[2015-09-30T09:16Z] Resource requests: bwa, sambamba, samtools; memory: 2.75; cores: 16, 1, 16
[2015-09-30T09:16Z] Configuring 1 jobs to run, using 8 cores each with 22.1g of memory reserved for each job
[2015-09-30T09:16Z] Timing: organize samples
[2015-09-30T09:16Z] multiprocessing: organize_samples
[2015-09-30T09:16Z] Using input YAML configuration: /home/cancer-dream-syn3/config/cancer-dream-syn3.yaml
[2015-09-30T09:16Z] Checking sample YAML configuration: /home/cancer-dream-syn3/config/cancer-dream-syn3.yaml
[2015-09-30T09:17Z] Testing minimum versions of installed programs
[2015-09-30T09:17Z] Timing: alignment preparation
[2015-09-30T09:17Z] multiprocessing: prep_align_inputs
[2015-09-30T09:17Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T09:17Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T09:17Z] bgzip input file
[2015-09-30T09:17Z] bgzip input file
[2015-09-30T09:34Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T09:34Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T09:34Z] Index input with grabix: synthetic_challenge_set3_normal_NGv3_1.fq.gz
[2015-09-30T09:34Z] Index input with grabix: synthetic_challenge_set3_normal_NGv3_2.fq.gz
[2015-09-30T09:36Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T09:36Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T09:36Z] bgzip input file
[2015-09-30T09:36Z] bgzip input file
[2015-09-30T09:51Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T09:51Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T09:51Z] Index input with grabix: synthetic_challenge_set3_tumor_NGv3_1.fq.gz
[2015-09-30T09:51Z] Index input with grabix: synthetic_challenge_set3_tumor_NGv3_2.fq.gz
[2015-09-30T09:53Z] multiprocessing: disambiguate_split
[2015-09-30T09:53Z] Timing: alignment
[2015-09-30T09:53Z] multiprocessing: process_alignment
[2015-09-30T09:53Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T09:53Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T09:53Z] samblaster: Version 0.1.22
[2015-09-30T09:53Z] samblaster: Inputting from stdin
[2015-09-30T09:53Z] samblaster: Outputting to stdout
[2015-09-30T09:53Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T09:53Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T09:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:54Z] [M::mem_pestat] (25, 50, 75) percentile: (240, 617, 1180)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3060)
[2015-09-30T09:54Z] [M::mem_pestat] mean and std.dev: (660.85, 558.37)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4000)
[2015-09-30T09:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:54Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 352)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 396)
[2015-09-30T09:54Z] [M::mem_pestat] mean and std.dev: (341.74, 14.85)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 418)
[2015-09-30T09:54Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:54Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:54Z] [M::mem_pestat] (25, 50, 75) percentile: (313, 646, 1055)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2539)
[2015-09-30T09:54Z] [M::mem_pestat] mean and std.dev: (710.73, 470.50)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3281)
[2015-09-30T09:54Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:54Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:54Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T09:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:54Z] [M::mem_pestat] (25, 50, 75) percentile: (192, 290, 783)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1965)
[2015-09-30T09:54Z] [M::mem_pestat] mean and std.dev: (472.40, 476.58)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2556)
[2015-09-30T09:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:54Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T09:54Z] [M::mem_pestat] mean and std.dev: (343.18, 15.07)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T09:54Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:54Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:54Z] [M::mem_pestat] (25, 50, 75) percentile: (342, 669, 1332)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3312)
[2015-09-30T09:54Z] [M::mem_pestat] mean and std.dev: (796.26, 687.93)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4302)
[2015-09-30T09:54Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:54Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:54Z] [M::mem_pestat] (25, 50, 75) percentile: (185, 318, 846)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2168)
[2015-09-30T09:54Z] [M::mem_pestat] mean and std.dev: (460.82, 408.58)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2829)
[2015-09-30T09:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:54Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T09:54Z] [M::mem_pestat] mean and std.dev: (343.30, 15.12)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T09:54Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:54Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:54Z] [M::mem_pestat] (25, 50, 75) percentile: (244, 441, 796)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1900)
[2015-09-30T09:54Z] [M::mem_pestat] mean and std.dev: (505.91, 364.58)
[2015-09-30T09:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2452)
[2015-09-30T09:54Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:54Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (176, 238, 689)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1715)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (370.00, 382.90)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2228)
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (343.89, 15.20)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (139, 274, 662)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1708)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (387.42, 406.00)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2231)
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (187, 304, 868)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2230)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (481.24, 431.77)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2911)
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (344.20, 15.14)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (241, 398, 1245)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3253)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (653.84, 625.21)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4257)
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (158, 226, 426)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 962)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (242.55, 161.01)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1230)
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (346.94, 15.69)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (182, 341, 946)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2474)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (476.87, 545.20)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3238)
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (188, 272, 1070)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2834)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (406.37, 459.98)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3716)
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (345.13, 15.54)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:55Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:55Z] [M::mem_pestat] (25, 50, 75) percentile: (264, 449, 8122)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 23838)
[2015-09-30T09:55Z] [M::mem_pestat] mean and std.dev: (2916.45, 3657.84)
[2015-09-30T09:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 31696)
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:55Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:56Z] [M::mem_pestat] (25, 50, 75) percentile: (158, 279, 974)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2606)
[2015-09-30T09:56Z] [M::mem_pestat] mean and std.dev: (402.13, 440.78)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3422)
[2015-09-30T09:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:56Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 354)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 398)
[2015-09-30T09:56Z] [M::mem_pestat] mean and std.dev: (344.06, 14.92)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (266, 420)
[2015-09-30T09:56Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:56Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:56Z] [M::mem_pestat] (25, 50, 75) percentile: (258, 808, 1279)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3321)
[2015-09-30T09:56Z] [M::mem_pestat] mean and std.dev: (752.86, 637.31)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4342)
[2015-09-30T09:56Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:56Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:56Z] [M::mem_pestat] (25, 50, 75) percentile: (126, 247, 697)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1839)
[2015-09-30T09:56Z] [M::mem_pestat] mean and std.dev: (325.55, 310.49)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2410)
[2015-09-30T09:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:56Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T09:56Z] [M::mem_pestat] mean and std.dev: (343.66, 15.12)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T09:56Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:56Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:56Z] [M::mem_pestat] (25, 50, 75) percentile: (274, 379, 731)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1645)
[2015-09-30T09:56Z] [M::mem_pestat] mean and std.dev: (413.65, 238.62)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2102)
[2015-09-30T09:56Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:56Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:56Z] [M::mem_pestat] (25, 50, 75) percentile: (125, 202, 285)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 605)
[2015-09-30T09:56Z] [M::mem_pestat] mean and std.dev: (182.02, 109.67)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 765)
[2015-09-30T09:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:56Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T09:56Z] [M::mem_pestat] mean and std.dev: (346.24, 15.53)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T09:56Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:56Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:56Z] [M::mem_pestat] (25, 50, 75) percentile: (224, 340, 819)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2009)
[2015-09-30T09:56Z] [M::mem_pestat] mean and std.dev: (422.63, 355.97)
[2015-09-30T09:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2604)
[2015-09-30T09:56Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:56Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (106, 201, 284)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 640)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (195.35, 125.50)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 818)
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (343.88, 15.21)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (727, 735, 748)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (685, 790)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (733.94, 12.97)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (664, 811)
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (199, 364, 807)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2023)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (429.26, 370.30)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2631)
[2015-09-30T09:57Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:57Z] [M::mem_pestat] skip orientation RF
[2015-09-30T09:57Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (148, 271, 844)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2236)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (447.33, 453.87)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2932)
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (345.07, 15.58)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T09:57Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (287, 354, 1234)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3128)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (665.52, 708.00)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4075)
[2015-09-30T09:57Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:57Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (153, 229, 429)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 981)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (293.44, 229.34)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1257)
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (345.61, 15.38)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T09:57Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:57Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:57Z] [M::mem_pestat] (25, 50, 75) percentile: (226, 336, 852)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2104)
[2015-09-30T09:57Z] [M::mem_pestat] mean and std.dev: (539.82, 422.49)
[2015-09-30T09:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2730)
[2015-09-30T09:57Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:57Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:57Z] [main] Version: 0.7.12-r1039
[2015-09-30T09:57Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 458061 discordant read pairs to /dev/fd/62
[2015-09-30T09:57Z] samblaster: Output 27468 split reads to /dev/fd/63
[2015-09-30T09:57Z]
[2015-09-30T09:57Z] [main] Real time: 254.604 sec; CPU: 1860.374 sec
[2015-09-30T09:57Z] samblaster: Marked 220038 of 5000000 (4.40%) read ids as duplicates using 147768k memory in 7.944S CPU seconds and 4M14S(254S) wall time.
[2015-09-30T09:58Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_20000000-sr.bam
[2015-09-30T09:58Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_20000000-disc.bam
[2015-09-30T09:58Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T09:58Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T09:58Z] samblaster: Version 0.1.22
[2015-09-30T09:58Z] samblaster: Inputting from stdin
[2015-09-30T09:58Z] samblaster: Outputting to stdout
[2015-09-30T09:58Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T09:58Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T09:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:58Z] [M::mem_pestat] (25, 50, 75) percentile: (229, 328, 892)
[2015-09-30T09:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2218)
[2015-09-30T09:58Z] [M::mem_pestat] mean and std.dev: (497.22, 424.39)
[2015-09-30T09:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2881)
[2015-09-30T09:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:58Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T09:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T09:58Z] [M::mem_pestat] mean and std.dev: (344.41, 15.26)
[2015-09-30T09:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T09:58Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:58Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:58Z] [M::mem_pestat] (25, 50, 75) percentile: (223, 317, 634)
[2015-09-30T09:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1456)
[2015-09-30T09:58Z] [M::mem_pestat] mean and std.dev: (378.41, 284.31)
[2015-09-30T09:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1867)
[2015-09-30T09:58Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:58Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:58Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T09:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:59Z] [M::mem_pestat] (25, 50, 75) percentile: (158, 265, 677)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1715)
[2015-09-30T09:59Z] [M::mem_pestat] mean and std.dev: (392.20, 318.10)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2234)
[2015-09-30T09:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:59Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T09:59Z] [M::mem_pestat] mean and std.dev: (346.36, 15.64)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T09:59Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:59Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:59Z] [M::mem_pestat] (25, 50, 75) percentile: (274, 628, 858)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2026)
[2015-09-30T09:59Z] [M::mem_pestat] mean and std.dev: (620.77, 452.44)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2610)
[2015-09-30T09:59Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:59Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:59Z] [M::mem_pestat] (25, 50, 75) percentile: (119, 194, 290)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 632)
[2015-09-30T09:59Z] [M::mem_pestat] mean and std.dev: (167.00, 92.32)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 803)
[2015-09-30T09:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:59Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T09:59Z] [M::mem_pestat] mean and std.dev: (344.40, 15.18)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T09:59Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:59Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:59Z] [M::mem_pestat] (25, 50, 75) percentile: (197, 383, 1187)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3167)
[2015-09-30T09:59Z] [M::mem_pestat] mean and std.dev: (685.03, 787.26)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4157)
[2015-09-30T09:59Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:59Z] [M::mem_pestat] skip orientation RR
[2015-09-30T09:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T09:59Z] [M::mem_pestat] (25, 50, 75) percentile: (109, 214, 745)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2017)
[2015-09-30T09:59Z] [M::mem_pestat] mean and std.dev: (309.15, 368.11)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2653)
[2015-09-30T09:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T09:59Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T09:59Z] [M::mem_pestat] mean and std.dev: (344.74, 15.27)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T09:59Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T09:59Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T09:59Z] [M::mem_pestat] (25, 50, 75) percentile: (283, 357, 649)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1381)
[2015-09-30T09:59Z] [M::mem_pestat] mean and std.dev: (393.40, 254.17)
[2015-09-30T09:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1747)
[2015-09-30T09:59Z] [M::mem_pestat] skip orientation FF
[2015-09-30T09:59Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (165, 271, 537)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1281)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (281.64, 268.00)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1653)
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (345.29, 15.34)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (1091, 1105, 1125)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1023, 1193)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (1113.82, 27.06)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (989, 1227)
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (215, 360, 1011)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2603)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (527.18, 497.38)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3399)
[2015-09-30T10:00Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:00Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:00Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (119, 176, 337)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 773)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (184.29, 133.65)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 991)
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (346.89, 15.39)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:00Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (196, 344, 605)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1423)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (341.23, 262.32)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1832)
[2015-09-30T10:00Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:00Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (111, 179, 299)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 675)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (181.29, 140.94)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 863)
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (347.00, 15.32)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:00Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:00Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:00Z] [M::mem_pestat] (25, 50, 75) percentile: (190, 343, 964)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2512)
[2015-09-30T10:00Z] [M::mem_pestat] mean and std.dev: (628.90, 649.79)
[2015-09-30T10:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3286)
[2015-09-30T10:00Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:00Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (156, 255, 647)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1629)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (328.90, 279.55)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2120)
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (344.08, 15.26)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (217, 417, 1052)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2722)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (590.40, 571.74)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3557)
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (183, 284, 692)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1710)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (380.00, 309.88)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2219)
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (343.45, 15.22)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (340, 613, 1022)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2386)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (629.02, 417.03)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3068)
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (149, 213, 404)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 914)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (201.06, 129.14)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1169)
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (344.86, 15.26)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (232, 479, 970)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2446)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (636.55, 577.55)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3184)
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (203, 281, 769)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1901)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (449.69, 443.02)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2467)
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (343.56, 15.13)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:01Z] [M::mem_pestat] (25, 50, 75) percentile: (277, 615, 995)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2431)
[2015-09-30T10:01Z] [M::mem_pestat] mean and std.dev: (671.24, 505.02)
[2015-09-30T10:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3149)
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:01Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:02Z] [M::mem_pestat] (25, 50, 75) percentile: (157, 222, 904)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2398)
[2015-09-30T10:02Z] [M::mem_pestat] mean and std.dev: (447.05, 624.63)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3145)
[2015-09-30T10:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:02Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:02Z] [M::mem_pestat] mean and std.dev: (344.17, 15.18)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:02Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:02Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:02Z] [M::mem_pestat] (25, 50, 75) percentile: (181, 319, 560)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1318)
[2015-09-30T10:02Z] [M::mem_pestat] mean and std.dev: (368.26, 312.49)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1697)
[2015-09-30T10:02Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:02Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:02Z] [M::mem_pestat] (25, 50, 75) percentile: (113, 204, 331)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 767)
[2015-09-30T10:02Z] [M::mem_pestat] mean and std.dev: (209.92, 128.18)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 985)
[2015-09-30T10:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:02Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T10:02Z] [M::mem_pestat] mean and std.dev: (347.02, 15.61)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T10:02Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:02Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:02Z] [M::mem_pestat] (25, 50, 75) percentile: (165, 256, 846)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2208)
[2015-09-30T10:02Z] [M::mem_pestat] mean and std.dev: (450.29, 573.24)
[2015-09-30T10:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2889)
[2015-09-30T10:02Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:02Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:02Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:02Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 469493 discordant read pairs to /dev/fd/62
[2015-09-30T10:02Z] samblaster: Output 32744 split reads to /dev/fd/63
[2015-09-30T10:02Z]
[2015-09-30T10:02Z] [main] Real time: 241.716 sec; CPU: 1842.236 sec
[2015-09-30T10:02Z] samblaster: Marked 213705 of 5000000 (4.27%) read ids as duplicates using 108644k memory in 7.922S CPU seconds and 4M2S(242S) wall time.
[2015-09-30T10:03Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-20000001_40000000-sr.bam
[2015-09-30T10:03Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-20000001_40000000-disc.bam
[2015-09-30T10:03Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:03Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T10:03Z] samblaster: Version 0.1.22
[2015-09-30T10:03Z] samblaster: Inputting from stdin
[2015-09-30T10:03Z] samblaster: Outputting to stdout
[2015-09-30T10:03Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:03Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:03Z] [M::mem_pestat] (25, 50, 75) percentile: (166, 222, 340)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 688)
[2015-09-30T10:03Z] [M::mem_pestat] mean and std.dev: (218.66, 121.84)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 862)
[2015-09-30T10:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:03Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:03Z] [M::mem_pestat] mean and std.dev: (344.76, 15.24)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:03Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:03Z] [M::mem_pestat] (25, 50, 75) percentile: (177, 306, 454)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1008)
[2015-09-30T10:03Z] [M::mem_pestat] mean and std.dev: (312.41, 209.26)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1285)
[2015-09-30T10:03Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:03Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:03Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:03Z] [M::mem_pestat] (25, 50, 75) percentile: (135, 207, 335)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 735)
[2015-09-30T10:03Z] [M::mem_pestat] mean and std.dev: (181.70, 130.11)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 935)
[2015-09-30T10:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:03Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T10:03Z] [M::mem_pestat] mean and std.dev: (346.29, 15.62)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T10:03Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:03Z] [M::mem_pestat] (25, 50, 75) percentile: (166, 306, 980)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2608)
[2015-09-30T10:03Z] [M::mem_pestat] mean and std.dev: (558.37, 599.82)
[2015-09-30T10:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3422)
[2015-09-30T10:03Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:03Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:04Z] [M::mem_pestat] (25, 50, 75) percentile: (163, 237, 473)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1093)
[2015-09-30T10:04Z] [M::mem_pestat] mean and std.dev: (287.58, 267.31)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1403)
[2015-09-30T10:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:04Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:04Z] [M::mem_pestat] mean and std.dev: (345.43, 15.34)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:04Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:04Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:04Z] [M::mem_pestat] (25, 50, 75) percentile: (261, 512, 1242)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3204)
[2015-09-30T10:04Z] [M::mem_pestat] mean and std.dev: (753.43, 700.36)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4185)
[2015-09-30T10:04Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:04Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:04Z] [M::mem_pestat] (25, 50, 75) percentile: (214, 308, 890)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2242)
[2015-09-30T10:04Z] [M::mem_pestat] mean and std.dev: (507.55, 462.81)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2918)
[2015-09-30T10:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:04Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 354)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:04Z] [M::mem_pestat] mean and std.dev: (342.96, 15.16)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:04Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:04Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:04Z] [M::mem_pestat] (25, 50, 75) percentile: (259, 660, 1422)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3748)
[2015-09-30T10:04Z] [M::mem_pestat] mean and std.dev: (841.63, 636.28)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4911)
[2015-09-30T10:04Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:04Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:04Z] [M::mem_pestat] (25, 50, 75) percentile: (102, 196, 331)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 789)
[2015-09-30T10:04Z] [M::mem_pestat] mean and std.dev: (200.92, 176.81)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1018)
[2015-09-30T10:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:04Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:04Z] [M::mem_pestat] mean and std.dev: (346.75, 15.41)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:04Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:04Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:04Z] [M::mem_pestat] (25, 50, 75) percentile: (169, 332, 787)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2023)
[2015-09-30T10:04Z] [M::mem_pestat] mean and std.dev: (377.19, 403.32)
[2015-09-30T10:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2641)
[2015-09-30T10:04Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:04Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:05Z] [M::mem_pestat] (25, 50, 75) percentile: (69, 167, 277)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 693)
[2015-09-30T10:05Z] [M::mem_pestat] mean and std.dev: (151.00, 123.29)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 901)
[2015-09-30T10:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:05Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:05Z] [M::mem_pestat] mean and std.dev: (346.85, 15.35)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:05Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:05Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:05Z] [M::mem_pestat] (25, 50, 75) percentile: (209, 336, 747)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1823)
[2015-09-30T10:05Z] [M::mem_pestat] mean and std.dev: (377.41, 352.19)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2361)
[2015-09-30T10:05Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:05Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:05Z] [M::mem_pestat] (25, 50, 75) percentile: (100, 200, 267)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 601)
[2015-09-30T10:05Z] [M::mem_pestat] mean and std.dev: (163.46, 111.40)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 768)
[2015-09-30T10:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:05Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:05Z] [M::mem_pestat] mean and std.dev: (347.02, 15.42)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:05Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:05Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:05Z] [M::mem_pestat] (25, 50, 75) percentile: (15, 265, 1670)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4980)
[2015-09-30T10:05Z] [M::mem_pestat] mean and std.dev: (863.97, 1189.73)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6635)
[2015-09-30T10:05Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:05Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:05Z] [M::mem_pestat] (25, 50, 75) percentile: (162, 258, 328)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 660)
[2015-09-30T10:05Z] [M::mem_pestat] mean and std.dev: (201.91, 108.08)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 826)
[2015-09-30T10:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:05Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:05Z] [M::mem_pestat] mean and std.dev: (344.88, 15.63)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:05Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:05Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:05Z] [M::mem_pestat] (25, 50, 75) percentile: (230, 335, 892)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2216)
[2015-09-30T10:05Z] [M::mem_pestat] mean and std.dev: (551.02, 533.81)
[2015-09-30T10:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2878)
[2015-09-30T10:05Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:05Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:06Z] [M::mem_pestat] (25, 50, 75) percentile: (124, 189, 290)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 622)
[2015-09-30T10:06Z] [M::mem_pestat] mean and std.dev: (169.05, 96.16)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 788)
[2015-09-30T10:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:06Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:06Z] [M::mem_pestat] mean and std.dev: (346.98, 15.40)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:06Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:06Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:06Z] [M::mem_pestat] (25, 50, 75) percentile: (224, 476, 1280)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3392)
[2015-09-30T10:06Z] [M::mem_pestat] mean and std.dev: (713.29, 749.30)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4448)
[2015-09-30T10:06Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:06Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:06Z] [M::mem_pestat] (25, 50, 75) percentile: (105, 186, 244)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 522)
[2015-09-30T10:06Z] [M::mem_pestat] mean and std.dev: (171.45, 94.30)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 661)
[2015-09-30T10:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:06Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:06Z] [M::mem_pestat] mean and std.dev: (346.71, 15.42)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:06Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:06Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:06Z] [M::mem_pestat] (25, 50, 75) percentile: (53, 296, 581)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1637)
[2015-09-30T10:06Z] [M::mem_pestat] mean and std.dev: (404.65, 428.70)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2165)
[2015-09-30T10:06Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:06Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:06Z] [M::mem_pestat] (25, 50, 75) percentile: (137, 200, 361)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 809)
[2015-09-30T10:06Z] [M::mem_pestat] mean and std.dev: (244.33, 187.54)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1033)
[2015-09-30T10:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:06Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:06Z] [M::mem_pestat] mean and std.dev: (344.95, 15.48)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:06Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:06Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:06Z] [M::mem_pestat] (25, 50, 75) percentile: (217, 324, 678)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1600)
[2015-09-30T10:06Z] [M::mem_pestat] mean and std.dev: (413.59, 349.22)
[2015-09-30T10:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2061)
[2015-09-30T10:06Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:06Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:07Z] [M::mem_pestat] (25, 50, 75) percentile: (179, 310, 790)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2012)
[2015-09-30T10:07Z] [M::mem_pestat] mean and std.dev: (419.59, 383.67)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2623)
[2015-09-30T10:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:07Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:07Z] [M::mem_pestat] mean and std.dev: (344.43, 15.19)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:07Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:07Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:07Z] [M::mem_pestat] (25, 50, 75) percentile: (171, 286, 522)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1224)
[2015-09-30T10:07Z] [M::mem_pestat] mean and std.dev: (303.18, 184.28)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1575)
[2015-09-30T10:07Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:07Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:07Z] [M::mem_pestat] (25, 50, 75) percentile: (234, 296, 884)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2184)
[2015-09-30T10:07Z] [M::mem_pestat] mean and std.dev: (549.62, 522.40)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2834)
[2015-09-30T10:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:07Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:07Z] [M::mem_pestat] mean and std.dev: (343.38, 15.18)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:07Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:07Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:07Z] [M::mem_pestat] (25, 50, 75) percentile: (290, 365, 823)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1889)
[2015-09-30T10:07Z] [M::mem_pestat] mean and std.dev: (474.37, 335.49)
[2015-09-30T10:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2422)
[2015-09-30T10:07Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:07Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:07Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:07Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 481551 discordant read pairs to /dev/fd/62
[2015-09-30T10:07Z] samblaster: Output 34332 split reads to /dev/fd/63
[2015-09-30T10:07Z]
[2015-09-30T10:07Z] [main] Real time: 245.531 sec; CPU: 1854.456 sec
[2015-09-30T10:07Z] samblaster: Marked 205473 of 5000000 (4.11%) read ids as duplicates using 108244k memory in 7.930S CPU seconds and 4M5S(245S) wall time.
[2015-09-30T10:07Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-40000001_60000000-sr.bam
[2015-09-30T10:08Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-40000001_60000000-disc.bam
[2015-09-30T10:08Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:08Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T10:08Z] samblaster: Version 0.1.22
[2015-09-30T10:08Z] samblaster: Inputting from stdin
[2015-09-30T10:08Z] samblaster: Outputting to stdout
[2015-09-30T10:08Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:08Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:08Z] [M::mem_pestat] (25, 50, 75) percentile: (138, 238, 512)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1260)
[2015-09-30T10:08Z] [M::mem_pestat] mean and std.dev: (275.70, 222.92)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1634)
[2015-09-30T10:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:08Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:08Z] [M::mem_pestat] mean and std.dev: (344.70, 15.27)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:08Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:08Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:08Z] [M::mem_pestat] (25, 50, 75) percentile: (242, 330, 1072)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2732)
[2015-09-30T10:08Z] [M::mem_pestat] mean and std.dev: (569.97, 515.89)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3562)
[2015-09-30T10:08Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:08Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:08Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:08Z] [M::mem_pestat] (25, 50, 75) percentile: (203, 287, 830)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2084)
[2015-09-30T10:08Z] [M::mem_pestat] mean and std.dev: (514.76, 540.33)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2711)
[2015-09-30T10:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:08Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:08Z] [M::mem_pestat] mean and std.dev: (343.26, 15.12)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:08Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:08Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:08Z] [M::mem_pestat] (25, 50, 75) percentile: (262, 362, 832)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1972)
[2015-09-30T10:08Z] [M::mem_pestat] mean and std.dev: (466.84, 317.06)
[2015-09-30T10:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2542)
[2015-09-30T10:08Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:08Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:09Z] [M::mem_pestat] (25, 50, 75) percentile: (175, 263, 759)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1927)
[2015-09-30T10:09Z] [M::mem_pestat] mean and std.dev: (381.44, 416.07)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2511)
[2015-09-30T10:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:09Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:09Z] [M::mem_pestat] mean and std.dev: (345.27, 15.59)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:09Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:09Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:09Z] [M::mem_pestat] (25, 50, 75) percentile: (178, 349, 979)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2581)
[2015-09-30T10:09Z] [M::mem_pestat] mean and std.dev: (585.15, 628.89)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3382)
[2015-09-30T10:09Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:09Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:09Z] [M::mem_pestat] (25, 50, 75) percentile: (115, 182, 268)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 574)
[2015-09-30T10:09Z] [M::mem_pestat] mean and std.dev: (161.95, 98.05)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 727)
[2015-09-30T10:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:09Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:09Z] [M::mem_pestat] mean and std.dev: (346.74, 15.42)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:09Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:09Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:09Z] [M::mem_pestat] (25, 50, 75) percentile: (30, 235, 532)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1536)
[2015-09-30T10:09Z] [M::mem_pestat] mean and std.dev: (288.22, 303.54)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2038)
[2015-09-30T10:09Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:09Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:09Z] [M::mem_pestat] (25, 50, 75) percentile: (117, 173, 287)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 627)
[2015-09-30T10:09Z] [M::mem_pestat] mean and std.dev: (170.04, 114.49)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 797)
[2015-09-30T10:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:09Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T10:09Z] [M::mem_pestat] mean and std.dev: (346.13, 15.55)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T10:09Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:09Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:09Z] [M::mem_pestat] (25, 50, 75) percentile: (253, 348, 1117)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2845)
[2015-09-30T10:09Z] [M::mem_pestat] mean and std.dev: (631.13, 655.90)
[2015-09-30T10:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3709)
[2015-09-30T10:09Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:09Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (160, 217, 302)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 586)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (216.05, 103.09)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 728)
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (343.30, 15.24)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (42, 42, 62)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (2, 102)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (47.10, 15.42)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 122)
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (170, 235, 890)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2330)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (490.56, 522.72)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3050)
[2015-09-30T10:10Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:10Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:10Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (147, 204, 293)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (206.03, 109.61)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 731)
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (345.52, 15.30)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:10Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (148, 240, 320)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 664)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (214.48, 123.55)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 836)
[2015-09-30T10:10Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:10Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (223, 335, 1316)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3502)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (828.87, 919.87)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4595)
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (343.78, 15.21)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:10Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:10Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:10Z] [M::mem_pestat] (25, 50, 75) percentile: (313, 809, 1878)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5008)
[2015-09-30T10:10Z] [M::mem_pestat] mean and std.dev: (1307.64, 1313.48)
[2015-09-30T10:10Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6573)
[2015-09-30T10:10Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:10Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (193, 266, 871)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2227)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (423.77, 444.24)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2905)
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (345.05, 15.64)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:11Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (241, 359, 1300)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3418)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (835.67, 814.08)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4477)
[2015-09-30T10:11Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:11Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (107, 214, 298)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 680)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (188.77, 117.87)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 871)
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 345, 356)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (345.42, 15.81)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (99, 164, 280)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 642)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (185.62, 103.69)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 823)
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (245, 368, 703)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1619)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (495.82, 407.83)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2077)
[2015-09-30T10:11Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:11Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:11Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (185, 261, 419)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 887)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (262.76, 160.03)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1121)
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (344.74, 15.27)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:11Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:11Z] [M::mem_pestat] (25, 50, 75) percentile: (241, 521, 1325)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3493)
[2015-09-30T10:11Z] [M::mem_pestat] mean and std.dev: (708.32, 631.02)
[2015-09-30T10:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4577)
[2015-09-30T10:11Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:11Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:12Z] [M::mem_pestat] (25, 50, 75) percentile: (177, 267, 750)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1896)
[2015-09-30T10:12Z] [M::mem_pestat] mean and std.dev: (399.50, 386.36)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2469)
[2015-09-30T10:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:12Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:12Z] [M::mem_pestat] mean and std.dev: (343.69, 15.29)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:12Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:12Z] [M::mem_pestat] (25, 50, 75) percentile: (59, 3712, 3718)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11036)
[2015-09-30T10:12Z] [M::mem_pestat] mean and std.dev: (2075.73, 1785.02)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 14695)
[2015-09-30T10:12Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:12Z] [M::mem_pestat] (25, 50, 75) percentile: (316, 568, 1020)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2428)
[2015-09-30T10:12Z] [M::mem_pestat] mean and std.dev: (649.64, 461.69)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3132)
[2015-09-30T10:12Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:12Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:12Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:12Z] [M::mem_pestat] (25, 50, 75) percentile: (142, 237, 309)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 643)
[2015-09-30T10:12Z] [M::mem_pestat] mean and std.dev: (205.89, 103.99)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 810)
[2015-09-30T10:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:12Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:12Z] [M::mem_pestat] mean and std.dev: (344.40, 15.32)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:12Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:12Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:12Z] [M::mem_pestat] (25, 50, 75) percentile: (230, 304, 721)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1703)
[2015-09-30T10:12Z] [M::mem_pestat] mean and std.dev: (395.47, 352.86)
[2015-09-30T10:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2194)
[2015-09-30T10:12Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:12Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:12Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:12Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 466461 discordant read pairs to /dev/fd/62
[2015-09-30T10:12Z]
[2015-09-30T10:12Z] [main] Real time: 259.925 sec; CPU: 1951.177 sec
[2015-09-30T10:12Z] samblaster: Output 31496 split reads to /dev/fd/63
[2015-09-30T10:12Z] samblaster: Marked 212326 of 5000000 (4.25%) read ids as duplicates using 124336k memory in 7.879S CPU seconds and 4M20S(260S) wall time.
[2015-09-30T10:13Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-60000001_80000000-sr.bam
[2015-09-30T10:13Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-60000001_80000000-disc.bam
[2015-09-30T10:13Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:13Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T10:13Z] samblaster: Version 0.1.22
[2015-09-30T10:13Z] samblaster: Inputting from stdin
[2015-09-30T10:13Z] samblaster: Outputting to stdout
[2015-09-30T10:13Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:13Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:13Z] [M::mem_pestat] (25, 50, 75) percentile: (172, 249, 814)
[2015-09-30T10:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2098)
[2015-09-30T10:13Z] [M::mem_pestat] mean and std.dev: (469.80, 514.98)
[2015-09-30T10:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2740)
[2015-09-30T10:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:13Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:13Z] [M::mem_pestat] mean and std.dev: (345.68, 15.29)
[2015-09-30T10:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:13Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:13Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:13Z] [M::mem_pestat] (25, 50, 75) percentile: (222, 364, 918)
[2015-09-30T10:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2310)
[2015-09-30T10:13Z] [M::mem_pestat] mean and std.dev: (511.30, 462.30)
[2015-09-30T10:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3006)
[2015-09-30T10:13Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:13Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:13Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:14Z] [M::mem_pestat] (25, 50, 75) percentile: (66, 190, 285)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 723)
[2015-09-30T10:14Z] [M::mem_pestat] mean and std.dev: (161.51, 111.08)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 942)
[2015-09-30T10:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:14Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 346, 357)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T10:14Z] [M::mem_pestat] mean and std.dev: (346.69, 15.73)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T10:14Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:14Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:14Z] [M::mem_pestat] (25, 50, 75) percentile: (214, 400, 788)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1936)
[2015-09-30T10:14Z] [M::mem_pestat] mean and std.dev: (429.85, 387.59)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2510)
[2015-09-30T10:14Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:14Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:14Z] [M::mem_pestat] (25, 50, 75) percentile: (193, 305, 908)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2338)
[2015-09-30T10:14Z] [M::mem_pestat] mean and std.dev: (492.90, 458.10)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3053)
[2015-09-30T10:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:14Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:14Z] [M::mem_pestat] mean and std.dev: (343.41, 15.33)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:14Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:14Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:14Z] [M::mem_pestat] (25, 50, 75) percentile: (290, 557, 1253)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3179)
[2015-09-30T10:14Z] [M::mem_pestat] mean and std.dev: (780.97, 712.76)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4142)
[2015-09-30T10:14Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:14Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:14Z] [M::mem_pestat] (25, 50, 75) percentile: (158, 231, 708)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1808)
[2015-09-30T10:14Z] [M::mem_pestat] mean and std.dev: (389.20, 390.18)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2358)
[2015-09-30T10:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:14Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:14Z] [M::mem_pestat] mean and std.dev: (345.37, 15.32)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:14Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:14Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:14Z] [M::mem_pestat] (25, 50, 75) percentile: (183, 341, 840)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2154)
[2015-09-30T10:14Z] [M::mem_pestat] mean and std.dev: (502.03, 472.84)
[2015-09-30T10:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2811)
[2015-09-30T10:14Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:14Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (166, 264, 866)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2266)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (494.89, 579.37)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2966)
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (345.57, 15.27)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (219, 405, 1123)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2931)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (694.42, 663.19)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3835)
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (179, 286, 417)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 893)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (256.79, 163.98)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1131)
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 344, 356)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (345.24, 15.26)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (228, 349, 1197)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3135)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (666.53, 571.43)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4104)
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (151, 250, 923)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2467)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (489.12, 528.03)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3239)
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (343.71, 15.17)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (292, 392, 1144)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2848)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (653.84, 529.80)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3700)
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (209, 283, 715)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1727)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (428.81, 379.43)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2233)
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (342.31, 15.06)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (836, 852, 859)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (790, 905)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (853.00, 19.94)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (767, 928)
[2015-09-30T10:15Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:15Z] [M::mem_pestat] (25, 50, 75) percentile: (248, 383, 1110)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2834)
[2015-09-30T10:15Z] [M::mem_pestat] mean and std.dev: (600.78, 583.05)
[2015-09-30T10:15Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3696)
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:15Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (159, 266, 935)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2487)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (458.10, 512.38)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3263)
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (343.32, 15.27)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (339, 623, 716)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1470)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (467.42, 288.28)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1847)
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (271, 434, 1073)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2677)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (638.54, 532.63)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3479)
[2015-09-30T10:16Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:16Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:16Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (132, 231, 685)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1791)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (372.66, 378.55)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2344)
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (345.43, 15.36)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:16Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (249, 381, 716)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1650)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (415.40, 271.34)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2117)
[2015-09-30T10:16Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:16Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (177, 245, 404)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 858)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (265.96, 177.15)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1085)
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (344.61, 15.30)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:16Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:16Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:16Z] [M::mem_pestat] (25, 50, 75) percentile: (190, 321, 594)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1402)
[2015-09-30T10:16Z] [M::mem_pestat] mean and std.dev: (373.19, 300.35)
[2015-09-30T10:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1806)
[2015-09-30T10:16Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:16Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:17Z] [M::mem_pestat] (25, 50, 75) percentile: (182, 246, 579)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1373)
[2015-09-30T10:17Z] [M::mem_pestat] mean and std.dev: (354.28, 299.45)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1770)
[2015-09-30T10:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:17Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:17Z] [M::mem_pestat] mean and std.dev: (345.04, 15.53)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:17Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:17Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:17Z] [M::mem_pestat] (25, 50, 75) percentile: (244, 322, 695)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1597)
[2015-09-30T10:17Z] [M::mem_pestat] mean and std.dev: (388.90, 338.75)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2048)
[2015-09-30T10:17Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:17Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:17Z] [M::mem_pestat] (25, 50, 75) percentile: (140, 203, 333)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 719)
[2015-09-30T10:17Z] [M::mem_pestat] mean and std.dev: (180.48, 106.27)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 912)
[2015-09-30T10:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:17Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:17Z] [M::mem_pestat] mean and std.dev: (344.66, 15.29)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:17Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:17Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:17Z] [M::mem_pestat] (25, 50, 75) percentile: (234, 297, 911)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2265)
[2015-09-30T10:17Z] [M::mem_pestat] mean and std.dev: (469.95, 424.31)
[2015-09-30T10:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2942)
[2015-09-30T10:17Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:17Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:17Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:17Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T10:17Z] [main] Real time: 250.695 sec; CPU: 1860.566 sec
[2015-09-30T10:17Z] samblaster: Output 459329 discordant read pairs to /dev/fd/62
[2015-09-30T10:17Z] samblaster: Output 30182 split reads to /dev/fd/63
[2015-09-30T10:17Z] samblaster: Marked 214986 of 5000000 (4.30%) read ids as duplicates using 109396k memory in 8.025S CPU seconds and 4M10S(250S) wall time.
[2015-09-30T10:18Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-80000001_100000000-sr.bam
[2015-09-30T10:18Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-80000001_100000000-disc.bam
[2015-09-30T10:18Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:18Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T10:18Z] samblaster: Version 0.1.22
[2015-09-30T10:18Z] samblaster: Inputting from stdin
[2015-09-30T10:18Z] samblaster: Outputting to stdout
[2015-09-30T10:18Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:18Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:18Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:18Z] [M::mem_pestat] (25, 50, 75) percentile: (217, 319, 1101)
[2015-09-30T10:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2869)
[2015-09-30T10:18Z] [M::mem_pestat] mean and std.dev: (631.79, 692.72)
[2015-09-30T10:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3753)
[2015-09-30T10:18Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:18Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:18Z] [M::mem_pestat] mean and std.dev: (343.58, 15.34)
[2015-09-30T10:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:18Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:18Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:18Z] [M::mem_pestat] (25, 50, 75) percentile: (268, 409, 932)
[2015-09-30T10:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2260)
[2015-09-30T10:18Z] [M::mem_pestat] mean and std.dev: (606.62, 489.69)
[2015-09-30T10:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2924)
[2015-09-30T10:18Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:18Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:18Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (185, 395, 1144)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3062)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (656.87, 624.27)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4021)
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 354)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (342.95, 15.25)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (205, 822, 837)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2101)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (631.94, 313.05)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2733)
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (336, 571, 1166)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2826)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (799.95, 655.01)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3656)
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (130, 207, 278)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 574)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (187.87, 94.94)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 722)
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (344.92, 15.53)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (262, 377, 1359)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3553)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (827.52, 850.44)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4650)
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (149, 237, 988)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2666)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (495.24, 589.52)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3505)
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (343.84, 15.22)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (263, 359, 1159)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2951)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (655.54, 603.36)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3847)
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (219, 298, 886)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2220)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (504.15, 441.19)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2887)
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 352)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 396)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (341.79, 14.69)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 418)
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:19Z] [M::mem_pestat] (25, 50, 75) percentile: (341, 576, 1132)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2714)
[2015-09-30T10:19Z] [M::mem_pestat] mean and std.dev: (663.11, 439.80)
[2015-09-30T10:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3505)
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:19Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:20Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:20Z] [M::mem_pestat] (25, 50, 75) percentile: (152, 209, 297)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 587)
[2015-09-30T10:20Z] [M::mem_pestat] mean and std.dev: (203.85, 93.19)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 732)
[2015-09-30T10:20Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:20Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:20Z] [M::mem_pestat] mean and std.dev: (344.26, 15.22)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:20Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:20Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:20Z] [M::mem_pestat] (25, 50, 75) percentile: (205, 412, 1039)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2707)
[2015-09-30T10:20Z] [M::mem_pestat] mean and std.dev: (518.33, 436.70)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3541)
[2015-09-30T10:20Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:20Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:20Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:20Z] [M::mem_pestat] (25, 50, 75) percentile: (184, 302, 880)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2272)
[2015-09-30T10:20Z] [M::mem_pestat] mean and std.dev: (487.89, 443.50)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2968)
[2015-09-30T10:20Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:20Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:20Z] [M::mem_pestat] mean and std.dev: (345.02, 15.61)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:20Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:20Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:20Z] [M::mem_pestat] (25, 50, 75) percentile: (304, 654, 940)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2212)
[2015-09-30T10:20Z] [M::mem_pestat] mean and std.dev: (591.40, 423.64)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2848)
[2015-09-30T10:20Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:20Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:20Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:20Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 219, 304)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 626)
[2015-09-30T10:20Z] [M::mem_pestat] mean and std.dev: (196.11, 84.39)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 787)
[2015-09-30T10:20Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:20Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:20Z] [M::mem_pestat] mean and std.dev: (344.19, 15.17)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:20Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:20Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:20Z] [M::mem_pestat] (25, 50, 75) percentile: (213, 363, 960)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2454)
[2015-09-30T10:20Z] [M::mem_pestat] mean and std.dev: (469.94, 437.92)
[2015-09-30T10:20Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3201)
[2015-09-30T10:20Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:20Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:21Z] [M::mem_pestat] (25, 50, 75) percentile: (149, 229, 621)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1565)
[2015-09-30T10:21Z] [M::mem_pestat] mean and std.dev: (286.94, 287.67)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2037)
[2015-09-30T10:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:21Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:21Z] [M::mem_pestat] mean and std.dev: (345.66, 15.36)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:21Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:21Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:21Z] [M::mem_pestat] (25, 50, 75) percentile: (179, 267, 671)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1655)
[2015-09-30T10:21Z] [M::mem_pestat] mean and std.dev: (357.98, 350.21)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2147)
[2015-09-30T10:21Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:21Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:21Z] [M::mem_pestat] (25, 50, 75) percentile: (163, 251, 433)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 973)
[2015-09-30T10:21Z] [M::mem_pestat] mean and std.dev: (248.11, 194.72)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1243)
[2015-09-30T10:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:21Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:21Z] [M::mem_pestat] mean and std.dev: (344.75, 15.32)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:21Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:21Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:21Z] [M::mem_pestat] (25, 50, 75) percentile: (244, 407, 909)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2239)
[2015-09-30T10:21Z] [M::mem_pestat] mean and std.dev: (559.71, 479.52)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2904)
[2015-09-30T10:21Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:21Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:21Z] [M::mem_pestat] (25, 50, 75) percentile: (170, 257, 925)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2435)
[2015-09-30T10:21Z] [M::mem_pestat] mean and std.dev: (455.60, 538.63)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3190)
[2015-09-30T10:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:21Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:21Z] [M::mem_pestat] mean and std.dev: (343.81, 15.20)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:21Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:21Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:21Z] [M::mem_pestat] (25, 50, 75) percentile: (270, 578, 1038)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2574)
[2015-09-30T10:21Z] [M::mem_pestat] mean and std.dev: (669.81, 556.77)
[2015-09-30T10:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3342)
[2015-09-30T10:21Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:21Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:22Z] [M::mem_pestat] (25, 50, 75) percentile: (165, 280, 730)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1860)
[2015-09-30T10:22Z] [M::mem_pestat] mean and std.dev: (406.79, 346.45)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2425)
[2015-09-30T10:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:22Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:22Z] [M::mem_pestat] mean and std.dev: (346.78, 15.40)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:22Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:22Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:22Z] [M::mem_pestat] (25, 50, 75) percentile: (259, 424, 753)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1741)
[2015-09-30T10:22Z] [M::mem_pestat] mean and std.dev: (513.27, 398.29)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2235)
[2015-09-30T10:22Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:22Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:22Z] [M::mem_pestat] (25, 50, 75) percentile: (201, 299, 1177)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3129)
[2015-09-30T10:22Z] [M::mem_pestat] mean and std.dev: (575.65, 521.08)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4105)
[2015-09-30T10:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:22Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:22Z] [M::mem_pestat] mean and std.dev: (344.23, 15.11)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:22Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:22Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:22Z] [M::mem_pestat] (25, 50, 75) percentile: (293, 810, 1284)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3266)
[2015-09-30T10:22Z] [M::mem_pestat] mean and std.dev: (826.24, 669.08)
[2015-09-30T10:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4257)
[2015-09-30T10:22Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:22Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:22Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:22Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 464467 discordant read pairs to /dev/fd/62
[2015-09-30T10:22Z] samblaster: Output 28266 split reads to /dev/fd/63
[2015-09-30T10:22Z]
[2015-09-30T10:22Z] [main] Real time: 244.580 sec; CPU: 1797.121 sec
[2015-09-30T10:22Z] samblaster: Marked 219621 of 5000000 (4.39%) read ids as duplicates using 111356k memory in 7.982S CPU seconds and 4M5S(245S) wall time.
[2015-09-30T10:22Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-100000001_120000000-sr.bam
[2015-09-30T10:22Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-100000001_120000000-disc.bam
[2015-09-30T10:22Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:23Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T10:23Z] samblaster: Version 0.1.22
[2015-09-30T10:23Z] samblaster: Inputting from stdin
[2015-09-30T10:23Z] samblaster: Outputting to stdout
[2015-09-30T10:23Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:23Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:23Z] [M::mem_pestat] (25, 50, 75) percentile: (218, 381, 1286)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3422)
[2015-09-30T10:23Z] [M::mem_pestat] mean and std.dev: (789.72, 784.92)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4490)
[2015-09-30T10:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:23Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:23Z] [M::mem_pestat] mean and std.dev: (343.60, 15.14)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:23Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:23Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:23Z] [M::mem_pestat] (25, 50, 75) percentile: (313, 746, 1934)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5176)
[2015-09-30T10:23Z] [M::mem_pestat] mean and std.dev: (1098.50, 1152.77)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6797)
[2015-09-30T10:23Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:23Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:23Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:23Z] [M::mem_pestat] (25, 50, 75) percentile: (172, 233, 364)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 748)
[2015-09-30T10:23Z] [M::mem_pestat] mean and std.dev: (238.11, 142.67)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 940)
[2015-09-30T10:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:23Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T10:23Z] [M::mem_pestat] mean and std.dev: (346.00, 15.69)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T10:23Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:23Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:23Z] [M::mem_pestat] (25, 50, 75) percentile: (186, 298, 663)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1617)
[2015-09-30T10:23Z] [M::mem_pestat] mean and std.dev: (420.39, 398.21)
[2015-09-30T10:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2094)
[2015-09-30T10:23Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:23Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:24Z] [M::mem_pestat] (25, 50, 75) percentile: (146, 263, 503)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1217)
[2015-09-30T10:24Z] [M::mem_pestat] mean and std.dev: (296.64, 257.77)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1574)
[2015-09-30T10:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:24Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:24Z] [M::mem_pestat] mean and std.dev: (345.81, 15.43)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:24Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:24Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:24Z] [M::mem_pestat] (25, 50, 75) percentile: (96, 327, 650)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1758)
[2015-09-30T10:24Z] [M::mem_pestat] mean and std.dev: (420.30, 433.02)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2312)
[2015-09-30T10:24Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:24Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:24Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 212, 612)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1548)
[2015-09-30T10:24Z] [M::mem_pestat] mean and std.dev: (357.94, 350.40)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2016)
[2015-09-30T10:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:24Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:24Z] [M::mem_pestat] mean and std.dev: (344.23, 15.26)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:24Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:24Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:24Z] [M::mem_pestat] (25, 50, 75) percentile: (288, 581, 1514)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3966)
[2015-09-30T10:24Z] [M::mem_pestat] mean and std.dev: (875.57, 821.13)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5192)
[2015-09-30T10:24Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:24Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:24Z] [M::mem_pestat] (25, 50, 75) percentile: (181, 280, 996)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2626)
[2015-09-30T10:24Z] [M::mem_pestat] mean and std.dev: (489.21, 524.49)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3441)
[2015-09-30T10:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:24Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T10:24Z] [M::mem_pestat] mean and std.dev: (345.95, 15.60)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T10:24Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:24Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:24Z] [M::mem_pestat] (25, 50, 75) percentile: (150, 259, 563)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1389)
[2015-09-30T10:24Z] [M::mem_pestat] mean and std.dev: (313.27, 327.76)
[2015-09-30T10:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1802)
[2015-09-30T10:24Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:24Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (187, 250, 610)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1456)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (303.47, 268.88)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1879)
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (344.81, 15.32)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:25Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (304, 483, 1280)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3232)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (654.59, 530.48)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4208)
[2015-09-30T10:25Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:25Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (229, 508, 1237)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3253)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (719.00, 650.91)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4261)
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 354)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (343.03, 15.20)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:25Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (376, 735, 1406)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3466)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (900.21, 669.39)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4496)
[2015-09-30T10:25Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:25Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (201, 270, 1111)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2931)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (587.18, 626.10)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3841)
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (344.45, 15.19)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (322, 333, 387)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (192, 517)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (338.29, 50.66)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (127, 582)
[2015-09-30T10:25Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:25Z] [M::mem_pestat] (25, 50, 75) percentile: (174, 296, 610)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1482)
[2015-09-30T10:25Z] [M::mem_pestat] mean and std.dev: (308.19, 241.41)
[2015-09-30T10:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1918)
[2015-09-30T10:25Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:25Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:25Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 196, 359)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 787)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (195.77, 163.52)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1001)
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (345.71, 15.28)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 350, 1243)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3439)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (610.82, 715.46)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4537)
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (141, 202, 414)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 960)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (223.32, 179.60)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1233)
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (344.29, 15.19)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (238, 631, 1165)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3019)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (681.91, 659.63)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3946)
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (166, 229, 292)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 544)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (201.78, 101.98)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 670)
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (344.16, 15.24)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (253, 455, 1189)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3061)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (586.77, 562.89)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3997)
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (205, 300, 933)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2389)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (551.28, 547.92)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3117)
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 353)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (342.01, 15.08)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:26Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:26Z] [M::mem_pestat] (25, 50, 75) percentile: (284, 602, 1088)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2696)
[2015-09-30T10:26Z] [M::mem_pestat] mean and std.dev: (751.69, 607.48)
[2015-09-30T10:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3500)
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:26Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:27Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:27Z] [M::mem_pestat] (25, 50, 75) percentile: (173, 314, 1354)
[2015-09-30T10:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3716)
[2015-09-30T10:27Z] [M::mem_pestat] mean and std.dev: (783.38, 906.16)
[2015-09-30T10:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4897)
[2015-09-30T10:27Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:27Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T10:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:27Z] [M::mem_pestat] mean and std.dev: (342.52, 15.09)
[2015-09-30T10:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:27Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:27Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:27Z] [M::mem_pestat] (25, 50, 75) percentile: (299, 564, 1250)
[2015-09-30T10:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3152)
[2015-09-30T10:27Z] [M::mem_pestat] mean and std.dev: (702.43, 574.87)
[2015-09-30T10:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4103)
[2015-09-30T10:27Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:27Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:27Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:27Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 459373 discordant read pairs to /dev/fd/62
[2015-09-30T10:27Z] samblaster: Output 28408 split reads to /dev/fd/63
[2015-09-30T10:27Z]
[2015-09-30T10:27Z] [main] Real time: 251.457 sec; CPU: 1894.170 sec
[2015-09-30T10:27Z] samblaster: Marked 216677 of 5000000 (4.33%) read ids as duplicates using 104136k memory in 7.941S CPU seconds and 4M12S(252S) wall time.
[2015-09-30T10:28Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-120000001_140000000-sr.bam
[2015-09-30T10:28Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-120000001_140000000-disc.bam
[2015-09-30T10:28Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:28Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T10:28Z] samblaster: Version 0.1.22
[2015-09-30T10:28Z] samblaster: Inputting from stdin
[2015-09-30T10:28Z] samblaster: Outputting to stdout
[2015-09-30T10:28Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:28Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:28Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:28Z] [M::mem_pestat] (25, 50, 75) percentile: (210, 647, 1440)
[2015-09-30T10:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3900)
[2015-09-30T10:28Z] [M::mem_pestat] mean and std.dev: (791.45, 739.68)
[2015-09-30T10:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5130)
[2015-09-30T10:28Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:28Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:28Z] [M::mem_pestat] mean and std.dev: (344.72, 15.22)
[2015-09-30T10:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:28Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:28Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:28Z] [M::mem_pestat] (25, 50, 75) percentile: (318, 605, 2259)
[2015-09-30T10:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6141)
[2015-09-30T10:28Z] [M::mem_pestat] mean and std.dev: (1253.70, 1215.22)
[2015-09-30T10:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8082)
[2015-09-30T10:28Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:28Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:28Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (188, 291, 696)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1712)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (393.54, 349.91)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2220)
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (342.61, 15.08)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:29Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (347, 651, 1199)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2903)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (774.42, 621.46)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3755)
[2015-09-30T10:29Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:29Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (185, 276, 825)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2105)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (464.51, 457.36)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2745)
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (343.61, 15.20)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (2740, 2754, 2761)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (2698, 2803)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (2753.36, 12.80)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (2677, 2824)
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (248, 440, 1139)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2921)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (714.98, 665.51)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3812)
[2015-09-30T10:29Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:29Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:29Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (211, 316, 1220)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3238)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (837.06, 875.03)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4247)
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (344.16, 15.12)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:29Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:29Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:29Z] [M::mem_pestat] (25, 50, 75) percentile: (329, 645, 1012)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2378)
[2015-09-30T10:29Z] [M::mem_pestat] mean and std.dev: (674.67, 473.44)
[2015-09-30T10:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3061)
[2015-09-30T10:29Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:29Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (201, 314, 872)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2214)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (479.69, 441.93)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2885)
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (342.14, 15.12)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (874, 1027, 1046)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (530, 1390)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (951.26, 136.08)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (358, 1562)
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (300, 479, 1142)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2826)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (635.02, 532.99)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3668)
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (175, 277, 769)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1957)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (437.25, 402.60)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2551)
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (343.29, 15.13)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (197, 438, 1306)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3524)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (661.15, 703.00)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4633)
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (162, 267, 926)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2454)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (513.43, 593.43)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3218)
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (343.16, 15.14)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (246, 340, 952)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2364)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (514.13, 457.51)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3070)
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (161, 232, 852)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2234)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (500.89, 582.33)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2925)
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (344.12, 15.17)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:30Z] [M::mem_pestat] (25, 50, 75) percentile: (293, 493, 1115)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2759)
[2015-09-30T10:30Z] [M::mem_pestat] mean and std.dev: (657.48, 596.34)
[2015-09-30T10:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3581)
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:30Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:31Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:31Z] [M::mem_pestat] (25, 50, 75) percentile: (118, 248, 703)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1873)
[2015-09-30T10:31Z] [M::mem_pestat] mean and std.dev: (419.09, 459.99)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2458)
[2015-09-30T10:31Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:31Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 353)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 397)
[2015-09-30T10:31Z] [M::mem_pestat] mean and std.dev: (343.00, 14.90)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 419)
[2015-09-30T10:31Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:31Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:31Z] [M::mem_pestat] (25, 50, 75) percentile: (250, 438, 850)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2050)
[2015-09-30T10:31Z] [M::mem_pestat] mean and std.dev: (550.35, 440.18)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2650)
[2015-09-30T10:31Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:31Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:31Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:31Z] [M::mem_pestat] (25, 50, 75) percentile: (93, 207, 327)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 795)
[2015-09-30T10:31Z] [M::mem_pestat] mean and std.dev: (180.33, 138.34)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1029)
[2015-09-30T10:31Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:31Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 355)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (283, 403)
[2015-09-30T10:31Z] [M::mem_pestat] mean and std.dev: (344.00, 15.51)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (259, 427)
[2015-09-30T10:31Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:31Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:31Z] [M::mem_pestat] (25, 50, 75) percentile: (257, 534, 1315)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3431)
[2015-09-30T10:31Z] [M::mem_pestat] mean and std.dev: (716.96, 672.14)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4489)
[2015-09-30T10:31Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:31Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:31Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:31Z] [M::mem_pestat] (25, 50, 75) percentile: (186, 269, 772)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1944)
[2015-09-30T10:31Z] [M::mem_pestat] mean and std.dev: (374.21, 352.28)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2530)
[2015-09-30T10:31Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:31Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:31Z] [M::mem_pestat] mean and std.dev: (343.13, 15.20)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:31Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:31Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:31Z] [M::mem_pestat] (25, 50, 75) percentile: (345, 758, 1494)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3792)
[2015-09-30T10:31Z] [M::mem_pestat] mean and std.dev: (962.42, 802.84)
[2015-09-30T10:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4941)
[2015-09-30T10:31Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:31Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:32Z] [M::mem_pestat] (25, 50, 75) percentile: (223, 285, 847)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2095)
[2015-09-30T10:32Z] [M::mem_pestat] mean and std.dev: (503.09, 452.95)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2719)
[2015-09-30T10:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:32Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:32Z] [M::mem_pestat] mean and std.dev: (342.78, 15.31)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:32Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:32Z] [M::mem_pestat] (25, 50, 75) percentile: (293, 488, 947)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2255)
[2015-09-30T10:32Z] [M::mem_pestat] mean and std.dev: (594.06, 453.73)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2909)
[2015-09-30T10:32Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:32Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:32Z] [M::mem_pestat] (25, 50, 75) percentile: (152, 217, 671)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1709)
[2015-09-30T10:32Z] [M::mem_pestat] mean and std.dev: (367.61, 410.74)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2228)
[2015-09-30T10:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:32Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T10:32Z] [M::mem_pestat] mean and std.dev: (346.14, 15.61)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T10:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:32Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:32Z] [M::mem_pestat] (25, 50, 75) percentile: (149, 285, 1927)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5483)
[2015-09-30T10:32Z] [M::mem_pestat] mean and std.dev: (881.94, 1057.53)
[2015-09-30T10:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7261)
[2015-09-30T10:32Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:32Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:32Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:32Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T10:32Z] [main] Real time: 261.655 sec; CPU: 1991.836 sec
[2015-09-30T10:32Z] samblaster: Output 441092 discordant read pairs to /dev/fd/62
[2015-09-30T10:32Z] samblaster: Output 23038 split reads to /dev/fd/63
[2015-09-30T10:32Z] samblaster: Marked 224516 of 5000000 (4.49%) read ids as duplicates using 119428k memory in 8.055S CPU seconds and 4M22S(262S) wall time.
[2015-09-30T10:33Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-140000001_160000000-sr.bam
[2015-09-30T10:33Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-140000001_160000000-disc.bam
[2015-09-30T10:33Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:33Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T10:33Z] samblaster: Version 0.1.22
[2015-09-30T10:33Z] samblaster: Inputting from stdin
[2015-09-30T10:33Z] samblaster: Outputting to stdout
[2015-09-30T10:33Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:33Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:33Z] [M::mem_pestat] (25, 50, 75) percentile: (197, 276, 1005)
[2015-09-30T10:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2621)
[2015-09-30T10:33Z] [M::mem_pestat] mean and std.dev: (547.60, 594.28)
[2015-09-30T10:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3429)
[2015-09-30T10:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:33Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:33Z] [M::mem_pestat] mean and std.dev: (344.71, 15.37)
[2015-09-30T10:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:33Z] [M::mem_pestat] (25, 50, 75) percentile: (146, 175, 187)
[2015-09-30T10:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (64, 269)
[2015-09-30T10:33Z] [M::mem_pestat] mean and std.dev: (169.00, 32.54)
[2015-09-30T10:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (23, 310)
[2015-09-30T10:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:33Z] [M::mem_pestat] (25, 50, 75) percentile: (274, 545, 917)
[2015-09-30T10:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2203)
[2015-09-30T10:33Z] [M::mem_pestat] mean and std.dev: (594.83, 425.66)
[2015-09-30T10:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2846)
[2015-09-30T10:33Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:33Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:33Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:33Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (229, 616, 1136)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2950)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (754.82, 624.56)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3857)
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (329, 340, 351)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 395)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (341.02, 14.71)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 417)
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (43, 50, 68)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 118)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (51.05, 16.19)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 143)
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (325, 729, 1389)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3517)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (904.53, 787.58)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4581)
[2015-09-30T10:34Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:34Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:34Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (247, 627, 1003)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2515)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (631.26, 515.72)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3271)
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (342.28, 15.04)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (235, 2838, 5902)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17236)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (3511.65, 2921.63)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 22903)
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (581, 1073, 1953)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4697)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (1337.71, 1042.46)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6069)
[2015-09-30T10:34Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:34Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:34Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (202, 343, 917)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2347)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (530.03, 447.36)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3062)
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 352)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 396)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (341.92, 14.68)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 418)
[2015-09-30T10:34Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:34Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:34Z] [M::mem_pestat] (25, 50, 75) percentile: (531, 962, 1386)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3096)
[2015-09-30T10:34Z] [M::mem_pestat] mean and std.dev: (995.75, 653.04)
[2015-09-30T10:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3951)
[2015-09-30T10:34Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:34Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:35Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:35Z] [M::mem_pestat] (25, 50, 75) percentile: (215, 478, 1253)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3329)
[2015-09-30T10:35Z] [M::mem_pestat] mean and std.dev: (777.55, 814.53)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4367)
[2015-09-30T10:35Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:35Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:35Z] [M::mem_pestat] mean and std.dev: (342.75, 15.19)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:35Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:35Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:35Z] [M::mem_pestat] (25, 50, 75) percentile: (297, 509, 1416)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3654)
[2015-09-30T10:35Z] [M::mem_pestat] mean and std.dev: (791.98, 775.01)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4773)
[2015-09-30T10:35Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:35Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:35Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:35Z] [M::mem_pestat] (25, 50, 75) percentile: (210, 308, 987)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2541)
[2015-09-30T10:35Z] [M::mem_pestat] mean and std.dev: (569.03, 573.01)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3318)
[2015-09-30T10:35Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:35Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:35Z] [M::mem_pestat] mean and std.dev: (342.21, 15.04)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:35Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:35Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:35Z] [M::mem_pestat] (25, 50, 75) percentile: (455, 813, 1149)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2537)
[2015-09-30T10:35Z] [M::mem_pestat] mean and std.dev: (770.42, 465.23)
[2015-09-30T10:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3231)
[2015-09-30T10:35Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:35Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (203, 328, 1063)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2783)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (558.13, 515.98)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3643)
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 352)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 396)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (341.74, 14.78)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 418)
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (476, 754, 1256)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2816)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (840.64, 525.36)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3596)
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (196, 299, 989)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2575)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (476.14, 405.11)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3368)
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 353)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 397)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (342.96, 14.90)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 419)
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (48, 9636, 9657)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 28875)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (5543.00, 4653.06)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 38484)
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (311, 583, 1290)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3248)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (834.98, 677.48)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4227)
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (148, 228, 340)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 724)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (217.82, 126.47)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 916)
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (344.14, 15.23)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (260, 340, 761)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1763)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (509.96, 428.27)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2264)
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (170, 280, 1076)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2888)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (536.68, 588.81)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3794)
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (343.66, 15.18)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:36Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:36Z] [M::mem_pestat] (25, 50, 75) percentile: (319, 561, 1292)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3238)
[2015-09-30T10:36Z] [M::mem_pestat] mean and std.dev: (827.29, 665.61)
[2015-09-30T10:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4211)
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:36Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:37Z] [M::mem_pestat] (25, 50, 75) percentile: (170, 256, 577)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1391)
[2015-09-30T10:37Z] [M::mem_pestat] mean and std.dev: (376.79, 354.75)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1798)
[2015-09-30T10:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:37Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:37Z] [M::mem_pestat] mean and std.dev: (344.02, 15.11)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:37Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:37Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:37Z] [M::mem_pestat] (25, 50, 75) percentile: (204, 336, 1024)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2664)
[2015-09-30T10:37Z] [M::mem_pestat] mean and std.dev: (535.59, 520.24)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3484)
[2015-09-30T10:37Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:37Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:37Z] [M::mem_pestat] (25, 50, 75) percentile: (211, 306, 958)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2452)
[2015-09-30T10:37Z] [M::mem_pestat] mean and std.dev: (478.03, 462.34)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3199)
[2015-09-30T10:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:37Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:37Z] [M::mem_pestat] mean and std.dev: (343.73, 15.45)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:37Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:37Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:37Z] [M::mem_pestat] (25, 50, 75) percentile: (283, 537, 1202)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3040)
[2015-09-30T10:37Z] [M::mem_pestat] mean and std.dev: (703.66, 580.83)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3959)
[2015-09-30T10:37Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:37Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:37Z] [M::mem_pestat] (25, 50, 75) percentile: (112, 287, 836)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2284)
[2015-09-30T10:37Z] [M::mem_pestat] mean and std.dev: (396.89, 376.57)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3008)
[2015-09-30T10:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:37Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:37Z] [M::mem_pestat] mean and std.dev: (343.35, 15.20)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:37Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:37Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:37Z] [M::mem_pestat] (25, 50, 75) percentile: (270, 491, 666)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1458)
[2015-09-30T10:37Z] [M::mem_pestat] mean and std.dev: (456.53, 301.29)
[2015-09-30T10:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1854)
[2015-09-30T10:37Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:37Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:37Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:37Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 448365 discordant read pairs to /dev/fd/62
[2015-09-30T10:37Z]
[2015-09-30T10:37Z] [main] Real time: 265.821 sec; CPU: 2005.657 sec
[2015-09-30T10:37Z] samblaster: Output 23096 split reads to /dev/fd/63
[2015-09-30T10:37Z] samblaster: Marked 235059 of 5000000 (4.70%) read ids as duplicates using 109680k memory in 8.062S CPU seconds and 4M25S(265S) wall time.
[2015-09-30T10:38Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-160000001_180000000-sr.bam
[2015-09-30T10:38Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-160000001_180000000-disc.bam
[2015-09-30T10:38Z] Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:38Z] bwa mem alignment from fastq: syn3-normal
[2015-09-30T10:38Z] samblaster: Version 0.1.22
[2015-09-30T10:38Z] samblaster: Inputting from stdin
[2015-09-30T10:38Z] samblaster: Outputting to stdout
[2015-09-30T10:38Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:38Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:39Z] [M::mem_pestat] (25, 50, 75) percentile: (254, 553, 1084)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2744)
[2015-09-30T10:39Z] [M::mem_pestat] mean and std.dev: (702.30, 636.83)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3574)
[2015-09-30T10:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:39Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T10:39Z] [M::mem_pestat] mean and std.dev: (342.24, 15.11)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T10:39Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:39Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:39Z] [M::mem_pestat] (25, 50, 75) percentile: (352, 688, 1082)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2542)
[2015-09-30T10:39Z] [M::mem_pestat] mean and std.dev: (700.89, 510.72)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3272)
[2015-09-30T10:39Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:39Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:39Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:39Z] [M::mem_pestat] (25, 50, 75) percentile: (208, 318, 963)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2473)
[2015-09-30T10:39Z] [M::mem_pestat] mean and std.dev: (493.03, 436.38)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3228)
[2015-09-30T10:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:39Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:39Z] [M::mem_pestat] mean and std.dev: (343.38, 15.10)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:39Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:39Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:39Z] [M::mem_pestat] (25, 50, 75) percentile: (299, 439, 1046)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2540)
[2015-09-30T10:39Z] [M::mem_pestat] mean and std.dev: (558.74, 439.03)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3287)
[2015-09-30T10:39Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:39Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:39Z] [M::mem_pestat] (25, 50, 75) percentile: (173, 273, 439)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 971)
[2015-09-30T10:39Z] [M::mem_pestat] mean and std.dev: (311.88, 221.18)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1237)
[2015-09-30T10:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:39Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 353)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 397)
[2015-09-30T10:39Z] [M::mem_pestat] mean and std.dev: (342.80, 14.80)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 419)
[2015-09-30T10:39Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:39Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:39Z] [M::mem_pestat] (25, 50, 75) percentile: (281, 470, 1360)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3518)
[2015-09-30T10:39Z] [M::mem_pestat] mean and std.dev: (829.20, 827.00)
[2015-09-30T10:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4597)
[2015-09-30T10:39Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:39Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (183, 283, 787)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1995)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (480.86, 443.24)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2599)
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (343.11, 15.19)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (133, 1980, 2364)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6826)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (1264.28, 976.02)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9057)
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (282, 621, 1178)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2970)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (764.13, 610.59)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3866)
[2015-09-30T10:40Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:40Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:40Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (213, 269, 847)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2115)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (470.17, 498.60)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2749)
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (345.16, 15.59)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:40Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (275, 447, 935)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2255)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (536.34, 469.18)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2915)
[2015-09-30T10:40Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:40Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (183, 303, 582)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1380)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (406.17, 366.92)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1779)
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (345.35, 15.24)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:40Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:40Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:40Z] [M::mem_pestat] (25, 50, 75) percentile: (179, 273, 1117)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2993)
[2015-09-30T10:40Z] [M::mem_pestat] mean and std.dev: (634.61, 709.66)
[2015-09-30T10:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3931)
[2015-09-30T10:40Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:40Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:41Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:41Z] [M::mem_pestat] (25, 50, 75) percentile: (132, 178, 293)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 615)
[2015-09-30T10:41Z] [M::mem_pestat] mean and std.dev: (156.38, 86.74)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 776)
[2015-09-30T10:41Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:41Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:41Z] [M::mem_pestat] mean and std.dev: (345.90, 15.34)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:41Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:41Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:41Z] [M::mem_pestat] (25, 50, 75) percentile: (176, 310, 638)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1562)
[2015-09-30T10:41Z] [M::mem_pestat] mean and std.dev: (364.21, 336.38)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2024)
[2015-09-30T10:41Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:41Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:41Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:41Z] [M::mem_pestat] (25, 50, 75) percentile: (162, 250, 364)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 768)
[2015-09-30T10:41Z] [M::mem_pestat] mean and std.dev: (230.48, 136.41)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 970)
[2015-09-30T10:41Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:41Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:41Z] [M::mem_pestat] mean and std.dev: (343.70, 15.31)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:41Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:41Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:41Z] [M::mem_pestat] (25, 50, 75) percentile: (275, 327, 776)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1778)
[2015-09-30T10:41Z] [M::mem_pestat] mean and std.dev: (471.32, 352.21)
[2015-09-30T10:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2279)
[2015-09-30T10:41Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:41Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:42Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-09-30T10:42Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:42Z] [M::mem_pestat] (25, 50, 75) percentile: (303, 339, 354)
[2015-09-30T10:42Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (201, 456)
[2015-09-30T10:42Z] [M::mem_pestat] mean and std.dev: (337.84, 35.03)
[2015-09-30T10:42Z] [M::mem_pestat] low and high boundaries for proper pairs: (150, 507)
[2015-09-30T10:42Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:42Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-09-30T10:43Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-09-30T10:43Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:43Z] [M::mem_pestat] (25, 50, 75) percentile: (295, 340, 355)
[2015-09-30T10:43Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (175, 475)
[2015-09-30T10:43Z] [M::mem_pestat] mean and std.dev: (328.19, 49.91)
[2015-09-30T10:43Z] [M::mem_pestat] low and high boundaries for proper pairs: (115, 535)
[2015-09-30T10:43Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:43Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-09-30T10:44Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:44Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:1\tPL:illumina\tPU:1_2014-08-13_dream-syn3\tSM:syn3-normal -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 981141 discordant read pairs to /dev/fd/62
[2015-09-30T10:44Z] samblaster: Output 140846 split reads to /dev/fd/63
[2015-09-30T10:44Z]
[2015-09-30T10:44Z] [main] Real time: 323.563 sec; CPU: 2414.196 sec
[2015-09-30T10:44Z] samblaster: Marked 143600 of 3857016 (3.72%) read ids as duplicates using 81236k memory in 6.592S CPU seconds and 5M23S(323S) wall time.
[2015-09-30T10:44Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-180000001_195428064-sr.bam
[2015-09-30T10:44Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-180000001_195428064-disc.bam
[2015-09-30T10:44Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:44Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T10:44Z] samblaster: Version 0.1.22
[2015-09-30T10:44Z] samblaster: Inputting from stdin
[2015-09-30T10:44Z] samblaster: Outputting to stdout
[2015-09-30T10:44Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:44Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:45Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:45Z] [M::mem_pestat] (25, 50, 75) percentile: (245, 682, 1241)
[2015-09-30T10:45Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3233)
[2015-09-30T10:45Z] [M::mem_pestat] mean and std.dev: (705.23, 607.97)
[2015-09-30T10:45Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4229)
[2015-09-30T10:45Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:45Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 352)
[2015-09-30T10:45Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 396)
[2015-09-30T10:45Z] [M::mem_pestat] mean and std.dev: (341.79, 14.87)
[2015-09-30T10:45Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 418)
[2015-09-30T10:45Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:45Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:45Z] [M::mem_pestat] (25, 50, 75) percentile: (354, 745, 1109)
[2015-09-30T10:45Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2619)
[2015-09-30T10:45Z] [M::mem_pestat] mean and std.dev: (772.94, 557.92)
[2015-09-30T10:45Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3374)
[2015-09-30T10:45Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:45Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:45Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (394, 1914, 2388)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6376)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (1489.69, 1063.20)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8370)
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (343.13, 15.02)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (451, 1575, 2258)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5872)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (1424.44, 897.96)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7679)
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (172, 304, 944)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2488)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (546.96, 541.96)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3260)
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (343.27, 15.15)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (4838, 4877, 4908)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (4698, 5048)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (4872.74, 47.25)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (4628, 5118)
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (307, 584, 1339)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3403)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (754.09, 676.36)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4435)
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (121, 205, 471)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1171)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (206.27, 180.29)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1521)
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (343.95, 15.16)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (171, 288, 702)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1764)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (392.54, 379.65)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2295)
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (232, 310, 2564)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7228)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (1575.68, 2203.20)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9560)
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (344.27, 15.14)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:46Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:46Z] [M::mem_pestat] (25, 50, 75) percentile: (248, 343, 1441)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3827)
[2015-09-30T10:46Z] [M::mem_pestat] mean and std.dev: (534.28, 536.34)
[2015-09-30T10:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5020)
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:46Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (171, 220, 328)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 642)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (224.90, 128.99)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 799)
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (346.91, 15.68)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (2860, 2990, 3074)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (2432, 3502)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (2977.58, 118.09)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (2218, 3716)
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (210, 303, 658)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1554)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (353.75, 318.57)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2002)
[2015-09-30T10:47Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:47Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:47Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (188, 266, 8103)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 23933)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (2566.72, 3656.58)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 31848)
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (345.33, 15.25)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:47Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (229, 311, 8161)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 24025)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (2848.09, 3607.13)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 31957)
[2015-09-30T10:47Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:47Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (179, 973, 4472)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13058)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (2136.78, 2189.91)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 17351)
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (344.05, 15.13)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (4856, 4932, 4969)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (4630, 5195)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (4934.21, 51.06)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (4517, 5308)
[2015-09-30T10:47Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:47Z] [M::mem_pestat] (25, 50, 75) percentile: (250, 2017, 4243)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12229)
[2015-09-30T10:47Z] [M::mem_pestat] mean and std.dev: (2287.16, 2065.88)
[2015-09-30T10:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 16222)
[2015-09-30T10:47Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:47Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:47Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (213, 558, 3724)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10746)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (2138.20, 2804.16)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 14257)
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 355)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (283, 403)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (343.65, 15.37)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (259, 427)
[2015-09-30T10:48Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (309, 830, 1917)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5133)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (1029.55, 1038.94)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6741)
[2015-09-30T10:48Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:48Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (123, 199, 337)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 765)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (170.95, 96.62)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 979)
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (346.11, 15.55)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T10:48Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (210, 265, 429)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 867)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (257.67, 160.07)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1086)
[2015-09-30T10:48Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:48Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (168, 212, 304)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 576)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (203.20, 99.64)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 712)
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (343.99, 15.17)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (731, 745, 2106)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4856)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (1171.21, 738.48)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6231)
[2015-09-30T10:48Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:48Z] [M::mem_pestat] (25, 50, 75) percentile: (185, 260, 864)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2222)
[2015-09-30T10:48Z] [M::mem_pestat] mean and std.dev: (512.96, 548.12)
[2015-09-30T10:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2901)
[2015-09-30T10:48Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:48Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:48Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:49Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:49Z] [M::mem_pestat] (25, 50, 75) percentile: (207, 263, 767)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1887)
[2015-09-30T10:49Z] [M::mem_pestat] mean and std.dev: (403.27, 366.07)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2447)
[2015-09-30T10:49Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:49Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:49Z] [M::mem_pestat] mean and std.dev: (345.04, 15.64)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:49Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:49Z] [M::mem_pestat] (25, 50, 75) percentile: (3461, 3488, 3517)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (3349, 3629)
[2015-09-30T10:49Z] [M::mem_pestat] mean and std.dev: (3482.76, 43.94)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (3293, 3685)
[2015-09-30T10:49Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:49Z] [M::mem_pestat] (25, 50, 75) percentile: (240, 333, 834)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2022)
[2015-09-30T10:49Z] [M::mem_pestat] mean and std.dev: (486.14, 403.43)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2616)
[2015-09-30T10:49Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:49Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:49Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:49Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:49Z] [M::mem_pestat] (25, 50, 75) percentile: (104, 221, 338)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 806)
[2015-09-30T10:49Z] [M::mem_pestat] mean and std.dev: (172.75, 118.92)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1040)
[2015-09-30T10:49Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:49Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T10:49Z] [M::mem_pestat] mean and std.dev: (345.68, 15.34)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T10:49Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:49Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:49Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 233, 360)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 794)
[2015-09-30T10:49Z] [M::mem_pestat] mean and std.dev: (255.67, 191.40)
[2015-09-30T10:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1011)
[2015-09-30T10:49Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:49Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:49Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:49Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 474821 discordant read pairs to /dev/fd/62
[2015-09-30T10:49Z] samblaster: Output 28142 split reads to /dev/fd/63
[2015-09-30T10:49Z]
[2015-09-30T10:49Z] [main] Real time: 260.298 sec; CPU: 1878.631 sec
[2015-09-30T10:49Z] samblaster: Marked 219925 of 5000000 (4.40%) read ids as duplicates using 148120k memory in 7.771S CPU seconds and 4M20S(260S) wall time.
[2015-09-30T10:50Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_20000000-sr.bam
[2015-09-30T10:50Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_20000000-disc.bam
[2015-09-30T10:50Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:50Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T10:50Z] samblaster: Version 0.1.22
[2015-09-30T10:50Z] samblaster: Inputting from stdin
[2015-09-30T10:50Z] samblaster: Outputting to stdout
[2015-09-30T10:50Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:50Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:50Z] [M::mem_pestat] (25, 50, 75) percentile: (159, 272, 1328)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3666)
[2015-09-30T10:50Z] [M::mem_pestat] mean and std.dev: (836.00, 995.82)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4835)
[2015-09-30T10:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:50Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:50Z] [M::mem_pestat] mean and std.dev: (344.39, 15.21)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:50Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:50Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:50Z] [M::mem_pestat] (25, 50, 75) percentile: (190, 585, 2315)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6565)
[2015-09-30T10:50Z] [M::mem_pestat] mean and std.dev: (1117.59, 1219.30)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8690)
[2015-09-30T10:50Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:50Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:50Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:50Z] [M::mem_pestat] (25, 50, 75) percentile: (273, 2012, 2454)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6816)
[2015-09-30T10:50Z] [M::mem_pestat] mean and std.dev: (1401.52, 1060.62)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8997)
[2015-09-30T10:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:50Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 346, 357)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T10:50Z] [M::mem_pestat] mean and std.dev: (346.34, 15.70)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T10:50Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:50Z] [M::mem_pestat] (25, 50, 75) percentile: (1132, 1180, 1992)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3712)
[2015-09-30T10:50Z] [M::mem_pestat] mean and std.dev: (1192.36, 173.16)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4572)
[2015-09-30T10:50Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:50Z] [M::mem_pestat] (25, 50, 75) percentile: (543, 2167, 2609)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6741)
[2015-09-30T10:50Z] [M::mem_pestat] mean and std.dev: (1721.38, 1241.54)
[2015-09-30T10:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8807)
[2015-09-30T10:50Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:50Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:50Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (171, 234, 788)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2022)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (399.75, 471.86)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2639)
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (344.37, 15.17)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:51Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (204, 310, 779)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1929)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (459.98, 404.51)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2504)
[2015-09-30T10:51Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:51Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (177, 262, 820)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2106)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (433.02, 470.08)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2749)
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (344.65, 15.54)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (7801, 7837, 7875)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (7653, 8023)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (7835.81, 52.11)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (7579, 8097)
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (281, 423, 1646)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4376)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (632.85, 705.01)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5741)
[2015-09-30T10:51Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:51Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:51Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (220, 289, 633)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1459)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (325.22, 245.51)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1872)
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (345.18, 15.62)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (1091, 1098, 1113)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1047, 1157)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (1101.91, 12.30)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1025, 1179)
[2015-09-30T10:51Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:51Z] [M::mem_pestat] (25, 50, 75) percentile: (200, 399, 1033)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2699)
[2015-09-30T10:51Z] [M::mem_pestat] mean and std.dev: (539.54, 529.36)
[2015-09-30T10:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3532)
[2015-09-30T10:51Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:51Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:51Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (154, 227, 317)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 643)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (188.71, 113.39)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 806)
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (346.83, 15.68)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (3803, 3857, 3950)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (3509, 4244)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (3830.18, 52.40)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (3362, 4391)
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (119, 238, 454)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1124)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (236.89, 210.85)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1459)
[2015-09-30T10:52Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:52Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:52Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (92, 198, 781)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2159)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (346.05, 453.72)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2848)
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (347.02, 15.64)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T10:52Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (151, 256, 803)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2107)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (333.73, 373.16)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2759)
[2015-09-30T10:52Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:52Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (165, 277, 724)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1842)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (356.44, 353.52)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2401)
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (344.09, 15.22)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (4851, 4879, 4894)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (4765, 4980)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (4880.94, 31.76)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (4722, 5023)
[2015-09-30T10:52Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:52Z] [M::mem_pestat] (25, 50, 75) percentile: (272, 490, 1015)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2501)
[2015-09-30T10:52Z] [M::mem_pestat] mean and std.dev: (521.09, 392.82)
[2015-09-30T10:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3244)
[2015-09-30T10:52Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:52Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:52Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (181, 781, 3108)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8962)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (1526.83, 1574.88)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 11889)
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (343.43, 15.26)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (309, 558, 2136)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5790)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (1231.81, 1245.92)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7617)
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (149, 234, 284)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 554)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (203.90, 101.49)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 689)
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (344.83, 15.54)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (260, 737, 1208)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3104)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (731.03, 642.12)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4052)
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (255, 1060, 5592)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16266)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (2887.95, 3076.58)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 21603)
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (343.52, 15.15)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (8355, 8396, 8436)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (8193, 8598)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (8404.64, 48.40)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (8112, 8679)
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (316, 1089, 5616)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16216)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (2942.40, 3010.16)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 21516)
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (153, 271, 1863)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5283)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (1123.85, 1444.87)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6993)
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (344.25, 15.23)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:53Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:53Z] [M::mem_pestat] (25, 50, 75) percentile: (233, 430, 1001)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2537)
[2015-09-30T10:53Z] [M::mem_pestat] mean and std.dev: (603.79, 580.39)
[2015-09-30T10:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3305)
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:53Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:54Z] [M::mem_pestat] (25, 50, 75) percentile: (217, 4792, 5110)
[2015-09-30T10:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14896)
[2015-09-30T10:54Z] [M::mem_pestat] mean and std.dev: (2724.79, 2409.58)
[2015-09-30T10:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 19789)
[2015-09-30T10:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:54Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T10:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T10:54Z] [M::mem_pestat] mean and std.dev: (347.03, 15.65)
[2015-09-30T10:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T10:54Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:54Z] [M::mem_pestat] (25, 50, 75) percentile: (1079, 2688, 2781)
[2015-09-30T10:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6185)
[2015-09-30T10:54Z] [M::mem_pestat] mean and std.dev: (1986.93, 848.01)
[2015-09-30T10:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7887)
[2015-09-30T10:54Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:54Z] [M::mem_pestat] (25, 50, 75) percentile: (303, 4743, 5052)
[2015-09-30T10:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14550)
[2015-09-30T10:54Z] [M::mem_pestat] mean and std.dev: (3056.63, 2318.50)
[2015-09-30T10:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 19299)
[2015-09-30T10:54Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:54Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:54Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:54Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:54Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T10:54Z] [main] Real time: 242.181 sec; CPU: 1833.716 sec
[2015-09-30T10:54Z] samblaster: Output 486439 discordant read pairs to /dev/fd/62
[2015-09-30T10:54Z] samblaster: Output 33018 split reads to /dev/fd/63
[2015-09-30T10:54Z] samblaster: Marked 211909 of 5000000 (4.24%) read ids as duplicates using 108616k memory in 7.874S CPU seconds and 4M2S(242S) wall time.
[2015-09-30T10:54Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-20000001_40000000-sr.bam
[2015-09-30T10:54Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-20000001_40000000-disc.bam
[2015-09-30T10:54Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T10:55Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T10:55Z] samblaster: Version 0.1.22
[2015-09-30T10:55Z] samblaster: Inputting from stdin
[2015-09-30T10:55Z] samblaster: Outputting to stdout
[2015-09-30T10:55Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T10:55Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T10:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:55Z] [M::mem_pestat] (25, 50, 75) percentile: (184, 276, 9341)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 27655)
[2015-09-30T10:55Z] [M::mem_pestat] mean and std.dev: (3138.71, 4130.25)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 36812)
[2015-09-30T10:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:55Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:55Z] [M::mem_pestat] mean and std.dev: (344.67, 15.29)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:55Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:55Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:55Z] [M::mem_pestat] (25, 50, 75) percentile: (265, 481, 9283)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 27319)
[2015-09-30T10:55Z] [M::mem_pestat] mean and std.dev: (3252.67, 4068.93)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 36337)
[2015-09-30T10:55Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:55Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:55Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T10:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:55Z] [M::mem_pestat] (25, 50, 75) percentile: (202, 248, 658)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1570)
[2015-09-30T10:55Z] [M::mem_pestat] mean and std.dev: (400.82, 375.99)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2026)
[2015-09-30T10:55Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:55Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 346, 357)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T10:55Z] [M::mem_pestat] mean and std.dev: (346.36, 15.64)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T10:55Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:55Z] [M::mem_pestat] (25, 50, 75) percentile: (1194, 1217, 1265)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1052, 1407)
[2015-09-30T10:55Z] [M::mem_pestat] mean and std.dev: (1221.20, 45.65)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (981, 1478)
[2015-09-30T10:55Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:55Z] [M::mem_pestat] (25, 50, 75) percentile: (121, 302, 612)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1594)
[2015-09-30T10:55Z] [M::mem_pestat] mean and std.dev: (390.54, 397.31)
[2015-09-30T10:55Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2085)
[2015-09-30T10:55Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:55Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:55Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (149, 225, 648)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1646)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (314.21, 351.08)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2145)
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 345, 356)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (345.30, 15.62)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (2299, 3046, 3106)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (685, 4720)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (2782.69, 414.62)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5527)
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (208, 302, 836)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2092)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (414.87, 360.10)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2720)
[2015-09-30T10:56Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:56Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:56Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (267, 1831, 4132)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11862)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (2362.28, 1946.16)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 15727)
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (343.09, 15.24)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (92, 115, 263)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 605)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (125.12, 70.84)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 776)
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (466, 2101, 4301)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11971)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (2416.92, 1818.36)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 15806)
[2015-09-30T10:56Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:56Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:56Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (179, 321, 1325)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3617)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (796.41, 943.49)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4763)
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (346.79, 15.40)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (6565, 6618, 6664)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (6367, 6862)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (6614.65, 52.04)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (6268, 6961)
[2015-09-30T10:56Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:56Z] [M::mem_pestat] (25, 50, 75) percentile: (254, 560, 1286)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3350)
[2015-09-30T10:56Z] [M::mem_pestat] mean and std.dev: (726.93, 731.97)
[2015-09-30T10:56Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4382)
[2015-09-30T10:56Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:56Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:56Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (132, 208, 1077)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2967)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (364.73, 500.24)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3912)
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (346.83, 15.64)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T10:57Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (206, 303, 819)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2045)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (386.89, 383.92)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2658)
[2015-09-30T10:57Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:57Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (121, 219, 296)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 646)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (181.59, 104.71)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 821)
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (346.90, 15.66)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (5161, 5196, 5242)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (4999, 5404)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (5203.71, 51.23)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (4918, 5485)
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (112, 254, 386)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 934)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (241.93, 194.96)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1208)
[2015-09-30T10:57Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:57Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:57Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (112, 216, 531)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1369)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (269.65, 286.38)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1788)
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (344.90, 15.57)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (1081, 1106, 1147)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (949, 1279)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (1117.95, 55.97)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (883, 1345)
[2015-09-30T10:57Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:57Z] [M::mem_pestat] (25, 50, 75) percentile: (185, 464, 1199)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3227)
[2015-09-30T10:57Z] [M::mem_pestat] mean and std.dev: (645.18, 704.68)
[2015-09-30T10:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4241)
[2015-09-30T10:57Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:57Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:57Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (103, 182, 290)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 664)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (172.73, 107.68)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 851)
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (346.92, 15.37)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T10:58Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (253, 576, 1490)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3964)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (902.41, 883.17)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5201)
[2015-09-30T10:58Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:58Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (173, 261, 3839)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11171)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (1972.92, 2756.42)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 14837)
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (346.63, 15.68)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (8255, 8294, 8318)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (8129, 8444)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (8285.03, 51.42)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (8066, 8507)
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (176, 565, 5425)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15923)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (2315.75, 2884.01)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 21172)
[2015-09-30T10:58Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:58Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:58Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (159, 239, 360)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 762)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (230.18, 146.18)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 963)
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (344.91, 15.50)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T10:58Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:58Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:58Z] [M::mem_pestat] (25, 50, 75) percentile: (264, 408, 915)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2217)
[2015-09-30T10:58Z] [M::mem_pestat] mean and std.dev: (570.21, 441.46)
[2015-09-30T10:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2868)
[2015-09-30T10:58Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:58Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:59Z] [M::mem_pestat] (25, 50, 75) percentile: (294, 2203, 8568)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 25116)
[2015-09-30T10:59Z] [M::mem_pestat] mean and std.dev: (4472.32, 3893.44)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 33390)
[2015-09-30T10:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:59Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T10:59Z] [M::mem_pestat] mean and std.dev: (344.33, 15.17)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T10:59Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T10:59Z] [M::mem_pestat] (25, 50, 75) percentile: (346, 374, 404)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (230, 520)
[2015-09-30T10:59Z] [M::mem_pestat] mean and std.dev: (374.46, 47.30)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (172, 578)
[2015-09-30T10:59Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:59Z] [M::mem_pestat] (25, 50, 75) percentile: (678, 2047, 8533)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 24243)
[2015-09-30T10:59Z] [M::mem_pestat] mean and std.dev: (4470.20, 3828.90)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 32098)
[2015-09-30T10:59Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:59Z] [M::mem_pestat] skip orientation RF
[2015-09-30T10:59Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T10:59Z] [M::mem_pestat] (25, 50, 75) percentile: (186, 291, 690)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1698)
[2015-09-30T10:59Z] [M::mem_pestat] mean and std.dev: (438.56, 397.29)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2202)
[2015-09-30T10:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T10:59Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T10:59Z] [M::mem_pestat] mean and std.dev: (343.67, 15.30)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T10:59Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T10:59Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T10:59Z] [M::mem_pestat] (25, 50, 75) percentile: (242, 470, 1051)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2669)
[2015-09-30T10:59Z] [M::mem_pestat] mean and std.dev: (621.39, 602.60)
[2015-09-30T10:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3478)
[2015-09-30T10:59Z] [M::mem_pestat] skip orientation FF
[2015-09-30T10:59Z] [M::mem_pestat] skip orientation RR
[2015-09-30T10:59Z] [main] Version: 0.7.12-r1039
[2015-09-30T10:59Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T10:59Z] [main] Real time: 253.605 sec; CPU: 1869.944 sec
[2015-09-30T10:59Z] samblaster: Output 494034 discordant read pairs to /dev/fd/62
[2015-09-30T10:59Z] samblaster: Output 35174 split reads to /dev/fd/63
[2015-09-30T10:59Z] samblaster: Marked 204211 of 5000000 (4.08%) read ids as duplicates using 108112k memory in 7.920S CPU seconds and 4M13S(253S) wall time.
[2015-09-30T10:59Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-40000001_60000000-sr.bam
[2015-09-30T10:59Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-40000001_60000000-disc.bam
[2015-09-30T10:59Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T11:00Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T11:00Z] samblaster: Version 0.1.22
[2015-09-30T11:00Z] samblaster: Inputting from stdin
[2015-09-30T11:00Z] samblaster: Outputting to stdout
[2015-09-30T11:00Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T11:00Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T11:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:00Z] [M::mem_pestat] (25, 50, 75) percentile: (279, 3180, 3630)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10332)
[2015-09-30T11:00Z] [M::mem_pestat] mean and std.dev: (2132.66, 1845.51)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 13683)
[2015-09-30T11:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:00Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:00Z] [M::mem_pestat] mean and std.dev: (344.56, 15.27)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:00Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:00Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:00Z] [M::mem_pestat] (25, 50, 75) percentile: (361, 3173, 3705)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10393)
[2015-09-30T11:00Z] [M::mem_pestat] mean and std.dev: (2275.30, 1610.97)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 13737)
[2015-09-30T11:00Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:00Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:00Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T11:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:00Z] [M::mem_pestat] (25, 50, 75) percentile: (203, 243, 321)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 557)
[2015-09-30T11:00Z] [M::mem_pestat] mean and std.dev: (209.29, 64.13)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 675)
[2015-09-30T11:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:00Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:00Z] [M::mem_pestat] mean and std.dev: (343.27, 15.15)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:00Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:00Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:00Z] [M::mem_pestat] (25, 50, 75) percentile: (238, 356, 720)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1684)
[2015-09-30T11:00Z] [M::mem_pestat] mean and std.dev: (435.56, 349.60)
[2015-09-30T11:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2166)
[2015-09-30T11:00Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:00Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (228, 1716, 2310)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6474)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (1289.72, 1108.34)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8556)
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (345.62, 15.38)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (9613, 9650, 9666)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (9507, 9772)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (9644.15, 44.08)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (9454, 9825)
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (321, 1702, 2105)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5673)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (1279.07, 1008.58)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7457)
[2015-09-30T11:01Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:01Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:01Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (175, 212, 272)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 466)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (182.50, 85.56)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 563)
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 346, 357)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (346.61, 15.65)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (740, 762, 776)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (668, 848)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (763.36, 34.69)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (625, 884)
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (221, 276, 674)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1580)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (332.40, 272.46)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2033)
[2015-09-30T11:01Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:01Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:01Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (165, 291, 2367)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6771)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (884.49, 1063.48)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8973)
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (346.08, 15.54)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T11:01Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:01Z] [M::mem_pestat] (25, 50, 75) percentile: (196, 260, 1370)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3718)
[2015-09-30T11:01Z] [M::mem_pestat] mean and std.dev: (801.68, 1005.99)
[2015-09-30T11:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4892)
[2015-09-30T11:01Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:01Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (183, 249, 634)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1536)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (376.27, 322.01)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1987)
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (343.42, 15.28)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (32, 42, 62)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 122)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (43.76, 20.90)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 152)
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (171, 241, 879)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2295)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (505.73, 516.44)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3003)
[2015-09-30T11:02Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:02Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:02Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (135, 239, 511)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1263)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (260.33, 252.74)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1639)
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (345.26, 15.29)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (1553, 1594, 1625)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1409, 1769)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (1591.04, 49.49)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1337, 1841)
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (149, 341, 787)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2063)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (461.81, 442.17)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2701)
[2015-09-30T11:02Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:02Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:02Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (315, 3115, 3475)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9795)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (2261.99, 1686.08)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 12955)
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (343.90, 15.12)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:02Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:02Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:02Z] [M::mem_pestat] (25, 50, 75) percentile: (525, 1980, 3371)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9063)
[2015-09-30T11:02Z] [M::mem_pestat] mean and std.dev: (1966.35, 1408.44)
[2015-09-30T11:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 11909)
[2015-09-30T11:02Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:02Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (138, 221, 865)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2319)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (448.76, 534.95)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3046)
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (344.96, 15.69)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (3563, 3605, 3661)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (3367, 3857)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (3603.97, 49.59)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (3269, 3955)
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (201, 351, 957)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2469)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (557.34, 576.20)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3225)
[2015-09-30T11:03Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:03Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:03Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (122, 232, 597)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1547)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (355.13, 401.49)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2022)
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (345.72, 15.43)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (99, 165, 281)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 645)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (187.19, 116.31)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 827)
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (136, 289, 738)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1942)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (424.83, 466.77)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2544)
[2015-09-30T11:03Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:03Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:03Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (131, 237, 381)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 881)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (179.39, 100.93)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1131)
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (344.77, 15.52)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (2801, 2848, 2895)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (2613, 3083)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (2867.76, 51.52)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (2519, 3177)
[2015-09-30T11:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:03Z] [M::mem_pestat] (25, 50, 75) percentile: (191, 372, 1079)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2855)
[2015-09-30T11:03Z] [M::mem_pestat] mean and std.dev: (524.12, 455.02)
[2015-09-30T11:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3743)
[2015-09-30T11:03Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:03Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:03Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:04Z] [M::mem_pestat] (25, 50, 75) percentile: (225, 362, 1814)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4992)
[2015-09-30T11:04Z] [M::mem_pestat] mean and std.dev: (553.94, 806.74)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6581)
[2015-09-30T11:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:04Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:04Z] [M::mem_pestat] mean and std.dev: (343.64, 15.31)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:04Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:04Z] [M::mem_pestat] (25, 50, 75) percentile: (58, 3726, 4957)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14755)
[2015-09-30T11:04Z] [M::mem_pestat] mean and std.dev: (3302.22, 2515.00)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 19654)
[2015-09-30T11:04Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:04Z] [M::mem_pestat] (25, 50, 75) percentile: (290, 425, 1272)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3236)
[2015-09-30T11:04Z] [M::mem_pestat] mean and std.dev: (516.51, 412.10)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4218)
[2015-09-30T11:04Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:04Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:04Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:04Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 256, 334)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 714)
[2015-09-30T11:04Z] [M::mem_pestat] mean and std.dev: (211.62, 123.81)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 904)
[2015-09-30T11:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:04Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:04Z] [M::mem_pestat] mean and std.dev: (344.41, 15.33)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:04Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:04Z] [M::mem_pestat] (25, 50, 75) percentile: (842, 875, 919)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (688, 1073)
[2015-09-30T11:04Z] [M::mem_pestat] mean and std.dev: (869.10, 47.23)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (611, 1150)
[2015-09-30T11:04Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:04Z] [M::mem_pestat] (25, 50, 75) percentile: (200, 511, 917)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2351)
[2015-09-30T11:04Z] [M::mem_pestat] mean and std.dev: (511.26, 443.15)
[2015-09-30T11:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3068)
[2015-09-30T11:04Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:04Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:04Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:04Z] [main] Version: 0.7.12-r1039
[2015-09-30T11:04Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T11:04Z] [main] Real time: 266.072 sec; CPU: 1945.312 sec
[2015-09-30T11:04Z] samblaster: Output 477488 discordant read pairs to /dev/fd/62
[2015-09-30T11:04Z] samblaster: Output 31374 split reads to /dev/fd/63
[2015-09-30T11:04Z] samblaster: Marked 211358 of 5000000 (4.23%) read ids as duplicates using 124208k memory in 7.962S CPU seconds and 4M26S(266S) wall time.
[2015-09-30T11:05Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-60000001_80000000-sr.bam
[2015-09-30T11:05Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-60000001_80000000-disc.bam
[2015-09-30T11:05Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T11:05Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T11:05Z] samblaster: Version 0.1.22
[2015-09-30T11:05Z] samblaster: Inputting from stdin
[2015-09-30T11:05Z] samblaster: Outputting to stdout
[2015-09-30T11:05Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T11:05Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (54, 186, 278)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 726)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (148.33, 105.44)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 950)
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (345.82, 15.33)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (215, 329, 928)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2354)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (501.89, 473.77)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3067)
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:06Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (154, 216, 297)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 583)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (187.94, 101.33)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 726)
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 358)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 406)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (346.90, 15.66)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 430)
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (6881, 6907, 6953)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (6737, 7097)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (6909.25, 51.05)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (6665, 7169)
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (165, 331, 779)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2007)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (328.96, 237.87)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2621)
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (1957, 2010, 2052)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1767, 2242)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (2013.11, 69.53)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1672, 2337)
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 357)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (282, 407)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (343.39, 15.88)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (257, 432)
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (1952, 2013, 2056)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1744, 2264)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (2008.51, 80.10)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1640, 2368)
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (159, 230, 335)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 687)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (226.92, 127.95)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 863)
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (345.34, 15.32)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (4097, 4109, 4141)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (4009, 4229)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (4121.50, 43.63)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (3947, 4273)
[2015-09-30T11:06Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:06Z] [M::mem_pestat] (25, 50, 75) percentile: (218, 324, 668)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1568)
[2015-09-30T11:06Z] [M::mem_pestat] mean and std.dev: (410.94, 339.61)
[2015-09-30T11:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2018)
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:06Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:07Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 284, 2293)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6589)
[2015-09-30T11:07Z] [M::mem_pestat] mean and std.dev: (954.10, 1085.42)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8737)
[2015-09-30T11:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:07Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:07Z] [M::mem_pestat] mean and std.dev: (345.57, 15.28)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:07Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:07Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:07Z] [M::mem_pestat] (25, 50, 75) percentile: (442, 1159, 2364)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6208)
[2015-09-30T11:07Z] [M::mem_pestat] mean and std.dev: (1399.54, 1059.00)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8130)
[2015-09-30T11:07Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:07Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:07Z] [M::mem_pestat] (25, 50, 75) percentile: (160, 236, 500)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1180)
[2015-09-30T11:07Z] [M::mem_pestat] mean and std.dev: (274.50, 230.13)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1520)
[2015-09-30T11:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:07Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:07Z] [M::mem_pestat] mean and std.dev: (345.27, 15.27)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:07Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:07Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:07Z] [M::mem_pestat] (25, 50, 75) percentile: (284, 357, 1154)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2894)
[2015-09-30T11:07Z] [M::mem_pestat] mean and std.dev: (727.49, 714.56)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3764)
[2015-09-30T11:07Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:07Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:07Z] [M::mem_pestat] (25, 50, 75) percentile: (170, 259, 608)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1484)
[2015-09-30T11:07Z] [M::mem_pestat] mean and std.dev: (303.24, 285.48)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1922)
[2015-09-30T11:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:07Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:07Z] [M::mem_pestat] mean and std.dev: (343.73, 15.16)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:07Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:07Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:07Z] [M::mem_pestat] (25, 50, 75) percentile: (198, 348, 901)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2307)
[2015-09-30T11:07Z] [M::mem_pestat] mean and std.dev: (557.25, 522.77)
[2015-09-30T11:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3010)
[2015-09-30T11:07Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:07Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (215, 279, 751)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1823)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (417.99, 368.96)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2359)
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (342.28, 15.03)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (2096, 2200, 2237)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1814, 2519)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (2213.22, 48.84)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1673, 2660)
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (272, 532, 1136)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2864)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (714.86, 664.09)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3728)
[2015-09-30T11:08Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:08Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:08Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (161, 260, 971)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2591)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (503.06, 582.35)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3401)
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (343.36, 15.30)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (1835, 1877, 1946)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1613, 2168)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (1876.54, 51.44)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1502, 2279)
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (264, 620, 1060)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2652)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (726.01, 611.54)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3448)
[2015-09-30T11:08Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:08Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:08Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (127, 222, 843)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2275)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (439.42, 533.30)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2991)
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (345.41, 15.36)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (9139, 9185, 9213)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (8991, 9361)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (9178.02, 47.19)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (8917, 9435)
[2015-09-30T11:08Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:08Z] [M::mem_pestat] (25, 50, 75) percentile: (261, 380, 1114)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2820)
[2015-09-30T11:08Z] [M::mem_pestat] mean and std.dev: (585.26, 456.54)
[2015-09-30T11:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3673)
[2015-09-30T11:08Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:08Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:08Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:09Z] [M::mem_pestat] (25, 50, 75) percentile: (158, 230, 828)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2168)
[2015-09-30T11:09Z] [M::mem_pestat] mean and std.dev: (365.48, 375.49)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2838)
[2015-09-30T11:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:09Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:09Z] [M::mem_pestat] mean and std.dev: (344.64, 15.29)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:09Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:09Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:09Z] [M::mem_pestat] (25, 50, 75) percentile: (270, 454, 725)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1635)
[2015-09-30T11:09Z] [M::mem_pestat] mean and std.dev: (550.16, 376.33)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2090)
[2015-09-30T11:09Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:09Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:09Z] [M::mem_pestat] (25, 50, 75) percentile: (171, 262, 1128)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3042)
[2015-09-30T11:09Z] [M::mem_pestat] mean and std.dev: (427.72, 581.11)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3999)
[2015-09-30T11:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:09Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T11:09Z] [M::mem_pestat] mean and std.dev: (345.04, 15.52)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T11:09Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:09Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:09Z] [M::mem_pestat] (25, 50, 75) percentile: (223, 354, 1368)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3658)
[2015-09-30T11:09Z] [M::mem_pestat] mean and std.dev: (500.17, 531.51)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4803)
[2015-09-30T11:09Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:09Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:09Z] [M::mem_pestat] (25, 50, 75) percentile: (183, 226, 856)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2202)
[2015-09-30T11:09Z] [M::mem_pestat] mean and std.dev: (473.61, 536.16)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2875)
[2015-09-30T11:09Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:09Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T11:09Z] [M::mem_pestat] mean and std.dev: (344.78, 15.57)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T11:09Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:09Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:09Z] [M::mem_pestat] (25, 50, 75) percentile: (300, 866, 1552)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4056)
[2015-09-30T11:09Z] [M::mem_pestat] mean and std.dev: (944.00, 916.42)
[2015-09-30T11:09Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5308)
[2015-09-30T11:09Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:09Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:09Z] [main] Version: 0.7.12-r1039
[2015-09-30T11:09Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T11:09Z] [main] Real time: 252.029 sec; CPU: 1853.832 sec
[2015-09-30T11:09Z] samblaster: Output 487445 discordant read pairs to /dev/fd/62
[2015-09-30T11:09Z] samblaster: Output 36860 split reads to /dev/fd/63
[2015-09-30T11:09Z] samblaster: Marked 214094 of 5000000 (4.28%) read ids as duplicates using 109548k memory in 8.010S CPU seconds and 4M12S(252S) wall time.
[2015-09-30T11:10Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-80000001_100000000-sr.bam
[2015-09-30T11:10Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-80000001_100000000-disc.bam
[2015-09-30T11:10Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T11:10Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T11:10Z] samblaster: Version 0.1.22
[2015-09-30T11:10Z] samblaster: Inputting from stdin
[2015-09-30T11:10Z] samblaster: Outputting to stdout
[2015-09-30T11:10Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T11:10Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (231, 371, 1982)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5484)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (782.20, 1117.98)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7235)
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (343.48, 15.29)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (290, 873, 6367)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18521)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (2494.67, 2809.66)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 24598)
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:11Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (150, 294, 873)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2319)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (513.46, 491.29)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3042)
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 354)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (343.05, 15.26)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (257, 821, 836)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1994)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (632.93, 305.76)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2573)
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (285, 594, 1261)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3213)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (754.46, 628.94)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4189)
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (118, 244, 773)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2083)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (349.21, 406.24)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2738)
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 345, 356)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (344.95, 15.58)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (5401, 5435, 5469)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (5265, 5605)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (5440.45, 53.79)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (5197, 5673)
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (165, 259, 1179)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3207)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (786.70, 984.69)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4221)
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (242, 4665, 5028)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14600)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (2900.31, 2369.23)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 19386)
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (343.82, 15.18)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:11Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:11Z] [M::mem_pestat] (25, 50, 75) percentile: (512, 4309, 4932)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13772)
[2015-09-30T11:11Z] [M::mem_pestat] mean and std.dev: (2904.04, 2151.75)
[2015-09-30T11:11Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 18192)
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:11Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:12Z] [M::mem_pestat] (25, 50, 75) percentile: (174, 261, 575)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1377)
[2015-09-30T11:12Z] [M::mem_pestat] mean and std.dev: (341.26, 260.39)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1778)
[2015-09-30T11:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:12Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 352)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 396)
[2015-09-30T11:12Z] [M::mem_pestat] mean and std.dev: (341.75, 14.73)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 418)
[2015-09-30T11:12Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:12Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:12Z] [M::mem_pestat] (25, 50, 75) percentile: (254, 580, 1150)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2942)
[2015-09-30T11:12Z] [M::mem_pestat] mean and std.dev: (720.82, 646.78)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3838)
[2015-09-30T11:12Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:12Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:12Z] [M::mem_pestat] (25, 50, 75) percentile: (171, 247, 1018)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2712)
[2015-09-30T11:12Z] [M::mem_pestat] mean and std.dev: (391.50, 451.90)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3559)
[2015-09-30T11:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:12Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T11:12Z] [M::mem_pestat] mean and std.dev: (344.42, 15.52)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T11:12Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:12Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:12Z] [M::mem_pestat] (25, 50, 75) percentile: (192, 342, 886)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2274)
[2015-09-30T11:12Z] [M::mem_pestat] mean and std.dev: (485.33, 490.48)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2968)
[2015-09-30T11:12Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:12Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:12Z] [M::mem_pestat] (25, 50, 75) percentile: (175, 300, 876)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2278)
[2015-09-30T11:12Z] [M::mem_pestat] mean and std.dev: (491.21, 488.50)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2979)
[2015-09-30T11:12Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:12Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T11:12Z] [M::mem_pestat] mean and std.dev: (344.92, 15.56)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T11:12Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:12Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:12Z] [M::mem_pestat] (25, 50, 75) percentile: (268, 465, 906)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2182)
[2015-09-30T11:12Z] [M::mem_pestat] mean and std.dev: (498.97, 348.31)
[2015-09-30T11:12Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2820)
[2015-09-30T11:12Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:12Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 234, 379)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 851)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (198.71, 142.91)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1087)
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (344.22, 15.14)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (229, 421, 864)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2134)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (557.86, 473.39)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2769)
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (123, 200, 622)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1620)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (292.42, 367.71)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2119)
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (345.83, 15.65)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (1930, 1959, 1988)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1814, 2104)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (1958.79, 52.08)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1750, 2162)
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (238, 429, 1729)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4711)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (961.28, 1126.78)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6202)
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 266, 1254)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3476)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (657.06, 884.26)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4587)
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (344.55, 15.34)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (278, 609, 1078)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2678)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (656.45, 586.81)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3478)
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (130, 236, 1184)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3292)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (578.98, 724.46)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4346)
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (343.97, 15.21)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:13Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:13Z] [M::mem_pestat] (25, 50, 75) percentile: (251, 418, 899)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2195)
[2015-09-30T11:13Z] [M::mem_pestat] mean and std.dev: (575.74, 499.59)
[2015-09-30T11:13Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2843)
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:13Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:14Z] [M::mem_pestat] (25, 50, 75) percentile: (190, 506, 3771)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10933)
[2015-09-30T11:14Z] [M::mem_pestat] mean and std.dev: (1445.68, 1778.10)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 14514)
[2015-09-30T11:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:14Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T11:14Z] [M::mem_pestat] mean and std.dev: (346.69, 15.41)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T11:14Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:14Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:14Z] [M::mem_pestat] (25, 50, 75) percentile: (312, 678, 4112)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11712)
[2015-09-30T11:14Z] [M::mem_pestat] mean and std.dev: (1700.46, 1811.53)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 15512)
[2015-09-30T11:14Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:14Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:14Z] [M::mem_pestat] (25, 50, 75) percentile: (175, 290, 1220)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3310)
[2015-09-30T11:14Z] [M::mem_pestat] mean and std.dev: (609.55, 578.62)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4355)
[2015-09-30T11:14Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:14Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:14Z] [M::mem_pestat] mean and std.dev: (344.24, 15.10)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:14Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:14Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:14Z] [M::mem_pestat] (25, 50, 75) percentile: (260, 987, 1276)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3308)
[2015-09-30T11:14Z] [M::mem_pestat] mean and std.dev: (920.81, 669.72)
[2015-09-30T11:14Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4324)
[2015-09-30T11:14Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:14Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:14Z] [main] Version: 0.7.12-r1039
[2015-09-30T11:14Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62samblaster: Output 477756 discordant read pairs to /dev/fd/62
[2015-09-30T11:14Z] samblaster: Output 28754 split reads to /dev/fd/63
[2015-09-30T11:14Z]
[2015-09-30T11:14Z] [main] Real time: 238.265 sec; CPU: 1761.728 sec
[2015-09-30T11:14Z] samblaster: Marked 220288 of 5000000 (4.41%) read ids as duplicates using 111444k memory in 7.848S CPU seconds and 3M58S(238S) wall time.
[2015-09-30T11:15Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-100000001_120000000-sr.bam
[2015-09-30T11:15Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-100000001_120000000-disc.bam
[2015-09-30T11:15Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T11:15Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T11:15Z] samblaster: Version 0.1.22
[2015-09-30T11:15Z] samblaster: Inputting from stdin
[2015-09-30T11:15Z] samblaster: Outputting to stdout
[2015-09-30T11:15Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T11:15Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (243, 1873, 2667)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7515)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (1216.27, 1096.62)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9939)
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (343.50, 15.19)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (700, 1996, 4414)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11842)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (3119.88, 3164.77)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 15556)
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:16Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (142, 220, 266)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 514)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (183.04, 97.97)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 638)
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (346.30, 15.60)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (206, 294, 607)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1409)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (394.79, 358.06)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1810)
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (155, 233, 503)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1199)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (271.98, 219.18)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1547)
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (345.56, 15.40)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (205, 379, 716)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1738)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (460.00, 424.88)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2249)
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (147, 267, 1593)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4485)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (565.33, 739.15)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5931)
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (344.54, 15.28)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:16Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:16Z] [M::mem_pestat] (25, 50, 75) percentile: (185, 387, 935)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2435)
[2015-09-30T11:16Z] [M::mem_pestat] mean and std.dev: (543.32, 531.92)
[2015-09-30T11:16Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3185)
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:16Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (169, 300, 4047)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11803)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (1640.32, 1845.01)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 15681)
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (345.82, 15.65)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (2602, 2638, 2671)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (2464, 2809)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (2634.98, 50.35)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (2395, 2878)
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (270, 2795, 4443)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12789)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (2514.33, 1975.51)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 16962)
[2015-09-30T11:17Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:17Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:17Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (185, 283, 1498)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4124)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (582.38, 798.00)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5437)
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (344.75, 15.28)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:17Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (244, 535, 1944)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5344)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (951.16, 1150.80)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7044)
[2015-09-30T11:17Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:17Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (226, 352, 1090)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2818)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (672.68, 650.78)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3682)
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 354)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (342.91, 15.18)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (189, 252, 334)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 624)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (246.38, 139.55)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 769)
[2015-09-30T11:17Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:17Z] [M::mem_pestat] (25, 50, 75) percentile: (252, 425, 1321)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3459)
[2015-09-30T11:17Z] [M::mem_pestat] mean and std.dev: (681.25, 663.97)
[2015-09-30T11:17Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4528)
[2015-09-30T11:17Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:17Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:17Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:18Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:18Z] [M::mem_pestat] (25, 50, 75) percentile: (141, 225, 492)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1194)
[2015-09-30T11:18Z] [M::mem_pestat] mean and std.dev: (254.71, 245.62)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1545)
[2015-09-30T11:18Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:18Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:18Z] [M::mem_pestat] mean and std.dev: (344.30, 15.22)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:18Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:18Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:18Z] [M::mem_pestat] (25, 50, 75) percentile: (280, 338, 670)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1450)
[2015-09-30T11:18Z] [M::mem_pestat] mean and std.dev: (386.67, 201.07)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1840)
[2015-09-30T11:18Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:18Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:18Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:18Z] [M::mem_pestat] (25, 50, 75) percentile: (228, 2397, 3226)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9222)
[2015-09-30T11:18Z] [M::mem_pestat] mean and std.dev: (1865.06, 1593.83)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 12220)
[2015-09-30T11:18Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:18Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T11:18Z] [M::mem_pestat] mean and std.dev: (345.94, 15.63)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T11:18Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:18Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:18Z] [M::mem_pestat] (25, 50, 75) percentile: (303, 2258, 3189)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8961)
[2015-09-30T11:18Z] [M::mem_pestat] mean and std.dev: (1972.10, 1704.82)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 11847)
[2015-09-30T11:18Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:18Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:18Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:18Z] [M::mem_pestat] (25, 50, 75) percentile: (150, 248, 613)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1539)
[2015-09-30T11:18Z] [M::mem_pestat] mean and std.dev: (351.53, 348.80)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2002)
[2015-09-30T11:18Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:18Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:18Z] [M::mem_pestat] mean and std.dev: (344.20, 15.19)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:18Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:18Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:18Z] [M::mem_pestat] (25, 50, 75) percentile: (226, 329, 568)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1252)
[2015-09-30T11:18Z] [M::mem_pestat] mean and std.dev: (361.85, 262.68)
[2015-09-30T11:18Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1594)
[2015-09-30T11:18Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:18Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (191, 281, 1030)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2708)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (459.27, 446.02)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3547)
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (344.13, 15.20)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:19Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (267, 510, 1328)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3450)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (674.23, 627.94)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4511)
[2015-09-30T11:19Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:19Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (978, 4765, 5065)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13239)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (3565.76, 2056.54)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 17326)
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 353)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (341.82, 15.10)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (247, 1189, 4525)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13081)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (2286.45, 2074.43)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 17359)
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (1028, 4713, 5000)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12944)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (3512.64, 2008.85)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 16916)
[2015-09-30T11:19Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:19Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:19Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (159, 273, 1354)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3744)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (703.10, 817.02)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4939)
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 353)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 397)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (342.87, 14.86)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 419)
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (3515, 3551, 3589)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (3367, 3737)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (3551.92, 47.21)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (3293, 3811)
[2015-09-30T11:19Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:19Z] [M::mem_pestat] (25, 50, 75) percentile: (232, 649, 1669)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4543)
[2015-09-30T11:19Z] [M::mem_pestat] mean and std.dev: (909.57, 927.12)
[2015-09-30T11:19Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5980)
[2015-09-30T11:19Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:19Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:19Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:19Z] [main] Version: 0.7.12-r1039
[2015-09-30T11:19Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T11:19Z] [main] Real time: 261.348 sec; CPU: 1899.057 sec
[2015-09-30T11:19Z] samblaster: Output 471958 discordant read pairs to /dev/fd/62
[2015-09-30T11:19Z] samblaster: Output 28874 split reads to /dev/fd/63
[2015-09-30T11:19Z] samblaster: Marked 215895 of 5000000 (4.32%) read ids as duplicates using 104128k memory in 7.924S CPU seconds and 4M21S(261S) wall time.
[2015-09-30T11:20Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-120000001_140000000-sr.bam
[2015-09-30T11:20Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-120000001_140000000-disc.bam
[2015-09-30T11:20Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T11:20Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T11:20Z] samblaster: Version 0.1.22
[2015-09-30T11:20Z] samblaster: Inputting from stdin
[2015-09-30T11:20Z] samblaster: Outputting to stdout
[2015-09-30T11:20Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T11:20Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T11:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:21Z] [M::mem_pestat] (25, 50, 75) percentile: (220, 934, 4075)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11785)
[2015-09-30T11:21Z] [M::mem_pestat] mean and std.dev: (2060.40, 2436.27)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 15640)
[2015-09-30T11:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:21Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:21Z] [M::mem_pestat] mean and std.dev: (344.78, 15.23)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:21Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:21Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:21Z] [M::mem_pestat] (25, 50, 75) percentile: (236, 544, 1218)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3182)
[2015-09-30T11:21Z] [M::mem_pestat] mean and std.dev: (637.45, 592.17)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4164)
[2015-09-30T11:21Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:21Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:21Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T11:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:21Z] [M::mem_pestat] (25, 50, 75) percentile: (187, 256, 686)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1684)
[2015-09-30T11:21Z] [M::mem_pestat] mean and std.dev: (372.94, 325.21)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2183)
[2015-09-30T11:21Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:21Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T11:21Z] [M::mem_pestat] mean and std.dev: (342.65, 15.10)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T11:21Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:21Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:21Z] [M::mem_pestat] (25, 50, 75) percentile: (420, 921, 1411)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3393)
[2015-09-30T11:21Z] [M::mem_pestat] mean and std.dev: (1016.96, 750.18)
[2015-09-30T11:21Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4384)
[2015-09-30T11:21Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:21Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (189, 270, 561)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1305)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (325.23, 247.14)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1677)
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (343.42, 15.21)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (1987, 2751, 4495)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9511)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (3160.87, 1178.08)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 12019)
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (242, 691, 1906)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5234)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (1132.13, 1304.10)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6898)
[2015-09-30T11:22Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:22Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:22Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (214, 284, 913)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2311)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (602.08, 652.88)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3010)
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (343.99, 15.19)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (2057, 2078, 2125)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1921, 2261)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (2085.60, 56.87)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1853, 2329)
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (289, 501, 1224)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3094)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (817.54, 698.63)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4029)
[2015-09-30T11:22Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:22Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:22Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (213, 442, 1214)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3216)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (722.65, 678.20)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4217)
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (342.11, 15.07)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (891, 1046, 1057)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (559, 1389)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (999.81, 146.72)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (393, 1555)
[2015-09-30T11:22Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:22Z] [M::mem_pestat] (25, 50, 75) percentile: (289, 496, 1068)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2626)
[2015-09-30T11:22Z] [M::mem_pestat] mean and std.dev: (658.79, 529.51)
[2015-09-30T11:22Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3405)
[2015-09-30T11:22Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:22Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:22Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (162, 285, 834)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2178)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (451.49, 469.74)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2850)
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (343.47, 15.15)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (4018, 4046, 4070)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (3914, 4174)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (4047.44, 41.93)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (3862, 4226)
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (249, 420, 924)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2274)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (595.25, 540.92)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2949)
[2015-09-30T11:23Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:23Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:23Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (174, 233, 747)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1893)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (302.06, 260.67)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2466)
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 355)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (283, 403)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (343.23, 15.40)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (259, 427)
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (5547, 5592, 5624)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (5393, 5778)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (5601.65, 48.18)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (5316, 5855)
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (291, 474, 2176)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5946)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (1389.69, 1782.40)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7831)
[2015-09-30T11:23Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:23Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:23Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (236, 405, 1959)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5405)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (1094.90, 1326.04)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7128)
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (344.01, 15.23)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (3981, 4068, 4109)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (3725, 4365)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (4081.62, 51.89)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (3597, 4493)
[2015-09-30T11:23Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:23Z] [M::mem_pestat] (25, 50, 75) percentile: (319, 951, 1668)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4366)
[2015-09-30T11:23Z] [M::mem_pestat] mean and std.dev: (1042.00, 806.81)
[2015-09-30T11:23Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5715)
[2015-09-30T11:23Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:23Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:23Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (225, 274, 633)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1449)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (393.21, 321.50)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1857)
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (343.09, 15.10)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (376, 743, 1640)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4168)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (1015.21, 862.66)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5432)
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (183, 236, 434)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 936)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (255.30, 168.12)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1187)
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 344, 355)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (283, 403)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (344.08, 15.55)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (259, 427)
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (7746, 7755, 7787)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (7664, 7869)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (7761.94, 29.78)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (7623, 7910)
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (249, 347, 1241)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3225)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (781.06, 840.94)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4217)
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (192, 310, 1291)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3489)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (611.00, 670.67)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4588)
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 354)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (343.02, 15.20)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (2868, 2958, 2980)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (2644, 3204)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (2964.86, 60.24)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (2532, 3316)
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (345, 913, 2753)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7569)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (1787.08, 2054.10)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9977)
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (271, 1114, 6501)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18961)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (2575.62, 2807.26)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 25191)
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 354)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (343.01, 15.28)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:24Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:24Z] [M::mem_pestat] (25, 50, 75) percentile: (293, 848, 1925)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5189)
[2015-09-30T11:24Z] [M::mem_pestat] mean and std.dev: (798.67, 766.67)
[2015-09-30T11:24Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6821)
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:24Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:25Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:25Z] [M::mem_pestat] (25, 50, 75) percentile: (290, 744, 2701)
[2015-09-30T11:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7523)
[2015-09-30T11:25Z] [M::mem_pestat] mean and std.dev: (1287.15, 1286.48)
[2015-09-30T11:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9934)
[2015-09-30T11:25Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:25Z] [M::mem_pestat] (25, 50, 75) percentile: (334, 346, 357)
[2015-09-30T11:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (288, 403)
[2015-09-30T11:25Z] [M::mem_pestat] mean and std.dev: (346.32, 15.39)
[2015-09-30T11:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 426)
[2015-09-30T11:25Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:25Z] [M::mem_pestat] (25, 50, 75) percentile: (4162, 4335, 4386)
[2015-09-30T11:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (3714, 4834)
[2015-09-30T11:25Z] [M::mem_pestat] mean and std.dev: (4290.82, 118.21)
[2015-09-30T11:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (3490, 5058)
[2015-09-30T11:25Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:25Z] [M::mem_pestat] (25, 50, 75) percentile: (222, 527, 2603)
[2015-09-30T11:25Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7365)
[2015-09-30T11:25Z] [M::mem_pestat] mean and std.dev: (1282.12, 1356.86)
[2015-09-30T11:25Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9746)
[2015-09-30T11:25Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:25Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:25Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:25Z] [main] Version: 0.7.12-r1039
[2015-09-30T11:25Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T11:25Z] [main] Real time: 280.556 sec; CPU: 2000.668 sec
[2015-09-30T11:25Z] samblaster: Output 458608 discordant read pairs to /dev/fd/62
[2015-09-30T11:25Z] samblaster: Output 23900 split reads to /dev/fd/63
[2015-09-30T11:25Z] samblaster: Marked 224024 of 5000000 (4.48%) read ids as duplicates using 119084k memory in 7.972S CPU seconds and 4M40S(280S) wall time.
[2015-09-30T11:25Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-140000001_160000000-sr.bam
[2015-09-30T11:25Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-140000001_160000000-disc.bam
[2015-09-30T11:25Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T11:26Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T11:26Z] samblaster: Version 0.1.22
[2015-09-30T11:26Z] samblaster: Inputting from stdin
[2015-09-30T11:26Z] samblaster: Outputting to stdout
[2015-09-30T11:26Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T11:26Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T11:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:26Z] [M::mem_pestat] (25, 50, 75) percentile: (194, 498, 5626)
[2015-09-30T11:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16490)
[2015-09-30T11:26Z] [M::mem_pestat] mean and std.dev: (2153.59, 2527.11)
[2015-09-30T11:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 21922)
[2015-09-30T11:26Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:26Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:26Z] [M::mem_pestat] mean and std.dev: (344.25, 15.42)
[2015-09-30T11:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:26Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:26Z] [M::mem_pestat] (25, 50, 75) percentile: (177, 5158, 5254)
[2015-09-30T11:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15408)
[2015-09-30T11:26Z] [M::mem_pestat] mean and std.dev: (2963.98, 2466.55)
[2015-09-30T11:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 20485)
[2015-09-30T11:26Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:26Z] [M::mem_pestat] (25, 50, 75) percentile: (374, 1750, 5724)
[2015-09-30T11:26Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16424)
[2015-09-30T11:26Z] [M::mem_pestat] mean and std.dev: (2821.79, 2524.55)
[2015-09-30T11:26Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 21774)
[2015-09-30T11:26Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:26Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:26Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:26Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (265, 452, 1265)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3265)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (730.22, 712.78)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4265)
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (329, 341, 352)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (283, 398)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (341.34, 14.98)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 421)
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (48, 59, 78)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 138)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (61.50, 23.41)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 168)
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (352, 808, 1295)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3181)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (850.27, 571.67)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4124)
[2015-09-30T11:27Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:27Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:27Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (227, 594, 1423)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3815)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (862.63, 852.05)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5011)
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (342.15, 15.01)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (2259, 2857, 5681)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12525)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (3471.29, 2412.91)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 15947)
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (313, 818, 1962)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5260)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (1129.06, 1060.12)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6909)
[2015-09-30T11:27Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:27Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:27Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (259, 676, 1086)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2740)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (699.43, 533.50)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3567)
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 352)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 396)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (341.89, 14.73)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 418)
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (2918, 2956, 2989)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (2776, 3131)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (2956.70, 51.57)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (2705, 3202)
[2015-09-30T11:27Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:27Z] [M::mem_pestat] (25, 50, 75) percentile: (539, 901, 1400)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3122)
[2015-09-30T11:27Z] [M::mem_pestat] mean and std.dev: (1016.09, 737.30)
[2015-09-30T11:27Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3983)
[2015-09-30T11:27Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:27Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:27Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (179, 282, 1174)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3164)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (627.74, 682.28)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4159)
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 353)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 397)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (342.89, 14.90)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 419)
[2015-09-30T11:28Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (303, 642, 1069)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2601)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (744.42, 558.73)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3367)
[2015-09-30T11:28Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:28Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (195, 410, 1270)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3420)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (604.52, 574.05)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4495)
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (342.24, 15.03)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T11:28Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (306, 502, 1126)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2766)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (694.06, 537.81)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3586)
[2015-09-30T11:28Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:28Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (296, 1373, 3586)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10166)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (2020.81, 1655.01)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 13456)
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 341, 352)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 396)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (341.74, 14.79)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 418)
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (5689, 5728, 5767)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (5533, 5923)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (5737.07, 49.66)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (5455, 6001)
[2015-09-30T11:28Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:28Z] [M::mem_pestat] (25, 50, 75) percentile: (484, 1256, 3725)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10207)
[2015-09-30T11:28Z] [M::mem_pestat] mean and std.dev: (2040.46, 1679.15)
[2015-09-30T11:28Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 13448)
[2015-09-30T11:28Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:28Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:28Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (218, 333, 805)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1979)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (437.40, 361.53)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2566)
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 353)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 397)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (343.03, 14.85)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 419)
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (4994, 9636, 9662)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18998)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (6197.22, 3865.04)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 23666)
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (318, 845, 1427)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3645)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (907.02, 760.97)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4754)
[2015-09-30T11:29Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:29Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:29Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (118, 210, 289)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 631)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (184.84, 102.45)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 802)
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (344.28, 15.24)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (4521, 4552, 4587)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (4389, 4719)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (4548.33, 44.96)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (4323, 4785)
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (256, 394, 805)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1903)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (482.81, 381.27)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2452)
[2015-09-30T11:29Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:29Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:29Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (139, 253, 1292)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3598)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (626.38, 809.66)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4751)
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 355)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (343.80, 15.11)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:29Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:29Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:29Z] [M::mem_pestat] (25, 50, 75) percentile: (221, 365, 918)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2312)
[2015-09-30T11:29Z] [M::mem_pestat] mean and std.dev: (492.16, 433.40)
[2015-09-30T11:29Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3009)
[2015-09-30T11:29Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:29Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (239, 385, 2750)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7772)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (860.85, 1482.84)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 10283)
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (343.77, 15.17)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (801, 4149, 4226)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11076)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (3111.69, 2033.49)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 14501)
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (300, 833, 8146)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 23838)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (3151.95, 3550.56)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 31684)
[2015-09-30T11:30Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:30Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:30Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (149, 234, 940)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2522)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (408.16, 442.91)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3313)
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 343, 355)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 401)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (344.15, 15.34)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (263, 424)
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (5292, 5321, 5367)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (5142, 5517)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (5330.90, 48.52)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (5067, 5592)
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (299, 602, 1288)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3266)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (857.92, 792.70)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4255)
[2015-09-30T11:30Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:30Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:30Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (245, 334, 1363)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3599)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (826.64, 907.05)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4717)
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 353)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 397)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (342.87, 14.96)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 419)
[2015-09-30T11:30Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:30Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:30Z] [M::mem_pestat] (25, 50, 75) percentile: (396, 743, 1695)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4293)
[2015-09-30T11:30Z] [M::mem_pestat] mean and std.dev: (974.57, 837.91)
[2015-09-30T11:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5592)
[2015-09-30T11:30Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:30Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:30Z] [main] Version: 0.7.12-r1039
[2015-09-30T11:30Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T11:30Z] [main] Real time: 274.809 sec; CPU: 2008.767 sec
[2015-09-30T11:30Z] samblaster: Output 468106 discordant read pairs to /dev/fd/62
[2015-09-30T11:30Z] samblaster: Output 23894 split reads to /dev/fd/63
[2015-09-30T11:30Z] samblaster: Marked 233078 of 5000000 (4.66%) read ids as duplicates using 109600k memory in 8.034S CPU seconds and 4M35S(275S) wall time.
[2015-09-30T11:31Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-160000001_180000000-sr.bam
[2015-09-30T11:31Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-160000001_180000000-disc.bam
[2015-09-30T11:31Z] Aligning lane 2_2014-08-13_dream-syn3 with bwa aligner
[2015-09-30T11:31Z] bwa mem alignment from fastq: syn3-tumor
[2015-09-30T11:31Z] samblaster: Version 0.1.22
[2015-09-30T11:31Z] samblaster: Inputting from stdin
[2015-09-30T11:31Z] samblaster: Outputting to stdout
[2015-09-30T11:31Z] samblaster: Opening /dev/fd/62 for write.
[2015-09-30T11:31Z] samblaster: Opening /dev/fd/63 for write.
[2015-09-30T11:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:32Z] [M::mem_pestat] (25, 50, 75) percentile: (343, 2019, 4382)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12460)
[2015-09-30T11:32Z] [M::mem_pestat] mean and std.dev: (2818.14, 2616.48)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 16499)
[2015-09-30T11:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:32Z] [M::mem_pestat] (25, 50, 75) percentile: (330, 342, 353)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 399)
[2015-09-30T11:32Z] [M::mem_pestat] mean and std.dev: (342.39, 15.02)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 422)
[2015-09-30T11:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:32Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:32Z] [M::mem_pestat] (25, 50, 75) percentile: (648, 2695, 3915)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10449)
[2015-09-30T11:32Z] [M::mem_pestat] mean and std.dev: (2580.66, 2053.45)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 13716)
[2015-09-30T11:32Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:32Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:32Z] samblaster: Loaded 84 header sequence entries.
[2015-09-30T11:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:32Z] [M::mem_pestat] (25, 50, 75) percentile: (182, 305, 1123)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3005)
[2015-09-30T11:32Z] [M::mem_pestat] mean and std.dev: (674.17, 748.75)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3946)
[2015-09-30T11:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:32Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:32Z] [M::mem_pestat] mean and std.dev: (343.45, 15.10)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:32Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:32Z] [M::mem_pestat] (25, 50, 75) percentile: (267, 562, 1141)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2889)
[2015-09-30T11:32Z] [M::mem_pestat] mean and std.dev: (620.13, 434.07)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3763)
[2015-09-30T11:32Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:32Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:32Z] [M::mem_pestat] (25, 50, 75) percentile: (214, 291, 1406)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3790)
[2015-09-30T11:32Z] [M::mem_pestat] mean and std.dev: (534.96, 642.85)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4982)
[2015-09-30T11:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:32Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 342, 353)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 397)
[2015-09-30T11:32Z] [M::mem_pestat] mean and std.dev: (342.74, 14.80)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (265, 419)
[2015-09-30T11:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:32Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:32Z] [M::mem_pestat] (25, 50, 75) percentile: (299, 665, 2478)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6836)
[2015-09-30T11:32Z] [M::mem_pestat] mean and std.dev: (1654.04, 1801.55)
[2015-09-30T11:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9015)
[2015-09-30T11:32Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:32Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (273, 502, 1059)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2631)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (579.53, 485.62)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3417)
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (343.43, 15.30)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (53, 583, 1783)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5243)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (869.50, 927.35)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 6973)
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (259, 576, 1228)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3166)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (708.20, 635.31)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 4135)
[2015-09-30T11:33Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:33Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:33Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (197, 236, 804)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2018)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (356.62, 382.04)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2625)
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 344, 356)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 404)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (345.06, 15.57)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (260, 428)
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (4625, 4637, 4660)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (4555, 4730)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (4644.53, 27.64)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (4520, 4765)
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (147, 329, 712)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1842)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (410.04, 429.01)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2407)
[2015-09-30T11:33Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:33Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:33Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (197, 249, 1646)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4544)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (808.33, 865.26)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5993)
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 356)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 402)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (345.42, 15.27)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (264, 425)
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (6981, 7002, 7051)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (6841, 7191)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (7015.36, 47.19)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (6771, 7261)
[2015-09-30T11:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:33Z] [M::mem_pestat] (25, 50, 75) percentile: (248, 689, 1944)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5336)
[2015-09-30T11:33Z] [M::mem_pestat] mean and std.dev: (1003.88, 906.99)
[2015-09-30T11:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 7032)
[2015-09-30T11:33Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:33Z] [M::mem_pestat] skip orientation RF
[2015-09-30T11:33Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:34Z] [M::mem_pestat] (25, 50, 75) percentile: (308, 8266, 8492)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 24860)
[2015-09-30T11:34Z] [M::mem_pestat] mean and std.dev: (5731.86, 3812.92)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 33044)
[2015-09-30T11:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:34Z] [M::mem_pestat] (25, 50, 75) percentile: (333, 345, 357)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 405)
[2015-09-30T11:34Z] [M::mem_pestat] mean and std.dev: (345.97, 15.59)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (261, 429)
[2015-09-30T11:34Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:34Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:34Z] [M::mem_pestat] (25, 50, 75) percentile: (315, 8245, 8576)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 25098)
[2015-09-30T11:34Z] [M::mem_pestat] mean and std.dev: (5638.68, 3906.73)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 33359)
[2015-09-30T11:34Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:34Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2015-09-30T11:34Z] [M::mem_pestat] (25, 50, 75) percentile: (162, 301, 1539)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4293)
[2015-09-30T11:34Z] [M::mem_pestat] mean and std.dev: (635.57, 782.71)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 5670)
[2015-09-30T11:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:34Z] [M::mem_pestat] (25, 50, 75) percentile: (331, 343, 354)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (285, 400)
[2015-09-30T11:34Z] [M::mem_pestat] mean and std.dev: (343.33, 15.24)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (262, 423)
[2015-09-30T11:34Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:34Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:34Z] [M::mem_pestat] (25, 50, 75) percentile: (262, 440, 986)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2434)
[2015-09-30T11:34Z] [M::mem_pestat] mean and std.dev: (536.85, 436.54)
[2015-09-30T11:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3158)
[2015-09-30T11:34Z] [M::mem_pestat] skip orientation FF
[2015-09-30T11:34Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:35Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-09-30T11:35Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:35Z] [M::mem_pestat] (25, 50, 75) percentile: (332, 355, 493)
[2015-09-30T11:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (10, 815)
[2015-09-30T11:35Z] [M::mem_pestat] mean and std.dev: (360.26, 109.90)
[2015-09-30T11:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 976)
[2015-09-30T11:35Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:35Z] [M::mem_pestat] analyzing insert size distribution for orientation RR...
[2015-09-30T11:35Z] [M::mem_pestat] (25, 50, 75) percentile: (1872, 2031, 2069)
[2015-09-30T11:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1478, 2463)
[2015-09-30T11:35Z] [M::mem_pestat] mean and std.dev: (2006.69, 94.66)
[2015-09-30T11:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (1281, 2660)
[2015-09-30T11:35Z] [M::mem_pestat] skip orientation RR
[2015-09-30T11:36Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2015-09-30T11:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2015-09-30T11:36Z] [M::mem_pestat] (25, 50, 75) percentile: (327, 349, 474)
[2015-09-30T11:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (33, 768)
[2015-09-30T11:36Z] [M::mem_pestat] mean and std.dev: (350.05, 99.48)
[2015-09-30T11:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 915)
[2015-09-30T11:36Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2015-09-30T11:36Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2015-09-30T11:37Z] [main] Version: 0.7.12-r1039
[2015-09-30T11:37Z] [main] CMD: /bin/bwa mem -c 250 -M -t 8 -R @RG\tID:2\tPL:illumina\tPU:2_2014-08-13_dream-syn3\tSM:syn3-tumor -v 1 /data/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /dev/fd/63 /dev/fd/62
[2015-09-30T11:37Z] [main] Real time: 344.918 sec; CPU: 2534.101 sec
[2015-09-30T11:37Z] samblaster: Output 979319 discordant read pairs to /dev/fd/62
[2015-09-30T11:37Z] samblaster: Output 141488 split reads to /dev/fd/63
[2015-09-30T11:37Z] samblaster: Marked 141264 of 3837526 (3.68%) read ids as duplicates using 80768k memory in 6.575S CPU seconds and 5M44S(344S) wall time.
[2015-09-30T11:38Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-180000001_195350104-sr.bam
[2015-09-30T11:38Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-180000001_195350104-disc.bam
[2015-09-30T11:38Z] multiprocessing: delayed_bam_merge
[2015-09-30T11:38Z] Merge bam files to 1_2014-08-13_dream-syn3-sort-sr.bam
[2015-09-30T11:38Z] Merge bam files to 1_2014-08-13_dream-syn3-sort-disc.bam
[2015-09-30T11:38Z] Merge bam files to 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:38Z] WARNING: PG line with id SAMBLASTER_0 has multiple children referencing it by PP tags.
[2015-09-30T11:38Z] WARNING: PG line with id SAMBLASTER_1 has multiple children referencing it by PP tags.
[2015-09-30T11:38Z] WARNING: PG line with id SAMBLASTER_2 has multiple children referencing it by PP tags.
[2015-09-30T11:38Z] WARNING: PG line with id SAMBLASTER_3 has multiple children referencing it by PP tags.
[2015-09-30T11:38Z] WARNING: PG line with id SAMBLASTER_4 has multiple children referencing it by PP tags.
[2015-09-30T11:38Z] WARNING: PG line with id SAMBLASTER_5 has multiple children referencing it by PP tags.
[2015-09-30T11:38Z] WARNING: PG line with id SAMBLASTER_6 has multiple children referencing it by PP tags.
[2015-09-30T11:38Z] WARNING: PG line with id SAMBLASTER_7 has multiple children referencing it by PP tags.
[2015-09-30T11:38Z] WARNING: PG line with id SAMBLASTER_8 has multiple children referencing it by PP tags.
[2015-09-30T11:38Z] [W] PG lines do not form a linear chain
[2015-09-30T11:38Z] [V] 1048576
[2015-09-30T11:39Z] [V] 2097152
[2015-09-30T11:39Z] [V] 1931360	23:91471800	MemUsage(size=3577.09,rss=1303.66,peak=3741.58)	AutoArrayMemUsage(memusage=2986.11,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 2897011	27:57405400	MemUsage(size=3577.09,rss=1392.11,peak=3741.58)	AutoArrayMemUsage(memusage=2987.33,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 3145728
[2015-09-30T11:39Z] [V] 3862484	30:88167400	MemUsage(size=3577.09,rss=1442.91,peak=3741.58)	AutoArrayMemUsage(memusage=2995.8,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 4194304
[2015-09-30T11:39Z] [V] 4828045	34:56911999	MemUsage(size=3577.09,rss=1462.68,peak=3741.58)	AutoArrayMemUsage(memusage=2995.8,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 5242880
[2015-09-30T11:39Z] [V] 5793682	38:23839499	MemUsage(size=3577.09,rss=1481.59,peak=3741.58)	AutoArrayMemUsage(memusage=3003.07,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 6291456
[2015-09-30T11:39Z] [V] 6759313	41:88761499	MemUsage(size=3577.09,rss=1481.66,peak=3741.58)	AutoArrayMemUsage(memusage=3003.07,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 7340032
[2015-09-30T11:39Z] [V] 7724973	44:72781599	MemUsage(size=3577.09,rss=1481.73,peak=3741.58)	AutoArrayMemUsage(memusage=3003.07,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 8388608
[2015-09-30T11:39Z] [V] 8690628	48:42408300	MemUsage(size=3577.09,rss=1481.82,peak=3741.58)	AutoArrayMemUsage(memusage=3003.07,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 9437184
[2015-09-30T11:39Z] [V] 9656202	52:26901900	MemUsage(size=3577.09,rss=1481.83,peak=3741.58)	AutoArrayMemUsage(memusage=3003.07,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 10485760
[2015-09-30T11:39Z] [V] 10625380	56:00251599	MemUsage(size=3577.09,rss=1481.83,peak=3741.58)	AutoArrayMemUsage(memusage=3003.07,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 11534336
[2015-09-30T11:39Z] [V] 11596606	59:67022200	MemUsage(size=3577.17,rss=1483.41,peak=3741.58)	AutoArrayMemUsage(memusage=3003.21,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 12582912
[2015-09-30T11:39Z] [V] 13631488
[2015-09-30T11:39Z] [V] 13538993	01:07:00979999	MemUsage(size=3577.21,rss=1498.81,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 14680064
[2015-09-30T11:39Z] [V] 14510228	01:10:65447399	MemUsage(size=3577.21,rss=1498.82,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 15481442	01:14:31053699	MemUsage(size=3577.21,rss=1498.84,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:39Z] [V] 15728640
[2015-09-30T11:40Z] [V] 16452677	01:17:07948199	MemUsage(size=3577.21,rss=1498.84,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 16777216
[2015-09-30T11:40Z] [V] 17423897	01:20:89821299	MemUsage(size=3577.21,rss=1498.86,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 17825792
[2015-09-30T11:40Z] [V] 18395154	01:24:60985700	MemUsage(size=3577.21,rss=1498.88,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 18874368
[2015-09-30T11:40Z] [V] 19366338	01:28:27720399	MemUsage(size=3577.21,rss=1498.88,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 19922944
[2015-09-30T11:40Z] [V] 20336659	01:32:10612600	MemUsage(size=3577.21,rss=1498.89,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 20971520
[2015-09-30T11:40Z] [V] 21304989	01:35:84707699	MemUsage(size=3577.21,rss=1499.13,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 22020096
[2015-09-30T11:40Z] [V] 22273417	01:39:54501399	MemUsage(size=3577.21,rss=1499.27,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 23068672
[2015-09-30T11:40Z] [V] 23241840	01:43:20907300	MemUsage(size=3577.21,rss=1499.28,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 24117248
[2015-09-30T11:40Z] [V] 24210261	01:46:94436399	MemUsage(size=3577.21,rss=1499.28,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 25165824
[2015-09-30T11:40Z] [V] 25178744	01:49:75977600	MemUsage(size=3577.21,rss=1499.29,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 26214400
[2015-09-30T11:40Z] [V] 27115371	01:57:18712899	MemUsage(size=3577.21,rss=1499.3,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 27262976
[2015-09-30T11:40Z] [V] 28083765	02:00:95312400	MemUsage(size=3577.21,rss=1499.3,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 28311552
[2015-09-30T11:40Z] [V] 29052212	02:04:69875500	MemUsage(size=3577.21,rss=1499.3,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 29360128
[2015-09-30T11:40Z] [V] 30020552	02:08:34381700	MemUsage(size=3577.21,rss=1499.3,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 30408704
[2015-09-30T11:40Z] [V] 30991169	02:11:97471999	MemUsage(size=3577.21,rss=1499.3,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 31457280
[2015-09-30T11:40Z] [V] 31961824	02:15:63048200	MemUsage(size=3577.21,rss=1499.45,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:40Z] [V] 32505856
[2015-09-30T11:41Z] [V] 32932522	02:19:28978599	MemUsage(size=3577.21,rss=1499.54,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 33554432
[2015-09-30T11:41Z] [V] 33903160	02:22:15538000	MemUsage(size=3577.21,rss=1499.55,peak=3741.58)	AutoArrayMemUsage(memusage=3003.29,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 34603008
[2015-09-30T11:41Z] [V] 34873844	02:25:92147900	MemUsage(size=3577.21,rss=1499.55,peak=3741.58)	AutoArrayMemUsage(memusage=3003.3,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 35651584
[2015-09-30T11:41Z] [V] 35844387	02:30:05301600	MemUsage(size=3577.21,rss=1499.55,peak=3741.58)	AutoArrayMemUsage(memusage=3003.3,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 36700160
[2015-09-30T11:41Z] [V] 36814997	02:33:74145200	MemUsage(size=3577.21,rss=1499.56,peak=3741.58)	AutoArrayMemUsage(memusage=3003.3,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 37748736
[2015-09-30T11:41Z] [V] 37785543	02:37:37214000	MemUsage(size=3577.21,rss=1499.56,peak=3741.58)	AutoArrayMemUsage(memusage=3003.3,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 38797312
[2015-09-30T11:41Z] [V] 39845888
[2015-09-30T11:41Z] [V] 39726746	02:44:67338699	MemUsage(size=3577.21,rss=1499.57,peak=3741.58)	AutoArrayMemUsage(memusage=3003.3,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 40894464
[2015-09-30T11:41Z] [V] 40688801	02:48:40970400	MemUsage(size=3577.21,rss=1499.57,peak=3741.58)	AutoArrayMemUsage(memusage=3003.3,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 41646165	02:52:18270000	MemUsage(size=3579.39,rss=1500.38,peak=3741.58)	AutoArrayMemUsage(memusage=3005.48,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 41943040
[2015-09-30T11:41Z] [V] 42603488	02:55:01937599	MemUsage(size=3581.57,rss=1500.9,peak=3741.58)	AutoArrayMemUsage(memusage=3007.66,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 42991616
[2015-09-30T11:41Z] [V] 43560896	02:58:92318800	MemUsage(size=3581.57,rss=1500.9,peak=3741.58)	AutoArrayMemUsage(memusage=3007.66,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 44040192
[2015-09-30T11:41Z] [V] 44518390	03:02:73135400	MemUsage(size=3581.57,rss=1500.91,peak=3741.58)	AutoArrayMemUsage(memusage=3007.66,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 45088768
[2015-09-30T11:41Z] [V] 45475663	03:06:41297399	MemUsage(size=3581.57,rss=1500.91,peak=3741.58)	AutoArrayMemUsage(memusage=3007.66,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 46137344
[2015-09-30T11:41Z] [V] 46432964	03:10:12692999	MemUsage(size=3581.57,rss=1500.91,peak=3741.58)	AutoArrayMemUsage(memusage=3007.66,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 47185920
[2015-09-30T11:41Z] [V] 47390290	03:13:93413200	MemUsage(size=3581.57,rss=1500.91,peak=3741.58)	AutoArrayMemUsage(memusage=3007.66,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:41Z] [V] 48234496
[2015-09-30T11:42Z] [V] 48350719	03:17:67312300	MemUsage(size=3581.57,rss=1500.91,peak=3741.58)	AutoArrayMemUsage(memusage=3007.66,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 49283072
[2015-09-30T11:42Z] [V] 49313981	03:21:34771599	MemUsage(size=3581.57,rss=1500.91,peak=3741.58)	AutoArrayMemUsage(memusage=3007.66,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 50331648
[2015-09-30T11:42Z] [V] 51240438	03:28:20156199	MemUsage(size=3583.75,rss=1501.7,peak=3741.58)	AutoArrayMemUsage(memusage=3009.84,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 51380224
[2015-09-30T11:42Z] [V] 52203665	03:31:88016799	MemUsage(size=3583.75,rss=1501.73,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 52428800
[2015-09-30T11:42Z] [V] 53166940	03:35:59100100	MemUsage(size=3583.75,rss=1501.74,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 53477376
[2015-09-30T11:42Z] [V] 54130104	03:39:32550900	MemUsage(size=3583.75,rss=1501.74,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 54525952
[2015-09-30T11:42Z] [V] 55093413	03:42:97649400	MemUsage(size=3583.75,rss=1501.74,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 55574528
[2015-09-30T11:42Z] [V] 56056679	03:46:60602900	MemUsage(size=3583.75,rss=1501.74,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 56623104
[2015-09-30T11:42Z] [V] 57020008	03:50:28160600	MemUsage(size=3583.75,rss=1501.74,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 57671680
[2015-09-30T11:42Z] [V] 57983047	03:54:49084300	MemUsage(size=3583.75,rss=1501.72,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 58720256
[2015-09-30T11:42Z] [V] 58944267	03:58:15723800	MemUsage(size=3583.75,rss=1502.09,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 59768832
[2015-09-30T11:42Z] [V] 59905567	04:01:02184800	MemUsage(size=3583.75,rss=1502.1,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 60817408
[2015-09-30T11:42Z] [V] 60866848	04:04:73785300	MemUsage(size=3583.75,rss=1502.1,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 61865984
[2015-09-30T11:42Z] [V] 62789268	04:12:10693399	MemUsage(size=3583.75,rss=1502.12,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 62914560
[2015-09-30T11:42Z] [V] 63750481	04:15:76845499	MemUsage(size=3583.75,rss=1502.11,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:42Z] [V] 63963136
[2015-09-30T11:43Z] [V] 64711760	04:19:36590599	MemUsage(size=3583.75,rss=1502.11,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 65011712
[2015-09-30T11:43Z] [V] 65673024	04:22:97255599	MemUsage(size=3583.75,rss=1502.11,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 66060288
[2015-09-30T11:43Z] [V] 66634211	04:27:70350600	MemUsage(size=3583.75,rss=1502.11,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 67108864
[2015-09-30T11:43Z] [V] 67595454	04:31:30897099	MemUsage(size=3583.75,rss=1502.11,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 68157440
[2015-09-30T11:43Z] [V] 68558576	04:34:04466000	MemUsage(size=3583.75,rss=1502.11,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 69206016
[2015-09-30T11:43Z] [V] 69522636	04:37:64248300	MemUsage(size=3583.75,rss=1502.14,peak=3741.58)	AutoArrayMemUsage(memusage=3009.85,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 70254592
[2015-09-30T11:43Z] [V] 70486657	04:41:30937799	MemUsage(size=3585.93,rss=1502.36,peak=3741.58)	AutoArrayMemUsage(memusage=3012.03,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 71303168
[2015-09-30T11:43Z] [V] 71450860	04:45:02244999	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.03,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 72351744
[2015-09-30T11:43Z] [V] 72415036	04:48:67684600	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.03,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 73400320
[2015-09-30T11:43Z] [V] 74448896
[2015-09-30T11:43Z] [V] 74343375	04:55:91128800	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.03,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 75497472
[2015-09-30T11:43Z] [V] 75307397	04:59:50380499	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.03,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 76271417	05:03:17140999	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.03,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 76546048
[2015-09-30T11:43Z] [V] 77235583	05:05:98146400	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 77594624
[2015-09-30T11:43Z] [V] 78200581	05:09:76019000	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 78643200
[2015-09-30T11:43Z] [V] 79167897	05:13:48427700	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:43Z] [V] 79691776
[2015-09-30T11:44Z] [V] 80135260	05:17:14102800	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 80740352
[2015-09-30T11:44Z] [V] 81102585	05:20:77162499	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 81788928
[2015-09-30T11:44Z] [V] 82069906	05:24:59172899	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 82837504
[2015-09-30T11:44Z] [V] 83037200	05:28:24202000	MemUsage(size=3585.93,rss=1502.42,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 83886080
[2015-09-30T11:44Z] [V] 84004460	05:31:78791699	MemUsage(size=3585.93,rss=1502.43,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 84934656
[2015-09-30T11:44Z] [V] 84971727	05:35:37846600	MemUsage(size=3585.93,rss=1502.44,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 85983232
[2015-09-30T11:44Z] [V] 86906272	05:41:79016400	MemUsage(size=3585.93,rss=1502.43,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 87031808
[2015-09-30T11:44Z] [V] 87873499	05:45:36757299	MemUsage(size=3585.93,rss=1502.43,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 88080384
[2015-09-30T11:44Z] [V] 88841653	05:49:04686199	MemUsage(size=3585.93,rss=1502.43,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 89128960
[2015-09-30T11:44Z] [V] 89809734	05:52:55050799	MemUsage(size=3585.93,rss=1502.46,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 90177536
[2015-09-30T11:44Z] [V] 90777916	05:56:18556300	MemUsage(size=3585.93,rss=1502.51,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 91226112
[2015-09-30T11:44Z] [V] 91746145	05:59:79923100	MemUsage(size=3585.93,rss=1502.51,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 92274688
[2015-09-30T11:44Z] [V] 92714271	06:03:31245200	MemUsage(size=3585.93,rss=1502.51,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 93323264
[2015-09-30T11:44Z] [V] 93682436	06:06:85971399	MemUsage(size=3585.93,rss=1502.53,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 94371840
[2015-09-30T11:44Z] [V] 94650500	06:09:73793799	MemUsage(size=3585.93,rss=1502.53,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 95420416
[2015-09-30T11:44Z] [V] 95618615	06:13:47408400	MemUsage(size=3585.93,rss=1502.53,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:44Z] [V] 96468992
[2015-09-30T11:44Z] [V] 96586890	06:17:00062200	MemUsage(size=3585.93,rss=1502.53,peak=3741.58)	AutoArrayMemUsage(memusage=3012.04,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:45Z] [V] 97517568
[2015-09-30T11:45Z] [V] 97555056	06:20:53590300	MemUsage(size=3585.93,rss=1502.53,peak=3741.58)	AutoArrayMemUsage(memusage=3012.05,peakmemusage=3200.03,maxmem=1.75922e+13)
[2015-09-30T11:45Z] [V] 97932849
[2015-09-30T11:45Z] [V] 97932849	06:21:40821599	MemUsage(size=3585.93,rss=1502.54,peak=3741.58)	AutoArrayMemUsage(memusage=3012.05,peakmemusage=3200.03,maxmem=1.75922e+13)	final
[2015-09-30T11:45Z] [V] flushing read ends lists...done.
[2015-09-30T11:45Z] [V] merging read ends lists/computing duplicates...done, time 20:29152900
[2015-09-30T11:45Z] [V] num dups 4576357
[2015-09-30T11:45Z] # bamsormadup
[2015-09-30T11:45Z]
[2015-09-30T11:45Z] ##METRICS
[2015-09-30T11:45Z] LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
[2015-09-30T11:45Z] Unknown Library	1478465	47374575	1486417	422579	2076889	0	0.0475576	524405745
[2015-09-30T11:45Z]
[2015-09-30T11:45Z] ## HISTOGRAM
[2015-09-30T11:45Z] BIN	VALUE
[2015-09-30T11:45Z] 1	1
[2015-09-30T11:45Z] 2	1.91362
[2015-09-30T11:45Z] 3	2.74832
[2015-09-30T11:45Z] 4	3.51093
[2015-09-30T11:45Z] 5	4.20766
[2015-09-30T11:45Z] 6	4.8442
[2015-09-30T11:45Z] 7	5.42576
[2015-09-30T11:45Z] 8	5.95709
[2015-09-30T11:45Z] 9	6.44252
[2015-09-30T11:45Z] 10	6.88602
[2015-09-30T11:45Z] 11	7.29122
[2015-09-30T11:45Z] 12	7.66141
[2015-09-30T11:45Z] 13	7.99962
[2015-09-30T11:45Z] 14	8.30862
[2015-09-30T11:45Z] 15	8.59093
[2015-09-30T11:45Z] 16	8.84885
[2015-09-30T11:45Z] 17	9.0845
[2015-09-30T11:45Z] 18	9.29979
[2015-09-30T11:45Z] 19	9.49648
[2015-09-30T11:45Z] 20	9.67618
[2015-09-30T11:45Z] 21	9.84036
[2015-09-30T11:45Z] 22	9.99036
[2015-09-30T11:45Z] 23	10.1274
[2015-09-30T11:45Z] 24	10.2526
[2015-09-30T11:45Z] 25	10.367
[2015-09-30T11:45Z] 26	10.4715
[2015-09-30T11:45Z] 27	10.567
[2015-09-30T11:45Z] 28	10.6542
[2015-09-30T11:45Z] 29	10.7339
[2015-09-30T11:45Z] 30	10.8067
[2015-09-30T11:45Z] 31	10.8733
[2015-09-30T11:45Z] 32	10.934
[2015-09-30T11:45Z] 33	10.9896
[2015-09-30T11:45Z] 34	11.0403
[2015-09-30T11:45Z] 35	11.0866
[2015-09-30T11:45Z] 36	11.129
[2015-09-30T11:45Z] 37	11.1677
[2015-09-30T11:45Z] 38	11.203
[2015-09-30T11:45Z] 39	11.2353
[2015-09-30T11:45Z] 40	11.2648
[2015-09-30T11:45Z] 41	11.2918
[2015-09-30T11:45Z] 42	11.3164
[2015-09-30T11:45Z] 43	11.3389
[2015-09-30T11:45Z] 44	11.3595
[2015-09-30T11:45Z] 45	11.3782
[2015-09-30T11:45Z] 46	11.3954
[2015-09-30T11:45Z] 47	11.4111
[2015-09-30T11:45Z] 48	11.4254
[2015-09-30T11:45Z] 49	11.4385
[2015-09-30T11:45Z] 50	11.4504
[2015-09-30T11:45Z] 51	11.4614
[2015-09-30T11:45Z] 52	11.4713
[2015-09-30T11:45Z] 53	11.4805
[2015-09-30T11:45Z] 54	11.4888
[2015-09-30T11:45Z] 55	11.4964
[2015-09-30T11:45Z] 56	11.5033
[2015-09-30T11:45Z] 57	11.5097
[2015-09-30T11:45Z] 58	11.5155
[2015-09-30T11:45Z] 59	11.5208
[2015-09-30T11:45Z] 60	11.5256
[2015-09-30T11:45Z] 61	11.5301
[2015-09-30T11:45Z] 62	11.5341
[2015-09-30T11:45Z] 63	11.5378
[2015-09-30T11:45Z] 64	11.5412
[2015-09-30T11:45Z] 65	11.5443
[2015-09-30T11:45Z] 66	11.5471
[2015-09-30T11:45Z] 67	11.5497
[2015-09-30T11:45Z] 68	11.552
[2015-09-30T11:45Z] 69	11.5542
[2015-09-30T11:45Z] 70	11.5561
[2015-09-30T11:45Z] 71	11.5579
[2015-09-30T11:45Z] 72	11.5595
[2015-09-30T11:45Z] 73	11.561
[2015-09-30T11:45Z] 74	11.5624
[2015-09-30T11:45Z] 75	11.5637
[2015-09-30T11:45Z] 76	11.5648
[2015-09-30T11:45Z] 77	11.5658
[2015-09-30T11:45Z] 78	11.5668
[2015-09-30T11:45Z] 79	11.5677
[2015-09-30T11:45Z] 80	11.5685
[2015-09-30T11:45Z] 81	11.5692
[2015-09-30T11:45Z] 82	11.5699
[2015-09-30T11:45Z] 83	11.5705
[2015-09-30T11:45Z] 84	11.571
[2015-09-30T11:45Z] 85	11.5715
[2015-09-30T11:45Z] 86	11.572
[2015-09-30T11:45Z] 87	11.5724
[2015-09-30T11:45Z] 88	11.5728
[2015-09-30T11:45Z] 89	11.5731
[2015-09-30T11:45Z] 90	11.5735
[2015-09-30T11:45Z] 91	11.5738
[2015-09-30T11:45Z] 92	11.574
[2015-09-30T11:45Z] 93	11.5743
[2015-09-30T11:45Z] 94	11.5745
[2015-09-30T11:45Z] 95	11.5747
[2015-09-30T11:45Z] 96	11.5749
[2015-09-30T11:45Z] 97	11.5751
[2015-09-30T11:45Z] 98	11.5752
[2015-09-30T11:45Z] 99	11.5754
[2015-09-30T11:45Z] 100	11.5755
[2015-09-30T11:45Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:45Z] WARNING: PG line with id SAMBLASTER_0 has multiple children referencing it by PP tags.
[2015-09-30T11:45Z] WARNING: PG line with id SAMBLASTER_1 has multiple children referencing it by PP tags.
[2015-09-30T11:45Z] WARNING: PG line with id SAMBLASTER_2 has multiple children referencing it by PP tags.
[2015-09-30T11:45Z] WARNING: PG line with id SAMBLASTER_3 has multiple children referencing it by PP tags.
[2015-09-30T11:45Z] WARNING: PG line with id SAMBLASTER_4 has multiple children referencing it by PP tags.
[2015-09-30T11:45Z] WARNING: PG line with id SAMBLASTER_5 has multiple children referencing it by PP tags.
[2015-09-30T11:45Z] WARNING: PG line with id SAMBLASTER_6 has multiple children referencing it by PP tags.
[2015-09-30T11:45Z] WARNING: PG line with id SAMBLASTER_7 has multiple children referencing it by PP tags.
[2015-09-30T11:45Z] WARNING: PG line with id SAMBLASTER_8 has multiple children referencing it by PP tags.
[2015-09-30T11:45Z] [V] blocks generated in time 06:48:83674600
[2015-09-30T11:45Z] [W] PG lines do not form a linear chain
[2015-09-30T11:45Z] [V] 1735034
[2015-09-30T11:45Z] [V] 2612188
[2015-09-30T11:45Z] [V] 3490951
[2015-09-30T11:45Z] [V] 4369719
[2015-09-30T11:45Z] [V] 5243259
[2015-09-30T11:45Z] [V] 6968535
[2015-09-30T11:45Z] [V] 7846519
[2015-09-30T11:45Z] [V] 8722999
[2015-09-30T11:45Z] [V] 9601097
[2015-09-30T11:46Z] [V] 11353522
[2015-09-30T11:46Z] [V] 12231738
[2015-09-30T11:46Z] [V] 13079450
[2015-09-30T11:46Z] [V] 13933637
[2015-09-30T11:46Z] [V] 14810614
[2015-09-30T11:46Z] [V] 16569022
[2015-09-30T11:46Z] [V] 17446471
[2015-09-30T11:46Z] [V] 18325639
[2015-09-30T11:46Z] [V] 19204790
[2015-09-30T11:46Z] [V] 20080523
[2015-09-30T11:46Z] [V] 21836865
[2015-09-30T11:46Z] [V] 22710960
[2015-09-30T11:46Z] [V] 23583743
[2015-09-30T11:46Z] [V] 24461437
[2015-09-30T11:46Z] [V] 25339715
[2015-09-30T11:46Z] [V] 26215868
[2015-09-30T11:46Z] [V] 27963979
[2015-09-30T11:46Z] [V] 28843093
[2015-09-30T11:46Z] [V] 29720916
[2015-09-30T11:46Z] [V] 30594541
[2015-09-30T11:46Z] [V] 31468506
[2015-09-30T11:46Z] [V] 33225097
[2015-09-30T11:47Z] [V] 34104151
[2015-09-30T11:47Z] [V] 34975726
[2015-09-30T11:47Z] [V] 35849247
[2015-09-30T11:47Z] [V] 36711522
[2015-09-30T11:47Z] [V] 38425578
[2015-09-30T11:47Z] [V] 39302743
[2015-09-30T11:47Z] [V] 40165289
[2015-09-30T11:47Z] [V] 41039881
[2015-09-30T11:47Z] [V] 42798800
[2015-09-30T11:47Z] [V] 43674027
[2015-09-30T11:47Z] [V] 44508244
[2015-09-30T11:47Z] [V] 45382861
[2015-09-30T11:47Z] [V] 46262144
[2015-09-30T11:47Z] [V] 48015455
[2015-09-30T11:47Z] [V] 48867333
[2015-09-30T11:47Z] [V] 49742865
[2015-09-30T11:47Z] [V] 50618587
[2015-09-30T11:47Z] [V] 51495614
[2015-09-30T11:47Z] [V] 53246450
[2015-09-30T11:47Z] [V] 54118675
[2015-09-30T11:47Z] [V] 54996002
[2015-09-30T11:47Z] [V] 55866712
[2015-09-30T11:47Z] [V] 56745537
[2015-09-30T11:48Z] [V] 58492319
[2015-09-30T11:48Z] [V] 59369735
[2015-09-30T11:48Z] [V] 60248477
[2015-09-30T11:48Z] [V] 61127887
[2015-09-30T11:48Z] [V] 62003635
[2015-09-30T11:48Z] [V] 63747847
[2015-09-30T11:48Z] [V] 64625483
[2015-09-30T11:48Z] [V] 65504659
[2015-09-30T11:48Z] [V] 66383620
[2015-09-30T11:48Z] [V] 67212591
[2015-09-30T11:48Z] [V] 68963544
[2015-09-30T11:48Z] [V] 69816572
[2015-09-30T11:48Z] [V] 70689905
[2015-09-30T11:48Z] [V] 71555421
[2015-09-30T11:48Z] [V] 72405336
[2015-09-30T11:48Z] [V] 74136146
[2015-09-30T11:48Z] [V] 75010274
[2015-09-30T11:48Z] [V] 75887187
[2015-09-30T11:48Z] [V] 76743903
[2015-09-30T11:48Z] [V] 77615353
[2015-09-30T11:48Z] [V] 79353434
[2015-09-30T11:49Z] [V] 80231472
[2015-09-30T11:49Z] [V] 81104279
[2015-09-30T11:49Z] [V] 81980019
[2015-09-30T11:49Z] [V] 82855028
[2015-09-30T11:49Z] [V] 84604812
[2015-09-30T11:49Z] [V] 85480598
[2015-09-30T11:49Z] [V] 86350532
[2015-09-30T11:49Z] [V] 87224474
[2015-09-30T11:49Z] [V] 88094840
[2015-09-30T11:49Z] [V] 89845926
[2015-09-30T11:49Z] [V] 90715190
[2015-09-30T11:49Z] [V] 91592700
[2015-09-30T11:49Z] [V] 92446061
[2015-09-30T11:49Z] [V] 94193926
[2015-09-30T11:49Z] [V] 95069351
[2015-09-30T11:49Z] [V] 95941654
[2015-09-30T11:49Z] [V] 96815891
[2015-09-30T11:49Z] [V] 97683830
[2015-09-30T11:49Z] [V] 97932849
[2015-09-30T11:50Z] [D]	md5	b3713ca7b37c0dc63fbe3768a1ace4eb
[2015-09-30T11:50Z] [V] checksum ok
[2015-09-30T11:50Z] [V] blocks merged in time 04:32:45812000
[2015-09-30T11:50Z] [V] run time 11:21:29908599 (681.299 s)	MemUsage(size=2205.07,rss=1169.73,peak=4887.26)
[2015-09-30T11:50Z] Index BAM file: 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T11:50Z] Merge bam files to 2_2014-08-13_dream-syn3-sort-sr.bam
[2015-09-30T11:50Z] Merge bam files to 2_2014-08-13_dream-syn3-sort-disc.bam
[2015-09-30T11:51Z] Merge bam files to 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:51Z] WARNING: PG line with id SAMBLASTER_0 has multiple children referencing it by PP tags.
[2015-09-30T11:51Z] WARNING: PG line with id SAMBLASTER_1 has multiple children referencing it by PP tags.
[2015-09-30T11:51Z] WARNING: PG line with id SAMBLASTER_2 has multiple children referencing it by PP tags.
[2015-09-30T11:51Z] WARNING: PG line with id SAMBLASTER_3 has multiple children referencing it by PP tags.
[2015-09-30T11:51Z] WARNING: PG line with id SAMBLASTER_4 has multiple children referencing it by PP tags.
[2015-09-30T11:51Z] WARNING: PG line with id SAMBLASTER_5 has multiple children referencing it by PP tags.
[2015-09-30T11:51Z] WARNING: PG line with id SAMBLASTER_6 has multiple children referencing it by PP tags.
[2015-09-30T11:51Z] WARNING: PG line with id SAMBLASTER_7 has multiple children referencing it by PP tags.
[2015-09-30T11:51Z] WARNING: PG line with id SAMBLASTER_8 has multiple children referencing it by PP tags.
[2015-09-30T11:51Z] [W] PG lines do not form a linear chain
[2015-09-30T11:51Z] [V] 1048576
[2015-09-30T11:51Z] [V] 2097152
[2015-09-30T11:51Z] [V] 1931483	22:23196099	MemUsage(size=3580.42,rss=1296.57,peak=3794.73)	AutoArrayMemUsage(memusage=2986.12,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:51Z] [V] 2897078	25:10491599	MemUsage(size=3580.42,rss=1370.38,peak=3794.73)	AutoArrayMemUsage(memusage=2987.33,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:51Z] [V] 3145728
[2015-09-30T11:51Z] [V] 3862719	28:77584399	MemUsage(size=3580.42,rss=1421.61,peak=3794.73)	AutoArrayMemUsage(memusage=2995.81,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:51Z] [V] 4194304
[2015-09-30T11:51Z] [V] 4828487	32:54496799	MemUsage(size=3580.42,rss=1441.39,peak=3794.73)	AutoArrayMemUsage(memusage=2995.81,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:51Z] [V] 5242880
[2015-09-30T11:51Z] [V] 5794309	36:33559100	MemUsage(size=3580.42,rss=1460.66,peak=3794.73)	AutoArrayMemUsage(memusage=3003.07,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 6291456
[2015-09-30T11:52Z] [V] 6759985	40:05042999	MemUsage(size=3580.42,rss=1475.5,peak=3794.73)	AutoArrayMemUsage(memusage=3003.08,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 7340032
[2015-09-30T11:52Z] [V] 7725692	43:69348800	MemUsage(size=3580.42,rss=1475.55,peak=3794.73)	AutoArrayMemUsage(memusage=3003.08,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 8388608
[2015-09-30T11:52Z] [V] 8691268	47:36749400	MemUsage(size=3580.42,rss=1475.62,peak=3794.73)	AutoArrayMemUsage(memusage=3003.08,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 9437184
[2015-09-30T11:52Z] [V] 9656861	51:05112900	MemUsage(size=3580.42,rss=1475.64,peak=3794.73)	AutoArrayMemUsage(memusage=3003.08,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 10485760
[2015-09-30T11:52Z] [V] 10619830	54:73246300	MemUsage(size=3580.42,rss=1475.64,peak=3794.73)	AutoArrayMemUsage(memusage=3003.08,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 11534336
[2015-09-30T11:52Z] [V] 11581051	57:51879399	MemUsage(size=3582.6,rss=1477.28,peak=3794.73)	AutoArrayMemUsage(memusage=3005.26,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 12582912
[2015-09-30T11:52Z] [V] 13503561	01:04:98811999	MemUsage(size=3584.78,rss=1478.49,peak=3794.73)	AutoArrayMemUsage(memusage=3007.44,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 13631488
[2015-09-30T11:52Z] [V] 14464880	01:08:61594599	MemUsage(size=3584.78,rss=1478.49,peak=3794.73)	AutoArrayMemUsage(memusage=3007.44,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 14680064
[2015-09-30T11:52Z] [V] 15426068	01:12:27479999	MemUsage(size=3584.78,rss=1478.5,peak=3794.73)	AutoArrayMemUsage(memusage=3007.44,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 15728640
[2015-09-30T11:52Z] [V] 16387378	01:15:98768599	MemUsage(size=3584.78,rss=1478.5,peak=3794.73)	AutoArrayMemUsage(memusage=3007.44,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 16777216
[2015-09-30T11:52Z] [V] 17348716	01:19:69106499	MemUsage(size=3584.78,rss=1478.51,peak=3794.73)	AutoArrayMemUsage(memusage=3007.44,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 17825792
[2015-09-30T11:52Z] [V] 18309839	01:23:37666099	MemUsage(size=3584.78,rss=1478.51,peak=3794.73)	AutoArrayMemUsage(memusage=3007.44,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 18874368
[2015-09-30T11:52Z] [V] 19271198	01:27:11042799	MemUsage(size=3584.78,rss=1478.52,peak=3794.73)	AutoArrayMemUsage(memusage=3007.44,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 19922944
[2015-09-30T11:52Z] [V] 20233129	01:29:99927700	MemUsage(size=3584.78,rss=1478.52,peak=3794.73)	AutoArrayMemUsage(memusage=3007.44,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 20971520
[2015-09-30T11:52Z] [V] 21197329	01:33:99552300	MemUsage(size=3586.96,rss=1479.02,peak=3794.73)	AutoArrayMemUsage(memusage=3009.62,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:52Z] [V] 22020096
[2015-09-30T11:53Z] [V] 22161490	01:37:70102400	MemUsage(size=3591.32,rss=1479.9,peak=3794.73)	AutoArrayMemUsage(memusage=3013.99,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 23068672
[2015-09-30T11:53Z] [V] 23125708	01:41:37947300	MemUsage(size=3591.32,rss=1479.91,peak=3794.73)	AutoArrayMemUsage(memusage=3013.99,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 24117248
[2015-09-30T11:53Z] [V] 25165824
[2015-09-30T11:53Z] [V] 25054012	01:48:78564500	MemUsage(size=3591.32,rss=1479.93,peak=3794.73)	AutoArrayMemUsage(memusage=3013.99,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 26018221	01:53:85874599	MemUsage(size=3591.32,rss=1479.95,peak=3794.73)	AutoArrayMemUsage(memusage=3013.99,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 26214400
[2015-09-30T11:53Z] [V] 26982384	01:57:51408299	MemUsage(size=3591.32,rss=1479.95,peak=3794.73)	AutoArrayMemUsage(memusage=3013.99,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 27262976
[2015-09-30T11:53Z] [V] 27946537	02:01:21815100	MemUsage(size=3591.32,rss=1479.95,peak=3794.73)	AutoArrayMemUsage(memusage=3013.99,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 28311552
[2015-09-30T11:53Z] [V] 28910707	02:04:01055300	MemUsage(size=3591.32,rss=1479.95,peak=3794.73)	AutoArrayMemUsage(memusage=3013.99,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 29360128
[2015-09-30T11:53Z] [V] 29874916	02:07:74810800	MemUsage(size=3591.32,rss=1479.96,peak=3794.73)	AutoArrayMemUsage(memusage=3013.99,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 30408704
[2015-09-30T11:53Z] [V] 30844357	02:11:58950200	MemUsage(size=3591.32,rss=1479.95,peak=3794.73)	AutoArrayMemUsage(memusage=3013.99,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 31457280
[2015-09-30T11:53Z] [V] 31814993	02:15:26362599	MemUsage(size=3591.4,rss=1480.29,peak=3794.73)	AutoArrayMemUsage(memusage=3014.13,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 32505856
[2015-09-30T11:53Z] [V] 32785576	02:19:19653600	MemUsage(size=3591.43,rss=1480.34,peak=3794.73)	AutoArrayMemUsage(memusage=3014.17,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 33554432
[2015-09-30T11:53Z] [V] 33756219	02:23:95063300	MemUsage(size=3591.43,rss=1480.35,peak=3794.73)	AutoArrayMemUsage(memusage=3014.17,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 34603008
[2015-09-30T11:53Z] [V] 34726775	02:27:63455300	MemUsage(size=3591.43,rss=1495.16,peak=3794.73)	AutoArrayMemUsage(memusage=3014.17,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 35651584
[2015-09-30T11:53Z] [V] 35697374	02:33:36734300	MemUsage(size=3591.43,rss=1495.16,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:53Z] [V] 36700160
[2015-09-30T11:54Z] [V] 37638567	02:40:63413800	MemUsage(size=3591.43,rss=1495.16,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 37748736
[2015-09-30T11:54Z] [V] 38609139	02:44:30254199	MemUsage(size=3591.43,rss=1495.16,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 38797312
[2015-09-30T11:54Z] [V] 39579753	02:47:93041199	MemUsage(size=3591.43,rss=1495.17,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 39845888
[2015-09-30T11:54Z] [V] 40548761	02:51:73215700	MemUsage(size=3591.43,rss=1495.17,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 40894464
[2015-09-30T11:54Z] [V] 41516037	02:55:32991400	MemUsage(size=3591.43,rss=1495.22,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 41943040
[2015-09-30T11:54Z] [V] 42483409	02:58:93148899	MemUsage(size=3591.43,rss=1495.3,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 42991616
[2015-09-30T11:54Z] [V] 43450720	03:02:66509800	MemUsage(size=3591.43,rss=1495.3,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 44040192
[2015-09-30T11:54Z] [V] 44418058	03:06:47318400	MemUsage(size=3591.43,rss=1495.3,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 45088768
[2015-09-30T11:54Z] [V] 45385348	03:09:35389499	MemUsage(size=3591.43,rss=1495.3,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 46137344
[2015-09-30T11:54Z] [V] 46352704	03:13:09155899	MemUsage(size=3591.43,rss=1495.32,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 47185920
[2015-09-30T11:54Z] [V] 47320017	03:16:72541499	MemUsage(size=3591.43,rss=1495.32,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 48234496
[2015-09-30T11:54Z] [V] 48287344	03:20:43150800	MemUsage(size=3591.43,rss=1495.32,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 49283072
[2015-09-30T11:54Z] [V] 50331648
[2015-09-30T11:54Z] [V] 50221358	03:27:70282499	MemUsage(size=3591.43,rss=1495.32,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 51184559	03:31:27884700	MemUsage(size=3591.43,rss=1495.58,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 51380224
[2015-09-30T11:54Z] [V] 52147808	03:34:85480999	MemUsage(size=3591.43,rss=1496.01,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:54Z] [V] 52428800
[2015-09-30T11:55Z] [V] 53110933	03:38:50343399	MemUsage(size=3591.43,rss=1496.01,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 53477376
[2015-09-30T11:55Z] [V] 54074049	03:41:24875299	MemUsage(size=3591.43,rss=1496.01,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 54525952
[2015-09-30T11:55Z] [V] 55037374	03:44:94359600	MemUsage(size=3591.43,rss=1496.01,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 55574528
[2015-09-30T11:55Z] [V] 56000584	03:48:87341599	MemUsage(size=3591.43,rss=1496.01,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 56623104
[2015-09-30T11:55Z] [V] 56963818	03:52:68661199	MemUsage(size=3591.43,rss=1496.01,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 57671680
[2015-09-30T11:55Z] [V] 57926978	03:56:49654000	MemUsage(size=3591.43,rss=1496.01,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 58720256
[2015-09-30T11:55Z] [V] 58890247	04:00:23035500	MemUsage(size=3591.43,rss=1496.01,peak=3794.73)	AutoArrayMemUsage(memusage=3014.18,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 59768832
[2015-09-30T11:55Z] [V] 59853558	04:03:87936899	MemUsage(size=3591.43,rss=1496.01,peak=3794.73)	AutoArrayMemUsage(memusage=3014.19,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 60817408
[2015-09-30T11:55Z] [V] 60820483	04:07:74601999	MemUsage(size=3591.43,rss=1496.02,peak=3794.73)	AutoArrayMemUsage(memusage=3014.19,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 61865984
[2015-09-30T11:55Z] [V] 62757021	04:14:14852099	MemUsage(size=3593.61,rss=1496.45,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 62914560
[2015-09-30T11:55Z] [V] 63725114	04:17:89220000	MemUsage(size=3593.61,rss=1496.44,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 63963136
[2015-09-30T11:55Z] [V] 64693366	04:21:50992899	MemUsage(size=3593.61,rss=1496.47,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 65011712
[2015-09-30T11:55Z] [V] 65661517	04:25:12301800	MemUsage(size=3593.61,rss=1496.47,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 66060288
[2015-09-30T11:55Z] [V] 66629757	04:28:72076600	MemUsage(size=3593.61,rss=1496.47,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 67108864
[2015-09-30T11:55Z] [V] 67597965	04:32:45210400	MemUsage(size=3593.61,rss=1496.47,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:55Z] [V] 68157440
[2015-09-30T11:55Z] [V] 68566203	04:36:12046900	MemUsage(size=3593.61,rss=1496.45,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 69206016
[2015-09-30T11:56Z] [V] 69534482	04:39:71637099	MemUsage(size=3593.61,rss=1496.46,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 70254592
[2015-09-30T11:56Z] [V] 70502794	04:43:37883299	MemUsage(size=3593.61,rss=1496.46,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 71303168
[2015-09-30T11:56Z] [V] 71471203	04:46:12537800	MemUsage(size=3593.61,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 72351744
[2015-09-30T11:56Z] [V] 72439603	04:49:71546399	MemUsage(size=3593.61,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 73400320
[2015-09-30T11:56Z] [V] 73407976	04:53:34013499	MemUsage(size=3593.61,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 74448896
[2015-09-30T11:56Z] [V] 75344774	05:00:51696500	MemUsage(size=3593.61,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 75497472
[2015-09-30T11:56Z] [V] 76313239	05:04:04980499	MemUsage(size=3593.61,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 76546048
[2015-09-30T11:56Z] [V] 77281550	05:07:62146899	MemUsage(size=3593.61,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 77594624
[2015-09-30T11:56Z] [V] 78250012	05:11:19757800	MemUsage(size=3593.61,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 78643200
[2015-09-30T11:56Z] [V] 79218300	05:14:77478500	MemUsage(size=3593.61,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 79691776
[2015-09-30T11:56Z] [V] 80185978	05:17:55185199	MemUsage(size=3593.61,rss=1496.48,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 80740352
[2015-09-30T11:56Z] [V] 81143298	05:21:12527499	MemUsage(size=3593.61,rss=1496.56,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 81788928
[2015-09-30T11:56Z] [V] 82100697	05:24:68989800	MemUsage(size=3593.61,rss=1496.56,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 82837504
[2015-09-30T11:56Z] [V] 83058034	05:28:27947899	MemUsage(size=3593.61,rss=1496.56,peak=3794.73)	AutoArrayMemUsage(memusage=3016.37,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 83886080
[2015-09-30T11:56Z] [V] 84015251	05:31:85826500	MemUsage(size=3593.61,rss=1496.56,peak=3794.73)	AutoArrayMemUsage(memusage=3016.38,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:56Z] [V] 84934656
[2015-09-30T11:56Z] [V] 84972605	05:35:44295599	MemUsage(size=3593.61,rss=1496.56,peak=3794.73)	AutoArrayMemUsage(memusage=3016.38,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 85983232
[2015-09-30T11:57Z] [V] 87031808
[2015-09-30T11:57Z] [V] 86887423	05:42:50776999	MemUsage(size=3593.61,rss=1496.49,peak=3794.73)	AutoArrayMemUsage(memusage=3016.38,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 88080384
[2015-09-30T11:57Z] [V] 87844809	05:46:15110900	MemUsage(size=3593.61,rss=1496.49,peak=3794.73)	AutoArrayMemUsage(memusage=3016.38,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 88815545	05:48:83598000	MemUsage(size=3593.61,rss=1496.49,peak=3794.73)	AutoArrayMemUsage(memusage=3016.38,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 89128960
[2015-09-30T11:57Z] [V] 89786757	05:52:28464700	MemUsage(size=3593.61,rss=1496.47,peak=3794.73)	AutoArrayMemUsage(memusage=3016.38,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 90177536
[2015-09-30T11:57Z] [V] 90757987	05:55:76607100	MemUsage(size=3593.62,rss=1481.83,peak=3794.73)	AutoArrayMemUsage(memusage=3016.4,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 91226112
[2015-09-30T11:57Z] [V] 91729161	05:59:30020999	MemUsage(size=3593.62,rss=1496.53,peak=3794.73)	AutoArrayMemUsage(memusage=3016.4,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 92274688
[2015-09-30T11:57Z] [V] 92700406	06:02:76430399	MemUsage(size=3593.62,rss=1496.53,peak=3794.73)	AutoArrayMemUsage(memusage=3016.4,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 93323264
[2015-09-30T11:57Z] [V] 93671649	06:06:31959599	MemUsage(size=3593.62,rss=1496.53,peak=3794.73)	AutoArrayMemUsage(memusage=3016.4,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 94371840
[2015-09-30T11:57Z] [V] 94642834	06:10:06210399	MemUsage(size=3593.62,rss=1496.53,peak=3794.73)	AutoArrayMemUsage(memusage=3016.4,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 95420416
[2015-09-30T11:57Z] [V] 95614121	06:13:55914000	MemUsage(size=3593.62,rss=1496.53,peak=3794.73)	AutoArrayMemUsage(memusage=3016.4,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 96468992
[2015-09-30T11:57Z] [V] 96585387	06:17:23707100	MemUsage(size=3593.62,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.41,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 97517568
[2015-09-30T11:57Z] [V] 97556597	06:19:92332900	MemUsage(size=3593.62,rss=1496.54,peak=3794.73)	AutoArrayMemUsage(memusage=3016.41,peakmemusage=3174.36,maxmem=1.75922e+13)
[2015-09-30T11:57Z] [V] 97899794
[2015-09-30T11:57Z] [V] 97899794	06:21:20218099	MemUsage(size=3593.62,rss=1496.61,peak=3794.73)	AutoArrayMemUsage(memusage=3016.41,peakmemusage=3174.36,maxmem=1.75922e+13)	final
[2015-09-30T11:57Z] [V] flushing read ends lists...done.
[2015-09-30T11:58Z] [V] merging read ends lists/computing duplicates...done, time 21:59765399
[2015-09-30T11:58Z] [V] num dups 4556301
[2015-09-30T11:58Z] # bamsormadup
[2015-09-30T11:58Z]
[2015-09-30T11:58Z] ##METRICS
[2015-09-30T11:58Z] LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
[2015-09-30T11:58Z] Unknown Library	1480311	47352803	1489135	422235	2067033	0	0.0473697	526491020
[2015-09-30T11:58Z]
[2015-09-30T11:58Z] ## HISTOGRAM
[2015-09-30T11:58Z] BIN	VALUE
[2015-09-30T11:58Z] 1	1
[2015-09-30T11:58Z] 2	1.91399
[2015-09-30T11:58Z] 3	2.74936
[2015-09-30T11:58Z] 4	3.51287
[2015-09-30T11:58Z] 5	4.21071
[2015-09-30T11:58Z] 6	4.84853
[2015-09-30T11:58Z] 7	5.43149
[2015-09-30T11:58Z] 8	5.9643
[2015-09-30T11:58Z] 9	6.45129
[2015-09-30T11:58Z] 10	6.89638
[2015-09-30T11:58Z] 11	7.3032
[2015-09-30T11:58Z] 12	7.67502
[2015-09-30T11:58Z] 13	8.01486
[2015-09-30T11:58Z] 14	8.32546
[2015-09-30T11:58Z] 15	8.60935
[2015-09-30T11:58Z] 16	8.86883
[2015-09-30T11:58Z] 17	9.10598
[2015-09-30T11:58Z] 18	9.32274
[2015-09-30T11:58Z] 19	9.52085
[2015-09-30T11:58Z] 20	9.70192
[2015-09-30T11:58Z] 21	9.86741
[2015-09-30T11:58Z] 22	10.0187
[2015-09-30T11:58Z] 23	10.1569
[2015-09-30T11:58Z] 24	10.2833
[2015-09-30T11:58Z] 25	10.3988
[2015-09-30T11:58Z] 26	10.5043
[2015-09-30T11:58Z] 27	10.6008
[2015-09-30T11:58Z] 28	10.689
[2015-09-30T11:58Z] 29	10.7696
[2015-09-30T11:58Z] 30	10.8432
[2015-09-30T11:58Z] 31	10.9106
[2015-09-30T11:58Z] 32	10.9721
[2015-09-30T11:58Z] 33	11.0283
[2015-09-30T11:58Z] 34	11.0797
[2015-09-30T11:58Z] 35	11.1267
[2015-09-30T11:58Z] 36	11.1697
[2015-09-30T11:58Z] 37	11.2089
[2015-09-30T11:58Z] 38	11.2448
[2015-09-30T11:58Z] 39	11.2776
[2015-09-30T11:58Z] 40	11.3075
[2015-09-30T11:58Z] 41	11.3349
[2015-09-30T11:58Z] 42	11.36
[2015-09-30T11:58Z] 43	11.3828
[2015-09-30T11:58Z] 44	11.4038
[2015-09-30T11:58Z] 45	11.4229
[2015-09-30T11:58Z] 46	11.4403
[2015-09-30T11:58Z] 47	11.4563
[2015-09-30T11:58Z] 48	11.4709
[2015-09-30T11:58Z] 49	11.4842
[2015-09-30T11:58Z] 50	11.4964
[2015-09-30T11:58Z] 51	11.5076
[2015-09-30T11:58Z] 52	11.5178
[2015-09-30T11:58Z] 53	11.5271
[2015-09-30T11:58Z] 54	11.5356
[2015-09-30T11:58Z] 55	11.5433
[2015-09-30T11:58Z] 56	11.5505
[2015-09-30T11:58Z] 57	11.557
[2015-09-30T11:58Z] 58	11.5629
[2015-09-30T11:58Z] 59	11.5683
[2015-09-30T11:58Z] 60	11.5733
[2015-09-30T11:58Z] 61	11.5778
[2015-09-30T11:58Z] 62	11.5819
[2015-09-30T11:58Z] 63	11.5857
[2015-09-30T11:58Z] 64	11.5892
[2015-09-30T11:58Z] 65	11.5924
[2015-09-30T11:58Z] 66	11.5952
[2015-09-30T11:58Z] 67	11.5979
[2015-09-30T11:58Z] 68	11.6003
[2015-09-30T11:58Z] 69	11.6025
[2015-09-30T11:58Z] 70	11.6045
[2015-09-30T11:58Z] 71	11.6064
[2015-09-30T11:58Z] 72	11.6081
[2015-09-30T11:58Z] 73	11.6096
[2015-09-30T11:58Z] 74	11.611
[2015-09-30T11:58Z] 75	11.6123
[2015-09-30T11:58Z] 76	11.6135
[2015-09-30T11:58Z] 77	11.6145
[2015-09-30T11:58Z] 78	11.6155
[2015-09-30T11:58Z] 79	11.6164
[2015-09-30T11:58Z] 80	11.6172
[2015-09-30T11:58Z] 81	11.618
[2015-09-30T11:58Z] 82	11.6187
[2015-09-30T11:58Z] 83	11.6193
[2015-09-30T11:58Z] 84	11.6199
[2015-09-30T11:58Z] 85	11.6204
[2015-09-30T11:58Z] 86	11.6209
[2015-09-30T11:58Z] 87	11.6213
[2015-09-30T11:58Z] 88	11.6217
[2015-09-30T11:58Z] 89	11.6221
[2015-09-30T11:58Z] 90	11.6224
[2015-09-30T11:58Z] 91	11.6227
[2015-09-30T11:58Z] 92	11.623
[2015-09-30T11:58Z] 93	11.6233
[2015-09-30T11:58Z] 94	11.6235
[2015-09-30T11:58Z] 95	11.6237
[2015-09-30T11:58Z] 96	11.6239
[2015-09-30T11:58Z] 97	11.6241
[2015-09-30T11:58Z] 98	11.6242
[2015-09-30T11:58Z] 99	11.6244
[2015-09-30T11:58Z] 100	11.6245
[2015-09-30T11:58Z] WARNING: SAM header designates more than one PG tree root by PP tags.
[2015-09-30T11:58Z] WARNING: PG line with id SAMBLASTER_0 has multiple children referencing it by PP tags.
[2015-09-30T11:58Z] WARNING: PG line with id SAMBLASTER_1 has multiple children referencing it by PP tags.
[2015-09-30T11:58Z] WARNING: PG line with id SAMBLASTER_2 has multiple children referencing it by PP tags.
[2015-09-30T11:58Z] WARNING: PG line with id SAMBLASTER_3 has multiple children referencing it by PP tags.
[2015-09-30T11:58Z] WARNING: PG line with id SAMBLASTER_4 has multiple children referencing it by PP tags.
[2015-09-30T11:58Z] WARNING: PG line with id SAMBLASTER_5 has multiple children referencing it by PP tags.
[2015-09-30T11:58Z] WARNING: PG line with id SAMBLASTER_6 has multiple children referencing it by PP tags.
[2015-09-30T11:58Z] WARNING: PG line with id SAMBLASTER_7 has multiple children referencing it by PP tags.
[2015-09-30T11:58Z] WARNING: PG line with id SAMBLASTER_8 has multiple children referencing it by PP tags.
[2015-09-30T11:58Z] [V] blocks generated in time 06:46:70272199
[2015-09-30T11:58Z] [W] PG lines do not form a linear chain
[2015-09-30T11:58Z] [V] 1735061
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[2015-09-30T12:02Z] [D]	md5	94f91998d7cba4d65ee0a403f00b200a
[2015-09-30T12:02Z] [V] checksum ok
[2015-09-30T12:02Z] [V] blocks merged in time 04:44:42496999
[2015-09-30T12:02Z] [V] run time 11:31:18154100 (691.182 s)	MemUsage(size=2196.23,rss=1161,peak=5138.38)
[2015-09-30T12:02Z] Index BAM file: 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:03Z] Timing: callable regions
[2015-09-30T12:03Z] multiprocessing: prep_samples
[2015-09-30T12:03Z] Prepare cleaned BED file : syn3-normal
[2015-09-30T12:03Z] bgzip NGv3.bed
[2015-09-30T12:03Z] tabix index NGv3.bed.gz
[2015-09-30T12:03Z] Prepare merged BED file : syn3-normal
[2015-09-30T12:03Z] bgzip NGv3-merged.bed
[2015-09-30T12:03Z] tabix index NGv3-merged.bed.gz
[2015-09-30T12:03Z] multiprocessing: postprocess_alignment
[2015-09-30T12:03Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T12:03Z] Configuring 8 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T12:03Z] multiprocessing: calc_callable_loci
[2015-09-30T12:03Z] bedtools genomecov: 1 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:03Z] bedtools genomecov: 3 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:03Z] bedtools genomecov: 5 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:03Z] bedtools genomecov: 4 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:03Z] bedtools genomecov: 2 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:03Z] bedtools genomecov: 6 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:03Z] bedtools genomecov: 7 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:03Z] bedtools genomecov: 8 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:04Z] bedtools groupby coverage: 8 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:04Z] bedtools groupby coverage: 4 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:04Z] bedtools groupby coverage: 5 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:04Z] bedtools groupby coverage: 7 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:04Z] bedtools groupby coverage: 6 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:04Z] bedtools genomecov: 9 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:04Z] bedtools genomecov: 10 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:04Z] bedtools genomecov: 11 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:04Z] bedtools groupby coverage: 3 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 12 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 13 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools groupby coverage: 2 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools groupby coverage: 13 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools groupby coverage: 1 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 14 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools groupby coverage: 9 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools groupby coverage: 10 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 15 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 16 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools groupby coverage: 11 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools groupby coverage: 12 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools groupby coverage: 14 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 17 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 18 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 19 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 20 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 21 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:05Z] bedtools genomecov: 22 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: 18 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: 15 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: 21 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools genomecov: X : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools genomecov: Y : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: Y : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: 20 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: 22 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: 16 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: 17 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: X : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] bedtools groupby coverage: 19 : 1_2014-08-13_dream-syn3-sort.bam
[2015-09-30T12:06Z] multiprocessing: combine_bed
[2015-09-30T12:12Z] Identify high coverage regions
[2015-09-30T12:12Z] Processing reference #1 (1)
[2015-09-30T12:12Z] Processing reference #2 (2)
[2015-09-30T12:13Z] Processing reference #3 (3)
[2015-09-30T12:13Z] Processing reference #4 (4)
[2015-09-30T12:13Z] Processing reference #5 (5)
[2015-09-30T12:13Z] Processing reference #6 (6)
[2015-09-30T12:14Z] Processing reference #7 (7)
[2015-09-30T12:14Z] Processing reference #8 (8)
[2015-09-30T12:14Z] Processing reference #9 (9)
[2015-09-30T12:14Z] Processing reference #10 (10)
[2015-09-30T12:14Z] Processing reference #11 (11)
[2015-09-30T12:15Z] Processing reference #12 (12)
[2015-09-30T12:15Z] Processing reference #13 (13)
[2015-09-30T12:15Z] Processing reference #14 (14)
[2015-09-30T12:15Z] Processing reference #15 (15)
[2015-09-30T12:15Z] Processing reference #16 (16)
[2015-09-30T12:16Z] Processing reference #17 (17)
[2015-09-30T12:16Z] Processing reference #18 (18)
[2015-09-30T12:16Z] Processing reference #19 (19)
[2015-09-30T12:16Z] Processing reference #20 (20)
[2015-09-30T12:16Z] Processing reference #21 (21)
[2015-09-30T12:16Z] Processing reference #22 (22)
[2015-09-30T12:16Z] Processing reference #23 (X)
[2015-09-30T12:17Z] Processing reference #24 (Y)
[2015-09-30T12:17Z] Processing reference #25 (MT)
[2015-09-30T12:17Z] Processing reference #26 (GL000207.1)
[2015-09-30T12:17Z] Processing reference #27 (GL000226.1)
[2015-09-30T12:17Z] Processing reference #28 (GL000229.1)
[2015-09-30T12:17Z] Processing reference #29 (GL000231.1)
[2015-09-30T12:17Z] Processing reference #30 (GL000210.1)
[2015-09-30T12:17Z] Processing reference #31 (GL000239.1)
[2015-09-30T12:17Z] Processing reference #32 (GL000235.1)
[2015-09-30T12:17Z] Processing reference #33 (GL000201.1)
[2015-09-30T12:17Z] Processing reference #34 (GL000247.1)
[2015-09-30T12:17Z] Processing reference #36 (GL000197.1)
[2015-09-30T12:17Z] Processing reference #37 (GL000203.1)
[2015-09-30T12:17Z] Processing reference #38 (GL000246.1)
[2015-09-30T12:17Z] Processing reference #40 (GL000196.1)
[2015-09-30T12:17Z] Processing reference #41 (GL000248.1)
[2015-09-30T12:17Z] Processing reference #42 (GL000244.1)
[2015-09-30T12:17Z] Processing reference #43 (GL000238.1)
[2015-09-30T12:17Z] Processing reference #44 (GL000202.1)
[2015-09-30T12:17Z] Processing reference #45 (GL000234.1)
[2015-09-30T12:17Z] Processing reference #46 (GL000232.1)
[2015-09-30T12:17Z] Processing reference #47 (GL000206.1)
[2015-09-30T12:17Z] Processing reference #48 (GL000240.1)
[2015-09-30T12:17Z] Processing reference #49 (GL000236.1)
[2015-09-30T12:17Z] Processing reference #50 (GL000241.1)
[2015-09-30T12:17Z] Processing reference #51 (GL000243.1)
[2015-09-30T12:17Z] Processing reference #52 (GL000242.1)
[2015-09-30T12:17Z] Processing reference #53 (GL000230.1)
[2015-09-30T12:17Z] Processing reference #54 (GL000237.1)
[2015-09-30T12:17Z] Processing reference #55 (GL000233.1)
[2015-09-30T12:17Z] Processing reference #56 (GL000204.1)
[2015-09-30T12:17Z] Processing reference #57 (GL000198.1)
[2015-09-30T12:17Z] Processing reference #58 (GL000208.1)
[2015-09-30T12:17Z] Processing reference #59 (GL000191.1)
[2015-09-30T12:17Z] Processing reference #60 (GL000227.1)
[2015-09-30T12:17Z] Processing reference #61 (GL000228.1)
[2015-09-30T12:17Z] Processing reference #62 (GL000214.1)
[2015-09-30T12:17Z] Processing reference #63 (GL000221.1)
[2015-09-30T12:17Z] Processing reference #64 (GL000209.1)
[2015-09-30T12:17Z] Processing reference #65 (GL000218.1)
[2015-09-30T12:17Z] Processing reference #66 (GL000220.1)
[2015-09-30T12:17Z] Processing reference #67 (GL000213.1)
[2015-09-30T12:17Z] Processing reference #68 (GL000211.1)
[2015-09-30T12:17Z] Processing reference #69 (GL000199.1)
[2015-09-30T12:17Z] Processing reference #70 (GL000217.1)
[2015-09-30T12:17Z] Processing reference #71 (GL000216.1)
[2015-09-30T12:17Z] Processing reference #72 (GL000215.1)
[2015-09-30T12:17Z] Processing reference #73 (GL000205.1)
[2015-09-30T12:17Z] Processing reference #74 (GL000219.1)
[2015-09-30T12:17Z] Processing reference #75 (GL000224.1)
[2015-09-30T12:17Z] Processing reference #76 (GL000223.1)
[2015-09-30T12:17Z] Processing reference #77 (GL000195.1)
[2015-09-30T12:17Z] Processing reference #78 (GL000212.1)
[2015-09-30T12:17Z] Processing reference #79 (GL000222.1)
[2015-09-30T12:17Z] Processing reference #81 (GL000193.1)
[2015-09-30T12:17Z] Processing reference #82 (GL000194.1)
[2015-09-30T12:17Z] Processing reference #83 (GL000225.1)
[2015-09-30T12:17Z] Processing reference #84 (GL000192.1)
[2015-09-30T12:17Z] Clean up raw coverage file
[2015-09-30T12:17Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T12:17Z] Configuring 8 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T12:22Z] Assigned coverage as 'regional' with 4.9% genome coverage and 17.7% offtarget coverage
[2015-09-30T12:22Z] Recalibrating ['', 'syn3-normal'] with GATK
[2015-09-30T12:22Z] GATK: BaseRecalibrator
[2015-09-30T12:22Z] INFO  13:22:37,884 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T12:22Z] INFO  13:22:37,887 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T12:22Z] INFO  13:22:37,887 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T12:22Z] INFO  13:22:37,888 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T12:22Z] INFO  13:22:37,891 HelpFormatter - Program Args: -T BaseRecalibrator -o /home/cancer-dream-syn3/work/align/syn3-normal/tx/tmpv65aPm/1_2014-08-13_dream-syn3-sort.grp -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --knownSites /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /home/cancer-dream-syn3/work/bedprep/NGv3.bed --interval_set_rule INTERSECTION -nct 8 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T12:22Z] INFO  13:22:37,902 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T12:22Z] INFO  13:22:37,902 HelpFormatter - Date/Time: 2015/09/30 13:22:37
[2015-09-30T12:22Z] INFO  13:22:37,902 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T12:22Z] INFO  13:22:37,902 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T12:22Z] INFO  13:22:38,029 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T12:22Z] INFO  13:22:38,126 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T12:22Z] INFO  13:22:38,143 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T12:22Z] INFO  13:22:38,223 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2015-09-30T12:22Z] INFO  13:22:39,089 IntervalUtils - Processing 150603778 bp from intervals
[2015-09-30T12:22Z] WARN  13:22:39,093 IndexDictionaryUtils - Track knownSites doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T12:22Z] INFO  13:22:39,100 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 8 CPU thread(s) for each of 1 data thread(s), of 16 processors available on this machine
[2015-09-30T12:22Z] INFO  13:22:39,223 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T12:22Z] INFO  13:22:39,542 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T12:22Z] INFO  13:22:39,542 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T12:22Z] INFO  13:22:39,543 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T12:22Z] INFO  13:22:39,543 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T12:22Z] INFO  13:22:39,569 BaseRecalibrator - The covariates being used here:
[2015-09-30T12:22Z] INFO  13:22:39,570 BaseRecalibrator - 	ReadGroupCovariate
[2015-09-30T12:22Z] INFO  13:22:39,570 BaseRecalibrator - 	QualityScoreCovariate
[2015-09-30T12:22Z] INFO  13:22:39,570 BaseRecalibrator - 	ContextCovariate
[2015-09-30T12:22Z] INFO  13:22:39,570 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T12:22Z] INFO  13:22:39,570 BaseRecalibrator - 	CycleCovariate
[2015-09-30T12:22Z] INFO  13:22:39,573 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:22Z] INFO  13:22:40,103 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:23Z] INFO  13:23:11,009 ProgressMeter -      1:11855105    600007.0    31.0 s      52.0 s        0.8%    67.4 m      66.9 m
[2015-09-30T12:23Z] INFO  13:23:41,779 ProgressMeter -      1:26846381   1600023.0    62.0 s      38.0 s        1.8%    56.8 m      55.8 m
[2015-09-30T12:24Z] INFO  13:24:12,027 ProgressMeter -      1:44304251   2400032.0    92.0 s      38.0 s        2.9%    53.1 m      51.6 m
[2015-09-30T12:24Z] INFO  13:24:42,870 ProgressMeter -      1:87211664   3300044.0     2.1 m      37.0 s        4.3%    48.2 m      46.2 m
[2015-09-30T12:25Z] INFO  13:25:13,564 ProgressMeter -     1:144918198   4100053.0     2.6 m      37.0 s        5.5%    46.4 m      43.9 m
[2015-09-30T12:25Z] INFO  13:25:44,288 ProgressMeter -     1:158047595   5100066.0     3.1 m      36.0 s        6.7%    45.9 m      42.8 m
[2015-09-30T12:26Z] INFO  13:26:14,476 ProgressMeter -     1:196251164   5900077.0     3.6 m      36.0 s        8.0%    44.5 m      40.9 m
[2015-09-30T12:26Z] INFO  13:26:46,661 ProgressMeter -     1:225705373   6800090.0     4.1 m      36.0 s        9.3%    44.4 m      40.3 m
[2015-09-30T12:27Z] INFO  13:27:05,766 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:27Z] INFO  13:27:06,005 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:27Z] INFO  13:27:16,662 ProgressMeter -      2:11702514   7600116.0     4.6 m      36.0 s       10.4%    44.4 m      39.8 m
[2015-09-30T12:27Z] INFO  13:27:46,678 ProgressMeter -      2:44549148   8500128.0     5.1 m      36.0 s       11.5%    44.3 m      39.2 m
[2015-09-30T12:28Z] INFO  13:28:16,679 ProgressMeter -      2:86517266   9300140.0     5.6 m      36.0 s       12.7%    44.2 m      38.5 m
[2015-09-30T12:28Z] INFO  13:28:46,680 ProgressMeter -     2:128350949   1.010015E7     6.1 m      36.0 s       14.1%    43.5 m      37.4 m
[2015-09-30T12:29Z] INFO  13:29:17,661 ProgressMeter -     2:175677277   1.0900162E7     6.6 m      36.0 s       15.4%    43.1 m      36.4 m
[2015-09-30T12:29Z] INFO  13:29:47,717 ProgressMeter -     2:216290125   1.1700171E7     7.1 m      36.0 s       16.8%    42.4 m      35.3 m
[2015-09-30T12:30Z] INFO  13:30:19,753 ProgressMeter -     2:241845965   1.2600183E7     7.7 m      36.0 s       17.9%    42.8 m      35.1 m
[2015-09-30T12:30Z] INFO  13:30:21,788 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:30Z] INFO  13:30:21,865 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:30Z] INFO  13:30:49,755 ProgressMeter -      3:37356764   1.3427107E7     8.2 m      36.0 s       19.0%    43.0 m      34.8 m
[2015-09-30T12:31Z] INFO  13:31:19,756 ProgressMeter -      3:50930497   1.432712E7     8.7 m      36.0 s       20.0%    43.3 m      34.7 m
[2015-09-30T12:31Z] INFO  13:31:49,757 ProgressMeter -     3:100105714   1.5027128E7     9.2 m      36.0 s       21.0%    43.6 m      34.4 m
[2015-09-30T12:32Z] INFO  13:32:20,527 ProgressMeter -     3:134256404   1.5927137E7     9.7 m      36.0 s       22.3%    43.3 m      33.6 m
[2015-09-30T12:32Z] INFO  13:32:51,549 ProgressMeter -     3:185655512   1.6727148E7    10.2 m      36.0 s       23.6%    43.2 m      33.0 m
[2015-09-30T12:33Z] INFO  13:33:00,550 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:33Z] INFO  13:33:00,962 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:33Z] INFO  13:33:21,796 ProgressMeter -       4:9889348   1.7562216E7    10.7 m      36.0 s       24.6%    43.5 m      32.8 m
[2015-09-30T12:33Z] INFO  13:33:52,108 ProgressMeter -      4:76571892   1.8262223E7    11.2 m      36.0 s       25.9%    43.3 m      32.1 m
[2015-09-30T12:34Z] INFO  13:34:22,171 ProgressMeter -     4:129048051   1.8962232E7    11.7 m      37.0 s       27.1%    43.2 m      31.5 m
[2015-09-30T12:34Z] INFO  13:34:41,108 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:34Z] INFO  13:34:41,166 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:34Z] INFO  13:34:52,172 ProgressMeter -       5:6744063   1.9756551E7    12.2 m      37.0 s       28.3%    43.1 m      30.9 m
[2015-09-30T12:35Z] INFO  13:35:22,179 ProgressMeter -      5:70953054   2.0456559E7    12.7 m      37.0 s       29.6%    42.9 m      30.2 m
[2015-09-30T12:35Z] INFO  13:35:52,226 ProgressMeter -     5:132160491   2.1256567E7    13.2 m      37.0 s       30.9%    42.8 m      29.6 m
[2015-09-30T12:36Z] INFO  13:36:22,230 ProgressMeter -     5:157117354   2.2056577E7    13.7 m      37.0 s       32.0%    42.8 m      29.1 m
[2015-09-30T12:36Z] INFO  13:36:39,166 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:36Z] INFO  13:36:39,240 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:36Z] INFO  13:36:52,231 ProgressMeter -      6:10876292   2.283935E7    14.2 m      37.0 s       33.0%    43.0 m      28.8 m
[2015-09-30T12:37Z] INFO  13:37:22,239 ProgressMeter -      6:34664534   2.373936E7    14.7 m      37.0 s       34.1%    43.1 m      28.4 m
[2015-09-30T12:37Z] INFO  13:37:53,133 ProgressMeter -      6:65596344   2.4539369E7    15.2 m      37.0 s       35.2%    43.2 m      28.0 m
[2015-09-30T12:38Z] INFO  13:38:23,570 ProgressMeter -     6:131915761   2.5339377E7    15.7 m      37.0 s       36.6%    43.0 m      27.3 m
[2015-09-30T12:38Z] INFO  13:38:50,174 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:38Z] INFO  13:38:50,247 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:38Z] INFO  13:38:53,838 ProgressMeter -       7:1197958   2.6150641E7    16.2 m      37.0 s       37.8%    43.0 m      26.8 m
[2015-09-30T12:39Z] INFO  13:39:23,839 ProgressMeter -      7:36588251   2.6850649E7    16.7 m      37.0 s       38.8%    43.1 m      26.4 m
[2015-09-30T12:39Z] INFO  13:39:53,903 ProgressMeter -      7:81144748   2.7650661E7    17.2 m      37.0 s       40.0%    43.1 m      25.9 m
[2015-09-30T12:40Z] INFO  13:40:23,942 ProgressMeter -     7:111474679   2.8550674E7    17.7 m      37.0 s       41.2%    43.0 m      25.3 m
[2015-09-30T12:40Z] INFO  13:40:54,339 ProgressMeter -     7:149507855   2.9350686E7    18.2 m      37.0 s       42.4%    43.0 m      24.8 m
[2015-09-30T12:41Z] INFO  13:41:04,745 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:41Z] INFO  13:41:04,796 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:41Z] INFO  13:41:25,440 ProgressMeter -      8:22502628   3.0069133E7    18.8 m      37.0 s       43.4%    43.2 m      24.4 m
[2015-09-30T12:41Z] INFO  13:41:55,839 ProgressMeter -      8:74897210   3.0869143E7    19.3 m      37.0 s       44.6%    43.2 m      23.9 m
[2015-09-30T12:42Z] INFO  13:42:25,841 ProgressMeter -     8:140630961   3.1669155E7    19.8 m      37.0 s       45.8%    43.1 m      23.4 m
[2015-09-30T12:42Z] INFO  13:42:34,234 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:42Z] INFO  13:42:34,966 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:42Z] INFO  13:42:56,087 ProgressMeter -      9:33386439   3.2337173E7    20.3 m      37.0 s       46.8%    43.3 m      23.0 m
[2015-09-30T12:43Z] INFO  13:43:26,439 ProgressMeter -      9:95782237   3.3137182E7    20.8 m      37.0 s       48.1%    43.2 m      22.4 m
[2015-09-30T12:43Z] INFO  13:43:58,336 ProgressMeter -     9:129455886   3.4037196E7    21.3 m      37.0 s       49.3%    43.2 m      21.9 m
[2015-09-30T12:44Z] INFO  13:44:29,492 ProgressMeter -     9:139909419   3.5037209E7    21.8 m      37.0 s       50.3%    43.4 m      21.6 m
[2015-09-30T12:44Z] INFO  13:44:31,225 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:44Z] INFO  13:44:31,378 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:44Z] INFO  13:44:59,539 ProgressMeter -     10:34601082   3.5713208E7    22.3 m      37.0 s       51.4%    43.4 m      21.1 m
[2015-09-30T12:45Z] INFO  13:45:29,749 ProgressMeter -     10:78630089   3.6513217E7    22.8 m      37.0 s       52.6%    43.4 m      20.6 m
[2015-09-30T12:45Z] INFO  13:45:59,750 ProgressMeter -    10:106057620   3.7413227E7    23.3 m      37.0 s       53.8%    43.4 m      20.0 m
[2015-09-30T12:46Z] INFO  13:46:22,071 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:46Z] INFO  13:46:22,135 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:46Z] INFO  13:46:31,005 ProgressMeter -       11:760488   3.819952E7    23.9 m      37.0 s       54.8%    43.5 m      19.6 m
[2015-09-30T12:47Z] INFO  13:47:02,293 ProgressMeter -     11:22272599   3.9099534E7    24.4 m      37.0 s       55.9%    43.6 m      19.2 m
[2015-09-30T12:47Z] INFO  13:47:32,422 ProgressMeter -     11:61719466   3.9999545E7    24.9 m      37.0 s       57.0%    43.6 m      18.7 m
[2015-09-30T12:48Z] INFO  13:48:02,439 ProgressMeter -     11:71947178   4.089956E7    25.4 m      37.0 s       58.0%    43.7 m      18.4 m
[2015-09-30T12:48Z] INFO  13:48:32,458 ProgressMeter -    11:113813850   4.1699569E7    25.9 m      37.0 s       59.2%    43.7 m      17.8 m
[2015-09-30T12:48Z] INFO  13:48:53,133 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:48Z] INFO  13:48:54,008 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:49Z] INFO  13:49:02,779 ProgressMeter -      12:4881407   4.2510344E7    26.4 m      37.0 s       60.3%    43.8 m      17.4 m
[2015-09-30T12:49Z] INFO  13:49:33,594 ProgressMeter -     12:41582185   4.3410355E7    26.9 m      37.0 s       61.5%    43.7 m      16.8 m
[2015-09-30T12:50Z] INFO  13:50:04,103 ProgressMeter -     12:57589125   4.4310365E7    27.4 m      37.0 s       62.6%    43.7 m      16.3 m
[2015-09-30T12:50Z] INFO  13:50:35,160 ProgressMeter -    12:107974961   4.5010373E7    27.9 m      37.0 s       64.0%    43.6 m      15.7 m
[2015-09-30T12:51Z] INFO  13:51:06,017 ProgressMeter -    12:129467921   4.5910384E7    28.4 m      37.0 s       65.1%    43.7 m      15.3 m
[2015-09-30T12:51Z] INFO  13:51:08,416 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:51Z] INFO  13:51:08,461 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:51Z] INFO  13:51:36,317 ProgressMeter -     13:51599323   4.6684346E7    28.9 m      37.0 s       66.3%    43.7 m      14.7 m
[2015-09-30T12:52Z] INFO  13:52:01,097 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:52Z] INFO  13:52:01,348 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:52Z] INFO  13:52:07,204 ProgressMeter -     14:21793625   4.7389226E7    29.5 m      37.0 s       67.3%    43.8 m      14.3 m
[2015-09-30T12:52Z] INFO  13:52:37,243 ProgressMeter -     14:61262715   4.8189235E7    30.0 m      37.0 s       68.5%    43.7 m      13.8 m
[2015-09-30T12:53Z] INFO  13:53:07,806 ProgressMeter -     14:96010207   4.9089246E7    30.5 m      37.0 s       69.7%    43.7 m      13.2 m
[2015-09-30T12:53Z] INFO  13:53:21,436 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:53Z] INFO  13:53:21,923 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:53Z] INFO  13:53:37,819 ProgressMeter -     15:34145789   4.9936253E7    31.0 m      37.0 s       70.9%    43.7 m      12.7 m
[2015-09-30T12:54Z] INFO  13:54:08,042 ProgressMeter -     15:59192352   5.0736263E7    31.5 m      37.0 s       72.1%    43.6 m      12.2 m
[2015-09-30T12:54Z] INFO  13:54:38,643 ProgressMeter -     15:80260009   5.1636275E7    32.0 m      37.0 s       73.2%    43.7 m      11.7 m
[2015-09-30T12:54Z] INFO  13:54:55,444 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:54Z] INFO  13:54:55,498 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:55Z] INFO  13:55:08,910 ProgressMeter -      16:1988871   5.2402749E7    32.5 m      37.0 s       74.3%    43.7 m      11.3 m
[2015-09-30T12:55Z] INFO  13:55:39,373 ProgressMeter -     16:20386135   5.3202759E7    33.0 m      37.0 s       75.3%    43.8 m      10.8 m
[2015-09-30T12:56Z] INFO  13:56:09,389 ProgressMeter -     16:53338776   5.4102771E7    33.5 m      37.0 s       76.4%    43.8 m      10.3 m
[2015-09-30T12:56Z] INFO  13:56:40,521 ProgressMeter -     16:74908468   5.4902783E7    34.0 m      37.0 s       77.5%    43.9 m       9.9 m
[2015-09-30T12:56Z] INFO  13:56:56,230 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:56Z] INFO  13:56:56,294 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:57Z] INFO  13:57:10,635 ProgressMeter -      17:4721436   5.5825015E7    34.5 m      37.0 s       78.4%    44.0 m       9.5 m
[2015-09-30T12:57Z] INFO  13:57:41,592 ProgressMeter -     17:18920518   5.6725027E7    35.0 m      37.0 s       79.5%    44.1 m       9.1 m
[2015-09-30T12:58Z] INFO  13:58:12,651 ProgressMeter -     17:39537974   5.7625037E7    35.6 m      37.0 s       80.7%    44.1 m       8.5 m
[2015-09-30T12:58Z] INFO  13:58:43,566 ProgressMeter -     17:54936339   5.8525047E7    36.1 m      36.0 s       81.7%    44.1 m       8.1 m
[2015-09-30T12:59Z] INFO  13:59:14,015 ProgressMeter -     17:74344946   5.9425059E7    36.6 m      36.0 s       82.9%    44.1 m       7.6 m
[2015-09-30T12:59Z] INFO  13:59:29,297 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T12:59Z] INFO  13:59:29,341 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T12:59Z] INFO  13:59:45,728 ProgressMeter -     18:19109644   6.018216E7    37.1 m      36.0 s       83.9%    44.2 m       7.1 m
[2015-09-30T13:00Z] INFO  14:00:11,405 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:00Z] INFO  14:00:11,604 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:00Z] INFO  14:00:15,746 ProgressMeter -       19:830979   6.1014208E7    37.6 m      36.0 s       85.1%    44.2 m       6.6 m
[2015-09-30T13:00Z] INFO  14:00:47,013 ProgressMeter -      19:8533546   6.1814217E7    38.1 m      37.0 s       86.0%    44.3 m       6.2 m
[2015-09-30T13:01Z] INFO  14:01:18,500 ProgressMeter -     19:17769228   6.2814228E7    38.6 m      36.0 s       87.0%    44.4 m       5.8 m
[2015-09-30T13:01Z] INFO  14:01:50,613 ProgressMeter -     19:39976640   6.3714242E7    39.2 m      36.0 s       88.0%    44.5 m       5.3 m
[2015-09-30T13:02Z] INFO  14:02:21,263 ProgressMeter -     19:49558373   6.4614253E7    39.7 m      36.0 s       89.0%    44.6 m       4.9 m
[2015-09-30T13:02Z] INFO  14:02:50,092 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:02Z] INFO  14:02:50,197 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:02Z] INFO  14:02:53,162 ProgressMeter -     19:59110668   6.5514266E7    40.2 m      36.0 s       90.1%    44.6 m       4.4 m
[2015-09-30T13:03Z] INFO  14:03:23,457 ProgressMeter -     20:32267607   6.6232537E7    40.7 m      36.0 s       91.1%    44.7 m       4.0 m
[2015-09-30T13:03Z] INFO  14:03:54,063 ProgressMeter -     20:56803389   6.7132549E7    41.2 m      36.0 s       92.2%    44.7 m       3.5 m
[2015-09-30T13:04Z] INFO  14:04:03,416 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:04Z] INFO  14:04:03,443 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:04Z] INFO  14:04:24,498 ProgressMeter -     21:40587303   6.7894928E7    41.7 m      36.0 s       93.2%    44.8 m       3.1 m
[2015-09-30T13:04Z] INFO  14:04:37,514 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:04Z] INFO  14:04:37,827 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:04Z] INFO  14:04:54,500 ProgressMeter -     22:22556145   6.8773788E7    42.2 m      36.0 s       94.2%    44.8 m       2.6 m
[2015-09-30T13:05Z] INFO  14:05:25,401 ProgressMeter -     22:38227856   6.9573797E7    42.8 m      36.0 s       95.1%    45.0 m       2.2 m
[2015-09-30T13:05Z] INFO  14:05:48,412 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:05Z] INFO  14:05:48,455 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:05Z] INFO  14:05:55,567 ProgressMeter -       X:8766979   7.0451556E7    43.3 m      36.0 s       96.1%    45.0 m     106.0 s
[2015-09-30T13:06Z] INFO  14:06:25,569 ProgressMeter -      X:54841329   7.1351565E7    43.8 m      36.0 s       97.4%    44.9 m      70.0 s
[2015-09-30T13:06Z] INFO  14:06:55,588 ProgressMeter -     X:119419357   7.2151576E7    44.3 m      36.0 s       98.6%    44.9 m      36.0 s
[2015-09-30T13:07Z] INFO  14:07:16,918 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:07Z] INFO  14:07:16,989 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:07Z] INFO  14:07:18,366 BaseRecalibrator - Calculating quantized quality scores...
[2015-09-30T13:07Z] INFO  14:07:18,426 BaseRecalibrator - Writing recalibration report...
[2015-09-30T13:07Z] INFO  14:07:19,502 BaseRecalibrator - ...done!
[2015-09-30T13:07Z] INFO  14:07:19,502 BaseRecalibrator - BaseRecalibrator was able to recalibrate 72880782 reads
[2015-09-30T13:07Z] INFO  14:07:19,504 ProgressMeter -            done   7.2880782E7    44.7 m      36.0 s      100.0%    44.7 m       0.0 s
[2015-09-30T13:07Z] INFO  14:07:19,504 ProgressMeter - Total runtime 2679.96 secs, 44.67 min, 0.74 hours
[2015-09-30T13:07Z] INFO  14:07:19,504 MicroScheduler - 7660039 reads were filtered out during the traversal out of approximately 80654968 total reads (9.50%)
[2015-09-30T13:07Z] INFO  14:07:19,505 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T13:07Z] INFO  14:07:19,505 MicroScheduler -   -> 3768483 reads (4.67% of total) failing DuplicateReadFilter
[2015-09-30T13:07Z] INFO  14:07:19,505 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T13:07Z] INFO  14:07:19,505 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T13:07Z] INFO  14:07:19,505 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T13:07Z] INFO  14:07:19,506 MicroScheduler -   -> 3891556 reads (4.82% of total) failing MappingQualityZeroFilter
[2015-09-30T13:07Z] INFO  14:07:19,506 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T13:07Z] INFO  14:07:19,506 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T13:07Z] INFO  14:07:21,057 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T13:07Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T13:07Z] Configuring 8 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T13:07Z] multiprocessing: calc_callable_loci
[2015-09-30T13:07Z] bedtools genomecov: 5 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:07Z] bedtools genomecov: 1 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:07Z] bedtools genomecov: 4 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:07Z] bedtools genomecov: 8 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:07Z] bedtools genomecov: 2 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:07Z] bedtools genomecov: 6 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:07Z] bedtools genomecov: 7 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:07Z] bedtools genomecov: 3 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:07Z] bedtools groupby coverage: 8 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 4 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 5 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools genomecov: 9 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 6 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 7 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools genomecov: 10 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 3 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools genomecov: 11 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools genomecov: 12 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 2 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools genomecov: 13 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools genomecov: 14 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 13 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 1 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 9 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools groupby coverage: 10 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools genomecov: 15 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:08Z] bedtools genomecov: 16 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 14 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools genomecov: 17 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools genomecov: 18 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 12 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 11 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools genomecov: 19 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 18 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 15 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools genomecov: 20 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools genomecov: 21 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools genomecov: 22 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools genomecov: X : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 16 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools genomecov: Y : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: Y : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 21 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 17 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 20 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 22 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: X : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:09Z] bedtools groupby coverage: 19 : 2_2014-08-13_dream-syn3-sort.bam
[2015-09-30T13:10Z] multiprocessing: combine_bed
[2015-09-30T13:15Z] Identify high coverage regions
[2015-09-30T13:15Z] Processing reference #1 (1)
[2015-09-30T13:16Z] Processing reference #2 (2)
[2015-09-30T13:16Z] Processing reference #3 (3)
[2015-09-30T13:16Z] Processing reference #4 (4)
[2015-09-30T13:17Z] Processing reference #5 (5)
[2015-09-30T13:17Z] Processing reference #6 (6)
[2015-09-30T13:17Z] Processing reference #7 (7)
[2015-09-30T13:17Z] Processing reference #8 (8)
[2015-09-30T13:17Z] Processing reference #9 (9)
[2015-09-30T13:18Z] Processing reference #10 (10)
[2015-09-30T13:18Z] Processing reference #11 (11)
[2015-09-30T13:18Z] Processing reference #12 (12)
[2015-09-30T13:18Z] Processing reference #13 (13)
[2015-09-30T13:18Z] Processing reference #14 (14)
[2015-09-30T13:19Z] Processing reference #15 (15)
[2015-09-30T13:19Z] Processing reference #16 (16)
[2015-09-30T13:19Z] Processing reference #17 (17)
[2015-09-30T13:19Z] Processing reference #18 (18)
[2015-09-30T13:19Z] Processing reference #19 (19)
[2015-09-30T13:19Z] Processing reference #20 (20)
[2015-09-30T13:20Z] Processing reference #21 (21)
[2015-09-30T13:20Z] Processing reference #22 (22)
[2015-09-30T13:20Z] Processing reference #23 (X)
[2015-09-30T13:20Z] Processing reference #24 (Y)
[2015-09-30T13:20Z] Processing reference #25 (MT)
[2015-09-30T13:20Z] Processing reference #26 (GL000207.1)
[2015-09-30T13:20Z] Processing reference #27 (GL000226.1)
[2015-09-30T13:20Z] Processing reference #28 (GL000229.1)
[2015-09-30T13:20Z] Processing reference #29 (GL000231.1)
[2015-09-30T13:20Z] Processing reference #31 (GL000239.1)
[2015-09-30T13:20Z] Processing reference #32 (GL000235.1)
[2015-09-30T13:20Z] Processing reference #34 (GL000247.1)
[2015-09-30T13:20Z] Processing reference #35 (GL000245.1)
[2015-09-30T13:20Z] Processing reference #37 (GL000203.1)
[2015-09-30T13:20Z] Processing reference #38 (GL000246.1)
[2015-09-30T13:20Z] Processing reference #41 (GL000248.1)
[2015-09-30T13:20Z] Processing reference #42 (GL000244.1)
[2015-09-30T13:20Z] Processing reference #43 (GL000238.1)
[2015-09-30T13:20Z] Processing reference #44 (GL000202.1)
[2015-09-30T13:20Z] Processing reference #45 (GL000234.1)
[2015-09-30T13:20Z] Processing reference #46 (GL000232.1)
[2015-09-30T13:20Z] Processing reference #48 (GL000240.1)
[2015-09-30T13:20Z] Processing reference #49 (GL000236.1)
[2015-09-30T13:20Z] Processing reference #50 (GL000241.1)
[2015-09-30T13:20Z] Processing reference #51 (GL000243.1)
[2015-09-30T13:20Z] Processing reference #52 (GL000242.1)
[2015-09-30T13:20Z] Processing reference #53 (GL000230.1)
[2015-09-30T13:20Z] Processing reference #54 (GL000237.1)
[2015-09-30T13:20Z] Processing reference #55 (GL000233.1)
[2015-09-30T13:20Z] Processing reference #56 (GL000204.1)
[2015-09-30T13:20Z] Processing reference #57 (GL000198.1)
[2015-09-30T13:20Z] Processing reference #58 (GL000208.1)
[2015-09-30T13:20Z] Processing reference #59 (GL000191.1)
[2015-09-30T13:20Z] Processing reference #60 (GL000227.1)
[2015-09-30T13:20Z] Processing reference #61 (GL000228.1)
[2015-09-30T13:20Z] Processing reference #62 (GL000214.1)
[2015-09-30T13:20Z] Processing reference #63 (GL000221.1)
[2015-09-30T13:20Z] Processing reference #64 (GL000209.1)
[2015-09-30T13:20Z] Processing reference #65 (GL000218.1)
[2015-09-30T13:20Z] Processing reference #66 (GL000220.1)
[2015-09-30T13:20Z] Processing reference #67 (GL000213.1)
[2015-09-30T13:20Z] Processing reference #68 (GL000211.1)
[2015-09-30T13:20Z] Processing reference #69 (GL000199.1)
[2015-09-30T13:20Z] Processing reference #70 (GL000217.1)
[2015-09-30T13:20Z] Processing reference #71 (GL000216.1)
[2015-09-30T13:20Z] Processing reference #72 (GL000215.1)
[2015-09-30T13:20Z] Processing reference #73 (GL000205.1)
[2015-09-30T13:20Z] Processing reference #74 (GL000219.1)
[2015-09-30T13:20Z] Processing reference #75 (GL000224.1)
[2015-09-30T13:20Z] Processing reference #76 (GL000223.1)
[2015-09-30T13:20Z] Processing reference #77 (GL000195.1)
[2015-09-30T13:20Z] Processing reference #78 (GL000212.1)
[2015-09-30T13:20Z] Processing reference #79 (GL000222.1)
[2015-09-30T13:20Z] Processing reference #81 (GL000193.1)
[2015-09-30T13:20Z] Processing reference #82 (GL000194.1)
[2015-09-30T13:20Z] Processing reference #83 (GL000225.1)
[2015-09-30T13:20Z] Processing reference #84 (GL000192.1)
[2015-09-30T13:20Z] Clean up raw coverage file
[2015-09-30T13:20Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T13:20Z] Configuring 8 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T13:26Z] Assigned coverage as 'regional' with 4.9% genome coverage and 17.8% offtarget coverage
[2015-09-30T13:26Z] Recalibrating ['', 'syn3-tumor'] with GATK
[2015-09-30T13:26Z] GATK: BaseRecalibrator
[2015-09-30T13:26Z] INFO  14:26:03,479 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T13:26Z] INFO  14:26:03,481 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T13:26Z] INFO  14:26:03,481 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T13:26Z] INFO  14:26:03,481 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T13:26Z] INFO  14:26:03,485 HelpFormatter - Program Args: -T BaseRecalibrator -o /home/cancer-dream-syn3/work/align/syn3-tumor/tx/tmplvaoTf/2_2014-08-13_dream-syn3-sort.grp -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --knownSites /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /home/cancer-dream-syn3/work/bedprep/NGv3.bed --interval_set_rule INTERSECTION -nct 8 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T13:26Z] INFO  14:26:03,522 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T13:26Z] INFO  14:26:03,522 HelpFormatter - Date/Time: 2015/09/30 14:26:03
[2015-09-30T13:26Z] INFO  14:26:03,523 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T13:26Z] INFO  14:26:03,817 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T13:26Z] INFO  14:26:03,900 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T13:26Z] INFO  14:26:03,969 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T13:26Z] INFO  14:26:03,976 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T13:26Z] INFO  14:26:03,991 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T13:26Z] INFO  14:26:04,722 IntervalUtils - Processing 150603778 bp from intervals
[2015-09-30T13:26Z] WARN  14:26:04,725 IndexDictionaryUtils - Track knownSites doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T13:26Z] INFO  14:26:04,732 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 8 CPU thread(s) for each of 1 data thread(s), of 16 processors available on this machine
[2015-09-30T13:26Z] INFO  14:26:04,790 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T13:26Z] INFO  14:26:05,143 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T13:26Z] INFO  14:26:05,144 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T13:26Z] INFO  14:26:05,144 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T13:26Z] INFO  14:26:05,144 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T13:26Z] INFO  14:26:05,164 BaseRecalibrator - The covariates being used here:
[2015-09-30T13:26Z] INFO  14:26:05,164 BaseRecalibrator - 	ReadGroupCovariate
[2015-09-30T13:26Z] INFO  14:26:05,164 BaseRecalibrator - 	QualityScoreCovariate
[2015-09-30T13:26Z] INFO  14:26:05,164 BaseRecalibrator - 	ContextCovariate
[2015-09-30T13:26Z] INFO  14:26:05,164 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T13:26Z] INFO  14:26:05,165 BaseRecalibrator - 	CycleCovariate
[2015-09-30T13:26Z] INFO  14:26:05,168 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:26Z] INFO  14:26:05,622 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:26Z] INFO  14:26:36,106 ProgressMeter -      1:11855117    600008.0    30.0 s      51.0 s        0.8%    65.2 m      64.7 m
[2015-09-30T13:27Z] INFO  14:27:06,250 ProgressMeter -      1:26800501   1600023.0    61.0 s      38.0 s        1.8%    56.0 m      55.0 m
[2015-09-30T13:27Z] INFO  14:27:36,251 ProgressMeter -      1:45266160   2500037.0    91.0 s      36.0 s        3.0%    51.4 m      49.9 m
[2015-09-30T13:28Z] INFO  14:28:06,605 ProgressMeter -      1:89325479   3300046.0     2.0 m      36.0 s        4.3%    47.1 m      45.1 m
[2015-09-30T13:28Z] INFO  14:28:36,647 ProgressMeter -     1:145586913   4200057.0     2.5 m      36.0 s        5.6%    45.0 m      42.5 m
[2015-09-30T13:29Z] INFO  14:29:06,672 ProgressMeter -     1:159904450   5100069.0     3.0 m      35.0 s        6.8%    44.4 m      41.4 m
[2015-09-30T13:29Z] INFO  14:29:36,686 ProgressMeter -     1:196255141   5900078.0     3.5 m      35.0 s        8.0%    43.9 m      40.4 m
[2015-09-30T13:30Z] INFO  14:30:08,594 ProgressMeter -     1:225965579   6800089.0     4.1 m      35.0 s        9.3%    43.7 m      39.6 m
[2015-09-30T13:30Z] INFO  14:30:25,062 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:30Z] INFO  14:30:25,234 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:30Z] INFO  14:30:38,595 ProgressMeter -      2:11706553   7598995.0     4.6 m      35.0 s       10.4%    43.7 m      39.2 m
[2015-09-30T13:31Z] INFO  14:31:08,921 ProgressMeter -      2:48687359   8499004.0     5.1 m      35.0 s       11.7%    43.3 m      38.3 m
[2015-09-30T13:31Z] INFO  14:31:38,941 ProgressMeter -      2:90413996   9299014.0     5.6 m      35.0 s       12.9%    43.0 m      37.5 m
[2015-09-30T13:32Z] INFO  14:32:08,942 ProgressMeter -     2:131414892   1.0199026E7     6.1 m      35.0 s       14.2%    42.6 m      36.5 m
[2015-09-30T13:32Z] INFO  14:32:40,342 ProgressMeter -     2:179472337   1.0999036E7     6.6 m      35.0 s       15.6%    42.3 m      35.7 m
[2015-09-30T13:33Z] INFO  14:33:11,696 ProgressMeter -     2:220131418   1.1899046E7     7.1 m      35.0 s       17.0%    41.6 m      34.5 m
[2015-09-30T13:33Z] INFO  14:33:38,242 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:33Z] INFO  14:33:38,320 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:33Z] INFO  14:33:42,278 ProgressMeter -       3:2967180   1.2814941E7     7.6 m      35.0 s       18.1%    42.1 m      34.5 m
[2015-09-30T13:34Z] INFO  14:34:12,335 ProgressMeter -      3:42240446   1.361495E7     8.1 m      35.0 s       19.3%    42.2 m      34.0 m
[2015-09-30T13:34Z] INFO  14:34:43,102 ProgressMeter -      3:53158198   1.4514966E7     8.6 m      35.0 s       20.3%    42.5 m      33.9 m
[2015-09-30T13:35Z] INFO  14:35:13,947 ProgressMeter -     3:120129949   1.5314976E7     9.1 m      35.0 s       21.5%    42.4 m      33.3 m
[2015-09-30T13:35Z] INFO  14:35:44,214 ProgressMeter -     3:152880905   1.6214989E7     9.7 m      35.0 s       22.8%    42.3 m      32.6 m
[2015-09-30T13:36Z] INFO  14:36:12,894 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:36Z] INFO  14:36:12,959 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:36Z] INFO  14:36:14,522 ProgressMeter -     3:197556523   1.7114999E7    10.2 m      35.0 s       24.0%    42.2 m      32.1 m
[2015-09-30T13:36Z] INFO  14:36:44,581 ProgressMeter -      4:39439523   1.7835577E7    10.7 m      35.0 s       25.0%    42.5 m      31.9 m
[2015-09-30T13:37Z] INFO  14:37:14,615 ProgressMeter -      4:95195605   1.8635586E7    11.2 m      35.0 s       26.4%    42.3 m      31.1 m
[2015-09-30T13:37Z] INFO  14:37:45,318 ProgressMeter -     4:170674953   1.9335594E7    11.7 m      36.0 s       27.8%    42.0 m      30.3 m
[2015-09-30T13:37Z] INFO  14:37:49,222 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:37Z] INFO  14:37:49,731 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:38Z] INFO  14:38:15,366 ProgressMeter -      5:37207808   2.0026344E7    12.2 m      36.0 s       28.8%    42.2 m      30.1 m
[2015-09-30T13:38Z] INFO  14:38:45,369 ProgressMeter -     5:102440172   2.0826353E7    12.7 m      36.0 s       30.3%    41.8 m      29.1 m
[2015-09-30T13:39Z] INFO  14:39:15,370 ProgressMeter -     5:142722138   2.1626364E7    13.2 m      36.0 s       31.5%    41.8 m      28.7 m
[2015-09-30T13:39Z] INFO  14:39:45,371 ProgressMeter -     5:179225647   2.2526376E7    13.7 m      36.0 s       32.6%    41.9 m      28.2 m
[2015-09-30T13:39Z] INFO  14:39:45,492 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:39Z] INFO  14:39:45,557 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:40Z] INFO  14:40:17,006 ProgressMeter -      6:31544470   2.3402834E7    14.2 m      36.0 s       33.7%    42.1 m      27.9 m
[2015-09-30T13:40Z] INFO  14:40:47,148 ProgressMeter -      6:44149388   2.4302843E7    14.7 m      36.0 s       34.7%    42.3 m      27.6 m
[2015-09-30T13:41Z] INFO  14:41:18,237 ProgressMeter -     6:109978129   2.500285E7    15.2 m      36.0 s       36.1%    42.1 m      26.9 m
[2015-09-30T13:41Z] INFO  14:41:48,238 ProgressMeter -     6:160450965   2.5802862E7    15.7 m      36.0 s       37.4%    42.0 m      26.3 m
[2015-09-30T13:41Z] INFO  14:41:53,772 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:41Z] INFO  14:41:54,023 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:42Z] INFO  14:42:18,556 ProgressMeter -      7:27194395   2.6609302E7    16.2 m      36.0 s       38.5%    42.1 m      25.9 m
[2015-09-30T13:42Z] INFO  14:42:48,557 ProgressMeter -      7:73450704   2.7409311E7    16.7 m      36.0 s       39.6%    42.2 m      25.5 m
[2015-09-30T13:43Z] INFO  14:43:18,877 ProgressMeter -     7:100965153   2.8309324E7    17.2 m      36.0 s       40.8%    42.2 m      25.0 m
[2015-09-30T13:43Z] INFO  14:43:50,286 ProgressMeter -     7:142168559   2.9109336E7    17.8 m      36.0 s       42.1%    42.1 m      24.4 m
[2015-09-30T13:44Z] INFO  14:44:07,123 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:44Z] INFO  14:44:07,171 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:44Z] INFO  14:44:20,308 ProgressMeter -      8:16025876   2.9921612E7    18.3 m      36.0 s       43.2%    42.3 m      24.0 m
[2015-09-30T13:44Z] INFO  14:44:50,412 ProgressMeter -      8:61749995   3.0721625E7    18.8 m      36.0 s       44.3%    42.3 m      23.5 m
[2015-09-30T13:45Z] INFO  14:45:21,444 ProgressMeter -     8:128750796   3.1421633E7    19.3 m      36.0 s       45.6%    42.2 m      22.9 m
[2015-09-30T13:45Z] INFO  14:45:36,652 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:45Z] INFO  14:45:36,718 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:45Z] INFO  14:45:52,504 ProgressMeter -      9:21440887   3.2245568E7    19.8 m      36.0 s       46.7%    42.4 m      22.6 m
[2015-09-30T13:46Z] INFO  14:46:23,640 ProgressMeter -      9:95420672   3.3145581E7    20.3 m      36.0 s       48.1%    42.2 m      21.9 m
[2015-09-30T13:46Z] INFO  14:46:53,697 ProgressMeter -     9:126501764   3.394559E7    20.8 m      36.0 s       49.2%    42.3 m      21.5 m
[2015-09-30T13:47Z] INFO  14:47:24,349 ProgressMeter -     9:139316136   3.4845603E7    21.3 m      36.0 s       50.2%    42.5 m      21.2 m
[2015-09-30T13:47Z] INFO  14:47:30,002 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:47Z] INFO  14:47:30,514 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:47Z] INFO  14:47:54,350 ProgressMeter -     10:27578733   3.5612415E7    21.8 m      36.0 s       51.2%    42.6 m      20.8 m
[2015-09-30T13:48Z] INFO  14:48:24,386 ProgressMeter -     10:75554440   3.6512427E7    22.3 m      36.0 s       52.5%    42.5 m      20.2 m
[2015-09-30T13:48Z] INFO  14:48:55,103 ProgressMeter -    10:105345069   3.7412438E7    22.8 m      36.0 s       53.8%    42.4 m      19.6 m
[2015-09-30T13:49Z] INFO  14:49:18,063 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:49Z] INFO  14:49:18,118 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:49Z] INFO  14:49:25,623 ProgressMeter -       11:759001   3.8190982E7    23.3 m      36.0 s       54.8%    42.6 m      19.2 m
[2015-09-30T13:49Z] INFO  14:49:57,190 ProgressMeter -     11:22364695   3.9090992E7    23.9 m      36.0 s       55.9%    42.7 m      18.8 m
[2015-09-30T13:50Z] INFO  14:50:27,226 ProgressMeter -     11:62361113   3.9991004E7    24.4 m      36.0 s       57.1%    42.7 m      18.3 m
[2015-09-30T13:50Z] INFO  14:50:57,429 ProgressMeter -     11:73590006   4.0891017E7    24.9 m      36.0 s       58.1%    42.8 m      17.9 m
[2015-09-30T13:51Z] INFO  14:51:27,939 ProgressMeter -    11:117242037   4.1691026E7    25.4 m      36.0 s       59.3%    42.8 m      17.4 m
[2015-09-30T13:51Z] INFO  14:51:43,762 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:51Z] INFO  14:51:43,814 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:51Z] INFO  14:51:59,141 ProgressMeter -      12:6782828   4.2687949E7    25.9 m      36.0 s       60.4%    42.9 m      17.0 m
[2015-09-30T13:52Z] INFO  14:52:29,769 ProgressMeter -     12:49076035   4.348796E7    26.4 m      36.0 s       61.8%    42.8 m      16.4 m
[2015-09-30T13:52Z] INFO  14:52:59,818 ProgressMeter -     12:62884069   4.4387971E7    26.9 m      36.0 s       62.8%    42.8 m      15.9 m
[2015-09-30T13:53Z] INFO  14:53:29,895 ProgressMeter -    12:110770425   4.518798E7    27.4 m      36.0 s       64.2%    42.7 m      15.3 m
[2015-09-30T13:53Z] INFO  14:53:57,865 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:53Z] INFO  14:53:57,898 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:53Z] INFO  14:53:59,958 ProgressMeter -    12:133795684   4.608799E7    27.9 m      36.0 s       65.3%    42.7 m      14.8 m
[2015-09-30T13:54Z] INFO  14:54:30,037 ProgressMeter -     13:73339989   4.6749826E7    28.4 m      36.0 s       66.4%    42.7 m      14.3 m
[2015-09-30T13:54Z] INFO  14:54:47,920 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:54Z] INFO  14:54:48,013 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:55Z] INFO  14:55:00,656 ProgressMeter -     14:24002894   4.7554477E7    28.9 m      36.0 s       67.6%    42.8 m      13.9 m
[2015-09-30T13:55Z] INFO  14:55:30,757 ProgressMeter -     14:68935747   4.8354488E7    29.4 m      36.0 s       68.8%    42.8 m      13.3 m
[2015-09-30T13:56Z] INFO  14:56:00,762 ProgressMeter -    14:102698305   4.92545E7    29.9 m      36.0 s       70.0%    42.8 m      12.8 m
[2015-09-30T13:56Z] INFO  14:56:07,608 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:56Z] INFO  14:56:07,671 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:56Z] INFO  14:56:30,922 ProgressMeter -     15:41190924   5.0097012E7    30.4 m      36.0 s       71.1%    42.8 m      12.3 m
[2015-09-30T13:57Z] INFO  14:57:00,924 ProgressMeter -     15:65743497   5.0997023E7    30.9 m      36.0 s       72.5%    42.7 m      11.8 m
[2015-09-30T13:57Z] INFO  14:57:31,802 ProgressMeter -     15:90344271   5.1797032E7    31.4 m      36.0 s       73.6%    42.7 m      11.2 m
[2015-09-30T13:57Z] INFO  14:57:37,207 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:57Z] INFO  14:57:37,391 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T13:58Z] INFO  14:58:02,542 ProgressMeter -      16:4519411   5.2762398E7    32.0 m      36.0 s       74.6%    42.8 m      10.9 m
[2015-09-30T13:58Z] INFO  14:58:34,014 ProgressMeter -     16:29842644   5.3562408E7    32.5 m      36.0 s       75.8%    42.8 m      10.3 m
[2015-09-30T13:59Z] INFO  14:59:04,430 ProgressMeter -     16:67695525   5.4462421E7    33.0 m      36.0 s       77.0%    42.9 m       9.9 m
[2015-09-30T13:59Z] INFO  14:59:35,161 ProgressMeter -     16:90057366   5.5362431E7    33.5 m      36.0 s       78.0%    42.9 m       9.4 m
[2015-09-30T13:59Z] INFO  14:59:35,167 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T13:59Z] INFO  14:59:35,233 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:00Z] INFO  15:00:05,793 ProgressMeter -      17:9538764   5.6180995E7    34.0 m      36.0 s       78.9%    43.1 m       9.1 m
[2015-09-30T14:00Z] INFO  15:00:35,849 ProgressMeter -     17:33312759   5.7181006E7    34.5 m      36.0 s       80.1%    43.1 m       8.6 m
[2015-09-30T14:01Z] INFO  15:01:06,064 ProgressMeter -     17:43517934   5.8081015E7    35.0 m      36.0 s       81.2%    43.1 m       8.1 m
[2015-09-30T14:01Z] INFO  15:01:36,257 ProgressMeter -     17:66397734   5.8881025E7    35.5 m      36.0 s       82.4%    43.1 m       7.6 m
[2015-09-30T14:02Z] INFO  15:02:04,602 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:02Z] INFO  15:02:05,969 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:02Z] INFO  15:02:06,425 ProgressMeter -     17:80400669   5.9781035E7    36.0 m      36.0 s       83.4%    43.2 m       7.2 m
[2015-09-30T14:02Z] INFO  15:02:36,883 ProgressMeter -     18:47463332   6.0532084E7    36.5 m      36.0 s       84.5%    43.2 m       6.7 m
[2015-09-30T14:02Z] INFO  15:02:47,843 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:02Z] INFO  15:02:47,901 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:03Z] INFO  15:03:06,888 ProgressMeter -      19:3852225   6.1364277E7    37.0 m      36.0 s       85.5%    43.3 m       6.3 m
[2015-09-30T14:03Z] INFO  15:03:37,180 ProgressMeter -     19:12859099   6.2264288E7    37.5 m      36.0 s       86.5%    43.4 m       5.9 m
[2015-09-30T14:04Z] INFO  15:04:07,268 ProgressMeter -     19:33603076   6.3064298E7    38.0 m      36.0 s       87.5%    43.5 m       5.5 m
[2015-09-30T14:04Z] INFO  15:04:38,724 ProgressMeter -     19:44281063   6.3964308E7    38.6 m      36.0 s       88.5%    43.6 m       5.0 m
[2015-09-30T14:05Z] INFO  15:05:09,814 ProgressMeter -     19:53271063   6.486432E7    39.1 m      36.0 s       89.5%    43.7 m       4.6 m
[2015-09-30T14:05Z] INFO  15:05:23,589 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:05Z] INFO  15:05:23,618 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:05Z] INFO  15:05:40,933 ProgressMeter -     20:17622277   6.5784588E7    39.6 m      36.0 s       90.6%    43.7 m       4.1 m
[2015-09-30T14:06Z] INFO  15:06:11,112 ProgressMeter -     20:43625996   6.6684605E7    40.1 m      36.0 s       91.7%    43.7 m       3.6 m
[2015-09-30T14:06Z] INFO  15:06:35,612 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:06Z] INFO  15:06:35,669 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:06Z] INFO  15:06:41,134 ProgressMeter -     20:62959645   6.7484617E7    40.6 m      36.0 s       92.6%    43.8 m       3.3 m
[2015-09-30T14:07Z] INFO  15:07:08,397 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:07Z] INFO  15:07:08,432 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:07Z] INFO  15:07:11,136 ProgressMeter -     21:48084501   6.8350257E7    41.1 m      36.0 s       93.7%    43.9 m       2.8 m
[2015-09-30T14:07Z] INFO  15:07:41,184 ProgressMeter -     22:30822898   6.922451E7    41.6 m      36.0 s       94.7%    43.9 m       2.3 m
[2015-09-30T14:08Z] INFO  15:08:11,186 ProgressMeter -     22:45759004   7.0024521E7    42.1 m      36.0 s       95.7%    44.0 m     114.0 s
[2015-09-30T14:08Z] INFO  15:08:16,777 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:08Z] INFO  15:08:16,838 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:08Z] INFO  15:08:41,614 ProgressMeter -      X:44108458   7.0893905E7    42.6 m      36.0 s       96.8%    44.0 m      83.0 s
[2015-09-30T14:09Z] INFO  15:09:11,863 ProgressMeter -     X:100667886   7.1793916E7    43.1 m      36.0 s       98.1%    43.9 m      49.0 s
[2015-09-30T14:09Z] INFO  15:09:41,927 ProgressMeter -     X:153639994   7.2693929E7    43.6 m      35.0 s       99.5%    43.8 m      13.0 s
[2015-09-30T14:09Z] INFO  15:09:42,932 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:09Z] INFO  15:09:42,941 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:09Z] INFO  15:09:44,254 BaseRecalibrator - Calculating quantized quality scores...
[2015-09-30T14:09Z] INFO  15:09:44,315 BaseRecalibrator - Writing recalibration report...
[2015-09-30T14:09Z] INFO  15:09:45,350 BaseRecalibrator - ...done!
[2015-09-30T14:09Z] INFO  15:09:45,351 BaseRecalibrator - BaseRecalibrator was able to recalibrate 72822191 reads
[2015-09-30T14:09Z] INFO  15:09:45,352 ProgressMeter -            done   7.2822191E7    43.7 m      35.0 s      100.0%    43.7 m       0.0 s
[2015-09-30T14:09Z] INFO  15:09:45,352 ProgressMeter - Total runtime 2620.21 secs, 43.67 min, 0.73 hours
[2015-09-30T14:09Z] INFO  15:09:45,353 MicroScheduler - 7638051 reads were filtered out during the traversal out of approximately 80577949 total reads (9.48%)
[2015-09-30T14:09Z] INFO  15:09:45,353 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:09Z] INFO  15:09:45,353 MicroScheduler -   -> 3752973 reads (4.66% of total) failing DuplicateReadFilter
[2015-09-30T14:09Z] INFO  15:09:45,353 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:09Z] INFO  15:09:45,353 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:09Z] INFO  15:09:45,354 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:09Z] INFO  15:09:45,354 MicroScheduler -   -> 3885078 reads (4.82% of total) failing MappingQualityZeroFilter
[2015-09-30T14:09Z] INFO  15:09:45,354 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:09Z] INFO  15:09:45,354 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:09Z] INFO  15:09:46,626 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:09Z] multiprocessing: combine_sample_regions
[2015-09-30T14:09Z] Identified 109 parallel analysis blocks
Block sizes:
  min: 986093
  5%: 10929224.6
  25%: 31018607.0
  median: 31035784.0
  75%: 31182805.0
  95%: 32106606.2
  99%: 33217824.64
  max: 49356624
Between block sizes:
  min: 273
  5%: 640.0
  25%: 2059.0
  median: 8040.0
  75%: 62645.0
  95%: 376499.0
  99%: 1414655.12
  max: 1434086

[2015-09-30T14:09Z] Timing: structural variation initial
[2015-09-30T14:09Z] Resource requests: freebayes, gatk, mutect, picard, vardict, varscan; memory: 2.00, 3.70, 2.50, 2.80, 6.00, 2.00; cores: 1, 1, 1, 1, 1, 1
[2015-09-30T14:09Z] Configuring 3 jobs to run, using 1 cores each with 6.00g of memory reserved for each job
[2015-09-30T14:09Z] Timing: alignment post-processing
[2015-09-30T14:10Z] multiprocessing: piped_bamprep
[2015-09-30T14:10Z] GATK pre-alignment ('1', 0, 31187470) : syn3-normal
[2015-09-30T14:10Z] GATK pre-alignment ('1', 62231753, 93258244) : syn3-normal
[2015-09-30T14:10Z] GATK pre-alignment ('1', 31187762, 62229084) : syn3-normal
[2015-09-30T14:10Z] INFO  15:10:03,625 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:10Z] INFO  15:10:03,627 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:10Z] INFO  15:10:03,627 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:10Z] INFO  15:10:03,628 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:10Z] INFO  15:10:03,631 HelpFormatter - Program Args: -T PrintReads -L 1:1-31187470 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmp8fSSiA/1_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam
[2015-09-30T14:10Z] INFO  15:10:03,639 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:10Z] INFO  15:10:03,640 HelpFormatter - Date/Time: 2015/09/30 15:10:03
[2015-09-30T14:10Z] INFO  15:10:03,640 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:10Z] INFO  15:10:03,640 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:10Z] INFO  15:10:03,754 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:10Z] INFO  15:10:04,326 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:10Z] INFO  15:10:04,328 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:10Z] INFO  15:10:04,328 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:10Z] INFO  15:10:04,328 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:10Z] INFO  15:10:04,332 HelpFormatter - Program Args: -T PrintReads -L 1:62231754-93258244 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmp6PNf0S/1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam
[2015-09-30T14:10Z] INFO  15:10:04,337 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:10Z] INFO  15:10:04,338 HelpFormatter - Date/Time: 2015/09/30 15:10:04
[2015-09-30T14:10Z] INFO  15:10:04,338 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:10Z] INFO  15:10:04,338 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:10Z] INFO  15:10:04,337 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:10Z] INFO  15:10:04,339 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:10Z] INFO  15:10:04,339 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:10Z] INFO  15:10:04,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:10Z] INFO  15:10:04,343 HelpFormatter - Program Args: -T PrintReads -L 1:31187763-62229084 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmp6U2bJ_/1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam
[2015-09-30T14:10Z] INFO  15:10:04,349 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:10Z] INFO  15:10:04,349 HelpFormatter - Date/Time: 2015/09/30 15:10:04
[2015-09-30T14:10Z] INFO  15:10:04,349 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:10Z] INFO  15:10:04,349 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:10Z] INFO  15:10:04,736 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:10Z] INFO  15:10:04,757 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:10Z] INFO  15:10:04,766 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:10Z] INFO  15:10:04,809 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:10Z] INFO  15:10:04,817 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:10Z] INFO  15:10:04,834 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:10Z] INFO  15:10:04,848 IntervalUtils - Processing 31187470 bp from intervals
[2015-09-30T14:10Z] INFO  15:10:04,917 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:10Z] INFO  15:10:05,098 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:10Z] INFO  15:10:05,098 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:10Z] INFO  15:10:05,099 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:10Z] INFO  15:10:05,099 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:10Z] INFO  15:10:05,110 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:10Z] INFO  15:10:05,536 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:10Z] INFO  15:10:05,670 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:10Z] INFO  15:10:05,687 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:10Z] INFO  15:10:05,721 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:10Z] INFO  15:10:05,729 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:10Z] INFO  15:10:05,737 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:10Z] INFO  15:10:05,744 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:10Z] INFO  15:10:05,744 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:10Z] INFO  15:10:05,757 IntervalUtils - Processing 31026491 bp from intervals
[2015-09-30T14:10Z] INFO  15:10:05,759 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:10Z] INFO  15:10:05,772 IntervalUtils - Processing 31041322 bp from intervals
[2015-09-30T14:10Z] INFO  15:10:05,942 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:10Z] INFO  15:10:05,966 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:10Z] INFO  15:10:06,133 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:10Z] INFO  15:10:06,133 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:10Z] INFO  15:10:06,134 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:10Z] INFO  15:10:06,134 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:10Z] INFO  15:10:06,145 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:10Z] INFO  15:10:06,150 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:10Z] INFO  15:10:06,150 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:10Z] INFO  15:10:06,151 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:10Z] INFO  15:10:06,151 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:10Z] INFO  15:10:06,162 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:10Z] INFO  15:10:06,344 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:10Z] INFO  15:10:06,351 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:10Z] INFO  15:10:35,121 ProgressMeter -       1:2100290    300003.0    30.0 s     100.0 s        6.7%     7.4 m       6.9 m
[2015-09-30T14:10Z] INFO  15:10:36,151 ProgressMeter -      1:33998982    200003.0    30.0 s       2.5 m        9.1%     5.5 m       5.0 m
[2015-09-30T14:10Z] INFO  15:10:36,182 ProgressMeter -      1:74819378    200005.0    30.0 s       2.5 m       40.6%    73.0 s      43.0 s
[2015-09-30T14:11Z] INFO  15:11:05,122 ProgressMeter -       1:8074911    600006.0    60.0 s     100.0 s       25.9%     3.9 m       2.9 m
[2015-09-30T14:11Z] INFO  15:11:06,176 ProgressMeter -      1:39380819    500008.0    60.0 s     120.0 s       26.4%     3.8 m       2.8 m
[2015-09-30T14:11Z] INFO  15:11:06,202 ProgressMeter -      1:91789907    500008.0    60.0 s     120.0 s       95.3%    62.0 s       2.0 s
[2015-09-30T14:11Z] INFO  15:11:10,460 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:11Z] INFO  15:11:10,662 ProgressMeter -            done    599350.0    64.0 s     107.0 s      100.0%    64.0 s       0.0 s
[2015-09-30T14:11Z] INFO  15:11:10,663 ProgressMeter - Total runtime 64.51 secs, 1.08 min, 0.02 hours
[2015-09-30T14:11Z] INFO  15:11:10,663 MicroScheduler - 1897 reads were filtered out during the traversal out of approximately 601247 total reads (0.32%)
[2015-09-30T14:11Z] INFO  15:11:10,663 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:11Z] INFO  15:11:10,663 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:11Z] INFO  15:11:10,664 MicroScheduler -   -> 1897 reads (0.32% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:11Z] INFO  15:11:11,773 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:11Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam
[2015-09-30T14:11Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam 1:62231754-93258244
[2015-09-30T14:11Z] GATK: RealignerTargetCreator
[2015-09-30T14:11Z] INFO  15:11:15,426 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:11Z] INFO  15:11:15,429 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:11Z] INFO  15:11:15,429 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:11Z] INFO  15:11:15,429 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:11Z] INFO  15:11:15,433 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpjPlfW2/1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign-realign.intervals -l INFO -L 1:62231754-93258244 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:11Z] INFO  15:11:15,438 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:11Z] INFO  15:11:15,438 HelpFormatter - Date/Time: 2015/09/30 15:11:15
[2015-09-30T14:11Z] INFO  15:11:15,438 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:11Z] INFO  15:11:15,439 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:11Z] INFO  15:11:15,558 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:11Z] INFO  15:11:15,677 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:11Z] INFO  15:11:15,685 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:11Z] INFO  15:11:15,701 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:11Z] INFO  15:11:17,008 IntervalUtils - Processing 31026491 bp from intervals
[2015-09-30T14:11Z] WARN  15:11:17,012 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:11Z] INFO  15:11:17,069 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:11Z] INFO  15:11:17,490 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:11Z] INFO  15:11:17,490 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:11Z] INFO  15:11:17,491 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:11Z] INFO  15:11:17,491 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:11Z] INFO  15:11:35,123 ProgressMeter -      1:12775700   1000010.0    90.0 s      90.0 s       41.0%     3.7 m       2.2 m
[2015-09-30T14:11Z] INFO  15:11:36,177 ProgressMeter -      1:43916534    800012.0    90.0 s     112.0 s       41.0%     3.7 m       2.2 m
[2015-09-30T14:11Z] INFO  15:11:42,725 ProgressMeter -            done   3.1026491E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T14:11Z] INFO  15:11:42,725 ProgressMeter - Total runtime 25.24 secs, 0.42 min, 0.01 hours
[2015-09-30T14:11Z] INFO  15:11:42,728 MicroScheduler - 43113 reads were filtered out during the traversal out of approximately 602996 total reads (7.15%)
[2015-09-30T14:11Z] INFO  15:11:42,728 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:11Z] INFO  15:11:42,729 MicroScheduler -   -> 8618 reads (1.43% of total) failing BadMateFilter
[2015-09-30T14:11Z] INFO  15:11:42,729 MicroScheduler -   -> 23458 reads (3.89% of total) failing DuplicateReadFilter
[2015-09-30T14:11Z] INFO  15:11:42,729 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:11Z] INFO  15:11:42,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:11Z] INFO  15:11:42,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:11Z] INFO  15:11:42,730 MicroScheduler -   -> 11037 reads (1.83% of total) failing MappingQualityZeroFilter
[2015-09-30T14:11Z] INFO  15:11:42,730 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:11Z] INFO  15:11:42,730 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:11Z] INFO  15:11:42,731 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:11Z] INFO  15:11:43,709 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:11Z] GATK: realign ('1', 62231753, 93258244) : syn3-normal
[2015-09-30T14:11Z] INFO  15:11:45,933 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:11Z] INFO  15:11:45,935 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:11Z] INFO  15:11:45,935 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:11Z] INFO  15:11:45,935 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:11Z] INFO  15:11:45,938 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign-realign.intervals -L 1:62231754-93258244 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmphmKtfL/1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam
[2015-09-30T14:11Z] INFO  15:11:45,944 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:11Z] INFO  15:11:45,944 HelpFormatter - Date/Time: 2015/09/30 15:11:45
[2015-09-30T14:11Z] INFO  15:11:45,944 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:11Z] INFO  15:11:45,944 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:11Z] INFO  15:11:46,076 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:11Z] INFO  15:11:46,148 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:11Z] INFO  15:11:46,156 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:11Z] INFO  15:11:46,173 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:11Z] INFO  15:11:46,400 IntervalUtils - Processing 31026491 bp from intervals
[2015-09-30T14:11Z] WARN  15:11:46,404 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:11Z] INFO  15:11:46,463 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:11Z] INFO  15:11:46,633 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:11Z] INFO  15:11:46,634 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:11Z] INFO  15:11:46,634 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:11Z] INFO  15:11:46,635 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:11Z] INFO  15:11:46,776 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:11Z] INFO  15:11:46,968 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:12Z] INFO  15:12:05,280 ProgressMeter -      1:17282039   1400016.0   120.0 s      85.0 s       55.4%     3.6 m      96.0 s
[2015-09-30T14:12Z] INFO  15:12:06,178 ProgressMeter -      1:47905485   1100029.0   120.0 s     109.0 s       53.9%     3.7 m     102.0 s
[2015-09-30T14:12Z] INFO  15:12:17,296 ProgressMeter -      1:92765897    500008.0    30.0 s      61.0 s       98.4%    30.0 s       0.0 s
[2015-09-30T14:12Z] INFO  15:12:18,218 ProgressMeter -            done    599350.0    31.0 s      52.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T14:12Z] INFO  15:12:18,218 ProgressMeter - Total runtime 31.58 secs, 0.53 min, 0.01 hours
[2015-09-30T14:12Z] INFO  15:12:18,221 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 599350 total reads (0.00%)
[2015-09-30T14:12Z] INFO  15:12:18,222 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:12Z] INFO  15:12:18,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:12Z] INFO  15:12:18,222 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:12Z] INFO  15:12:19,366 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:12Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam
[2015-09-30T14:12Z] GATK pre-alignment ('1', 93297335, 142653959) : syn3-normal
[2015-09-30T14:12Z] INFO  15:12:23,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:12Z] INFO  15:12:23,363 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:12Z] INFO  15:12:23,363 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:12Z] INFO  15:12:23,363 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:12Z] INFO  15:12:23,366 HelpFormatter - Program Args: -T PrintReads -L 1:93297336-142653959 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpa4AQhN/1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam
[2015-09-30T14:12Z] INFO  15:12:23,372 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:12Z] INFO  15:12:23,372 HelpFormatter - Date/Time: 2015/09/30 15:12:23
[2015-09-30T14:12Z] INFO  15:12:23,372 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:12Z] INFO  15:12:23,373 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:12Z] INFO  15:12:23,479 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:12Z] INFO  15:12:24,180 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:12Z] INFO  15:12:24,229 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:12Z] INFO  15:12:24,237 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:12Z] INFO  15:12:24,252 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:12Z] INFO  15:12:24,265 IntervalUtils - Processing 49356624 bp from intervals
[2015-09-30T14:12Z] INFO  15:12:24,324 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:12Z] INFO  15:12:24,504 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:12Z] INFO  15:12:24,504 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:12Z] INFO  15:12:24,505 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:12Z] INFO  15:12:24,505 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:12Z] INFO  15:12:24,516 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:12Z] INFO  15:12:24,765 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:12Z] INFO  15:12:35,281 ProgressMeter -      1:22168674   1700019.0     2.5 m      88.0 s       71.1%     3.5 m      61.0 s
[2015-09-30T14:12Z] INFO  15:12:46,143 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:12Z] INFO  15:12:46,179 ProgressMeter -      1:62228360   1600034.0     2.7 m     100.0 s      100.0%     2.7 m       0.0 s
[2015-09-30T14:12Z] INFO  15:12:46,446 ProgressMeter -            done   1606223.0     2.7 m      99.0 s      100.0%     2.7 m       0.0 s
[2015-09-30T14:12Z] INFO  15:12:46,446 ProgressMeter - Total runtime 160.31 secs, 2.67 min, 0.04 hours
[2015-09-30T14:12Z] INFO  15:12:46,447 MicroScheduler - 2863 reads were filtered out during the traversal out of approximately 1609086 total reads (0.18%)
[2015-09-30T14:12Z] INFO  15:12:46,447 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:12Z] INFO  15:12:46,447 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:12Z] INFO  15:12:46,447 MicroScheduler -   -> 2863 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:12Z] INFO  15:12:47,445 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:12Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam
[2015-09-30T14:12Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam 1:31187763-62229084
[2015-09-30T14:12Z] GATK: RealignerTargetCreator
[2015-09-30T14:12Z] INFO  15:12:53,317 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:12Z] INFO  15:12:53,319 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:12Z] INFO  15:12:53,319 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:12Z] INFO  15:12:53,320 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:12Z] INFO  15:12:53,323 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmp6pbZQK/1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign-realign.intervals -l INFO -L 1:31187763-62229084 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:12Z] INFO  15:12:53,330 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:12Z] INFO  15:12:53,330 HelpFormatter - Date/Time: 2015/09/30 15:12:53
[2015-09-30T14:12Z] INFO  15:12:53,330 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:12Z] INFO  15:12:53,330 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:12Z] INFO  15:12:53,520 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:12Z] INFO  15:12:53,723 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:12Z] INFO  15:12:53,731 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:12Z] INFO  15:12:53,867 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2015-09-30T14:12Z] INFO  15:12:54,518 ProgressMeter -     1:108704326    200003.0    30.0 s       2.5 m       31.2%    96.0 s      66.0 s
[2015-09-30T14:12Z] INFO  15:12:54,567 IntervalUtils - Processing 31041322 bp from intervals
[2015-09-30T14:12Z] WARN  15:12:54,571 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:12Z] INFO  15:12:54,628 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:12Z] INFO  15:12:54,926 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:12Z] INFO  15:12:54,926 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:12Z] INFO  15:12:54,927 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:12Z] INFO  15:12:54,927 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:13Z] INFO  15:13:05,563 ProgressMeter -      1:26871954   2100026.0     3.0 m      85.0 s       86.2%     3.5 m      28.0 s
[2015-09-30T14:13Z] INFO  15:13:23,196 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:13Z] INFO  15:13:23,333 ProgressMeter -            done   2398410.0     3.3 m      82.0 s      100.0%     3.3 m       0.0 s
[2015-09-30T14:13Z] INFO  15:13:23,334 ProgressMeter - Total runtime 198.24 secs, 3.30 min, 0.06 hours
[2015-09-30T14:13Z] INFO  15:13:23,334 MicroScheduler - 3522 reads were filtered out during the traversal out of approximately 2401932 total reads (0.15%)
[2015-09-30T14:13Z] INFO  15:13:23,334 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:13Z] INFO  15:13:23,335 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:13Z] INFO  15:13:23,335 MicroScheduler -   -> 3522 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:13Z] INFO  15:13:24,352 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:13Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam
[2015-09-30T14:13Z] INFO  15:13:24,547 ProgressMeter -     1:113063724    500008.0    60.0 s     120.0 s       40.0%     2.5 m      89.0 s
[2015-09-30T14:13Z] INFO  15:13:24,930 ProgressMeter -      1:52437901   2.1241038E7    30.0 s       1.0 s       68.5%    43.0 s      13.0 s
[2015-09-30T14:13Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam 1:1-31187470
[2015-09-30T14:13Z] GATK: RealignerTargetCreator
[2015-09-30T14:13Z] INFO  15:13:32,398 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:13Z] INFO  15:13:32,401 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:13Z] INFO  15:13:32,401 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:13Z] INFO  15:13:32,401 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:13Z] INFO  15:13:32,405 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmp6uPr1n/1_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign-realign.intervals -l INFO -L 1:1-31187470 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:13Z] INFO  15:13:32,410 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:13Z] INFO  15:13:32,410 HelpFormatter - Date/Time: 2015/09/30 15:13:32
[2015-09-30T14:13Z] INFO  15:13:32,411 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:13Z] INFO  15:13:32,411 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:13Z] INFO  15:13:32,470 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:13Z] INFO  15:13:32,586 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:13Z] INFO  15:13:32,593 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:13Z] INFO  15:13:32,610 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:13Z] INFO  15:13:32,871 IntervalUtils - Processing 31187470 bp from intervals
[2015-09-30T14:13Z] WARN  15:13:32,875 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:13Z] INFO  15:13:32,944 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:13Z] INFO  15:13:33,204 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:13Z] INFO  15:13:33,205 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:13Z] INFO  15:13:33,205 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:13Z] INFO  15:13:33,206 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:13Z] INFO  15:13:34,442 ProgressMeter -            done   3.1041322E7    39.0 s       1.0 s      100.0%    39.0 s       0.0 s
[2015-09-30T14:13Z] INFO  15:13:34,442 ProgressMeter - Total runtime 39.52 secs, 0.66 min, 0.01 hours
[2015-09-30T14:13Z] INFO  15:13:34,445 MicroScheduler - 125874 reads were filtered out during the traversal out of approximately 1615993 total reads (7.79%)
[2015-09-30T14:13Z] INFO  15:13:34,446 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:13Z] INFO  15:13:34,446 MicroScheduler -   -> 15292 reads (0.95% of total) failing BadMateFilter
[2015-09-30T14:13Z] INFO  15:13:34,446 MicroScheduler -   -> 77552 reads (4.80% of total) failing DuplicateReadFilter
[2015-09-30T14:13Z] INFO  15:13:34,447 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:13Z] INFO  15:13:34,447 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:13Z] INFO  15:13:34,447 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:13Z] INFO  15:13:34,447 MicroScheduler -   -> 33030 reads (2.04% of total) failing MappingQualityZeroFilter
[2015-09-30T14:13Z] INFO  15:13:34,448 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:13Z] INFO  15:13:34,448 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:13Z] INFO  15:13:34,448 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:13Z] INFO  15:13:36,450 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:13Z] GATK: realign ('1', 31187762, 62229084) : syn3-normal
[2015-09-30T14:13Z] INFO  15:13:39,542 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:13Z] INFO  15:13:39,544 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:13Z] INFO  15:13:39,544 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:13Z] INFO  15:13:39,544 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:13Z] INFO  15:13:39,548 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign-realign.intervals -L 1:31187763-62229084 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpRS7pVt/1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam
[2015-09-30T14:13Z] INFO  15:13:39,554 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:13Z] INFO  15:13:39,554 HelpFormatter - Date/Time: 2015/09/30 15:13:39
[2015-09-30T14:13Z] INFO  15:13:39,555 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:13Z] INFO  15:13:39,555 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:13Z] INFO  15:13:39,664 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:13Z] INFO  15:13:39,733 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:13Z] INFO  15:13:39,741 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:13Z] INFO  15:13:39,757 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:13Z] INFO  15:13:39,986 IntervalUtils - Processing 31041322 bp from intervals
[2015-09-30T14:13Z] WARN  15:13:39,990 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:13Z] INFO  15:13:40,047 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:13Z] INFO  15:13:40,250 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:13Z] INFO  15:13:40,251 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:13Z] INFO  15:13:40,251 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:13Z] INFO  15:13:40,251 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:13Z] INFO  15:13:40,395 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:13Z] INFO  15:13:40,586 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:13Z] INFO  15:13:54,548 ProgressMeter -     1:121106669    800012.0    90.0 s     112.0 s       56.3%     2.7 m      69.0 s
[2015-09-30T14:13Z] INFO  15:13:55,484 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:13Z] INFO  15:13:55,725 ProgressMeter -            done    884519.0    91.0 s     103.0 s      100.0%    91.0 s       0.0 s
[2015-09-30T14:13Z] INFO  15:13:55,726 ProgressMeter - Total runtime 91.22 secs, 1.52 min, 0.03 hours
[2015-09-30T14:13Z] INFO  15:13:55,726 MicroScheduler - 2158 reads were filtered out during the traversal out of approximately 886677 total reads (0.24%)
[2015-09-30T14:13Z] INFO  15:13:55,726 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:13Z] INFO  15:13:55,727 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:13Z] INFO  15:13:55,727 MicroScheduler -   -> 2158 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:13Z] INFO  15:13:56,697 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:13Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam
[2015-09-30T14:13Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam 1:93297336-142653959
[2015-09-30T14:13Z] GATK: RealignerTargetCreator
[2015-09-30T14:14Z] INFO  15:14:00,904 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:00,906 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:14Z] INFO  15:14:00,907 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:14Z] INFO  15:14:00,907 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:14Z] INFO  15:14:00,910 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpoFyahE/1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign-realign.intervals -l INFO -L 1:93297336-142653959 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:14Z] INFO  15:14:00,917 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:14Z] INFO  15:14:00,917 HelpFormatter - Date/Time: 2015/09/30 15:14:00
[2015-09-30T14:14Z] INFO  15:14:00,917 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:00,917 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:00,975 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:14Z] INFO  15:14:01,083 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:14Z] INFO  15:14:01,091 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:14Z] INFO  15:14:01,107 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:14Z] INFO  15:14:01,645 IntervalUtils - Processing 49356624 bp from intervals
[2015-09-30T14:14Z] WARN  15:14:01,648 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:14Z] INFO  15:14:01,705 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:14Z] INFO  15:14:01,853 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:14Z] INFO  15:14:01,853 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:14Z] INFO  15:14:01,853 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:14Z] INFO  15:14:01,854 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:14Z] INFO  15:14:03,208 ProgressMeter -      1:17402009   1.7399808E7    30.0 s       1.0 s       55.8%    53.0 s      23.0 s
[2015-09-30T14:14Z] INFO  15:14:10,298 ProgressMeter -      1:39826202    500008.0    30.0 s      60.0 s       27.8%   107.0 s      77.0 s
[2015-09-30T14:14Z] INFO  15:14:24,649 ProgressMeter -            done   3.118747E7    51.0 s       1.0 s      100.0%    51.0 s       0.0 s
[2015-09-30T14:14Z] INFO  15:14:24,649 ProgressMeter - Total runtime 51.44 secs, 0.86 min, 0.01 hours
[2015-09-30T14:14Z] INFO  15:14:24,650 MicroScheduler - 275231 reads were filtered out during the traversal out of approximately 2412717 total reads (11.41%)
[2015-09-30T14:14Z] INFO  15:14:24,650 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:14Z] INFO  15:14:24,650 MicroScheduler -   -> 19854 reads (0.82% of total) failing BadMateFilter
[2015-09-30T14:14Z] INFO  15:14:24,651 MicroScheduler -   -> 121530 reads (5.04% of total) failing DuplicateReadFilter
[2015-09-30T14:14Z] INFO  15:14:24,651 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:14Z] INFO  15:14:24,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:14Z] INFO  15:14:24,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:14Z] INFO  15:14:24,652 MicroScheduler -   -> 133847 reads (5.55% of total) failing MappingQualityZeroFilter
[2015-09-30T14:14Z] INFO  15:14:24,652 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:14Z] INFO  15:14:24,652 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:14Z] INFO  15:14:24,652 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:14Z] INFO  15:14:25,611 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:14Z] GATK: realign ('1', 0, 31187470) : syn3-normal
[2015-09-30T14:14Z] INFO  15:14:28,017 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:28,019 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:14Z] INFO  15:14:28,019 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:14Z] INFO  15:14:28,020 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:14Z] INFO  15:14:28,023 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign-realign.intervals -L 1:1-31187470 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpqwaTGl/1_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam
[2015-09-30T14:14Z] INFO  15:14:28,029 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:14Z] INFO  15:14:28,029 HelpFormatter - Date/Time: 2015/09/30 15:14:28
[2015-09-30T14:14Z] INFO  15:14:28,029 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:28,029 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:28,164 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:14Z] INFO  15:14:28,231 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:14Z] INFO  15:14:28,239 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:14Z] INFO  15:14:28,256 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:14Z] INFO  15:14:28,728 IntervalUtils - Processing 31187470 bp from intervals
[2015-09-30T14:14Z] WARN  15:14:28,732 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:14Z] INFO  15:14:28,791 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:14Z] INFO  15:14:28,940 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:14Z] INFO  15:14:28,940 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:14Z] INFO  15:14:28,941 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:14Z] INFO  15:14:28,941 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:14Z] INFO  15:14:29,087 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:14Z] INFO  15:14:29,290 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:14Z] INFO  15:14:31,856 ProgressMeter -     1:125576661   2.8190025E7    30.0 s       1.0 s       65.4%    45.0 s      15.0 s
[2015-09-30T14:14Z] INFO  15:14:38,780 ProgressMeter -            done   4.9356624E7    36.0 s       0.0 s      100.0%    36.0 s       0.0 s
[2015-09-30T14:14Z] INFO  15:14:38,781 ProgressMeter - Total runtime 36.93 secs, 0.62 min, 0.01 hours
[2015-09-30T14:14Z] INFO  15:14:38,784 MicroScheduler - 99051 reads were filtered out during the traversal out of approximately 889332 total reads (11.14%)
[2015-09-30T14:14Z] INFO  15:14:38,784 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:14Z] INFO  15:14:38,785 MicroScheduler -   -> 10615 reads (1.19% of total) failing BadMateFilter
[2015-09-30T14:14Z] INFO  15:14:38,785 MicroScheduler -   -> 37299 reads (4.19% of total) failing DuplicateReadFilter
[2015-09-30T14:14Z] INFO  15:14:38,785 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:14Z] INFO  15:14:38,785 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:14Z] INFO  15:14:38,786 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:14Z] INFO  15:14:38,786 MicroScheduler -   -> 51137 reads (5.75% of total) failing MappingQualityZeroFilter
[2015-09-30T14:14Z] INFO  15:14:38,786 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:14Z] INFO  15:14:38,786 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:14Z] INFO  15:14:38,787 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:14Z] INFO  15:14:39,955 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:14Z] GATK: realign ('1', 93297335, 142653959) : syn3-normal
[2015-09-30T14:14Z] INFO  15:14:41,305 ProgressMeter -      1:52870065   1200030.0    61.0 s      50.0 s       69.8%    87.0 s      26.0 s
[2015-09-30T14:14Z] INFO  15:14:42,211 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:42,213 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:14Z] INFO  15:14:42,213 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:14Z] INFO  15:14:42,213 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:14Z] INFO  15:14:42,217 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign-realign.intervals -L 1:93297336-142653959 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpIXT1QW/1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam
[2015-09-30T14:14Z] INFO  15:14:42,222 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:14Z] INFO  15:14:42,222 HelpFormatter - Date/Time: 2015/09/30 15:14:42
[2015-09-30T14:14Z] INFO  15:14:42,223 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:42,223 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:42,346 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:14Z] INFO  15:14:42,407 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:14Z] INFO  15:14:42,415 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:14Z] INFO  15:14:42,431 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:14Z] INFO  15:14:42,662 IntervalUtils - Processing 49356624 bp from intervals
[2015-09-30T14:14Z] WARN  15:14:42,666 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:14Z] INFO  15:14:42,720 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:14Z] INFO  15:14:42,875 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:14Z] INFO  15:14:42,876 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:14Z] INFO  15:14:42,876 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:14Z] INFO  15:14:42,876 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:14Z] INFO  15:14:43,010 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:14Z] INFO  15:14:43,248 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:14Z] INFO  15:14:51,390 ProgressMeter -            done   1606223.0    71.0 s      44.0 s      100.0%    71.0 s       0.0 s
[2015-09-30T14:14Z] INFO  15:14:51,390 ProgressMeter - Total runtime 71.14 secs, 1.19 min, 0.02 hours
[2015-09-30T14:14Z] INFO  15:14:51,394 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1606223 total reads (0.00%)
[2015-09-30T14:14Z] INFO  15:14:51,394 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:14Z] INFO  15:14:51,394 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:14Z] INFO  15:14:51,395 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:14Z] INFO  15:14:52,647 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:14Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam
[2015-09-30T14:14Z] GATK pre-alignment ('1', 142666976, 173685474) : syn3-normal
[2015-09-30T14:14Z] INFO  15:14:58,776 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:58,778 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:14Z] INFO  15:14:58,778 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:14Z] INFO  15:14:58,778 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:14Z] INFO  15:14:58,782 HelpFormatter - Program Args: -T PrintReads -L 1:142666977-173685474 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmp5TXAuk/1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam
[2015-09-30T14:14Z] INFO  15:14:58,788 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:14Z] INFO  15:14:58,788 HelpFormatter - Date/Time: 2015/09/30 15:14:58
[2015-09-30T14:14Z] INFO  15:14:58,788 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:58,788 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:14Z] INFO  15:14:58,899 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:14Z] INFO  15:14:59,319 ProgressMeter -       1:6027517    400004.0    30.0 s      75.0 s       19.3%     2.6 m       2.1 m
[2015-09-30T14:15Z] INFO  15:15:00,031 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:15Z] INFO  15:15:00,080 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:15Z] INFO  15:15:00,088 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:15Z] INFO  15:15:00,103 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:15Z] INFO  15:15:00,116 IntervalUtils - Processing 31018498 bp from intervals
[2015-09-30T14:15Z] INFO  15:15:00,173 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:15Z] INFO  15:15:00,366 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:15Z] INFO  15:15:00,366 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:15Z] INFO  15:15:00,366 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:15Z] INFO  15:15:00,367 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:15Z] INFO  15:15:00,378 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:15Z] INFO  15:15:00,578 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:15Z] INFO  15:15:12,879 ProgressMeter -     1:111999119    500008.0    30.0 s      60.0 s       37.9%    79.0 s      49.0 s
[2015-09-30T14:15Z] INFO  15:15:27,498 ProgressMeter -            done    884519.0    44.0 s      50.0 s      100.0%    44.0 s       0.0 s
[2015-09-30T14:15Z] INFO  15:15:27,498 ProgressMeter - Total runtime 44.62 secs, 0.74 min, 0.01 hours
[2015-09-30T14:15Z] INFO  15:15:27,501 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 884519 total reads (0.00%)
[2015-09-30T14:15Z] INFO  15:15:27,502 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:15Z] INFO  15:15:27,502 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:15Z] INFO  15:15:27,502 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:15Z] INFO  15:15:28,891 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:15Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam
[2015-09-30T14:15Z] INFO  15:15:30,369 ProgressMeter -     1:146502414    200002.0    30.0 s       2.5 m       12.4%     4.0 m       3.5 m
[2015-09-30T14:15Z] INFO  15:15:30,593 ProgressMeter -      1:16162004   1100011.0    61.0 s      56.0 s       51.8%   117.0 s      56.0 s
[2015-09-30T14:15Z] GATK pre-alignment ('1', 173702591, 204798081) : syn3-normal
[2015-09-30T14:15Z] INFO  15:15:33,453 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:15Z] INFO  15:15:33,455 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:15Z] INFO  15:15:33,455 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:15Z] INFO  15:15:33,455 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:15Z] INFO  15:15:33,459 HelpFormatter - Program Args: -T PrintReads -L 1:173702592-204798081 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmphiPb5c/1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam
[2015-09-30T14:15Z] INFO  15:15:33,464 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:15Z] INFO  15:15:33,465 HelpFormatter - Date/Time: 2015/09/30 15:15:33
[2015-09-30T14:15Z] INFO  15:15:33,465 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:15Z] INFO  15:15:33,465 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:15Z] INFO  15:15:33,571 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:15Z] INFO  15:15:34,853 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:15Z] INFO  15:15:34,904 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:15Z] INFO  15:15:34,911 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:15Z] INFO  15:15:34,926 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:15Z] INFO  15:15:34,938 IntervalUtils - Processing 31095490 bp from intervals
[2015-09-30T14:15Z] INFO  15:15:34,995 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:15Z] INFO  15:15:35,180 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:15Z] INFO  15:15:35,180 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:15Z] INFO  15:15:35,180 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:15Z] INFO  15:15:35,180 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:15Z] INFO  15:15:35,191 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:15Z] INFO  15:15:35,377 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:16Z] INFO  15:16:00,370 ProgressMeter -     1:151254830    500006.0    60.0 s     120.0 s       27.7%     3.6 m       2.6 m
[2015-09-30T14:16Z] INFO  15:16:00,594 ProgressMeter -      1:23758549   1900023.0    91.0 s      48.0 s       76.2%   119.0 s      28.0 s
[2015-09-30T14:16Z] INFO  15:16:05,183 ProgressMeter -     1:181020045    200003.0    30.0 s       2.5 m       23.5%     2.1 m      97.0 s
[2015-09-30T14:16Z] INFO  15:16:19,239 ProgressMeter -            done   2398410.0   110.0 s      45.0 s      100.0%   110.0 s       0.0 s
[2015-09-30T14:16Z] INFO  15:16:19,239 ProgressMeter - Total runtime 110.30 secs, 1.84 min, 0.03 hours
[2015-09-30T14:16Z] INFO  15:16:19,243 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2398410 total reads (0.00%)
[2015-09-30T14:16Z] INFO  15:16:19,243 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:16Z] INFO  15:16:19,243 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:16Z] INFO  15:16:19,243 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:16Z] INFO  15:16:20,396 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:16Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam
[2015-09-30T14:16Z] GATK pre-alignment ('1', 204839842, 235860787) : syn3-normal
[2015-09-30T14:16Z] INFO  15:16:28,283 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:16Z] INFO  15:16:28,285 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:16Z] INFO  15:16:28,285 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:16Z] INFO  15:16:28,285 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:16Z] INFO  15:16:28,289 HelpFormatter - Program Args: -T PrintReads -L 1:204839843-235860787 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpjowKLc/1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam
[2015-09-30T14:16Z] INFO  15:16:28,295 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:16Z] INFO  15:16:28,295 HelpFormatter - Date/Time: 2015/09/30 15:16:28
[2015-09-30T14:16Z] INFO  15:16:28,295 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:16Z] INFO  15:16:28,295 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:16Z] INFO  15:16:28,922 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:16Z] INFO  15:16:29,649 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:16Z] INFO  15:16:29,702 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:16Z] INFO  15:16:29,710 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:16Z] INFO  15:16:29,725 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:16Z] INFO  15:16:29,739 IntervalUtils - Processing 31020945 bp from intervals
[2015-09-30T14:16Z] INFO  15:16:29,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:16Z] INFO  15:16:29,981 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:16Z] INFO  15:16:29,981 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:16Z] INFO  15:16:29,982 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:16Z] INFO  15:16:29,982 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:16Z] INFO  15:16:29,993 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:16Z] INFO  15:16:30,182 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:16Z] INFO  15:16:30,383 ProgressMeter -     1:154406839    800011.0    90.0 s     112.0 s       37.8%     4.0 m       2.5 m
[2015-09-30T14:16Z] INFO  15:16:35,184 ProgressMeter -     1:197482524    500006.0    60.0 s     120.0 s       76.5%    78.0 s      18.0 s
[2015-09-30T14:16Z] INFO  15:16:59,984 ProgressMeter -     1:207889054    200002.0    30.0 s       2.5 m        9.8%     5.1 m       4.6 m
[2015-09-30T14:17Z] INFO  15:17:00,404 ProgressMeter -     1:156347129   1100016.0   120.0 s     109.0 s       44.1%     4.5 m       2.5 m
[2015-09-30T14:17Z] INFO  15:17:05,359 ProgressMeter -     1:203017839    800011.0    90.0 s     112.0 s       94.3%    95.0 s       5.0 s
[2015-09-30T14:17Z] INFO  15:17:16,989 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:17Z] INFO  15:17:17,184 ProgressMeter -            done   1005084.0   102.0 s     101.0 s      100.0%   102.0 s       0.0 s
[2015-09-30T14:17Z] INFO  15:17:17,184 ProgressMeter - Total runtime 102.00 secs, 1.70 min, 0.03 hours
[2015-09-30T14:17Z] INFO  15:17:17,184 MicroScheduler - 2245 reads were filtered out during the traversal out of approximately 1007329 total reads (0.22%)
[2015-09-30T14:17Z] INFO  15:17:17,185 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:17Z] INFO  15:17:17,185 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:17Z] INFO  15:17:17,185 MicroScheduler -   -> 2245 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:17Z] INFO  15:17:18,322 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:17Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam
[2015-09-30T14:17Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam 1:173702592-204798081
[2015-09-30T14:17Z] GATK: RealignerTargetCreator
[2015-09-30T14:17Z] INFO  15:17:22,855 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:17Z] INFO  15:17:22,857 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:17Z] INFO  15:17:22,857 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:17Z] INFO  15:17:22,858 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:17Z] INFO  15:17:22,861 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpUDIIQw/1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign-realign.intervals -l INFO -L 1:173702592-204798081 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:17Z] INFO  15:17:22,867 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:17Z] INFO  15:17:22,868 HelpFormatter - Date/Time: 2015/09/30 15:17:22
[2015-09-30T14:17Z] INFO  15:17:22,868 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:17Z] INFO  15:17:22,868 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:17Z] INFO  15:17:22,926 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:17Z] INFO  15:17:23,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:17Z] INFO  15:17:23,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:17Z] INFO  15:17:23,479 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:17Z] INFO  15:17:23,735 IntervalUtils - Processing 31095490 bp from intervals
[2015-09-30T14:17Z] WARN  15:17:23,739 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:17Z] INFO  15:17:23,797 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:17Z] INFO  15:17:23,944 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:17Z] INFO  15:17:23,945 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:17Z] INFO  15:17:23,945 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:17Z] INFO  15:17:23,946 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:17Z] INFO  15:17:29,985 ProgressMeter -     1:221053228    500007.0    60.0 s     120.0 s       52.3%   114.0 s      54.0 s
[2015-09-30T14:17Z] INFO  15:17:30,405 ProgressMeter -     1:160192589   1400019.0     2.5 m     107.0 s       56.5%     4.4 m     115.0 s
[2015-09-30T14:17Z] INFO  15:17:53,948 ProgressMeter -     1:204495505   3.0786113E7    30.0 s       0.0 s       99.0%    30.0 s       0.0 s
[2015-09-30T14:17Z] INFO  15:17:54,469 ProgressMeter -            done   3.109549E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T14:17Z] INFO  15:17:54,470 ProgressMeter - Total runtime 30.53 secs, 0.51 min, 0.01 hours
[2015-09-30T14:17Z] INFO  15:17:54,473 MicroScheduler - 73614 reads were filtered out during the traversal out of approximately 1011672 total reads (7.28%)
[2015-09-30T14:17Z] INFO  15:17:54,474 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:17Z] INFO  15:17:54,474 MicroScheduler -   -> 10836 reads (1.07% of total) failing BadMateFilter
[2015-09-30T14:17Z] INFO  15:17:54,474 MicroScheduler -   -> 45102 reads (4.46% of total) failing DuplicateReadFilter
[2015-09-30T14:17Z] INFO  15:17:54,475 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:17Z] INFO  15:17:54,475 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:17Z] INFO  15:17:54,475 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:17Z] INFO  15:17:54,475 MicroScheduler -   -> 17676 reads (1.75% of total) failing MappingQualityZeroFilter
[2015-09-30T14:17Z] INFO  15:17:54,475 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:17Z] INFO  15:17:54,476 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:17Z] INFO  15:17:54,476 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:17Z] INFO  15:17:56,892 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:17Z] GATK: realign ('1', 173702591, 204798081) : syn3-normal
[2015-09-30T14:17Z] INFO  15:17:58,840 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:17Z] INFO  15:17:58,842 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:17Z] INFO  15:17:58,843 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:17Z] INFO  15:17:58,843 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:17Z] INFO  15:17:58,846 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign-realign.intervals -L 1:173702592-204798081 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmp9N0Ulx/1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam
[2015-09-30T14:17Z] INFO  15:17:58,852 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:17Z] INFO  15:17:58,852 HelpFormatter - Date/Time: 2015/09/30 15:17:58
[2015-09-30T14:17Z] INFO  15:17:58,852 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:17Z] INFO  15:17:58,853 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:17Z] INFO  15:17:59,158 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:17Z] INFO  15:17:59,220 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:17Z] INFO  15:17:59,228 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:17Z] INFO  15:17:59,244 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:17Z] INFO  15:17:59,473 IntervalUtils - Processing 31095490 bp from intervals
[2015-09-30T14:17Z] WARN  15:17:59,477 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:17Z] INFO  15:17:59,533 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:17Z] INFO  15:17:59,679 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:17Z] INFO  15:17:59,679 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:17Z] INFO  15:17:59,680 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:17Z] INFO  15:17:59,680 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:17Z] INFO  15:17:59,824 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:17Z] INFO  15:17:59,986 ProgressMeter -     1:228527615    800010.0    90.0 s     112.0 s       76.4%   117.0 s      27.0 s
[2015-09-30T14:18Z] INFO  15:18:00,012 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:18Z] INFO  15:18:10,406 ProgressMeter -     1:170135978   1800024.0     3.2 m     105.0 s       88.6%     3.6 m      24.0 s
[2015-09-30T14:18Z] INFO  15:18:19,523 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:18Z] INFO  15:18:19,664 ProgressMeter -            done   1977353.0     3.3 m     100.0 s      100.0%     3.3 m       0.0 s
[2015-09-30T14:18Z] INFO  15:18:19,665 ProgressMeter - Total runtime 199.30 secs, 3.32 min, 0.06 hours
[2015-09-30T14:18Z] INFO  15:18:19,665 MicroScheduler - 3355 reads were filtered out during the traversal out of approximately 1980708 total reads (0.17%)
[2015-09-30T14:18Z] INFO  15:18:19,665 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:18Z] INFO  15:18:19,665 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:18Z] INFO  15:18:19,666 MicroScheduler -   -> 3355 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:18Z] INFO  15:18:20,692 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:18Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam
[2015-09-30T14:18Z] INFO  15:18:22,053 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:18Z] INFO  15:18:22,217 ProgressMeter -            done   1105676.0   112.0 s     101.0 s      100.0%   112.0 s       0.0 s
[2015-09-30T14:18Z] INFO  15:18:22,218 ProgressMeter - Total runtime 112.24 secs, 1.87 min, 0.03 hours
[2015-09-30T14:18Z] INFO  15:18:22,218 MicroScheduler - 2362 reads were filtered out during the traversal out of approximately 1108038 total reads (0.21%)
[2015-09-30T14:18Z] INFO  15:18:22,218 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:18Z] INFO  15:18:22,219 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:18Z] INFO  15:18:22,219 MicroScheduler -   -> 2362 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:18Z] INFO  15:18:23,355 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:18Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam
[2015-09-30T14:18Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam 1:142666977-173685474
[2015-09-30T14:18Z] GATK: RealignerTargetCreator
[2015-09-30T14:18Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam 1:204839843-235860787
[2015-09-30T14:18Z] GATK: RealignerTargetCreator
[2015-09-30T14:18Z] INFO  15:18:28,113 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:18Z] INFO  15:18:28,115 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:18Z] INFO  15:18:28,115 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:18Z] INFO  15:18:28,115 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:18Z] INFO  15:18:28,119 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmp9EMdee/1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign-realign.intervals -l INFO -L 1:204839843-235860787 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:18Z] INFO  15:18:28,125 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:18Z] INFO  15:18:28,125 HelpFormatter - Date/Time: 2015/09/30 15:18:28
[2015-09-30T14:18Z] INFO  15:18:28,125 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:18Z] INFO  15:18:28,125 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:18Z] INFO  15:18:28,182 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:18Z] INFO  15:18:28,290 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:18Z] INFO  15:18:28,298 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:18Z] INFO  15:18:28,314 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:18Z] INFO  15:18:28,346 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:18Z] INFO  15:18:28,348 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:18Z] INFO  15:18:28,348 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:18Z] INFO  15:18:28,348 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:18Z] INFO  15:18:28,351 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpKJYfRC/1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign-realign.intervals -l INFO -L 1:142666977-173685474 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:18Z] INFO  15:18:28,357 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:18Z] INFO  15:18:28,357 HelpFormatter - Date/Time: 2015/09/30 15:18:28
[2015-09-30T14:18Z] INFO  15:18:28,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:18Z] INFO  15:18:28,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:18Z] INFO  15:18:28,417 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:18Z] INFO  15:18:28,528 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:18Z] INFO  15:18:28,536 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:18Z] INFO  15:18:28,553 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:18Z] INFO  15:18:28,807 IntervalUtils - Processing 31018498 bp from intervals
[2015-09-30T14:18Z] WARN  15:18:28,811 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:18Z] INFO  15:18:28,869 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:18Z] INFO  15:18:28,988 IntervalUtils - Processing 31020945 bp from intervals
[2015-09-30T14:18Z] WARN  15:18:28,992 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:18Z] INFO  15:18:29,038 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:18Z] INFO  15:18:29,039 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:18Z] INFO  15:18:29,039 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:18Z] INFO  15:18:29,040 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:18Z] INFO  15:18:29,049 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:18Z] INFO  15:18:29,196 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:18Z] INFO  15:18:29,196 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:18Z] INFO  15:18:29,197 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:18Z] INFO  15:18:29,197 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:18Z] INFO  15:18:30,534 ProgressMeter -     1:200556971    500006.0    30.0 s      61.0 s       86.4%    34.0 s       4.0 s
[2015-09-30T14:18Z] INFO  15:18:45,300 ProgressMeter -            done   1005084.0    45.0 s      45.0 s      100.0%    45.0 s       0.0 s
[2015-09-30T14:18Z] INFO  15:18:45,301 ProgressMeter - Total runtime 45.62 secs, 0.76 min, 0.01 hours
[2015-09-30T14:18Z] INFO  15:18:45,304 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1005084 total reads (0.00%)
[2015-09-30T14:18Z] INFO  15:18:45,304 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:18Z] INFO  15:18:45,305 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:18Z] INFO  15:18:45,305 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:18Z] INFO  15:18:46,530 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:18Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam
[2015-09-30T14:18Z] GATK pre-alignment ('1', 235865791, 249250621) : syn3-normal
[2015-09-30T14:18Z] INFO  15:18:50,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:18Z] INFO  15:18:50,952 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:18Z] INFO  15:18:50,953 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:18Z] INFO  15:18:50,953 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:18Z] INFO  15:18:50,956 HelpFormatter - Program Args: -T PrintReads -L 1:235865792-249250621 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpkpVP3b/1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam
[2015-09-30T14:18Z] INFO  15:18:50,962 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:18Z] INFO  15:18:50,962 HelpFormatter - Date/Time: 2015/09/30 15:18:50
[2015-09-30T14:18Z] INFO  15:18:50,962 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:18Z] INFO  15:18:50,963 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:18Z] INFO  15:18:51,070 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:18Z] INFO  15:18:52,340 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:18Z] INFO  15:18:52,389 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:18Z] INFO  15:18:52,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:18Z] INFO  15:18:52,412 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:18Z] INFO  15:18:52,425 IntervalUtils - Processing 13384830 bp from intervals
[2015-09-30T14:18Z] INFO  15:18:52,482 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:18Z] INFO  15:18:52,615 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:18Z] INFO  15:18:52,616 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:18Z] INFO  15:18:52,616 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:18Z] INFO  15:18:52,616 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:18Z] INFO  15:18:52,627 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:18Z] INFO  15:18:52,717 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:18Z] INFO  15:18:59,042 ProgressMeter -     1:160276889   1.7601312E7    30.0 s       1.0 s       56.8%    52.0 s      22.0 s
[2015-09-30T14:18Z] INFO  15:18:59,199 ProgressMeter -     1:234940677   3.0090334E7    30.0 s       0.0 s       97.0%    30.0 s       0.0 s
[2015-09-30T14:19Z] INFO  15:19:00,428 ProgressMeter -            done   3.1020945E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T14:19Z] INFO  15:19:00,429 ProgressMeter - Total runtime 31.23 secs, 0.52 min, 0.01 hours
[2015-09-30T14:19Z] INFO  15:19:00,432 MicroScheduler - 92341 reads were filtered out during the traversal out of approximately 1111456 total reads (8.31%)
[2015-09-30T14:19Z] INFO  15:19:00,433 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:19Z] INFO  15:19:00,433 MicroScheduler -   -> 11771 reads (1.06% of total) failing BadMateFilter
[2015-09-30T14:19Z] INFO  15:19:00,433 MicroScheduler -   -> 50349 reads (4.53% of total) failing DuplicateReadFilter
[2015-09-30T14:19Z] INFO  15:19:00,433 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:19Z] INFO  15:19:00,434 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:19Z] INFO  15:19:00,434 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:19Z] INFO  15:19:00,434 MicroScheduler -   -> 30221 reads (2.72% of total) failing MappingQualityZeroFilter
[2015-09-30T14:19Z] INFO  15:19:00,434 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:19Z] INFO  15:19:00,434 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:19Z] INFO  15:19:00,435 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:19Z] INFO  15:19:01,438 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:19Z] GATK: realign ('1', 204839842, 235860787) : syn3-normal
[2015-09-30T14:19Z] INFO  15:19:03,216 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:03,218 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:19Z] INFO  15:19:03,218 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:19Z] INFO  15:19:03,219 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:19Z] INFO  15:19:03,222 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign-realign.intervals -L 1:204839843-235860787 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpyH3741/1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam
[2015-09-30T14:19Z] INFO  15:19:03,227 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:19Z] INFO  15:19:03,227 HelpFormatter - Date/Time: 2015/09/30 15:19:03
[2015-09-30T14:19Z] INFO  15:19:03,228 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:03,228 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:03,355 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:19Z] INFO  15:19:03,425 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:19Z] INFO  15:19:03,433 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:19Z] INFO  15:19:03,450 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:19Z] INFO  15:19:03,853 IntervalUtils - Processing 31020945 bp from intervals
[2015-09-30T14:19Z] WARN  15:19:03,857 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:19Z] INFO  15:19:03,917 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:19Z] INFO  15:19:04,072 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:19Z] INFO  15:19:04,072 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:19Z] INFO  15:19:04,072 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:19Z] INFO  15:19:04,073 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:19Z] INFO  15:19:04,214 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:19Z] INFO  15:19:04,409 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:19Z] INFO  15:19:13,332 ProgressMeter -            done   3.1018498E7    44.0 s       1.0 s      100.0%    44.0 s       0.0 s
[2015-09-30T14:19Z] INFO  15:19:13,332 ProgressMeter - Total runtime 44.29 secs, 0.74 min, 0.01 hours
[2015-09-30T14:19Z] INFO  15:19:13,336 MicroScheduler - 275519 reads were filtered out during the traversal out of approximately 1988092 total reads (13.86%)
[2015-09-30T14:19Z] INFO  15:19:13,336 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:19Z] INFO  15:19:13,336 MicroScheduler -   -> 16156 reads (0.81% of total) failing BadMateFilter
[2015-09-30T14:19Z] INFO  15:19:13,336 MicroScheduler -   -> 87708 reads (4.41% of total) failing DuplicateReadFilter
[2015-09-30T14:19Z] INFO  15:19:13,337 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:19Z] INFO  15:19:13,337 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:19Z] INFO  15:19:13,337 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:19Z] INFO  15:19:13,337 MicroScheduler -   -> 171655 reads (8.63% of total) failing MappingQualityZeroFilter
[2015-09-30T14:19Z] INFO  15:19:13,337 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:19Z] INFO  15:19:13,338 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:19Z] INFO  15:19:13,338 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:19Z] INFO  15:19:14,292 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:19Z] GATK: realign ('1', 142666976, 173685474) : syn3-normal
[2015-09-30T14:19Z] INFO  15:19:16,099 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:16,101 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:19Z] INFO  15:19:16,101 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:19Z] INFO  15:19:16,101 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:19Z] INFO  15:19:16,105 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign-realign.intervals -L 1:142666977-173685474 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpl4thmz/1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam
[2015-09-30T14:19Z] INFO  15:19:16,110 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:19Z] INFO  15:19:16,110 HelpFormatter - Date/Time: 2015/09/30 15:19:16
[2015-09-30T14:19Z] INFO  15:19:16,111 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:16,111 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:16,239 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:19Z] INFO  15:19:16,307 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:19Z] INFO  15:19:16,314 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:19Z] INFO  15:19:16,329 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:19Z] INFO  15:19:16,562 IntervalUtils - Processing 31018498 bp from intervals
[2015-09-30T14:19Z] WARN  15:19:16,566 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:19Z] INFO  15:19:16,622 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:19Z] INFO  15:19:16,772 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:19Z] INFO  15:19:16,773 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:19Z] INFO  15:19:16,773 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:19Z] INFO  15:19:16,773 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:19Z] INFO  15:19:16,916 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:19Z] INFO  15:19:17,106 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:19Z] INFO  15:19:22,636 ProgressMeter -     1:245533487    200002.0    30.0 s       2.5 m       72.2%    41.0 s      11.0 s
[2015-09-30T14:19Z] INFO  15:19:34,139 ProgressMeter -     1:222843336    500007.0    30.0 s      60.0 s       58.0%    51.0 s      21.0 s
[2015-09-30T14:19Z] INFO  15:19:34,399 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:19Z] INFO  15:19:34,506 ProgressMeter -            done    372567.0    41.0 s     112.0 s       99.9%    41.0 s       0.0 s
[2015-09-30T14:19Z] INFO  15:19:34,506 ProgressMeter - Total runtime 41.89 secs, 0.70 min, 0.01 hours
[2015-09-30T14:19Z] INFO  15:19:34,507 MicroScheduler - 1057 reads were filtered out during the traversal out of approximately 373624 total reads (0.28%)
[2015-09-30T14:19Z] INFO  15:19:34,507 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:19Z] INFO  15:19:34,507 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:19Z] INFO  15:19:34,507 MicroScheduler -   -> 1057 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:19Z] INFO  15:19:35,500 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:19Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam
[2015-09-30T14:19Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam 1:235865792-249250621
[2015-09-30T14:19Z] GATK: RealignerTargetCreator
[2015-09-30T14:19Z] INFO  15:19:40,074 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:40,076 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:19Z] INFO  15:19:40,076 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:19Z] INFO  15:19:40,076 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:19Z] INFO  15:19:40,080 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmpIgrrmU/1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign-realign.intervals -l INFO -L 1:235865792-249250621 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:19Z] INFO  15:19:40,086 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:19Z] INFO  15:19:40,086 HelpFormatter - Date/Time: 2015/09/30 15:19:40
[2015-09-30T14:19Z] INFO  15:19:40,086 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:40,086 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:40,145 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:19Z] INFO  15:19:40,254 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:19Z] INFO  15:19:40,262 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:19Z] INFO  15:19:40,278 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:19Z] INFO  15:19:40,531 IntervalUtils - Processing 13384830 bp from intervals
[2015-09-30T14:19Z] WARN  15:19:40,536 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:19Z] INFO  15:19:40,596 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:19Z] INFO  15:19:40,689 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:19Z] INFO  15:19:40,690 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:19Z] INFO  15:19:40,690 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:19Z] INFO  15:19:40,691 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:19Z] INFO  15:19:47,160 ProgressMeter -     1:151022857    500006.0    30.0 s      60.0 s       26.9%   111.0 s      81.0 s
[2015-09-30T14:19Z] INFO  15:19:53,823 ProgressMeter -            done   1.338483E7    13.0 s       0.0 s      100.0%    13.0 s       0.0 s
[2015-09-30T14:19Z] INFO  15:19:53,823 ProgressMeter - Total runtime 13.13 secs, 0.22 min, 0.00 hours
[2015-09-30T14:19Z] INFO  15:19:53,826 MicroScheduler - 33732 reads were filtered out during the traversal out of approximately 375190 total reads (8.99%)
[2015-09-30T14:19Z] INFO  15:19:53,826 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:19Z] INFO  15:19:53,827 MicroScheduler -   -> 4636 reads (1.24% of total) failing BadMateFilter
[2015-09-30T14:19Z] INFO  15:19:53,827 MicroScheduler -   -> 16397 reads (4.37% of total) failing DuplicateReadFilter
[2015-09-30T14:19Z] INFO  15:19:53,827 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:19Z] INFO  15:19:53,828 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:19Z] INFO  15:19:53,828 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:19Z] INFO  15:19:53,828 MicroScheduler -   -> 12699 reads (3.38% of total) failing MappingQualityZeroFilter
[2015-09-30T14:19Z] INFO  15:19:53,828 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:19Z] INFO  15:19:53,828 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:19Z] INFO  15:19:53,829 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:19Z] INFO  15:19:54,796 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:19Z] GATK: realign ('1', 235865791, 249250621) : syn3-normal
[2015-09-30T14:19Z] INFO  15:19:56,362 ProgressMeter -            done   1105676.0    52.0 s      47.0 s      100.0%    52.0 s       0.0 s
[2015-09-30T14:19Z] INFO  15:19:56,363 ProgressMeter - Total runtime 52.29 secs, 0.87 min, 0.01 hours
[2015-09-30T14:19Z] INFO  15:19:56,366 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1105676 total reads (0.00%)
[2015-09-30T14:19Z] INFO  15:19:56,366 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:19Z] INFO  15:19:56,367 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:19Z] INFO  15:19:56,367 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:19Z] INFO  15:19:56,716 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:56,718 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:19Z] INFO  15:19:56,718 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:19Z] INFO  15:19:56,718 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:19Z] INFO  15:19:56,721 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign-realign.intervals -L 1:235865792-249250621 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/tx/tmp6V_A61/1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam
[2015-09-30T14:19Z] INFO  15:19:56,727 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:19Z] INFO  15:19:56,727 HelpFormatter - Date/Time: 2015/09/30 15:19:56
[2015-09-30T14:19Z] INFO  15:19:56,727 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:56,727 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:19Z] INFO  15:19:56,852 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:19Z] INFO  15:19:56,918 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:19Z] INFO  15:19:56,925 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:19Z] INFO  15:19:56,940 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:19Z] INFO  15:19:57,407 IntervalUtils - Processing 13384830 bp from intervals
[2015-09-30T14:19Z] WARN  15:19:57,410 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:19Z] INFO  15:19:57,438 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:19Z] INFO  15:19:57,465 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:19Z] INFO  15:19:57,558 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:19Z] INFO  15:19:57,558 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:19Z] INFO  15:19:57,558 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:19Z] INFO  15:19:57,559 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:19Z] INFO  15:19:57,677 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:19Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam
[2015-09-30T14:19Z] INFO  15:19:57,783 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:20Z] GATK pre-alignment ('2', 0, 31134137) : syn3-normal
[2015-09-30T14:20Z] INFO  15:20:02,626 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:20Z] INFO  15:20:02,628 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:20Z] INFO  15:20:02,628 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:20Z] INFO  15:20:02,628 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:20Z] INFO  15:20:02,632 HelpFormatter - Program Args: -T PrintReads -L 2:1-31134137 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpNyaYLe/1_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam
[2015-09-30T14:20Z] INFO  15:20:02,638 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:20Z] INFO  15:20:02,638 HelpFormatter - Date/Time: 2015/09/30 15:20:02
[2015-09-30T14:20Z] INFO  15:20:02,638 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:20Z] INFO  15:20:02,638 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:20Z] INFO  15:20:03,093 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:20Z] INFO  15:20:03,828 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:20Z] INFO  15:20:03,881 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:20Z] INFO  15:20:03,889 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:20Z] INFO  15:20:03,905 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:20Z] INFO  15:20:03,919 IntervalUtils - Processing 31134137 bp from intervals
[2015-09-30T14:20Z] INFO  15:20:03,977 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:20Z] INFO  15:20:04,220 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:20Z] INFO  15:20:04,221 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:20Z] INFO  15:20:04,221 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:20Z] INFO  15:20:04,221 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:20Z] INFO  15:20:04,232 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:20Z] INFO  15:20:04,440 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:20Z] INFO  15:20:17,718 ProgressMeter -     1:156714782   1200017.0    60.0 s      50.0 s       45.3%     2.2 m      72.0 s
[2015-09-30T14:20Z] INFO  15:20:18,390 ProgressMeter -            done    372567.0    20.0 s      55.0 s       99.9%    20.0 s       0.0 s
[2015-09-30T14:20Z] INFO  15:20:18,390 ProgressMeter - Total runtime 20.83 secs, 0.35 min, 0.01 hours
[2015-09-30T14:20Z] INFO  15:20:18,393 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 372567 total reads (0.00%)
[2015-09-30T14:20Z] INFO  15:20:18,394 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:20Z] INFO  15:20:18,394 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:20Z] INFO  15:20:18,394 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:20Z] INFO  15:20:19,489 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:20Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam
[2015-09-30T14:20Z] GATK pre-alignment ('2', 31134801, 62196287) : syn3-normal
[2015-09-30T14:20Z] INFO  15:20:24,109 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:20Z] INFO  15:20:24,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:20Z] INFO  15:20:24,111 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:20Z] INFO  15:20:24,111 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:20Z] INFO  15:20:24,114 HelpFormatter - Program Args: -T PrintReads -L 2:31134802-62196287 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpVlv8pg/1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam
[2015-09-30T14:20Z] INFO  15:20:24,120 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:20Z] INFO  15:20:24,120 HelpFormatter - Date/Time: 2015/09/30 15:20:24
[2015-09-30T14:20Z] INFO  15:20:24,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:20Z] INFO  15:20:24,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:20Z] INFO  15:20:24,225 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:20Z] INFO  15:20:24,985 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:20Z] INFO  15:20:25,035 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:20Z] INFO  15:20:25,043 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:20Z] INFO  15:20:25,058 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:20Z] INFO  15:20:25,071 IntervalUtils - Processing 31061486 bp from intervals
[2015-09-30T14:20Z] INFO  15:20:25,129 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:20Z] INFO  15:20:25,339 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:20Z] INFO  15:20:25,340 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:20Z] INFO  15:20:25,340 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:20Z] INFO  15:20:25,340 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:20Z] INFO  15:20:25,351 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:20Z] INFO  15:20:25,554 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:20Z] INFO  15:20:34,224 ProgressMeter -      2:10977152    200002.0    30.0 s       2.5 m       35.3%    85.0 s      55.0 s
[2015-09-30T14:20Z] INFO  15:20:47,001 ProgressMeter -            done   1977353.0    90.0 s      45.0 s      100.0%    90.0 s       0.0 s
[2015-09-30T14:20Z] INFO  15:20:47,002 ProgressMeter - Total runtime 90.23 secs, 1.50 min, 0.03 hours
[2015-09-30T14:20Z] INFO  15:20:47,005 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1977353 total reads (0.00%)
[2015-09-30T14:20Z] INFO  15:20:47,005 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:20Z] INFO  15:20:47,006 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:20Z] INFO  15:20:47,006 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:20Z] INFO  15:20:48,130 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:20Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam
[2015-09-30T14:20Z] GATK pre-alignment ('2', 62227535, 95457199) : syn3-normal
[2015-09-30T14:20Z] INFO  15:20:55,343 ProgressMeter -      2:39251147    200253.0    30.0 s       2.5 m       26.1%   114.0 s      84.0 s
[2015-09-30T14:20Z] INFO  15:20:55,503 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:20Z] INFO  15:20:55,505 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:20Z] INFO  15:20:55,505 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:20Z] INFO  15:20:55,505 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:20Z] INFO  15:20:55,509 HelpFormatter - Program Args: -T PrintReads -L 2:62227536-95457199 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpNIn3dl/1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam
[2015-09-30T14:20Z] INFO  15:20:55,514 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:20Z] INFO  15:20:55,515 HelpFormatter - Date/Time: 2015/09/30 15:20:55
[2015-09-30T14:20Z] INFO  15:20:55,515 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:20Z] INFO  15:20:55,515 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:20Z] INFO  15:20:55,617 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:20Z] INFO  15:20:56,647 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:20Z] INFO  15:20:56,697 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:20Z] INFO  15:20:56,704 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:20Z] INFO  15:20:56,719 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:20Z] INFO  15:20:56,732 IntervalUtils - Processing 33229664 bp from intervals
[2015-09-30T14:20Z] INFO  15:20:56,789 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:20Z] INFO  15:20:56,982 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:20Z] INFO  15:20:56,982 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:20Z] INFO  15:20:56,983 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:20Z] INFO  15:20:56,983 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:20Z] INFO  15:20:56,994 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:20Z] INFO  15:20:57,195 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:21Z] INFO  15:21:04,568 ProgressMeter -      2:25498521    500008.0    60.0 s     120.0 s       81.9%    73.0 s      13.0 s
[2015-09-30T14:21Z] INFO  15:21:25,343 ProgressMeter -      2:54849508    500260.0    60.0 s     119.0 s       76.3%    78.0 s      18.0 s
[2015-09-30T14:21Z] INFO  15:21:26,985 ProgressMeter -      2:71376882    200004.0    30.0 s       2.5 m       27.5%   108.0 s      78.0 s
[2015-09-30T14:21Z] INFO  15:21:40,222 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:21Z] INFO  15:21:40,333 ProgressMeter -            done    743867.0    74.0 s     100.0 s      100.0%    74.0 s       0.0 s
[2015-09-30T14:21Z] INFO  15:21:40,334 ProgressMeter - Total runtime 74.99 secs, 1.25 min, 0.02 hours
[2015-09-30T14:21Z] INFO  15:21:40,334 MicroScheduler - 8032 reads were filtered out during the traversal out of approximately 751899 total reads (1.07%)
[2015-09-30T14:21Z] INFO  15:21:40,334 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:21Z] INFO  15:21:40,334 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:21Z] INFO  15:21:40,335 MicroScheduler -   -> 8032 reads (1.07% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:21Z] INFO  15:21:40,557 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:21Z] INFO  15:21:40,632 ProgressMeter -            done    937527.0    96.0 s     102.0 s      100.0%    96.0 s       0.0 s
[2015-09-30T14:21Z] INFO  15:21:40,633 ProgressMeter - Total runtime 96.41 secs, 1.61 min, 0.03 hours
[2015-09-30T14:21Z] INFO  15:21:40,633 MicroScheduler - 1946 reads were filtered out during the traversal out of approximately 939473 total reads (0.21%)
[2015-09-30T14:21Z] INFO  15:21:40,633 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:21Z] INFO  15:21:40,634 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:21Z] INFO  15:21:40,634 MicroScheduler -   -> 1946 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:21Z] INFO  15:21:41,477 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:21Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam
[2015-09-30T14:21Z] INFO  15:21:41,643 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:21Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam
[2015-09-30T14:21Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam 2:31134802-62196287
[2015-09-30T14:21Z] GATK: RealignerTargetCreator
[2015-09-30T14:21Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam 2:1-31134137
[2015-09-30T14:21Z] GATK: RealignerTargetCreator
[2015-09-30T14:21Z] INFO  15:21:45,777 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:21Z] INFO  15:21:45,779 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:21Z] INFO  15:21:45,780 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:21Z] INFO  15:21:45,780 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:21Z] INFO  15:21:45,783 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpgIWNat/1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign-realign.intervals -l INFO -L 2:31134802-62196287 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:21Z] INFO  15:21:45,789 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:21Z] INFO  15:21:45,789 HelpFormatter - Date/Time: 2015/09/30 15:21:45
[2015-09-30T14:21Z] INFO  15:21:45,789 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:21Z] INFO  15:21:45,789 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:21Z] INFO  15:21:45,848 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:21Z] INFO  15:21:45,960 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:21Z] INFO  15:21:45,968 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:21Z] INFO  15:21:45,984 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:21Z] INFO  15:21:46,895 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:21Z] INFO  15:21:46,897 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:21Z] INFO  15:21:46,897 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:21Z] INFO  15:21:46,897 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:21Z] INFO  15:21:46,901 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpSFX0a4/1_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign-realign.intervals -l INFO -L 2:1-31134137 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:21Z] INFO  15:21:46,907 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:21Z] INFO  15:21:46,907 HelpFormatter - Date/Time: 2015/09/30 15:21:46
[2015-09-30T14:21Z] INFO  15:21:46,907 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:21Z] INFO  15:21:46,908 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:21Z] INFO  15:21:46,965 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:21Z] INFO  15:21:47,076 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:21Z] INFO  15:21:47,085 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:21Z] INFO  15:21:47,087 IntervalUtils - Processing 31061486 bp from intervals
[2015-09-30T14:21Z] WARN  15:21:47,091 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:21Z] INFO  15:21:47,101 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:21Z] INFO  15:21:47,149 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:21Z] INFO  15:21:47,313 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:21Z] INFO  15:21:47,314 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:21Z] INFO  15:21:47,314 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:21Z] INFO  15:21:47,314 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:21Z] INFO  15:21:47,348 IntervalUtils - Processing 31134137 bp from intervals
[2015-09-30T14:21Z] WARN  15:21:47,352 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:21Z] INFO  15:21:47,411 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:21Z] INFO  15:21:47,557 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:21Z] INFO  15:21:47,558 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:21Z] INFO  15:21:47,558 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:21Z] INFO  15:21:47,558 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:21Z] INFO  15:21:57,049 ProgressMeter -      2:75937948    500010.0    60.0 s     120.0 s       41.3%     2.4 m      85.0 s
[2015-09-30T14:22Z] INFO  15:22:14,314 ProgressMeter -            done   3.1061486E7    26.0 s       0.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T14:22Z] INFO  15:22:14,314 ProgressMeter - Total runtime 27.00 secs, 0.45 min, 0.01 hours
[2015-09-30T14:22Z] INFO  15:22:14,317 MicroScheduler - 77347 reads were filtered out during the traversal out of approximately 748453 total reads (10.33%)
[2015-09-30T14:22Z] INFO  15:22:14,318 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:22Z] INFO  15:22:14,318 MicroScheduler -   -> 17360 reads (2.32% of total) failing BadMateFilter
[2015-09-30T14:22Z] INFO  15:22:14,318 MicroScheduler -   -> 29948 reads (4.00% of total) failing DuplicateReadFilter
[2015-09-30T14:22Z] INFO  15:22:14,318 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:22Z] INFO  15:22:14,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:22Z] INFO  15:22:14,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:22Z] INFO  15:22:14,319 MicroScheduler -   -> 30039 reads (4.01% of total) failing MappingQualityZeroFilter
[2015-09-30T14:22Z] INFO  15:22:14,319 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:22Z] INFO  15:22:14,320 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:22Z] INFO  15:22:14,320 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:22Z] INFO  15:22:15,343 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:22Z] GATK: realign ('2', 31134801, 62196287) : syn3-normal
[2015-09-30T14:22Z] INFO  15:22:16,382 ProgressMeter -            done   3.1134137E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T14:22Z] INFO  15:22:16,382 ProgressMeter - Total runtime 28.82 secs, 0.48 min, 0.01 hours
[2015-09-30T14:22Z] INFO  15:22:16,385 MicroScheduler - 71332 reads were filtered out during the traversal out of approximately 943163 total reads (7.56%)
[2015-09-30T14:22Z] INFO  15:22:16,386 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:22Z] INFO  15:22:16,386 MicroScheduler -   -> 10840 reads (1.15% of total) failing BadMateFilter
[2015-09-30T14:22Z] INFO  15:22:16,386 MicroScheduler -   -> 44135 reads (4.68% of total) failing DuplicateReadFilter
[2015-09-30T14:22Z] INFO  15:22:16,387 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:22Z] INFO  15:22:16,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:22Z] INFO  15:22:16,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:22Z] INFO  15:22:16,387 MicroScheduler -   -> 16357 reads (1.73% of total) failing MappingQualityZeroFilter
[2015-09-30T14:22Z] INFO  15:22:16,387 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:22Z] INFO  15:22:16,388 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:22Z] INFO  15:22:16,388 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:22Z] INFO  15:22:17,166 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:22Z] INFO  15:22:17,168 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:22Z] INFO  15:22:17,168 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:22Z] INFO  15:22:17,168 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:22Z] INFO  15:22:17,172 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign-realign.intervals -L 2:31134802-62196287 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpGY1zxl/1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam
[2015-09-30T14:22Z] INFO  15:22:17,177 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:22Z] INFO  15:22:17,178 HelpFormatter - Date/Time: 2015/09/30 15:22:17
[2015-09-30T14:22Z] INFO  15:22:17,178 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:22Z] INFO  15:22:17,178 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:22Z] INFO  15:22:17,317 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:22Z] GATK: realign ('2', 0, 31134137) : syn3-normal
[2015-09-30T14:22Z] INFO  15:22:17,492 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:22Z] INFO  15:22:17,558 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:22Z] INFO  15:22:17,566 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:22Z] INFO  15:22:17,582 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:22Z] INFO  15:22:17,814 IntervalUtils - Processing 31061486 bp from intervals
[2015-09-30T14:22Z] WARN  15:22:17,818 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:22Z] INFO  15:22:17,978 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:22Z] INFO  15:22:18,132 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:22Z] INFO  15:22:18,132 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:22Z] INFO  15:22:18,133 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:22Z] INFO  15:22:18,133 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:22Z] INFO  15:22:18,275 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:22Z] INFO  15:22:18,477 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:22Z] INFO  15:22:19,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:22Z] INFO  15:22:19,134 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:22Z] INFO  15:22:19,134 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:22Z] INFO  15:22:19,134 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:22Z] INFO  15:22:19,138 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign-realign.intervals -L 2:1-31134137 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpXI2QJy/1_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam
[2015-09-30T14:22Z] INFO  15:22:19,144 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:22Z] INFO  15:22:19,144 HelpFormatter - Date/Time: 2015/09/30 15:22:19
[2015-09-30T14:22Z] INFO  15:22:19,144 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:22Z] INFO  15:22:19,145 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:22Z] INFO  15:22:19,275 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:22Z] INFO  15:22:19,348 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:22Z] INFO  15:22:19,356 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:22Z] INFO  15:22:19,373 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:22Z] INFO  15:22:19,614 IntervalUtils - Processing 31134137 bp from intervals
[2015-09-30T14:22Z] WARN  15:22:19,618 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:22Z] INFO  15:22:19,676 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:22Z] INFO  15:22:19,825 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:22Z] INFO  15:22:19,826 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:22Z] INFO  15:22:19,826 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:22Z] INFO  15:22:19,827 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:22Z] INFO  15:22:19,970 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:22Z] INFO  15:22:20,164 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:22Z] INFO  15:22:27,050 ProgressMeter -      2:89385342    800014.0    90.0 s     112.0 s       81.7%   110.0 s      20.0 s
[2015-09-30T14:22Z] INFO  15:22:29,040 IndelRealigner - Not attempting realignment in interval 2:33141303-33141675 because there are too many reads.
[2015-09-30T14:22Z] INFO  15:22:35,948 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:22Z] INFO  15:22:36,199 ProgressMeter -            done    946848.0    99.0 s     104.0 s      100.0%    99.0 s       0.0 s
[2015-09-30T14:22Z] INFO  15:22:36,199 ProgressMeter - Total runtime 99.22 secs, 1.65 min, 0.03 hours
[2015-09-30T14:22Z] INFO  15:22:36,200 MicroScheduler - 2415 reads were filtered out during the traversal out of approximately 949263 total reads (0.25%)
[2015-09-30T14:22Z] INFO  15:22:36,200 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:22Z] INFO  15:22:36,200 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:22Z] INFO  15:22:36,200 MicroScheduler -   -> 2415 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:22Z] INFO  15:22:37,310 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:22Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam
[2015-09-30T14:22Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam 2:62227536-95457199
[2015-09-30T14:22Z] GATK: RealignerTargetCreator
[2015-09-30T14:22Z] INFO  15:22:41,682 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:22Z] INFO  15:22:41,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:22Z] INFO  15:22:41,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:22Z] INFO  15:22:41,685 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:22Z] INFO  15:22:41,688 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmp8a2ZVb/1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign-realign.intervals -l INFO -L 2:62227536-95457199 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:22Z] INFO  15:22:41,695 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:22Z] INFO  15:22:41,695 HelpFormatter - Date/Time: 2015/09/30 15:22:41
[2015-09-30T14:22Z] INFO  15:22:41,695 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:22Z] INFO  15:22:41,695 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:22Z] INFO  15:22:41,751 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:22Z] INFO  15:22:41,858 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:22Z] INFO  15:22:41,866 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:22Z] INFO  15:22:41,882 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:22Z] INFO  15:22:42,140 IntervalUtils - Processing 33229664 bp from intervals
[2015-09-30T14:22Z] WARN  15:22:42,144 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:22Z] INFO  15:22:42,200 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:22Z] INFO  15:22:42,352 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:22Z] INFO  15:22:42,352 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:22Z] INFO  15:22:42,352 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:22Z] INFO  15:22:42,353 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:22Z] INFO  15:22:48,958 ProgressMeter -      2:54872123    500260.0    30.0 s      61.0 s       76.4%    39.0 s       9.0 s
[2015-09-30T14:22Z] INFO  15:22:51,009 ProgressMeter -      2:26535936    500008.0    31.0 s      62.0 s       85.2%    36.0 s       5.0 s
[2015-09-30T14:22Z] INFO  15:22:56,058 ProgressMeter -            done    743867.0    37.0 s      50.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T14:22Z] INFO  15:22:56,059 ProgressMeter - Total runtime 37.93 secs, 0.63 min, 0.01 hours
[2015-09-30T14:22Z] INFO  15:22:56,062 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 743867 total reads (0.00%)
[2015-09-30T14:22Z] INFO  15:22:56,063 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:22Z] INFO  15:22:56,063 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:22Z] INFO  15:22:56,063 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:22Z] INFO  15:22:57,160 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:22Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam
[2015-09-30T14:23Z] GATK pre-alignment ('2', 95457728, 127315933) : syn3-normal
[2015-09-30T14:23Z] INFO  15:23:02,677 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:23Z] INFO  15:23:02,679 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:23Z] INFO  15:23:02,679 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:23Z] INFO  15:23:02,680 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:23Z] INFO  15:23:02,683 HelpFormatter - Program Args: -T PrintReads -L 2:95457729-127315933 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpYdO4au/1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam
[2015-09-30T14:23Z] INFO  15:23:02,688 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:23Z] INFO  15:23:02,688 HelpFormatter - Date/Time: 2015/09/30 15:23:02
[2015-09-30T14:23Z] INFO  15:23:02,688 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:23Z] INFO  15:23:02,689 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:23Z] INFO  15:23:02,788 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:23Z] INFO  15:23:03,740 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:23Z] INFO  15:23:03,792 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:23Z] INFO  15:23:03,799 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:23Z] INFO  15:23:03,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:23Z] INFO  15:23:03,826 ProgressMeter -            done    937527.0    43.0 s      46.0 s      100.0%    43.0 s       0.0 s
[2015-09-30T14:23Z] INFO  15:23:03,826 ProgressMeter - Total runtime 44.00 secs, 0.73 min, 0.01 hours
[2015-09-30T14:23Z] INFO  15:23:03,827 IntervalUtils - Processing 31858205 bp from intervals
[2015-09-30T14:23Z] INFO  15:23:03,829 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 937527 total reads (0.00%)
[2015-09-30T14:23Z] INFO  15:23:03,830 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:23Z] INFO  15:23:03,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:23Z] INFO  15:23:03,830 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:23Z] INFO  15:23:03,883 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:23Z] INFO  15:23:04,080 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:23Z] INFO  15:23:04,081 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:23Z] INFO  15:23:04,081 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:23Z] INFO  15:23:04,081 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:23Z] INFO  15:23:04,092 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:23Z] INFO  15:23:04,288 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:23Z] INFO  15:23:04,958 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:23Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam
[2015-09-30T14:23Z] GATK pre-alignment ('2', 127413596, 158444156) : syn3-normal
[2015-09-30T14:23Z] INFO  15:23:09,453 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:23Z] INFO  15:23:09,455 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:23Z] INFO  15:23:09,455 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:23Z] INFO  15:23:09,455 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:23Z] INFO  15:23:09,458 HelpFormatter - Program Args: -T PrintReads -L 2:127413597-158444156 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpel4T5j/1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam
[2015-09-30T14:23Z] INFO  15:23:09,464 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:23Z] INFO  15:23:09,464 HelpFormatter - Date/Time: 2015/09/30 15:23:09
[2015-09-30T14:23Z] INFO  15:23:09,464 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:23Z] INFO  15:23:09,464 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:23Z] INFO  15:23:09,571 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:23Z] INFO  15:23:10,766 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:23Z] INFO  15:23:10,815 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:23Z] INFO  15:23:10,822 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:23Z] INFO  15:23:10,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:23Z] INFO  15:23:10,850 IntervalUtils - Processing 31030560 bp from intervals
[2015-09-30T14:23Z] INFO  15:23:10,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:23Z] INFO  15:23:11,093 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:23Z] INFO  15:23:11,094 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:23Z] INFO  15:23:11,094 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:23Z] INFO  15:23:11,094 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:23Z] INFO  15:23:11,105 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:23Z] INFO  15:23:11,293 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:23Z] INFO  15:23:11,821 ProgressMeter -            done   3.3229664E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T14:23Z] INFO  15:23:11,822 ProgressMeter - Total runtime 29.47 secs, 0.49 min, 0.01 hours
[2015-09-30T14:23Z] INFO  15:23:11,825 MicroScheduler - 130625 reads were filtered out during the traversal out of approximately 952543 total reads (13.71%)
[2015-09-30T14:23Z] INFO  15:23:11,825 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:23Z] INFO  15:23:11,826 MicroScheduler -   -> 10484 reads (1.10% of total) failing BadMateFilter
[2015-09-30T14:23Z] INFO  15:23:11,826 MicroScheduler -   -> 41352 reads (4.34% of total) failing DuplicateReadFilter
[2015-09-30T14:23Z] INFO  15:23:11,826 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:23Z] INFO  15:23:11,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:23Z] INFO  15:23:11,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:23Z] INFO  15:23:11,827 MicroScheduler -   -> 78789 reads (8.27% of total) failing MappingQualityZeroFilter
[2015-09-30T14:23Z] INFO  15:23:11,827 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:23Z] INFO  15:23:11,827 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:23Z] INFO  15:23:11,827 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:23Z] INFO  15:23:12,835 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:23Z] GATK: realign ('2', 62227535, 95457199) : syn3-normal
[2015-09-30T14:23Z] INFO  15:23:15,709 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:23Z] INFO  15:23:15,711 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:23Z] INFO  15:23:15,712 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:23Z] INFO  15:23:15,712 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:23Z] INFO  15:23:15,715 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign-realign.intervals -L 2:62227536-95457199 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpKCxi7X/1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam
[2015-09-30T14:23Z] INFO  15:23:15,722 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:23Z] INFO  15:23:15,722 HelpFormatter - Date/Time: 2015/09/30 15:23:15
[2015-09-30T14:23Z] INFO  15:23:15,722 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:23Z] INFO  15:23:15,722 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:23Z] INFO  15:23:16,208 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:23Z] INFO  15:23:16,274 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:23Z] INFO  15:23:16,282 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:23Z] INFO  15:23:16,298 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:23Z] INFO  15:23:16,538 IntervalUtils - Processing 33229664 bp from intervals
[2015-09-30T14:23Z] WARN  15:23:16,542 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:23Z] INFO  15:23:16,598 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:23Z] INFO  15:23:16,745 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:23Z] INFO  15:23:16,746 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:23Z] INFO  15:23:16,746 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:23Z] INFO  15:23:16,747 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:23Z] INFO  15:23:16,884 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:23Z] INFO  15:23:17,079 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:23Z] INFO  15:23:34,083 ProgressMeter -      2:97875649    200002.0    30.0 s       2.5 m        7.6%     6.6 m       6.1 m
[2015-09-30T14:23Z] INFO  15:23:41,097 ProgressMeter -     2:132044832    200002.0    30.0 s       2.5 m       14.9%     3.4 m       2.9 m
[2015-09-30T14:23Z] INFO  15:23:47,716 ProgressMeter -      2:79242687    500010.0    30.0 s      61.0 s       51.2%    58.0 s      28.0 s
[2015-09-30T14:24Z] INFO  15:24:02,957 ProgressMeter -            done    946848.0    46.0 s      48.0 s      100.0%    46.0 s       0.0 s
[2015-09-30T14:24Z] INFO  15:24:02,958 ProgressMeter - Total runtime 46.21 secs, 0.77 min, 0.01 hours
[2015-09-30T14:24Z] INFO  15:24:02,961 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 946848 total reads (0.00%)
[2015-09-30T14:24Z] INFO  15:24:02,962 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:24Z] INFO  15:24:02,962 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:24Z] INFO  15:24:02,962 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:24Z] INFO  15:24:04,059 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:24Z] INFO  15:24:04,087 ProgressMeter -     2:107788211    500006.0    60.0 s     120.0 s       38.7%     2.6 m      95.0 s
[2015-09-30T14:24Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam
[2015-09-30T14:24Z] GATK pre-alignment ('2', 158484801, 189599894) : syn3-normal
[2015-09-30T14:24Z] INFO  15:24:08,256 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:08,258 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:24Z] INFO  15:24:08,259 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:24Z] INFO  15:24:08,259 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:24Z] INFO  15:24:08,262 HelpFormatter - Program Args: -T PrintReads -L 2:158484802-189599894 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmphpc_dC/1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam
[2015-09-30T14:24Z] INFO  15:24:08,268 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:24Z] INFO  15:24:08,268 HelpFormatter - Date/Time: 2015/09/30 15:24:08
[2015-09-30T14:24Z] INFO  15:24:08,269 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:08,269 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:08,377 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:24Z] INFO  15:24:09,730 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:24Z] INFO  15:24:09,780 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:24Z] INFO  15:24:09,787 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:24Z] INFO  15:24:09,802 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:24Z] INFO  15:24:09,815 IntervalUtils - Processing 31115093 bp from intervals
[2015-09-30T14:24Z] INFO  15:24:09,871 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:24Z] INFO  15:24:10,206 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:24Z] INFO  15:24:10,206 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:24Z] INFO  15:24:10,206 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:24Z] INFO  15:24:10,207 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:24Z] INFO  15:24:10,218 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:24Z] INFO  15:24:10,429 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:24Z] INFO  15:24:11,097 ProgressMeter -     2:152381186    500007.0    60.0 s     120.0 s       80.5%    74.0 s      14.0 s
[2015-09-30T14:24Z] INFO  15:24:20,772 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:24Z] INFO  15:24:20,845 ProgressMeter -            done    659816.0    69.0 s     105.0 s      100.0%    69.0 s       0.0 s
[2015-09-30T14:24Z] INFO  15:24:20,845 ProgressMeter - Total runtime 69.75 secs, 1.16 min, 0.02 hours
[2015-09-30T14:24Z] INFO  15:24:20,845 MicroScheduler - 1862 reads were filtered out during the traversal out of approximately 661678 total reads (0.28%)
[2015-09-30T14:24Z] INFO  15:24:20,846 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:24Z] INFO  15:24:20,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:24Z] INFO  15:24:20,846 MicroScheduler -   -> 1862 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:24Z] INFO  15:24:22,150 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:24Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam
[2015-09-30T14:24Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam 2:127413597-158444156
[2015-09-30T14:24Z] GATK: RealignerTargetCreator
[2015-09-30T14:24Z] INFO  15:24:26,107 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:26,109 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:24Z] INFO  15:24:26,109 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:24Z] INFO  15:24:26,109 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:24Z] INFO  15:24:26,113 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpb5vKAa/1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign-realign.intervals -l INFO -L 2:127413597-158444156 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:24Z] INFO  15:24:26,119 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:24Z] INFO  15:24:26,119 HelpFormatter - Date/Time: 2015/09/30 15:24:26
[2015-09-30T14:24Z] INFO  15:24:26,119 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:26,119 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:26,177 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:24Z] INFO  15:24:26,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:24Z] INFO  15:24:26,294 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:24Z] INFO  15:24:26,310 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:24Z] INFO  15:24:26,562 IntervalUtils - Processing 31030560 bp from intervals
[2015-09-30T14:24Z] WARN  15:24:26,566 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:24Z] INFO  15:24:26,622 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:24Z] INFO  15:24:26,763 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:24Z] INFO  15:24:26,763 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:24Z] INFO  15:24:26,764 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:24Z] INFO  15:24:26,764 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:24Z] INFO  15:24:34,088 ProgressMeter -     2:114475315    800009.0    90.0 s     112.0 s       59.7%     2.5 m      60.0 s
[2015-09-30T14:24Z] INFO  15:24:40,236 ProgressMeter -     2:169760922    200003.0    30.0 s       2.5 m       36.2%    82.0 s      52.0 s
[2015-09-30T14:24Z] INFO  15:24:48,053 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:24Z] INFO  15:24:48,211 ProgressMeter -            done   1036542.0   104.0 s     100.0 s      100.0%   104.0 s       0.0 s
[2015-09-30T14:24Z] INFO  15:24:48,212 ProgressMeter - Total runtime 104.13 secs, 1.74 min, 0.03 hours
[2015-09-30T14:24Z] INFO  15:24:48,212 MicroScheduler - 2412 reads were filtered out during the traversal out of approximately 1038954 total reads (0.23%)
[2015-09-30T14:24Z] INFO  15:24:48,212 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:24Z] INFO  15:24:48,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:24Z] INFO  15:24:48,213 MicroScheduler -   -> 2412 reads (0.23% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:24Z] INFO  15:24:49,204 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:24Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam
[2015-09-30T14:24Z] INFO  15:24:51,030 ProgressMeter -            done   3.103056E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T14:24Z] INFO  15:24:51,031 ProgressMeter - Total runtime 24.27 secs, 0.40 min, 0.01 hours
[2015-09-30T14:24Z] INFO  15:24:51,034 MicroScheduler - 85383 reads were filtered out during the traversal out of approximately 663460 total reads (12.87%)
[2015-09-30T14:24Z] INFO  15:24:51,034 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:24Z] INFO  15:24:51,034 MicroScheduler -   -> 9048 reads (1.36% of total) failing BadMateFilter
[2015-09-30T14:24Z] INFO  15:24:51,034 MicroScheduler -   -> 27970 reads (4.22% of total) failing DuplicateReadFilter
[2015-09-30T14:24Z] INFO  15:24:51,035 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:24Z] INFO  15:24:51,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:24Z] INFO  15:24:51,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:24Z] INFO  15:24:51,035 MicroScheduler -   -> 48365 reads (7.29% of total) failing MappingQualityZeroFilter
[2015-09-30T14:24Z] INFO  15:24:51,036 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:24Z] INFO  15:24:51,036 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:24Z] INFO  15:24:51,036 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:24Z] INFO  15:24:52,155 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:24Z] GATK: realign ('2', 127413596, 158444156) : syn3-normal
[2015-09-30T14:24Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam 2:95457729-127315933
[2015-09-30T14:24Z] GATK: RealignerTargetCreator
[2015-09-30T14:24Z] INFO  15:24:54,471 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:54,473 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:24Z] INFO  15:24:54,473 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:24Z] INFO  15:24:54,473 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:24Z] INFO  15:24:54,477 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpXsR6m7/1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign-realign.intervals -l INFO -L 2:95457729-127315933 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:24Z] INFO  15:24:54,476 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:54,478 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:24Z] INFO  15:24:54,478 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:24Z] INFO  15:24:54,479 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:24Z] INFO  15:24:54,482 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:24Z] INFO  15:24:54,482 HelpFormatter - Date/Time: 2015/09/30 15:24:54
[2015-09-30T14:24Z] INFO  15:24:54,482 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:54,482 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign-realign.intervals -L 2:127413597-158444156 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpnJmoNs/1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam
[2015-09-30T14:24Z] INFO  15:24:54,482 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:54,487 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:24Z] INFO  15:24:54,487 HelpFormatter - Date/Time: 2015/09/30 15:24:54
[2015-09-30T14:24Z] INFO  15:24:54,487 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:54,487 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:24Z] INFO  15:24:54,540 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:24Z] INFO  15:24:54,608 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:24Z] INFO  15:24:54,643 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:24Z] INFO  15:24:54,651 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:24Z] INFO  15:24:54,668 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:24Z] INFO  15:24:54,670 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:24Z] INFO  15:24:54,678 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:24Z] INFO  15:24:54,694 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:24Z] INFO  15:24:54,915 IntervalUtils - Processing 31030560 bp from intervals
[2015-09-30T14:24Z] WARN  15:24:54,919 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:24Z] INFO  15:24:55,178 IntervalUtils - Processing 31858205 bp from intervals
[2015-09-30T14:24Z] WARN  15:24:55,182 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:24Z] INFO  15:24:55,225 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:24Z] INFO  15:24:55,236 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:24Z] INFO  15:24:55,363 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:24Z] INFO  15:24:55,363 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:24Z] INFO  15:24:55,363 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:24Z] INFO  15:24:55,364 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:24Z] INFO  15:24:55,379 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:24Z] INFO  15:24:55,379 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:24Z] INFO  15:24:55,380 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:24Z] INFO  15:24:55,380 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:24Z] INFO  15:24:55,506 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:24Z] INFO  15:24:55,691 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:25Z] INFO  15:25:10,236 ProgressMeter -     2:178977573    500007.0    60.0 s     120.0 s       65.9%    91.0 s      31.0 s
[2015-09-30T14:25Z] INFO  15:25:24,358 ProgressMeter -            done   3.1858205E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T14:25Z] INFO  15:25:24,358 ProgressMeter - Total runtime 28.98 secs, 0.48 min, 0.01 hours
[2015-09-30T14:25Z] INFO  15:25:24,361 MicroScheduler - 174576 reads were filtered out during the traversal out of approximately 1043466 total reads (16.73%)
[2015-09-30T14:25Z] INFO  15:25:24,361 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:25Z] INFO  15:25:24,362 MicroScheduler -   -> 10289 reads (0.99% of total) failing BadMateFilter
[2015-09-30T14:25Z] INFO  15:25:24,362 MicroScheduler -   -> 43325 reads (4.15% of total) failing DuplicateReadFilter
[2015-09-30T14:25Z] INFO  15:25:24,362 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:25Z] INFO  15:25:24,363 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:25Z] INFO  15:25:24,363 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:25Z] INFO  15:25:24,363 MicroScheduler -   -> 120962 reads (11.59% of total) failing MappingQualityZeroFilter
[2015-09-30T14:25Z] INFO  15:25:24,363 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:25Z] INFO  15:25:24,363 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:25Z] INFO  15:25:24,364 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:25Z] INFO  15:25:25,798 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:25Z] INFO  15:25:25,810 ProgressMeter -     2:152547230    500007.0    30.0 s      60.0 s       81.0%    37.0 s       7.0 s
[2015-09-30T14:25Z] GATK: realign ('2', 95457728, 127315933) : syn3-normal
[2015-09-30T14:25Z] INFO  15:25:27,527 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:25Z] INFO  15:25:27,529 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:25Z] INFO  15:25:27,529 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:25Z] INFO  15:25:27,529 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:25Z] INFO  15:25:27,533 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign-realign.intervals -L 2:95457729-127315933 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpeh6Yob/1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam
[2015-09-30T14:25Z] INFO  15:25:27,539 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:25Z] INFO  15:25:27,539 HelpFormatter - Date/Time: 2015/09/30 15:25:27
[2015-09-30T14:25Z] INFO  15:25:27,539 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:25Z] INFO  15:25:27,539 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:25Z] INFO  15:25:27,670 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:25Z] INFO  15:25:27,734 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:25Z] INFO  15:25:27,742 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:25Z] INFO  15:25:27,762 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:25Z] INFO  15:25:28,047 ProgressMeter -            done    659816.0    32.0 s      49.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T14:25Z] INFO  15:25:28,047 ProgressMeter - Total runtime 32.68 secs, 0.54 min, 0.01 hours
[2015-09-30T14:25Z] INFO  15:25:28,050 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 659816 total reads (0.00%)
[2015-09-30T14:25Z] INFO  15:25:28,051 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:25Z] INFO  15:25:28,051 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:25Z] INFO  15:25:28,051 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:25Z] INFO  15:25:28,342 IntervalUtils - Processing 31858205 bp from intervals
[2015-09-30T14:25Z] WARN  15:25:28,346 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:25Z] INFO  15:25:28,401 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:25Z] INFO  15:25:28,547 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:25Z] INFO  15:25:28,547 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:25Z] INFO  15:25:28,548 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:25Z] INFO  15:25:28,548 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:25Z] INFO  15:25:28,690 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:25Z] INFO  15:25:28,884 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:25Z] INFO  15:25:29,311 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:25Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam
[2015-09-30T14:25Z] GATK pre-alignment ('2', 189838937, 221056966) : syn3-normal
[2015-09-30T14:25Z] INFO  15:25:32,826 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:25Z] INFO  15:25:32,943 ProgressMeter -            done    790984.0    82.0 s     104.0 s      100.0%    82.0 s       0.0 s
[2015-09-30T14:25Z] INFO  15:25:32,944 ProgressMeter - Total runtime 82.74 secs, 1.38 min, 0.02 hours
[2015-09-30T14:25Z] INFO  15:25:32,944 MicroScheduler - 2398 reads were filtered out during the traversal out of approximately 793382 total reads (0.30%)
[2015-09-30T14:25Z] INFO  15:25:32,944 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:25Z] INFO  15:25:32,945 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:25Z] INFO  15:25:32,945 MicroScheduler -   -> 2398 reads (0.30% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:25Z] INFO  15:25:33,372 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:25Z] INFO  15:25:33,375 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:25Z] INFO  15:25:33,375 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:25Z] INFO  15:25:33,375 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:25Z] INFO  15:25:33,379 HelpFormatter - Program Args: -T PrintReads -L 2:189838938-221056966 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpTXQek5/1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam
[2015-09-30T14:25Z] INFO  15:25:33,384 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:25Z] INFO  15:25:33,384 HelpFormatter - Date/Time: 2015/09/30 15:25:33
[2015-09-30T14:25Z] INFO  15:25:33,385 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:25Z] INFO  15:25:33,385 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:25Z] INFO  15:25:33,499 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:25Z] INFO  15:25:34,693 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:25Z] INFO  15:25:34,745 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:25Z] INFO  15:25:34,753 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:25Z] INFO  15:25:34,768 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:25Z] INFO  15:25:34,781 IntervalUtils - Processing 31218029 bp from intervals
[2015-09-30T14:25Z] INFO  15:25:34,841 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:25Z] INFO  15:25:34,863 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:25Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam
[2015-09-30T14:25Z] INFO  15:25:35,069 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:25Z] INFO  15:25:35,069 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:25Z] INFO  15:25:35,070 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:25Z] INFO  15:25:35,070 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:25Z] INFO  15:25:35,081 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:25Z] INFO  15:25:35,283 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:25Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam 2:158484802-189599894
[2015-09-30T14:25Z] GATK: RealignerTargetCreator
[2015-09-30T14:25Z] INFO  15:25:39,438 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:25Z] INFO  15:25:39,440 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:25Z] INFO  15:25:39,440 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:25Z] INFO  15:25:39,440 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:25Z] INFO  15:25:39,444 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpp6RToz/1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign-realign.intervals -l INFO -L 2:158484802-189599894 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:25Z] INFO  15:25:39,449 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:25Z] INFO  15:25:39,449 HelpFormatter - Date/Time: 2015/09/30 15:25:39
[2015-09-30T14:25Z] INFO  15:25:39,449 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:25Z] INFO  15:25:39,450 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:25Z] INFO  15:25:39,508 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:25Z] INFO  15:25:39,623 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:25Z] INFO  15:25:39,631 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:25Z] INFO  15:25:39,647 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:25Z] INFO  15:25:39,912 IntervalUtils - Processing 31115093 bp from intervals
[2015-09-30T14:25Z] WARN  15:25:39,916 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:25Z] INFO  15:25:40,326 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:25Z] INFO  15:25:40,512 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:25Z] INFO  15:25:40,513 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:25Z] INFO  15:25:40,513 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:25Z] INFO  15:25:40,514 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:25Z] INFO  15:25:59,402 ProgressMeter -     2:103348919    400005.0    30.0 s      77.0 s       24.8%     2.0 m      91.0 s
[2015-09-30T14:26Z] INFO  15:26:05,072 ProgressMeter -     2:201284165    200006.0    30.0 s       2.5 m       36.7%    81.0 s      51.0 s
[2015-09-30T14:26Z] INFO  15:26:08,994 ProgressMeter -            done   3.1115093E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T14:26Z] INFO  15:26:08,995 ProgressMeter - Total runtime 28.48 secs, 0.47 min, 0.01 hours
[2015-09-30T14:26Z] INFO  15:26:08,998 MicroScheduler - 55795 reads were filtered out during the traversal out of approximately 795793 total reads (7.01%)
[2015-09-30T14:26Z] INFO  15:26:08,998 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:26Z] INFO  15:26:08,998 MicroScheduler -   -> 9484 reads (1.19% of total) failing BadMateFilter
[2015-09-30T14:26Z] INFO  15:26:08,999 MicroScheduler -   -> 31307 reads (3.93% of total) failing DuplicateReadFilter
[2015-09-30T14:26Z] INFO  15:26:08,999 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:26Z] INFO  15:26:08,999 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:26Z] INFO  15:26:08,999 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:26Z] INFO  15:26:08,999 MicroScheduler -   -> 15004 reads (1.89% of total) failing MappingQualityZeroFilter
[2015-09-30T14:26Z] INFO  15:26:09,000 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:26Z] INFO  15:26:09,000 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:26Z] INFO  15:26:09,000 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:26Z] INFO  15:26:09,965 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:26Z] GATK: realign ('2', 158484801, 189599894) : syn3-normal
[2015-09-30T14:26Z] INFO  15:26:12,505 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:26Z] INFO  15:26:12,507 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:26Z] INFO  15:26:12,507 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:26Z] INFO  15:26:12,507 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:26Z] INFO  15:26:12,510 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign-realign.intervals -L 2:158484802-189599894 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpjxKepU/1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam
[2015-09-30T14:26Z] INFO  15:26:12,516 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:26Z] INFO  15:26:12,516 HelpFormatter - Date/Time: 2015/09/30 15:26:12
[2015-09-30T14:26Z] INFO  15:26:12,516 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:26Z] INFO  15:26:12,516 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:26Z] INFO  15:26:12,641 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:26Z] INFO  15:26:12,703 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:26Z] INFO  15:26:12,711 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:26Z] INFO  15:26:12,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:26Z] INFO  15:26:12,955 IntervalUtils - Processing 31115093 bp from intervals
[2015-09-30T14:26Z] WARN  15:26:12,959 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:26Z] INFO  15:26:13,011 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:26Z] INFO  15:26:13,158 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:26Z] INFO  15:26:13,159 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:26Z] INFO  15:26:13,159 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:26Z] INFO  15:26:13,160 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:26Z] INFO  15:26:13,303 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:26Z] INFO  15:26:13,489 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:26Z] INFO  15:26:20,966 ProgressMeter -            done   1036542.0    52.0 s      50.0 s      100.0%    52.0 s       0.0 s
[2015-09-30T14:26Z] INFO  15:26:20,966 ProgressMeter - Total runtime 52.42 secs, 0.87 min, 0.01 hours
[2015-09-30T14:26Z] INFO  15:26:20,970 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1036542 total reads (0.00%)
[2015-09-30T14:26Z] INFO  15:26:20,970 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:26Z] INFO  15:26:20,970 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:26Z] INFO  15:26:20,970 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:26Z] INFO  15:26:22,107 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:26Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam
[2015-09-30T14:26Z] GATK pre-alignment ('2', 221341378, 243199373) : syn3-normal
[2015-09-30T14:26Z] INFO  15:26:27,331 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:26Z] INFO  15:26:27,333 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:26Z] INFO  15:26:27,333 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:26Z] INFO  15:26:27,333 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:26Z] INFO  15:26:27,337 HelpFormatter - Program Args: -T PrintReads -L 2:221341379-243199373 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpZSmQGk/1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam
[2015-09-30T14:26Z] INFO  15:26:27,343 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:26Z] INFO  15:26:27,343 HelpFormatter - Date/Time: 2015/09/30 15:26:27
[2015-09-30T14:26Z] INFO  15:26:27,343 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:26Z] INFO  15:26:27,343 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:26Z] INFO  15:26:27,450 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:26Z] INFO  15:26:28,631 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:26Z] INFO  15:26:28,680 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:26Z] INFO  15:26:28,688 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:26Z] INFO  15:26:28,702 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:26Z] INFO  15:26:28,715 IntervalUtils - Processing 21857995 bp from intervals
[2015-09-30T14:26Z] INFO  15:26:28,772 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:26Z] INFO  15:26:28,949 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:26Z] INFO  15:26:28,950 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:26Z] INFO  15:26:28,950 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:26Z] INFO  15:26:28,950 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:26Z] INFO  15:26:28,961 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:26Z] INFO  15:26:29,103 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:26Z] INFO  15:26:35,700 ProgressMeter -     2:208432601    500009.0    60.0 s       2.0 m       59.6%   100.0 s      40.0 s
[2015-09-30T14:26Z] INFO  15:26:43,162 ProgressMeter -     2:176988894    500007.0    30.0 s      60.0 s       59.5%    50.0 s      20.0 s
[2015-09-30T14:26Z] INFO  15:26:53,100 ProgressMeter -            done    790984.0    39.0 s      50.0 s      100.0%    39.0 s       0.0 s
[2015-09-30T14:26Z] INFO  15:26:53,101 ProgressMeter - Total runtime 39.94 secs, 0.67 min, 0.01 hours
[2015-09-30T14:26Z] INFO  15:26:53,104 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 790984 total reads (0.00%)
[2015-09-30T14:26Z] INFO  15:26:53,104 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:26Z] INFO  15:26:53,104 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:26Z] INFO  15:26:53,105 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:26Z] INFO  15:26:54,164 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:26Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam
[2015-09-30T14:26Z] GATK pre-alignment ('3', 0, 31203562) : syn3-normal
[2015-09-30T14:26Z] INFO  15:26:58,221 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:26Z] INFO  15:26:58,223 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:26Z] INFO  15:26:58,223 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:26Z] INFO  15:26:58,224 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:26Z] INFO  15:26:58,227 HelpFormatter - Program Args: -T PrintReads -L 3:1-31203562 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpJ1ooqX/1_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam
[2015-09-30T14:26Z] INFO  15:26:58,233 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:26Z] INFO  15:26:58,233 HelpFormatter - Date/Time: 2015/09/30 15:26:58
[2015-09-30T14:26Z] INFO  15:26:58,233 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:26Z] INFO  15:26:58,233 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:26Z] INFO  15:26:58,354 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:26Z] INFO  15:26:58,953 ProgressMeter -     2:231775581    200002.0    30.0 s       2.5 m       47.7%    62.0 s      32.0 s
[2015-09-30T14:26Z] INFO  15:26:59,595 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:26Z] INFO  15:26:59,645 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:26Z] INFO  15:26:59,653 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:26Z] INFO  15:26:59,668 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:26Z] INFO  15:26:59,682 IntervalUtils - Processing 31203562 bp from intervals
[2015-09-30T14:26Z] INFO  15:26:59,741 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:26Z] INFO  15:26:59,950 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:26Z] INFO  15:26:59,950 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:26Z] INFO  15:26:59,951 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:26Z] INFO  15:26:59,951 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:26Z] INFO  15:26:59,962 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:27Z] INFO  15:27:00,163 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:27Z] INFO  15:27:05,701 ProgressMeter -     2:219270629    800012.0    90.0 s     113.0 s       94.3%    95.0 s       5.0 s
[2015-09-30T14:27Z] INFO  15:27:26,613 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:27Z] INFO  15:27:26,949 ProgressMeter -            done   1086431.0   111.0 s     102.0 s      100.0%   111.0 s       0.0 s
[2015-09-30T14:27Z] INFO  15:27:26,949 ProgressMeter - Total runtime 111.88 secs, 1.86 min, 0.03 hours
[2015-09-30T14:27Z] INFO  15:27:26,949 MicroScheduler - 2405 reads were filtered out during the traversal out of approximately 1088836 total reads (0.22%)
[2015-09-30T14:27Z] INFO  15:27:26,950 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:27Z] INFO  15:27:26,950 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:27Z] INFO  15:27:26,950 MicroScheduler -   -> 2405 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:27Z] INFO  15:27:27,989 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:27Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam
[2015-09-30T14:27Z] INFO  15:27:29,245 ProgressMeter -     2:238270650    500005.0    60.0 s     120.0 s       77.5%    77.0 s      17.0 s
[2015-09-30T14:27Z] INFO  15:27:29,960 ProgressMeter -      3:10059673    200002.0    30.0 s       2.5 m       32.2%    93.0 s      63.0 s
[2015-09-30T14:27Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam 2:189838938-221056966
[2015-09-30T14:27Z] GATK: RealignerTargetCreator
[2015-09-30T14:27Z] INFO  15:27:33,092 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:27Z] INFO  15:27:33,095 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:27Z] INFO  15:27:33,095 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:27Z] INFO  15:27:33,095 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:27Z] INFO  15:27:33,099 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpZhUK6M/1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign-realign.intervals -l INFO -L 2:189838938-221056966 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:27Z] INFO  15:27:33,105 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:27Z] INFO  15:27:33,105 HelpFormatter - Date/Time: 2015/09/30 15:27:33
[2015-09-30T14:27Z] INFO  15:27:33,105 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:27Z] INFO  15:27:33,106 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:27Z] INFO  15:27:33,166 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:27Z] INFO  15:27:33,547 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:27Z] INFO  15:27:33,554 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:27Z] INFO  15:27:33,570 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:27Z] INFO  15:27:33,809 IntervalUtils - Processing 31218029 bp from intervals
[2015-09-30T14:27Z] WARN  15:27:33,813 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:27Z] INFO  15:27:33,870 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:27Z] INFO  15:27:34,032 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:27Z] INFO  15:27:34,032 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:27Z] INFO  15:27:34,032 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:27Z] INFO  15:27:34,033 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:27Z] INFO  15:27:59,246 ProgressMeter -     2:242102415    800011.0    90.0 s     112.0 s       95.0%    94.0 s       4.0 s
[2015-09-30T14:27Z] INFO  15:27:59,961 ProgressMeter -      3:15472533    500005.0    60.0 s     120.0 s       49.6%     2.0 m      61.0 s
[2015-09-30T14:28Z] INFO  15:28:04,036 ProgressMeter -     2:220158909   3.0312871E7    30.0 s       0.0 s       97.1%    30.0 s       0.0 s
[2015-09-30T14:28Z] INFO  15:28:06,014 ProgressMeter -            done   3.1218029E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T14:28Z] INFO  15:28:06,014 ProgressMeter - Total runtime 31.98 secs, 0.53 min, 0.01 hours
[2015-09-30T14:28Z] INFO  15:28:06,018 MicroScheduler - 78105 reads were filtered out during the traversal out of approximately 1093385 total reads (7.14%)
[2015-09-30T14:28Z] INFO  15:28:06,018 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:28Z] INFO  15:28:06,018 MicroScheduler -   -> 11772 reads (1.08% of total) failing BadMateFilter
[2015-09-30T14:28Z] INFO  15:28:06,019 MicroScheduler -   -> 47551 reads (4.35% of total) failing DuplicateReadFilter
[2015-09-30T14:28Z] INFO  15:28:06,019 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:28Z] INFO  15:28:06,019 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:28Z] INFO  15:28:06,019 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:28Z] INFO  15:28:06,020 MicroScheduler -   -> 18782 reads (1.72% of total) failing MappingQualityZeroFilter
[2015-09-30T14:28Z] INFO  15:28:06,020 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:28Z] INFO  15:28:06,020 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:28Z] INFO  15:28:06,020 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:28Z] INFO  15:28:07,021 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:28Z] GATK: realign ('2', 189838937, 221056966) : syn3-normal
[2015-09-30T14:28Z] INFO  15:28:08,816 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:28Z] INFO  15:28:09,012 ProgressMeter -            done    968082.0   100.0 s     103.0 s       99.8%   100.0 s       0.0 s
[2015-09-30T14:28Z] INFO  15:28:09,012 ProgressMeter - Total runtime 100.06 secs, 1.67 min, 0.03 hours
[2015-09-30T14:28Z] INFO  15:28:09,012 MicroScheduler - 1907 reads were filtered out during the traversal out of approximately 969989 total reads (0.20%)
[2015-09-30T14:28Z] INFO  15:28:09,013 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:28Z] INFO  15:28:09,013 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:28Z] INFO  15:28:09,013 MicroScheduler -   -> 1907 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:28Z] INFO  15:28:09,047 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:09,049 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:28Z] INFO  15:28:09,049 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:28Z] INFO  15:28:09,049 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:28Z] INFO  15:28:09,053 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign-realign.intervals -L 2:189838938-221056966 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmp3N8ECS/1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam
[2015-09-30T14:28Z] INFO  15:28:09,059 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:28Z] INFO  15:28:09,059 HelpFormatter - Date/Time: 2015/09/30 15:28:09
[2015-09-30T14:28Z] INFO  15:28:09,059 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:09,059 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:09,192 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:28Z] INFO  15:28:09,255 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:28Z] INFO  15:28:09,263 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:28Z] INFO  15:28:09,278 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:28Z] INFO  15:28:09,516 IntervalUtils - Processing 31218029 bp from intervals
[2015-09-30T14:28Z] WARN  15:28:09,520 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:28Z] INFO  15:28:09,574 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:28Z] INFO  15:28:09,724 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:28Z] INFO  15:28:09,724 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:28Z] INFO  15:28:09,725 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:28Z] INFO  15:28:09,725 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:28Z] INFO  15:28:09,868 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:28Z] INFO  15:28:10,026 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:28Z] INFO  15:28:10,059 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:28Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam
[2015-09-30T14:28Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam 2:221341379-243199373
[2015-09-30T14:28Z] GATK: RealignerTargetCreator
[2015-09-30T14:28Z] INFO  15:28:14,943 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:14,946 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:28Z] INFO  15:28:14,946 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:28Z] INFO  15:28:14,946 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:28Z] INFO  15:28:14,949 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmpZWdKO9/1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign-realign.intervals -l INFO -L 2:221341379-243199373 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:28Z] INFO  15:28:14,955 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:28Z] INFO  15:28:14,955 HelpFormatter - Date/Time: 2015/09/30 15:28:14
[2015-09-30T14:28Z] INFO  15:28:14,955 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:14,955 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:15,013 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:28Z] INFO  15:28:15,126 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:28Z] INFO  15:28:15,134 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:28Z] INFO  15:28:15,150 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:28Z] INFO  15:28:15,622 IntervalUtils - Processing 21857995 bp from intervals
[2015-09-30T14:28Z] WARN  15:28:15,626 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:28Z] INFO  15:28:15,683 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:28Z] INFO  15:28:15,847 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:28Z] INFO  15:28:15,848 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:28Z] INFO  15:28:15,848 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:28Z] INFO  15:28:15,849 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:28Z] INFO  15:28:17,842 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:28Z] INFO  15:28:17,953 ProgressMeter -            done    770460.0    78.0 s     101.0 s      100.0%    78.0 s       0.0 s
[2015-09-30T14:28Z] INFO  15:28:17,953 ProgressMeter - Total runtime 78.00 secs, 1.30 min, 0.02 hours
[2015-09-30T14:28Z] INFO  15:28:17,954 MicroScheduler - 1765 reads were filtered out during the traversal out of approximately 772225 total reads (0.23%)
[2015-09-30T14:28Z] INFO  15:28:17,954 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:28Z] INFO  15:28:17,954 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:28Z] INFO  15:28:17,954 MicroScheduler -   -> 1765 reads (0.23% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:28Z] INFO  15:28:19,067 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:28Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam
[2015-09-30T14:28Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam 3:1-31203562
[2015-09-30T14:28Z] GATK: RealignerTargetCreator
[2015-09-30T14:28Z] INFO  15:28:23,629 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:23,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:28Z] INFO  15:28:23,631 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:28Z] INFO  15:28:23,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:28Z] INFO  15:28:23,635 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmptDO0lu/1_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign-realign.intervals -l INFO -L 3:1-31203562 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:28Z] INFO  15:28:23,641 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:28Z] INFO  15:28:23,641 HelpFormatter - Date/Time: 2015/09/30 15:28:23
[2015-09-30T14:28Z] INFO  15:28:23,641 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:23,642 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:23,703 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:28Z] INFO  15:28:23,812 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:28Z] INFO  15:28:23,820 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:28Z] INFO  15:28:23,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:28Z] INFO  15:28:24,090 IntervalUtils - Processing 31203562 bp from intervals
[2015-09-30T14:28Z] WARN  15:28:24,094 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:28Z] INFO  15:28:24,153 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:28Z] INFO  15:28:24,294 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:28Z] INFO  15:28:24,295 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:28Z] INFO  15:28:24,295 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:28Z] INFO  15:28:24,295 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:28Z] INFO  15:28:39,753 ProgressMeter -     2:207116705    400008.0    30.0 s      75.0 s       55.3%    54.0 s      24.0 s
[2015-09-30T14:28Z] INFO  15:28:41,341 ProgressMeter -            done   2.1857995E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T14:28Z] INFO  15:28:41,341 ProgressMeter - Total runtime 25.49 secs, 0.42 min, 0.01 hours
[2015-09-30T14:28Z] INFO  15:28:41,344 MicroScheduler - 79804 reads were filtered out during the traversal out of approximately 973776 total reads (8.20%)
[2015-09-30T14:28Z] INFO  15:28:41,345 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:28Z] INFO  15:28:41,345 MicroScheduler -   -> 9089 reads (0.93% of total) failing BadMateFilter
[2015-09-30T14:28Z] INFO  15:28:41,345 MicroScheduler -   -> 47674 reads (4.90% of total) failing DuplicateReadFilter
[2015-09-30T14:28Z] INFO  15:28:41,346 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:28Z] INFO  15:28:41,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:28Z] INFO  15:28:41,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:28Z] INFO  15:28:41,346 MicroScheduler -   -> 23041 reads (2.37% of total) failing MappingQualityZeroFilter
[2015-09-30T14:28Z] INFO  15:28:41,346 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:28Z] INFO  15:28:41,347 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:28Z] INFO  15:28:41,347 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:28Z] INFO  15:28:42,798 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:28Z] GATK: realign ('2', 221341378, 243199373) : syn3-normal
[2015-09-30T14:28Z] INFO  15:28:44,487 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:44,490 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:28Z] INFO  15:28:44,490 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:28Z] INFO  15:28:44,490 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:28Z] INFO  15:28:44,493 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign-realign.intervals -L 2:221341379-243199373 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/tx/tmp92JHVP/1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam
[2015-09-30T14:28Z] INFO  15:28:44,500 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:28Z] INFO  15:28:44,500 HelpFormatter - Date/Time: 2015/09/30 15:28:44
[2015-09-30T14:28Z] INFO  15:28:44,500 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:44,500 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:44,656 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:28Z] INFO  15:28:44,721 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:28Z] INFO  15:28:44,728 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:28Z] INFO  15:28:44,744 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:28Z] INFO  15:28:45,061 IntervalUtils - Processing 21857995 bp from intervals
[2015-09-30T14:28Z] WARN  15:28:45,065 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:28Z] INFO  15:28:45,120 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:28Z] INFO  15:28:45,241 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:28Z] INFO  15:28:45,241 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:28Z] INFO  15:28:45,242 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:28Z] INFO  15:28:45,242 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:28Z] INFO  15:28:45,378 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:28Z] INFO  15:28:45,527 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:28Z] INFO  15:28:52,051 ProgressMeter -            done   3.1203562E7    27.0 s       0.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T14:28Z] INFO  15:28:52,052 ProgressMeter - Total runtime 27.76 secs, 0.46 min, 0.01 hours
[2015-09-30T14:28Z] INFO  15:28:52,055 MicroScheduler - 59375 reads were filtered out during the traversal out of approximately 775301 total reads (7.66%)
[2015-09-30T14:28Z] INFO  15:28:52,055 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:28Z] INFO  15:28:52,055 MicroScheduler -   -> 9776 reads (1.26% of total) failing BadMateFilter
[2015-09-30T14:28Z] INFO  15:28:52,056 MicroScheduler -   -> 35887 reads (4.63% of total) failing DuplicateReadFilter
[2015-09-30T14:28Z] INFO  15:28:52,056 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:28Z] INFO  15:28:52,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:28Z] INFO  15:28:52,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:28Z] INFO  15:28:52,057 MicroScheduler -   -> 13712 reads (1.77% of total) failing MappingQualityZeroFilter
[2015-09-30T14:28Z] INFO  15:28:52,057 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:28Z] INFO  15:28:52,057 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:28Z] INFO  15:28:52,057 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:28Z] INFO  15:28:53,065 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:28Z] GATK: realign ('3', 0, 31203562) : syn3-normal
[2015-09-30T14:28Z] INFO  15:28:54,864 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:54,866 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:28Z] INFO  15:28:54,866 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:28Z] INFO  15:28:54,866 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:28Z] INFO  15:28:54,870 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign-realign.intervals -L 3:1-31203562 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpkxHmKJ/1_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam
[2015-09-30T14:28Z] INFO  15:28:54,876 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:28Z] INFO  15:28:54,876 HelpFormatter - Date/Time: 2015/09/30 15:28:54
[2015-09-30T14:28Z] INFO  15:28:54,876 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:54,877 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:28Z] INFO  15:28:55,007 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:28Z] INFO  15:28:55,074 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:28Z] INFO  15:28:55,082 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:28Z] INFO  15:28:55,098 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:28Z] INFO  15:28:55,619 IntervalUtils - Processing 31203562 bp from intervals
[2015-09-30T14:28Z] WARN  15:28:55,623 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:28Z] INFO  15:28:55,681 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:28Z] INFO  15:28:55,825 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:28Z] INFO  15:28:55,825 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:28Z] INFO  15:28:55,826 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:28Z] INFO  15:28:55,826 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:28Z] INFO  15:28:55,971 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:28Z] INFO  15:28:56,164 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:29Z] INFO  15:29:03,158 ProgressMeter -            done   1086431.0    53.0 s      49.0 s      100.0%    53.0 s       0.0 s
[2015-09-30T14:29Z] INFO  15:29:03,158 ProgressMeter - Total runtime 53.43 secs, 0.89 min, 0.01 hours
[2015-09-30T14:29Z] INFO  15:29:03,162 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1086431 total reads (0.00%)
[2015-09-30T14:29Z] INFO  15:29:03,162 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:29Z] INFO  15:29:03,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:29Z] INFO  15:29:03,162 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:29Z] INFO  15:29:04,224 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:29Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam
[2015-09-30T14:29Z] GATK pre-alignment ('3', 31494593, 62516713) : syn3-normal
[2015-09-30T14:29Z] INFO  15:29:09,203 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:29Z] INFO  15:29:09,205 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:29Z] INFO  15:29:09,205 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:29Z] INFO  15:29:09,205 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:29Z] INFO  15:29:09,208 HelpFormatter - Program Args: -T PrintReads -L 3:31494594-62516713 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpj2CpNj/1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam
[2015-09-30T14:29Z] INFO  15:29:09,214 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:29Z] INFO  15:29:09,214 HelpFormatter - Date/Time: 2015/09/30 15:29:09
[2015-09-30T14:29Z] INFO  15:29:09,214 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:29Z] INFO  15:29:09,215 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:29Z] INFO  15:29:09,321 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:29Z] INFO  15:29:10,457 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:29Z] INFO  15:29:10,509 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:29Z] INFO  15:29:10,517 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:29Z] INFO  15:29:10,532 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:29Z] INFO  15:29:10,546 IntervalUtils - Processing 31022120 bp from intervals
[2015-09-30T14:29Z] INFO  15:29:10,606 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:29Z] INFO  15:29:11,531 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:29Z] INFO  15:29:11,532 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:29Z] INFO  15:29:11,532 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:29Z] INFO  15:29:11,533 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:29Z] INFO  15:29:11,544 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:29Z] INFO  15:29:11,753 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:29Z] INFO  15:29:15,666 ProgressMeter -     2:238838809    500005.0    30.0 s      60.0 s       80.1%    37.0 s       7.0 s
[2015-09-30T14:29Z] INFO  15:29:25,829 ProgressMeter -      3:14581610    500005.0    30.0 s      60.0 s       46.7%    64.0 s      34.0 s
[2015-09-30T14:29Z] INFO  15:29:30,483 ProgressMeter -            done    968082.0    45.0 s      46.0 s       99.8%    45.0 s       0.0 s
[2015-09-30T14:29Z] INFO  15:29:30,483 ProgressMeter - Total runtime 45.24 secs, 0.75 min, 0.01 hours
[2015-09-30T14:29Z] INFO  15:29:30,486 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 968082 total reads (0.00%)
[2015-09-30T14:29Z] INFO  15:29:30,487 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:29Z] INFO  15:29:30,487 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:29Z] INFO  15:29:30,487 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:29Z] INFO  15:29:31,573 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:29Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam
[2015-09-30T14:29Z] INFO  15:29:34,862 ProgressMeter -            done    770460.0    39.0 s      50.0 s      100.0%    39.0 s       0.0 s
[2015-09-30T14:29Z] INFO  15:29:34,862 ProgressMeter - Total runtime 39.04 secs, 0.65 min, 0.01 hours
[2015-09-30T14:29Z] INFO  15:29:34,865 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 770460 total reads (0.00%)
[2015-09-30T14:29Z] INFO  15:29:34,865 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:29Z] INFO  15:29:34,865 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:29Z] INFO  15:29:34,866 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:29Z] GATK pre-alignment ('3', 62518267, 93593495) : syn3-normal
[2015-09-30T14:29Z] INFO  15:29:35,995 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:29Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam
[2015-09-30T14:29Z] INFO  15:29:38,053 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:29Z] INFO  15:29:38,055 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:29Z] INFO  15:29:38,055 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:29Z] INFO  15:29:38,055 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:29Z] INFO  15:29:38,059 HelpFormatter - Program Args: -T PrintReads -L 3:62518268-93593495 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmp4JJ6NB/1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam
[2015-09-30T14:29Z] INFO  15:29:38,064 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:29Z] INFO  15:29:38,064 HelpFormatter - Date/Time: 2015/09/30 15:29:38
[2015-09-30T14:29Z] INFO  15:29:38,065 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:29Z] INFO  15:29:38,065 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:29Z] INFO  15:29:38,168 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:29Z] GATK pre-alignment ('3', 93595554, 124625281) : syn3-normal
[2015-09-30T14:29Z] INFO  15:29:39,405 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:29Z] INFO  15:29:39,453 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:29Z] INFO  15:29:39,460 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:29Z] INFO  15:29:39,475 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:29Z] INFO  15:29:39,487 IntervalUtils - Processing 31075228 bp from intervals
[2015-09-30T14:29Z] INFO  15:29:39,543 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:29Z] INFO  15:29:39,728 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:29Z] INFO  15:29:39,728 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:29Z] INFO  15:29:39,729 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:29Z] INFO  15:29:39,729 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:29Z] INFO  15:29:39,740 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:29Z] INFO  15:29:39,935 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:29Z] INFO  15:29:40,590 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:29Z] INFO  15:29:40,593 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:29Z] INFO  15:29:40,593 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:29Z] INFO  15:29:40,593 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:29Z] INFO  15:29:40,596 HelpFormatter - Program Args: -T PrintReads -L 3:93595555-124625281 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpZW6vL2/1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam
[2015-09-30T14:29Z] INFO  15:29:40,602 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:29Z] INFO  15:29:40,602 HelpFormatter - Date/Time: 2015/09/30 15:29:40
[2015-09-30T14:29Z] INFO  15:29:40,602 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:29Z] INFO  15:29:40,602 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:29Z] INFO  15:29:40,702 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:29Z] INFO  15:29:41,535 ProgressMeter -      3:38387897    200002.0    30.0 s       2.5 m       22.2%     2.3 m     105.0 s
[2015-09-30T14:29Z] INFO  15:29:42,450 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:29Z] INFO  15:29:42,498 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:29Z] INFO  15:29:42,505 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:29Z] INFO  15:29:42,520 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:29Z] INFO  15:29:42,532 IntervalUtils - Processing 31029727 bp from intervals
[2015-09-30T14:29Z] INFO  15:29:43,067 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:29Z] INFO  15:29:43,257 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:29Z] INFO  15:29:43,258 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:29Z] INFO  15:29:43,258 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:29Z] INFO  15:29:43,258 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:29Z] INFO  15:29:43,269 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:29Z] INFO  15:29:43,464 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:30Z] INFO  15:30:09,742 ProgressMeter -      3:86064411    200002.0    30.0 s       2.5 m       75.8%    39.0 s       9.0 s
[2015-09-30T14:30Z] INFO  15:30:11,536 ProgressMeter -      3:45031050    500005.0    60.0 s     120.0 s       43.6%     2.3 m      77.0 s
[2015-09-30T14:30Z] INFO  15:30:11,885 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:30Z] INFO  15:30:12,064 ProgressMeter -            done    289069.0    32.0 s     111.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T14:30Z] INFO  15:30:12,064 ProgressMeter - Total runtime 32.34 secs, 0.54 min, 0.01 hours
[2015-09-30T14:30Z] INFO  15:30:12,065 MicroScheduler - 1149 reads were filtered out during the traversal out of approximately 290218 total reads (0.40%)
[2015-09-30T14:30Z] INFO  15:30:12,065 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:30Z] INFO  15:30:12,065 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:30Z] INFO  15:30:12,065 MicroScheduler -   -> 1149 reads (0.40% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:30Z] INFO  15:30:13,260 ProgressMeter -     3:110611561    200002.0    30.0 s       2.5 m       54.8%    54.0 s      24.0 s
[2015-09-30T14:30Z] INFO  15:30:13,328 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:30Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam
[2015-09-30T14:30Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam 3:62518268-93593495
[2015-09-30T14:30Z] GATK: RealignerTargetCreator
[2015-09-30T14:30Z] INFO  15:30:16,360 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:30Z] INFO  15:30:16,362 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:30Z] INFO  15:30:16,363 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:30Z] INFO  15:30:16,363 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:30Z] INFO  15:30:16,366 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmp2ga6hM/1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign-realign.intervals -l INFO -L 3:62518268-93593495 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:30Z] INFO  15:30:16,373 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:30Z] INFO  15:30:16,373 HelpFormatter - Date/Time: 2015/09/30 15:30:16
[2015-09-30T14:30Z] INFO  15:30:16,373 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:30Z] INFO  15:30:16,373 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:30Z] INFO  15:30:16,432 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:30Z] INFO  15:30:16,546 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:30Z] INFO  15:30:16,554 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:30Z] INFO  15:30:16,570 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:30Z] INFO  15:30:16,833 IntervalUtils - Processing 31075228 bp from intervals
[2015-09-30T14:30Z] WARN  15:30:16,837 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:30Z] INFO  15:30:16,892 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:30Z] INFO  15:30:17,012 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:30Z] INFO  15:30:17,013 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:30Z] INFO  15:30:17,013 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:30Z] INFO  15:30:17,014 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:30Z] INFO  15:30:35,868 ProgressMeter -            done   3.1075228E7    18.0 s       0.0 s      100.0%    18.0 s       0.0 s
[2015-09-30T14:30Z] INFO  15:30:35,868 ProgressMeter - Total runtime 18.86 secs, 0.31 min, 0.01 hours
[2015-09-30T14:30Z] INFO  15:30:35,871 MicroScheduler - 41947 reads were filtered out during the traversal out of approximately 290705 total reads (14.43%)
[2015-09-30T14:30Z] INFO  15:30:35,871 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:30Z] INFO  15:30:35,872 MicroScheduler -   -> 5937 reads (2.04% of total) failing BadMateFilter
[2015-09-30T14:30Z] INFO  15:30:35,872 MicroScheduler -   -> 11093 reads (3.82% of total) failing DuplicateReadFilter
[2015-09-30T14:30Z] INFO  15:30:35,872 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:30Z] INFO  15:30:35,872 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:30Z] INFO  15:30:35,872 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:30Z] INFO  15:30:35,873 MicroScheduler -   -> 24917 reads (8.57% of total) failing MappingQualityZeroFilter
[2015-09-30T14:30Z] INFO  15:30:35,873 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:30Z] INFO  15:30:35,873 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:30Z] INFO  15:30:35,873 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:30Z] INFO  15:30:36,825 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:30Z] GATK: realign ('3', 62518267, 93593495) : syn3-normal
[2015-09-30T14:30Z] INFO  15:30:38,727 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:30Z] INFO  15:30:38,729 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:30Z] INFO  15:30:38,729 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:30Z] INFO  15:30:38,730 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:30Z] INFO  15:30:38,733 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign-realign.intervals -L 3:62518268-93593495 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpyLkWFj/1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam
[2015-09-30T14:30Z] INFO  15:30:38,738 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:30Z] INFO  15:30:38,739 HelpFormatter - Date/Time: 2015/09/30 15:30:38
[2015-09-30T14:30Z] INFO  15:30:38,739 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:30Z] INFO  15:30:38,739 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:30Z] INFO  15:30:38,870 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:30Z] INFO  15:30:38,934 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:30Z] INFO  15:30:38,941 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:30Z] INFO  15:30:38,957 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:30Z] INFO  15:30:39,193 IntervalUtils - Processing 31075228 bp from intervals
[2015-09-30T14:30Z] WARN  15:30:39,197 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:30Z] INFO  15:30:39,251 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:30Z] INFO  15:30:39,371 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:30Z] INFO  15:30:39,372 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:30Z] INFO  15:30:39,372 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:30Z] INFO  15:30:39,372 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:30Z] INFO  15:30:39,515 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:30Z] INFO  15:30:39,687 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:30Z] INFO  15:30:43,261 ProgressMeter -     3:121643756    500005.0    60.0 s     120.0 s       90.4%    66.0 s       6.0 s
[2015-09-30T14:30Z] INFO  15:30:51,537 ProgressMeter -      3:49062172    900010.0   100.0 s     111.0 s       56.6%     2.9 m      76.0 s
[2015-09-30T14:30Z] INFO  15:30:56,331 ProgressMeter -            done    289069.0    16.0 s      58.0 s      100.0%    16.0 s       0.0 s
[2015-09-30T14:30Z] INFO  15:30:56,331 ProgressMeter - Total runtime 16.96 secs, 0.28 min, 0.00 hours
[2015-09-30T14:30Z] INFO  15:30:56,334 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 289069 total reads (0.00%)
[2015-09-30T14:30Z] INFO  15:30:56,335 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:30Z] INFO  15:30:56,335 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:30Z] INFO  15:30:56,335 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:30Z] INFO  15:30:57,536 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:30Z] INFO  15:30:58,805 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:30Z] INFO  15:30:58,901 ProgressMeter -            done    750584.0    75.0 s     100.0 s      100.0%    75.0 s       0.0 s
[2015-09-30T14:30Z] INFO  15:30:58,901 ProgressMeter - Total runtime 75.64 secs, 1.26 min, 0.02 hours
[2015-09-30T14:30Z] INFO  15:30:58,901 MicroScheduler - 2001 reads were filtered out during the traversal out of approximately 752585 total reads (0.27%)
[2015-09-30T14:30Z] INFO  15:30:58,902 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:30Z] INFO  15:30:58,902 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:30Z] INFO  15:30:58,902 MicroScheduler -   -> 2001 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:30Z] INFO  15:30:59,922 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:31Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam
[2015-09-30T14:31Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam
[2015-09-30T14:31Z] GATK pre-alignment ('3', 124626733, 155649953) : syn3-normal
[2015-09-30T14:31Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam 3:93595555-124625281
[2015-09-30T14:31Z] GATK: RealignerTargetCreator
[2015-09-30T14:31Z] INFO  15:31:06,652 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:31Z] INFO  15:31:06,655 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:31Z] INFO  15:31:06,655 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:31Z] INFO  15:31:06,655 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:31Z] INFO  15:31:06,658 HelpFormatter - Program Args: -T PrintReads -L 3:124626734-155649953 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmp07PNA_/1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam
[2015-09-30T14:31Z] INFO  15:31:06,664 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:31Z] INFO  15:31:06,664 HelpFormatter - Date/Time: 2015/09/30 15:31:06
[2015-09-30T14:31Z] INFO  15:31:06,664 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:31Z] INFO  15:31:06,664 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:31Z] INFO  15:31:06,766 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:31Z] INFO  15:31:06,866 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:31Z] INFO  15:31:06,868 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:31Z] INFO  15:31:06,868 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:31Z] INFO  15:31:06,869 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:31Z] INFO  15:31:06,872 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpJjFTF4/1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign-realign.intervals -l INFO -L 3:93595555-124625281 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:31Z] INFO  15:31:06,878 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:31Z] INFO  15:31:06,878 HelpFormatter - Date/Time: 2015/09/30 15:31:06
[2015-09-30T14:31Z] INFO  15:31:06,878 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:31Z] INFO  15:31:06,878 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:31Z] INFO  15:31:06,937 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:31Z] INFO  15:31:07,046 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:31Z] INFO  15:31:07,054 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:31Z] INFO  15:31:07,070 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:31Z] INFO  15:31:07,466 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:31Z] INFO  15:31:07,517 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:31Z] INFO  15:31:07,524 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:31Z] INFO  15:31:07,539 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:31Z] INFO  15:31:07,552 IntervalUtils - Processing 31023220 bp from intervals
[2015-09-30T14:31Z] INFO  15:31:07,609 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:31Z] INFO  15:31:07,846 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:31Z] INFO  15:31:07,847 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:31Z] INFO  15:31:07,847 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:31Z] INFO  15:31:07,847 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:31Z] INFO  15:31:07,859 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:31Z] INFO  15:31:07,979 IntervalUtils - Processing 31029727 bp from intervals
[2015-09-30T14:31Z] WARN  15:31:07,983 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:31Z] INFO  15:31:08,040 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:31Z] INFO  15:31:08,066 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:31Z] INFO  15:31:08,482 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:31Z] INFO  15:31:08,483 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:31Z] INFO  15:31:08,483 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:31Z] INFO  15:31:08,483 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:31Z] INFO  15:31:21,538 ProgressMeter -      3:51690608   1200019.0     2.2 m     108.0 s       65.1%     3.3 m      69.0 s
[2015-09-30T14:31Z] INFO  15:31:35,000 ProgressMeter -            done   3.1029727E7    26.0 s       0.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T14:31Z] INFO  15:31:35,001 ProgressMeter - Total runtime 26.52 secs, 0.44 min, 0.01 hours
[2015-09-30T14:31Z] INFO  15:31:35,004 MicroScheduler - 55117 reads were filtered out during the traversal out of approximately 755558 total reads (7.29%)
[2015-09-30T14:31Z] INFO  15:31:35,004 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:31Z] INFO  15:31:35,004 MicroScheduler -   -> 9274 reads (1.23% of total) failing BadMateFilter
[2015-09-30T14:31Z] INFO  15:31:35,005 MicroScheduler -   -> 32021 reads (4.24% of total) failing DuplicateReadFilter
[2015-09-30T14:31Z] INFO  15:31:35,005 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:31Z] INFO  15:31:35,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:31Z] INFO  15:31:35,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:31Z] INFO  15:31:35,005 MicroScheduler -   -> 13822 reads (1.83% of total) failing MappingQualityZeroFilter
[2015-09-30T14:31Z] INFO  15:31:35,006 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:31Z] INFO  15:31:35,006 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:31Z] INFO  15:31:35,006 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:31Z] INFO  15:31:35,972 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:31Z] GATK: realign ('3', 93595554, 124625281) : syn3-normal
[2015-09-30T14:31Z] INFO  15:31:37,850 ProgressMeter -     3:128684997    200019.0    30.0 s       2.5 m       13.1%     3.8 m       3.3 m
[2015-09-30T14:31Z] INFO  15:31:38,106 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:31Z] INFO  15:31:38,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:31Z] INFO  15:31:38,109 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:31Z] INFO  15:31:38,109 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:31Z] INFO  15:31:38,112 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign-realign.intervals -L 3:93595555-124625281 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmp9bchSq/1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam
[2015-09-30T14:31Z] INFO  15:31:38,118 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:31Z] INFO  15:31:38,118 HelpFormatter - Date/Time: 2015/09/30 15:31:38
[2015-09-30T14:31Z] INFO  15:31:38,118 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:31Z] INFO  15:31:38,119 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:31Z] INFO  15:31:38,245 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:31Z] INFO  15:31:38,314 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:31Z] INFO  15:31:38,321 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:31Z] INFO  15:31:38,337 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:31Z] INFO  15:31:38,569 IntervalUtils - Processing 31029727 bp from intervals
[2015-09-30T14:31Z] WARN  15:31:38,573 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:31Z] INFO  15:31:38,628 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:31Z] INFO  15:31:38,772 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:31Z] INFO  15:31:38,773 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:31Z] INFO  15:31:38,773 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:31Z] INFO  15:31:38,774 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:31Z] INFO  15:31:38,920 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:31Z] INFO  15:31:39,110 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:31Z] INFO  15:31:51,766 ProgressMeter -      3:53911213   1500024.0     2.7 m     106.0 s       72.3%     3.7 m      61.0 s
[2015-09-30T14:32Z] INFO  15:32:07,850 ProgressMeter -     3:134881000    500023.0    60.0 s     120.0 s       33.1%     3.0 m       2.0 m
[2015-09-30T14:32Z] INFO  15:32:09,133 ProgressMeter -     3:121192603    500005.0    30.0 s      60.0 s       88.9%    33.0 s       3.0 s
[2015-09-30T14:32Z] INFO  15:32:12,533 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:32Z] INFO  15:32:12,830 ProgressMeter -            done   1820958.0     3.0 m      99.0 s      100.0%     3.0 m       0.0 s
[2015-09-30T14:32Z] INFO  15:32:12,831 ProgressMeter - Total runtime 181.30 secs, 3.02 min, 0.05 hours
[2015-09-30T14:32Z] INFO  15:32:12,831 MicroScheduler - 3066 reads were filtered out during the traversal out of approximately 1824024 total reads (0.17%)
[2015-09-30T14:32Z] INFO  15:32:12,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:32Z] INFO  15:32:12,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:32Z] INFO  15:32:12,832 MicroScheduler -   -> 3066 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:32Z] INFO  15:32:13,900 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:32Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam
[2015-09-30T14:32Z] INFO  15:32:17,069 ProgressMeter -            done    750584.0    38.0 s      51.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T14:32Z] INFO  15:32:17,070 ProgressMeter - Total runtime 38.30 secs, 0.64 min, 0.01 hours
[2015-09-30T14:32Z] INFO  15:32:17,073 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 750584 total reads (0.00%)
[2015-09-30T14:32Z] INFO  15:32:17,074 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:32Z] INFO  15:32:17,074 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:32Z] INFO  15:32:17,074 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:32Z] INFO  15:32:18,091 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:32Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam
[2015-09-30T14:32Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam 3:31494594-62516713
[2015-09-30T14:32Z] GATK: RealignerTargetCreator
[2015-09-30T14:32Z] GATK pre-alignment ('3', 155652401, 186761310) : syn3-normal
[2015-09-30T14:32Z] INFO  15:32:21,836 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:32Z] INFO  15:32:21,838 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:32Z] INFO  15:32:21,838 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:32Z] INFO  15:32:21,838 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:32Z] INFO  15:32:21,842 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpgQOCwB/1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign-realign.intervals -l INFO -L 3:31494594-62516713 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:32Z] INFO  15:32:21,848 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:32Z] INFO  15:32:21,849 HelpFormatter - Date/Time: 2015/09/30 15:32:21
[2015-09-30T14:32Z] INFO  15:32:21,849 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:32Z] INFO  15:32:21,849 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:32Z] INFO  15:32:21,908 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:32Z] INFO  15:32:22,021 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:32Z] INFO  15:32:22,029 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:32Z] INFO  15:32:22,046 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:32Z] INFO  15:32:22,311 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:32Z] INFO  15:32:22,313 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:32Z] INFO  15:32:22,313 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:32Z] INFO  15:32:22,313 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:32Z] INFO  15:32:22,317 HelpFormatter - Program Args: -T PrintReads -L 3:155652402-186761310 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpLrzsnf/1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam
[2015-09-30T14:32Z] INFO  15:32:22,322 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:32Z] INFO  15:32:22,322 HelpFormatter - Date/Time: 2015/09/30 15:32:22
[2015-09-30T14:32Z] INFO  15:32:22,323 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:32Z] INFO  15:32:22,323 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:32Z] INFO  15:32:23,245 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:32Z] INFO  15:32:23,261 IntervalUtils - Processing 31022120 bp from intervals
[2015-09-30T14:32Z] WARN  15:32:23,265 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:32Z] INFO  15:32:23,322 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:32Z] INFO  15:32:23,479 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:32Z] INFO  15:32:23,480 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:32Z] INFO  15:32:23,480 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:32Z] INFO  15:32:23,481 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:32Z] INFO  15:32:23,953 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:32Z] INFO  15:32:24,002 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:32Z] INFO  15:32:24,010 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:32Z] INFO  15:32:24,024 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:32Z] INFO  15:32:24,037 IntervalUtils - Processing 31108909 bp from intervals
[2015-09-30T14:32Z] INFO  15:32:24,094 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:32Z] INFO  15:32:24,324 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:32Z] INFO  15:32:24,324 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:32Z] INFO  15:32:24,324 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:32Z] INFO  15:32:24,324 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:32Z] INFO  15:32:24,336 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:32Z] INFO  15:32:24,532 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:32Z] INFO  15:32:37,851 ProgressMeter -     3:148895756    800027.0    90.0 s     112.0 s       78.2%   115.0 s      25.0 s
[2015-09-30T14:32Z] INFO  15:32:49,858 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:32Z] INFO  15:32:50,042 ProgressMeter -            done    987038.0   102.0 s     103.0 s      100.0%   102.0 s       0.0 s
[2015-09-30T14:32Z] INFO  15:32:50,043 ProgressMeter - Total runtime 102.20 secs, 1.70 min, 0.03 hours
[2015-09-30T14:32Z] INFO  15:32:50,043 MicroScheduler - 2483 reads were filtered out during the traversal out of approximately 989521 total reads (0.25%)
[2015-09-30T14:32Z] INFO  15:32:50,043 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:32Z] INFO  15:32:50,043 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:32Z] INFO  15:32:50,044 MicroScheduler -   -> 2483 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:32Z] INFO  15:32:51,067 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:32Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam
[2015-09-30T14:32Z] INFO  15:32:53,483 ProgressMeter -      3:50645645   1.9148351E7    30.0 s       1.0 s       61.7%    48.0 s      18.0 s
[2015-09-30T14:32Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam 3:124626734-155649953
[2015-09-30T14:32Z] GATK: RealignerTargetCreator
[2015-09-30T14:32Z] INFO  15:32:54,327 ProgressMeter -     3:170826071    200004.0    30.0 s       2.5 m       48.8%    61.0 s      31.0 s
[2015-09-30T14:32Z] INFO  15:32:55,614 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:32Z] INFO  15:32:55,616 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:32Z] INFO  15:32:55,616 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:32Z] INFO  15:32:55,616 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:32Z] INFO  15:32:55,620 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpoRZJwk/1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign-realign.intervals -l INFO -L 3:124626734-155649953 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:32Z] INFO  15:32:55,625 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:32Z] INFO  15:32:55,626 HelpFormatter - Date/Time: 2015/09/30 15:32:55
[2015-09-30T14:32Z] INFO  15:32:55,626 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:32Z] INFO  15:32:55,626 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:32Z] INFO  15:32:55,683 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:32Z] INFO  15:32:55,799 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:32Z] INFO  15:32:55,807 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:32Z] INFO  15:32:55,822 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:32Z] INFO  15:32:56,084 IntervalUtils - Processing 31023220 bp from intervals
[2015-09-30T14:32Z] WARN  15:32:56,088 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:32Z] INFO  15:32:56,144 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:32Z] INFO  15:32:56,294 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:32Z] INFO  15:32:56,295 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:32Z] INFO  15:32:56,295 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:32Z] INFO  15:32:56,296 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:33Z] INFO  15:33:08,603 ProgressMeter -            done   3.102212E7    45.0 s       1.0 s      100.0%    45.0 s       0.0 s
[2015-09-30T14:33Z] INFO  15:33:08,603 ProgressMeter - Total runtime 45.12 secs, 0.75 min, 0.01 hours
[2015-09-30T14:33Z] INFO  15:33:08,607 MicroScheduler - 138556 reads were filtered out during the traversal out of approximately 1832468 total reads (7.56%)
[2015-09-30T14:33Z] INFO  15:33:08,607 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:33Z] INFO  15:33:08,607 MicroScheduler -   -> 16703 reads (0.91% of total) failing BadMateFilter
[2015-09-30T14:33Z] INFO  15:33:08,608 MicroScheduler -   -> 90452 reads (4.94% of total) failing DuplicateReadFilter
[2015-09-30T14:33Z] INFO  15:33:08,608 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:33Z] INFO  15:33:08,608 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:33Z] INFO  15:33:08,608 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:33Z] INFO  15:33:08,608 MicroScheduler -   -> 31401 reads (1.71% of total) failing MappingQualityZeroFilter
[2015-09-30T14:33Z] INFO  15:33:08,609 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:33Z] INFO  15:33:08,609 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:33Z] INFO  15:33:08,609 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:33Z] INFO  15:33:09,588 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:33Z] GATK: realign ('3', 31494593, 62516713) : syn3-normal
[2015-09-30T14:33Z] INFO  15:33:11,322 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:33Z] INFO  15:33:11,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:33Z] INFO  15:33:11,324 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:33Z] INFO  15:33:11,325 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:33Z] INFO  15:33:11,328 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign-realign.intervals -L 3:31494594-62516713 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpVWxZU_/1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam
[2015-09-30T14:33Z] INFO  15:33:11,334 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:33Z] INFO  15:33:11,334 HelpFormatter - Date/Time: 2015/09/30 15:33:11
[2015-09-30T14:33Z] INFO  15:33:11,334 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:33Z] INFO  15:33:11,335 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:33Z] INFO  15:33:11,461 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:33Z] INFO  15:33:11,531 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:33Z] INFO  15:33:11,539 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:33Z] INFO  15:33:11,555 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:33Z] INFO  15:33:11,794 IntervalUtils - Processing 31022120 bp from intervals
[2015-09-30T14:33Z] WARN  15:33:11,798 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:33Z] INFO  15:33:11,852 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:33Z] INFO  15:33:12,001 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:33Z] INFO  15:33:12,001 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:33Z] INFO  15:33:12,002 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:33Z] INFO  15:33:12,002 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:33Z] INFO  15:33:12,147 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:33Z] INFO  15:33:12,346 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:33Z] INFO  15:33:24,328 ProgressMeter -     3:184298050    500008.0    60.0 s     120.0 s       92.1%    65.0 s       5.0 s
[2015-09-30T14:33Z] INFO  15:33:26,298 ProgressMeter -     3:154886453   3.0251219E7    30.0 s       0.0 s       97.5%    30.0 s       0.0 s
[2015-09-30T14:33Z] INFO  15:33:27,179 ProgressMeter -            done   3.102322E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T14:33Z] INFO  15:33:27,179 ProgressMeter - Total runtime 30.88 secs, 0.51 min, 0.01 hours
[2015-09-30T14:33Z] INFO  15:33:27,182 MicroScheduler - 73929 reads were filtered out during the traversal out of approximately 993316 total reads (7.44%)
[2015-09-30T14:33Z] INFO  15:33:27,183 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:33Z] INFO  15:33:27,183 MicroScheduler -   -> 11274 reads (1.13% of total) failing BadMateFilter
[2015-09-30T14:33Z] INFO  15:33:27,183 MicroScheduler -   -> 44528 reads (4.48% of total) failing DuplicateReadFilter
[2015-09-30T14:33Z] INFO  15:33:27,184 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:33Z] INFO  15:33:27,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:33Z] INFO  15:33:27,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:33Z] INFO  15:33:27,184 MicroScheduler -   -> 18127 reads (1.82% of total) failing MappingQualityZeroFilter
[2015-09-30T14:33Z] INFO  15:33:27,184 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:33Z] INFO  15:33:27,185 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:33Z] INFO  15:33:27,185 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:33Z] INFO  15:33:28,159 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:33Z] GATK: realign ('3', 124626733, 155649953) : syn3-normal
[2015-09-30T14:33Z] INFO  15:33:29,860 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:33Z] INFO  15:33:29,862 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:33Z] INFO  15:33:29,862 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:33Z] INFO  15:33:29,862 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:33Z] INFO  15:33:29,866 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign-realign.intervals -L 3:124626734-155649953 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmppQGAkR/1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam
[2015-09-30T14:33Z] INFO  15:33:29,872 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:33Z] INFO  15:33:29,872 HelpFormatter - Date/Time: 2015/09/30 15:33:29
[2015-09-30T14:33Z] INFO  15:33:29,872 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:33Z] INFO  15:33:29,872 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:33Z] INFO  15:33:30,000 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:33Z] INFO  15:33:30,065 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:33Z] INFO  15:33:30,072 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:33Z] INFO  15:33:30,087 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:33Z] INFO  15:33:30,319 IntervalUtils - Processing 31023220 bp from intervals
[2015-09-30T14:33Z] WARN  15:33:30,322 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:33Z] INFO  15:33:30,378 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:33Z] INFO  15:33:30,527 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:33Z] INFO  15:33:30,528 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:33Z] INFO  15:33:30,528 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:33Z] INFO  15:33:30,529 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:33Z] INFO  15:33:30,679 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:33Z] INFO  15:33:30,866 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:33Z] INFO  15:33:35,343 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:33Z] INFO  15:33:35,423 ProgressMeter -            done    649060.0    71.0 s     109.0 s      100.0%    71.0 s       0.0 s
[2015-09-30T14:33Z] INFO  15:33:35,424 ProgressMeter - Total runtime 71.10 secs, 1.18 min, 0.02 hours
[2015-09-30T14:33Z] INFO  15:33:35,424 MicroScheduler - 1795 reads were filtered out during the traversal out of approximately 650855 total reads (0.28%)
[2015-09-30T14:33Z] INFO  15:33:35,424 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:33Z] INFO  15:33:35,425 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:33Z] INFO  15:33:35,425 MicroScheduler -   -> 1795 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:33Z] INFO  15:33:36,403 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:33Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam
[2015-09-30T14:33Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam 3:155652402-186761310
[2015-09-30T14:33Z] GATK: RealignerTargetCreator
[2015-09-30T14:33Z] INFO  15:33:41,145 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:33Z] INFO  15:33:41,147 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:33Z] INFO  15:33:41,147 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:33Z] INFO  15:33:41,147 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:33Z] INFO  15:33:41,151 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpRiVVHJ/1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign-realign.intervals -l INFO -L 3:155652402-186761310 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:33Z] INFO  15:33:41,157 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:33Z] INFO  15:33:41,157 HelpFormatter - Date/Time: 2015/09/30 15:33:41
[2015-09-30T14:33Z] INFO  15:33:41,157 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:33Z] INFO  15:33:41,157 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:33Z] INFO  15:33:41,225 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:33Z] INFO  15:33:41,349 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:33Z] INFO  15:33:41,357 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:33Z] INFO  15:33:41,372 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:33Z] INFO  15:33:42,089 IntervalUtils - Processing 31108909 bp from intervals
[2015-09-30T14:33Z] WARN  15:33:42,093 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:33Z] INFO  15:33:42,150 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:33Z] INFO  15:33:42,327 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:33Z] INFO  15:33:42,328 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:33Z] INFO  15:33:42,328 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:33Z] INFO  15:33:42,328 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:33Z] INFO  15:33:42,820 ProgressMeter -      3:41954149    300003.0    30.0 s     102.0 s       33.7%    88.0 s      58.0 s
[2015-09-30T14:34Z] INFO  15:34:01,492 ProgressMeter -     3:136139680    500023.0    30.0 s      61.0 s       37.1%    80.0 s      50.0 s
[2015-09-30T14:34Z] INFO  15:34:06,920 ProgressMeter -            done   3.1108909E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T14:34Z] INFO  15:34:06,921 ProgressMeter - Total runtime 24.59 secs, 0.41 min, 0.01 hours
[2015-09-30T14:34Z] INFO  15:34:06,924 MicroScheduler - 48137 reads were filtered out during the traversal out of approximately 653412 total reads (7.37%)
[2015-09-30T14:34Z] INFO  15:34:06,924 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:34Z] INFO  15:34:06,925 MicroScheduler -   -> 9274 reads (1.42% of total) failing BadMateFilter
[2015-09-30T14:34Z] INFO  15:34:06,925 MicroScheduler -   -> 27452 reads (4.20% of total) failing DuplicateReadFilter
[2015-09-30T14:34Z] INFO  15:34:06,925 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:34Z] INFO  15:34:06,925 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:34Z] INFO  15:34:06,926 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:34Z] INFO  15:34:06,926 MicroScheduler -   -> 11411 reads (1.75% of total) failing MappingQualityZeroFilter
[2015-09-30T14:34Z] INFO  15:34:06,926 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:34Z] INFO  15:34:06,926 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:34Z] INFO  15:34:06,927 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:34Z] INFO  15:34:08,022 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:34Z] GATK: realign ('3', 155652401, 186761310) : syn3-normal
[2015-09-30T14:34Z] INFO  15:34:09,721 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:09,723 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:34Z] INFO  15:34:09,723 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:34Z] INFO  15:34:09,723 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:34Z] INFO  15:34:09,726 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign-realign.intervals -L 3:155652402-186761310 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpERR0pl/1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam
[2015-09-30T14:34Z] INFO  15:34:09,732 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:34Z] INFO  15:34:09,732 HelpFormatter - Date/Time: 2015/09/30 15:34:09
[2015-09-30T14:34Z] INFO  15:34:09,732 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:09,732 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:09,857 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:34Z] INFO  15:34:09,918 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:34Z] INFO  15:34:09,925 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:34Z] INFO  15:34:09,940 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:34Z] INFO  15:34:10,173 IntervalUtils - Processing 31108909 bp from intervals
[2015-09-30T14:34Z] WARN  15:34:10,177 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:34Z] INFO  15:34:10,232 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:34Z] INFO  15:34:10,374 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:34Z] INFO  15:34:10,374 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:34Z] INFO  15:34:10,374 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:34Z] INFO  15:34:10,375 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:34Z] INFO  15:34:10,519 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:34Z] INFO  15:34:10,709 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:34Z] INFO  15:34:12,860 ProgressMeter -      3:49867019   1000013.0    60.0 s      60.0 s       59.2%   101.0 s      41.0 s
[2015-09-30T14:34Z] INFO  15:34:17,422 ProgressMeter -            done    987038.0    46.0 s      47.0 s      100.0%    46.0 s       0.0 s
[2015-09-30T14:34Z] INFO  15:34:17,422 ProgressMeter - Total runtime 46.89 secs, 0.78 min, 0.01 hours
[2015-09-30T14:34Z] INFO  15:34:17,425 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 987038 total reads (0.00%)
[2015-09-30T14:34Z] INFO  15:34:17,426 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:34Z] INFO  15:34:17,426 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:34Z] INFO  15:34:17,426 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:34Z] INFO  15:34:18,642 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:34Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam
[2015-09-30T14:34Z] GATK pre-alignment ('3', 186768753, 198022430) : syn3-normal
[2015-09-30T14:34Z] INFO  15:34:23,862 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:23,864 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:34Z] INFO  15:34:23,865 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:34Z] INFO  15:34:23,865 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:34Z] INFO  15:34:23,868 HelpFormatter - Program Args: -T PrintReads -L 3:186768754-198022430 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpNJEiym/1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam
[2015-09-30T14:34Z] INFO  15:34:23,873 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:34Z] INFO  15:34:23,874 HelpFormatter - Date/Time: 2015/09/30 15:34:23
[2015-09-30T14:34Z] INFO  15:34:23,874 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:23,874 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:23,979 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:34Z] INFO  15:34:25,088 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:34Z] INFO  15:34:25,138 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:34Z] INFO  15:34:25,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:34Z] INFO  15:34:25,161 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:34Z] INFO  15:34:25,174 IntervalUtils - Processing 11253677 bp from intervals
[2015-09-30T14:34Z] INFO  15:34:25,231 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:34Z] INFO  15:34:25,374 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:34Z] INFO  15:34:25,374 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:34Z] INFO  15:34:25,374 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:34Z] INFO  15:34:25,375 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:34Z] INFO  15:34:25,386 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:34Z] INFO  15:34:25,465 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:34Z] INFO  15:34:40,181 ProgressMeter -            done   1820958.0    88.0 s      48.0 s      100.0%    88.0 s       0.0 s
[2015-09-30T14:34Z] INFO  15:34:40,181 ProgressMeter - Total runtime 88.18 secs, 1.47 min, 0.02 hours
[2015-09-30T14:34Z] INFO  15:34:40,184 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1820958 total reads (0.00%)
[2015-09-30T14:34Z] INFO  15:34:40,185 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:34Z] INFO  15:34:40,185 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:34Z] INFO  15:34:40,185 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:34Z] INFO  15:34:41,302 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:34Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam
[2015-09-30T14:34Z] INFO  15:34:41,923 ProgressMeter -     3:186299874    600010.0    31.0 s      52.0 s       98.5%    31.0 s       0.0 s
[2015-09-30T14:34Z] INFO  15:34:43,028 ProgressMeter -            done    649060.0    32.0 s      50.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T14:34Z] INFO  15:34:43,028 ProgressMeter - Total runtime 32.65 secs, 0.54 min, 0.01 hours
[2015-09-30T14:34Z] INFO  15:34:43,032 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 649060 total reads (0.00%)
[2015-09-30T14:34Z] INFO  15:34:43,032 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:34Z] INFO  15:34:43,032 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:34Z] INFO  15:34:43,032 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:34Z] INFO  15:34:44,211 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:34Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam
[2015-09-30T14:34Z] GATK pre-alignment ('4', 0, 31018607) : syn3-normal
[2015-09-30T14:34Z] GATK pre-alignment ('4', 31031389, 62067173) : syn3-normal
[2015-09-30T14:34Z] INFO  15:34:47,779 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:47,782 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:34Z] INFO  15:34:47,782 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:34Z] INFO  15:34:47,782 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:34Z] INFO  15:34:47,786 HelpFormatter - Program Args: -T PrintReads -L 4:1-31018607 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmphxUg2C/1_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam
[2015-09-30T14:34Z] INFO  15:34:47,791 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:34Z] INFO  15:34:47,791 HelpFormatter - Date/Time: 2015/09/30 15:34:47
[2015-09-30T14:34Z] INFO  15:34:47,792 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:47,792 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:47,811 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:47,814 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:34Z] INFO  15:34:47,814 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:34Z] INFO  15:34:47,814 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:34Z] INFO  15:34:47,818 HelpFormatter - Program Args: -T PrintReads -L 4:31031390-62067173 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpRbZOB_/1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam
[2015-09-30T14:34Z] INFO  15:34:47,824 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:34Z] INFO  15:34:47,825 HelpFormatter - Date/Time: 2015/09/30 15:34:47
[2015-09-30T14:34Z] INFO  15:34:47,825 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:47,825 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:34Z] INFO  15:34:47,913 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:34Z] INFO  15:34:48,877 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:34Z] INFO  15:34:50,306 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:34Z] INFO  15:34:50,357 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:34Z] INFO  15:34:50,365 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:34Z] INFO  15:34:50,380 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:34Z] INFO  15:34:50,394 IntervalUtils - Processing 31018607 bp from intervals
[2015-09-30T14:34Z] INFO  15:34:50,554 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:34Z] INFO  15:34:50,606 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:34Z] INFO  15:34:50,614 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:34Z] INFO  15:34:50,630 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:34Z] INFO  15:34:50,644 IntervalUtils - Processing 31035784 bp from intervals
[2015-09-30T14:34Z] INFO  15:34:51,010 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:34Z] INFO  15:34:51,239 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:34Z] INFO  15:34:51,239 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:34Z] INFO  15:34:51,239 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:34Z] INFO  15:34:51,240 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:34Z] INFO  15:34:51,240 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:34Z] INFO  15:34:51,252 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:34Z] INFO  15:34:51,426 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:34Z] INFO  15:34:51,426 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:34Z] INFO  15:34:51,426 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:34Z] INFO  15:34:51,427 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:34Z] INFO  15:34:51,438 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:34Z] INFO  15:34:51,444 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:34Z] INFO  15:34:51,634 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:34Z] INFO  15:34:55,396 ProgressMeter -     3:195517161    200005.0    30.0 s       2.5 m       77.7%    38.0 s       8.0 s
[2015-09-30T14:35Z] INFO  15:35:09,492 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:35Z] INFO  15:35:09,587 ProgressMeter -            done    400596.0    44.0 s     110.0 s       99.4%    44.0 s       0.0 s
[2015-09-30T14:35Z] INFO  15:35:09,587 ProgressMeter - Total runtime 44.21 secs, 0.74 min, 0.01 hours
[2015-09-30T14:35Z] INFO  15:35:09,588 MicroScheduler - 845 reads were filtered out during the traversal out of approximately 401441 total reads (0.21%)
[2015-09-30T14:35Z] INFO  15:35:09,588 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:35Z] INFO  15:35:09,588 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:35Z] INFO  15:35:09,588 MicroScheduler -   -> 845 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:35Z] INFO  15:35:10,699 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:35Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam
[2015-09-30T14:35Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam 3:186768754-198022430
[2015-09-30T14:35Z] GATK: RealignerTargetCreator
[2015-09-30T14:35Z] INFO  15:35:14,018 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:14,020 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:35Z] INFO  15:35:14,020 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:35Z] INFO  15:35:14,020 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:35Z] INFO  15:35:14,023 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpJ1gt7V/1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign-realign.intervals -l INFO -L 3:186768754-198022430 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:35Z] INFO  15:35:14,029 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:35Z] INFO  15:35:14,029 HelpFormatter - Date/Time: 2015/09/30 15:35:14
[2015-09-30T14:35Z] INFO  15:35:14,029 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:14,029 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:14,083 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:35Z] INFO  15:35:14,184 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:35Z] INFO  15:35:14,191 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:35Z] INFO  15:35:14,206 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:35Z] INFO  15:35:14,969 IntervalUtils - Processing 11253677 bp from intervals
[2015-09-30T14:35Z] WARN  15:35:14,973 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:35Z] INFO  15:35:15,027 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:35Z] INFO  15:35:15,163 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:35Z] INFO  15:35:15,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:35Z] INFO  15:35:15,164 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:35Z] INFO  15:35:15,164 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:35Z] INFO  15:35:21,242 ProgressMeter -       4:2746248    200002.0    30.0 s       2.5 m        8.9%     5.6 m       5.1 m
[2015-09-30T14:35Z] INFO  15:35:21,429 ProgressMeter -      4:48574645    200002.0    30.0 s       2.5 m       56.5%    53.0 s      23.0 s
[2015-09-30T14:35Z] INFO  15:35:26,680 ProgressMeter -            done   1.1253677E7    11.0 s       1.0 s      100.0%    11.0 s       0.0 s
[2015-09-30T14:35Z] INFO  15:35:26,680 ProgressMeter - Total runtime 11.52 secs, 0.19 min, 0.00 hours
[2015-09-30T14:35Z] INFO  15:35:26,683 MicroScheduler - 43940 reads were filtered out during the traversal out of approximately 403619 total reads (10.89%)
[2015-09-30T14:35Z] INFO  15:35:26,683 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:35Z] INFO  15:35:26,684 MicroScheduler -   -> 4440 reads (1.10% of total) failing BadMateFilter
[2015-09-30T14:35Z] INFO  15:35:26,684 MicroScheduler -   -> 17918 reads (4.44% of total) failing DuplicateReadFilter
[2015-09-30T14:35Z] INFO  15:35:26,684 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:35Z] INFO  15:35:26,684 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:35Z] INFO  15:35:26,685 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:35Z] INFO  15:35:26,685 MicroScheduler -   -> 21582 reads (5.35% of total) failing MappingQualityZeroFilter
[2015-09-30T14:35Z] INFO  15:35:26,685 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:35Z] INFO  15:35:26,685 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:35Z] INFO  15:35:26,686 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:35Z] INFO  15:35:27,628 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:35Z] GATK: realign ('3', 186768753, 198022430) : syn3-normal
[2015-09-30T14:35Z] INFO  15:35:30,791 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:30,793 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:35Z] INFO  15:35:30,793 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:35Z] INFO  15:35:30,793 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:35Z] INFO  15:35:30,797 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign-realign.intervals -L 3:186768754-198022430 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/tx/tmpCKc0QG/1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam
[2015-09-30T14:35Z] INFO  15:35:30,802 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:35Z] INFO  15:35:30,802 HelpFormatter - Date/Time: 2015/09/30 15:35:30
[2015-09-30T14:35Z] INFO  15:35:30,802 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:30,802 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:30,919 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:35Z] INFO  15:35:30,980 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:35Z] INFO  15:35:30,988 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:35Z] INFO  15:35:31,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:35Z] INFO  15:35:31,224 IntervalUtils - Processing 11253677 bp from intervals
[2015-09-30T14:35Z] WARN  15:35:31,228 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:35Z] INFO  15:35:31,282 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:35Z] INFO  15:35:31,612 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:35Z] INFO  15:35:31,612 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:35Z] INFO  15:35:31,613 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:35Z] INFO  15:35:31,613 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:35Z] INFO  15:35:31,719 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:35Z] INFO  15:35:31,802 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:35Z] INFO  15:35:34,765 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:35Z] INFO  15:35:34,832 ProgressMeter -            done    451257.0    43.0 s      96.0 s      100.0%    43.0 s       0.0 s
[2015-09-30T14:35Z] INFO  15:35:34,832 ProgressMeter - Total runtime 43.41 secs, 0.72 min, 0.01 hours
[2015-09-30T14:35Z] INFO  15:35:34,833 MicroScheduler - 2350 reads were filtered out during the traversal out of approximately 453607 total reads (0.52%)
[2015-09-30T14:35Z] INFO  15:35:34,833 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:35Z] INFO  15:35:34,833 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:35Z] INFO  15:35:34,833 MicroScheduler -   -> 2350 reads (0.52% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:35Z] INFO  15:35:35,977 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:35Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam
[2015-09-30T14:35Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam 4:31031390-62067173
[2015-09-30T14:35Z] GATK: RealignerTargetCreator
[2015-09-30T14:35Z] INFO  15:35:39,100 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:39,102 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:35Z] INFO  15:35:39,102 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:35Z] INFO  15:35:39,102 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:35Z] INFO  15:35:39,106 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmp0T7rCR/1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign-realign.intervals -l INFO -L 4:31031390-62067173 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:35Z] INFO  15:35:39,112 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:35Z] INFO  15:35:39,112 HelpFormatter - Date/Time: 2015/09/30 15:35:39
[2015-09-30T14:35Z] INFO  15:35:39,112 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:39,112 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:39,183 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:35Z] INFO  15:35:39,828 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:35Z] INFO  15:35:39,836 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:35Z] INFO  15:35:39,853 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:35Z] INFO  15:35:40,109 IntervalUtils - Processing 31035784 bp from intervals
[2015-09-30T14:35Z] WARN  15:35:40,113 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:35Z] INFO  15:35:40,172 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:35Z] INFO  15:35:40,306 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:35Z] INFO  15:35:40,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:35Z] INFO  15:35:40,307 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:35Z] INFO  15:35:40,307 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:35Z] INFO  15:35:51,243 ProgressMeter -       4:8288445    500006.0    60.0 s     120.0 s       26.7%     3.7 m       2.7 m
[2015-09-30T14:35Z] INFO  15:35:53,114 ProgressMeter -            done    400596.0    21.0 s      53.0 s       99.4%    21.0 s       0.0 s
[2015-09-30T14:35Z] INFO  15:35:53,114 ProgressMeter - Total runtime 21.50 secs, 0.36 min, 0.01 hours
[2015-09-30T14:35Z] INFO  15:35:53,117 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 400596 total reads (0.00%)
[2015-09-30T14:35Z] INFO  15:35:53,118 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:35Z] INFO  15:35:53,118 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:35Z] INFO  15:35:53,118 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:35Z] INFO  15:35:54,303 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:35Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam
[2015-09-30T14:35Z] GATK pre-alignment ('4', 62292837, 93511697) : syn3-normal
[2015-09-30T14:35Z] INFO  15:35:57,891 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:57,893 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:35Z] INFO  15:35:57,893 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:35Z] INFO  15:35:57,893 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:35Z] INFO  15:35:57,897 HelpFormatter - Program Args: -T PrintReads -L 4:62292838-93511697 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmp4K6kzA/1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam
[2015-09-30T14:35Z] INFO  15:35:57,907 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:35Z] INFO  15:35:57,907 HelpFormatter - Date/Time: 2015/09/30 15:35:57
[2015-09-30T14:35Z] INFO  15:35:57,908 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:57,908 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:35Z] INFO  15:35:58,042 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:35Z] INFO  15:35:59,264 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:35Z] INFO  15:35:59,313 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:35Z] INFO  15:35:59,321 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:35Z] INFO  15:35:59,336 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:35Z] INFO  15:35:59,349 IntervalUtils - Processing 31218860 bp from intervals
[2015-09-30T14:35Z] INFO  15:35:59,408 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:35Z] INFO  15:35:59,600 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:35Z] INFO  15:35:59,600 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:35Z] INFO  15:35:59,600 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:35Z] INFO  15:35:59,601 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:35Z] INFO  15:35:59,612 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:35Z] INFO  15:35:59,807 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:36Z] INFO  15:36:01,736 ProgressMeter -            done   3.1035784E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T14:36Z] INFO  15:36:01,736 ProgressMeter - Total runtime 21.43 secs, 0.36 min, 0.01 hours
[2015-09-30T14:36Z] INFO  15:36:01,739 MicroScheduler - 38480 reads were filtered out during the traversal out of approximately 454088 total reads (8.47%)
[2015-09-30T14:36Z] INFO  15:36:01,739 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:36Z] INFO  15:36:01,740 MicroScheduler -   -> 8554 reads (1.88% of total) failing BadMateFilter
[2015-09-30T14:36Z] INFO  15:36:01,740 MicroScheduler -   -> 18089 reads (3.98% of total) failing DuplicateReadFilter
[2015-09-30T14:36Z] INFO  15:36:01,740 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:36Z] INFO  15:36:01,740 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:36Z] INFO  15:36:01,741 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:36Z] INFO  15:36:01,741 MicroScheduler -   -> 11837 reads (2.61% of total) failing MappingQualityZeroFilter
[2015-09-30T14:36Z] INFO  15:36:01,741 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:36Z] INFO  15:36:01,741 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:36Z] INFO  15:36:01,742 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:36Z] INFO  15:36:03,037 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:36Z] GATK: realign ('4', 31031389, 62067173) : syn3-normal
[2015-09-30T14:36Z] INFO  15:36:05,207 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:05,209 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:36Z] INFO  15:36:05,209 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:36Z] INFO  15:36:05,209 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:36Z] INFO  15:36:05,212 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign-realign.intervals -L 4:31031390-62067173 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpgAQBbV/1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam
[2015-09-30T14:36Z] INFO  15:36:05,218 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:36Z] INFO  15:36:05,218 HelpFormatter - Date/Time: 2015/09/30 15:36:05
[2015-09-30T14:36Z] INFO  15:36:05,218 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:05,218 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:05,339 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:36Z] INFO  15:36:05,633 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:36Z] INFO  15:36:05,641 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:36Z] INFO  15:36:05,656 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:36Z] INFO  15:36:05,875 IntervalUtils - Processing 31035784 bp from intervals
[2015-09-30T14:36Z] WARN  15:36:05,879 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:36Z] INFO  15:36:05,933 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:36Z] INFO  15:36:06,070 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:36Z] INFO  15:36:06,071 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:36Z] INFO  15:36:06,071 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:36Z] INFO  15:36:06,072 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:36Z] INFO  15:36:06,209 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:36Z] INFO  15:36:06,386 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:36Z] INFO  15:36:15,591 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:36Z] INFO  15:36:15,788 ProgressMeter -            done    923754.0    84.0 s      91.0 s      100.0%    84.0 s       0.0 s
[2015-09-30T14:36Z] INFO  15:36:15,789 ProgressMeter - Total runtime 84.55 secs, 1.41 min, 0.02 hours
[2015-09-30T14:36Z] INFO  15:36:15,789 MicroScheduler - 1846 reads were filtered out during the traversal out of approximately 925600 total reads (0.20%)
[2015-09-30T14:36Z] INFO  15:36:15,789 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:36Z] INFO  15:36:15,790 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:36Z] INFO  15:36:15,790 MicroScheduler -   -> 1846 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:36Z] INFO  15:36:17,010 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:36Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam
[2015-09-30T14:36Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam 4:1-31018607
[2015-09-30T14:36Z] GATK: RealignerTargetCreator
[2015-09-30T14:36Z] INFO  15:36:21,550 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:21,553 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:36Z] INFO  15:36:21,553 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:36Z] INFO  15:36:21,553 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:36Z] INFO  15:36:21,556 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmp8fR8lU/1_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign-realign.intervals -l INFO -L 4:1-31018607 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:36Z] INFO  15:36:21,562 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:36Z] INFO  15:36:21,563 HelpFormatter - Date/Time: 2015/09/30 15:36:21
[2015-09-30T14:36Z] INFO  15:36:21,563 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:21,563 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:21,617 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:36Z] INFO  15:36:21,725 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:36Z] INFO  15:36:21,733 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:36Z] INFO  15:36:21,748 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:36Z] INFO  15:36:21,994 IntervalUtils - Processing 31018607 bp from intervals
[2015-09-30T14:36Z] WARN  15:36:21,998 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:36Z] INFO  15:36:22,050 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:36Z] INFO  15:36:22,185 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:36Z] INFO  15:36:22,185 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:36Z] INFO  15:36:22,186 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:36Z] INFO  15:36:22,186 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:36Z] INFO  15:36:29,609 ProgressMeter -      4:76851489    200002.0    30.0 s       2.5 m       46.6%    64.0 s      34.0 s
[2015-09-30T14:36Z] INFO  15:36:29,617 ProgressMeter -            done    451257.0    23.0 s      52.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T14:36Z] INFO  15:36:29,618 ProgressMeter - Total runtime 23.55 secs, 0.39 min, 0.01 hours
[2015-09-30T14:36Z] INFO  15:36:29,621 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 451257 total reads (0.00%)
[2015-09-30T14:36Z] INFO  15:36:29,621 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:36Z] INFO  15:36:29,621 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:36Z] INFO  15:36:29,622 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:36Z] INFO  15:36:30,777 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:36Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam
[2015-09-30T14:36Z] GATK pre-alignment ('4', 94005855, 125588163) : syn3-normal
[2015-09-30T14:36Z] INFO  15:36:35,809 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:35,811 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:36Z] INFO  15:36:35,811 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:36Z] INFO  15:36:35,812 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:36Z] INFO  15:36:35,815 HelpFormatter - Program Args: -T PrintReads -L 4:94005856-125588163 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmplCUA8i/1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam
[2015-09-30T14:36Z] INFO  15:36:35,821 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:36Z] INFO  15:36:35,821 HelpFormatter - Date/Time: 2015/09/30 15:36:35
[2015-09-30T14:36Z] INFO  15:36:35,821 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:35,821 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:36,660 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:36Z] INFO  15:36:37,404 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:36Z] INFO  15:36:37,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:36Z] INFO  15:36:37,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:36Z] INFO  15:36:37,480 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:36Z] INFO  15:36:37,493 IntervalUtils - Processing 31582308 bp from intervals
[2015-09-30T14:36Z] INFO  15:36:37,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:36Z] INFO  15:36:37,752 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:36Z] INFO  15:36:37,752 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:36Z] INFO  15:36:37,752 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:36Z] INFO  15:36:37,753 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:36Z] INFO  15:36:37,764 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:36Z] INFO  15:36:37,970 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:36Z] INFO  15:36:52,188 ProgressMeter -      4:30788937   3.0785536E7    30.0 s       0.0 s       99.3%    30.0 s       0.0 s
[2015-09-30T14:36Z] INFO  15:36:52,534 ProgressMeter -            done   3.1018607E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T14:36Z] INFO  15:36:52,535 ProgressMeter - Total runtime 30.35 secs, 0.51 min, 0.01 hours
[2015-09-30T14:36Z] INFO  15:36:52,538 MicroScheduler - 82502 reads were filtered out during the traversal out of approximately 929040 total reads (8.88%)
[2015-09-30T14:36Z] INFO  15:36:52,538 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:36Z] INFO  15:36:52,539 MicroScheduler -   -> 10703 reads (1.15% of total) failing BadMateFilter
[2015-09-30T14:36Z] INFO  15:36:52,539 MicroScheduler -   -> 45850 reads (4.94% of total) failing DuplicateReadFilter
[2015-09-30T14:36Z] INFO  15:36:52,539 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:36Z] INFO  15:36:52,539 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:36Z] INFO  15:36:52,540 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:36Z] INFO  15:36:52,540 MicroScheduler -   -> 25949 reads (2.79% of total) failing MappingQualityZeroFilter
[2015-09-30T14:36Z] INFO  15:36:52,540 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:36Z] INFO  15:36:52,540 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:36Z] INFO  15:36:52,540 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:36Z] INFO  15:36:53,499 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:36Z] GATK: realign ('4', 0, 31018607) : syn3-normal
[2015-09-30T14:36Z] INFO  15:36:55,889 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:55,891 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:36Z] INFO  15:36:55,892 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:36Z] INFO  15:36:55,892 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:36Z] INFO  15:36:55,895 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign-realign.intervals -L 4:1-31018607 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpeBT4Y4/1_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam
[2015-09-30T14:36Z] INFO  15:36:55,901 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:36Z] INFO  15:36:55,901 HelpFormatter - Date/Time: 2015/09/30 15:36:55
[2015-09-30T14:36Z] INFO  15:36:55,901 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:55,901 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:36Z] INFO  15:36:56,031 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:36Z] INFO  15:36:56,095 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:36Z] INFO  15:36:56,103 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:36Z] INFO  15:36:56,119 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:36Z] INFO  15:36:56,838 IntervalUtils - Processing 31018607 bp from intervals
[2015-09-30T14:36Z] WARN  15:36:56,841 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:36Z] INFO  15:36:56,897 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:36Z] INFO  15:36:57,034 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:36Z] INFO  15:36:57,034 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:36Z] INFO  15:36:57,035 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:36Z] INFO  15:36:57,035 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:36Z] INFO  15:36:57,179 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:36Z] INFO  15:36:57,366 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:36Z] INFO  15:36:59,610 ProgressMeter -      4:89183430    500010.0    60.0 s     120.0 s       86.1%    69.0 s       9.0 s
[2015-09-30T14:37Z] INFO  15:37:04,220 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:37Z] INFO  15:37:04,391 ProgressMeter -            done    627350.0    64.0 s     103.0 s      100.0%    64.0 s       0.0 s
[2015-09-30T14:37Z] INFO  15:37:04,392 ProgressMeter - Total runtime 64.79 secs, 1.08 min, 0.02 hours
[2015-09-30T14:37Z] INFO  15:37:04,392 MicroScheduler - 1953 reads were filtered out during the traversal out of approximately 629303 total reads (0.31%)
[2015-09-30T14:37Z] INFO  15:37:04,392 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:37Z] INFO  15:37:04,393 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:37Z] INFO  15:37:04,393 MicroScheduler -   -> 1953 reads (0.31% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:37Z] INFO  15:37:05,425 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:37Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam
[2015-09-30T14:37Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam 4:62292838-93511697
[2015-09-30T14:37Z] GATK: RealignerTargetCreator
[2015-09-30T14:37Z] INFO  15:37:07,755 ProgressMeter -     4:109762843    200003.0    30.0 s       2.5 m       49.9%    60.0 s      30.0 s
[2015-09-30T14:37Z] INFO  15:37:09,191 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:09,193 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:37Z] INFO  15:37:09,193 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:37Z] INFO  15:37:09,193 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:37Z] INFO  15:37:09,197 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmp4dTeHb/1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign-realign.intervals -l INFO -L 4:62292838-93511697 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:37Z] INFO  15:37:09,202 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:37Z] INFO  15:37:09,202 HelpFormatter - Date/Time: 2015/09/30 15:37:09
[2015-09-30T14:37Z] INFO  15:37:09,202 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:09,203 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:09,258 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:37Z] INFO  15:37:09,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:37Z] INFO  15:37:09,368 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:37Z] INFO  15:37:09,383 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:37Z] INFO  15:37:09,926 IntervalUtils - Processing 31218860 bp from intervals
[2015-09-30T14:37Z] WARN  15:37:09,929 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:37Z] INFO  15:37:09,986 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:37Z] INFO  15:37:10,140 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:37Z] INFO  15:37:10,140 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:37Z] INFO  15:37:10,140 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:37Z] INFO  15:37:10,141 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:37Z] INFO  15:37:27,037 ProgressMeter -       4:8288445    500006.0    30.0 s      60.0 s       26.7%   112.0 s      82.0 s
[2015-09-30T14:37Z] INFO  15:37:30,846 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:37Z] INFO  15:37:30,969 ProgressMeter -            done    487976.0    53.0 s     109.0 s      100.0%    53.0 s       0.0 s
[2015-09-30T14:37Z] INFO  15:37:30,969 ProgressMeter - Total runtime 53.22 secs, 0.89 min, 0.01 hours
[2015-09-30T14:37Z] INFO  15:37:30,969 MicroScheduler - 1666 reads were filtered out during the traversal out of approximately 489642 total reads (0.34%)
[2015-09-30T14:37Z] INFO  15:37:30,970 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:37Z] INFO  15:37:30,970 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:37Z] INFO  15:37:30,970 MicroScheduler -   -> 1666 reads (0.34% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:37Z] INFO  15:37:31,986 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:37Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam
[2015-09-30T14:37Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam 4:94005856-125588163
[2015-09-30T14:37Z] GATK: RealignerTargetCreator
[2015-09-30T14:37Z] INFO  15:37:35,272 ProgressMeter -            done   3.121886E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T14:37Z] INFO  15:37:35,272 ProgressMeter - Total runtime 25.13 secs, 0.42 min, 0.01 hours
[2015-09-30T14:37Z] INFO  15:37:35,275 MicroScheduler - 46545 reads were filtered out during the traversal out of approximately 631104 total reads (7.38%)
[2015-09-30T14:37Z] INFO  15:37:35,276 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:37Z] INFO  15:37:35,276 MicroScheduler -   -> 8898 reads (1.41% of total) failing BadMateFilter
[2015-09-30T14:37Z] INFO  15:37:35,276 MicroScheduler -   -> 24616 reads (3.90% of total) failing DuplicateReadFilter
[2015-09-30T14:37Z] INFO  15:37:35,277 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:37Z] INFO  15:37:35,277 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:37Z] INFO  15:37:35,277 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:37Z] INFO  15:37:35,277 MicroScheduler -   -> 13031 reads (2.06% of total) failing MappingQualityZeroFilter
[2015-09-30T14:37Z] INFO  15:37:35,277 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:37Z] INFO  15:37:35,278 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:37Z] INFO  15:37:35,278 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:37Z] INFO  15:37:35,995 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:35,997 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:37Z] INFO  15:37:35,997 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:37Z] INFO  15:37:35,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:37Z] INFO  15:37:36,001 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpenJVyO/1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign-realign.intervals -l INFO -L 4:94005856-125588163 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:37Z] INFO  15:37:36,006 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:37Z] INFO  15:37:36,006 HelpFormatter - Date/Time: 2015/09/30 15:37:35
[2015-09-30T14:37Z] INFO  15:37:36,007 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:36,007 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:36,062 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:37Z] INFO  15:37:36,169 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:37Z] INFO  15:37:36,176 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:37Z] INFO  15:37:36,191 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:37Z] INFO  15:37:36,276 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:37Z] INFO  15:37:36,880 IntervalUtils - Processing 31582308 bp from intervals
[2015-09-30T14:37Z] WARN  15:37:36,884 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:37Z] GATK: realign ('4', 62292837, 93511697) : syn3-normal
[2015-09-30T14:37Z] INFO  15:37:36,938 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:37Z] INFO  15:37:37,381 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:37Z] INFO  15:37:37,382 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:37Z] INFO  15:37:37,382 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:37Z] INFO  15:37:37,383 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:37Z] INFO  15:37:38,658 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:38,660 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:37Z] INFO  15:37:38,660 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:37Z] INFO  15:37:38,660 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:37Z] INFO  15:37:38,664 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign-realign.intervals -L 4:62292838-93511697 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpVHldfL/1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam
[2015-09-30T14:37Z] INFO  15:37:38,669 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:37Z] INFO  15:37:38,669 HelpFormatter - Date/Time: 2015/09/30 15:37:38
[2015-09-30T14:37Z] INFO  15:37:38,669 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:38,669 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:38,791 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:37Z] INFO  15:37:38,853 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:37Z] INFO  15:37:38,860 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:37Z] INFO  15:37:38,876 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:37Z] INFO  15:37:39,102 IntervalUtils - Processing 31218860 bp from intervals
[2015-09-30T14:37Z] WARN  15:37:39,106 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:37Z] INFO  15:37:39,161 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:37Z] INFO  15:37:39,299 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:37Z] INFO  15:37:39,300 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:37Z] INFO  15:37:39,300 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:37Z] INFO  15:37:39,300 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:37Z] INFO  15:37:39,450 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:37Z] INFO  15:37:39,636 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:37Z] INFO  15:37:40,347 ProgressMeter -            done    923754.0    43.0 s      46.0 s      100.0%    43.0 s       0.0 s
[2015-09-30T14:37Z] INFO  15:37:40,347 ProgressMeter - Total runtime 43.31 secs, 0.72 min, 0.01 hours
[2015-09-30T14:37Z] INFO  15:37:40,350 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 923754 total reads (0.00%)
[2015-09-30T14:37Z] INFO  15:37:40,351 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:37Z] INFO  15:37:40,351 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:37Z] INFO  15:37:40,351 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:37Z] INFO  15:37:41,472 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:37Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam
[2015-09-30T14:37Z] GATK pre-alignment ('4', 125589908, 156618518) : syn3-normal
[2015-09-30T14:37Z] INFO  15:37:45,824 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:45,826 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:37Z] INFO  15:37:45,826 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:37Z] INFO  15:37:45,826 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:37Z] INFO  15:37:45,830 HelpFormatter - Program Args: -T PrintReads -L 4:125589909-156618518 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpig8mbZ/1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam
[2015-09-30T14:37Z] INFO  15:37:45,835 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:37Z] INFO  15:37:45,835 HelpFormatter - Date/Time: 2015/09/30 15:37:45
[2015-09-30T14:37Z] INFO  15:37:45,836 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:45,836 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:37Z] INFO  15:37:45,937 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:37Z] INFO  15:37:47,215 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:37Z] INFO  15:37:47,264 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:37Z] INFO  15:37:47,271 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:37Z] INFO  15:37:47,285 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:37Z] INFO  15:37:47,298 IntervalUtils - Processing 31028610 bp from intervals
[2015-09-30T14:37Z] INFO  15:37:47,356 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:37Z] INFO  15:37:47,550 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:37Z] INFO  15:37:47,550 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:37Z] INFO  15:37:47,550 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:37Z] INFO  15:37:47,550 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:37Z] INFO  15:37:47,562 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:37Z] INFO  15:37:47,752 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:38Z] INFO  15:38:00,370 ProgressMeter -            done   3.1582308E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T14:38Z] INFO  15:38:00,371 ProgressMeter - Total runtime 22.99 secs, 0.38 min, 0.01 hours
[2015-09-30T14:38Z] INFO  15:38:00,374 MicroScheduler - 36421 reads were filtered out during the traversal out of approximately 490696 total reads (7.42%)
[2015-09-30T14:38Z] INFO  15:38:00,374 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:38Z] INFO  15:38:00,375 MicroScheduler -   -> 7795 reads (1.59% of total) failing BadMateFilter
[2015-09-30T14:38Z] INFO  15:38:00,375 MicroScheduler -   -> 18565 reads (3.78% of total) failing DuplicateReadFilter
[2015-09-30T14:38Z] INFO  15:38:00,375 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:38Z] INFO  15:38:00,375 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:38Z] INFO  15:38:00,375 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:38Z] INFO  15:38:00,376 MicroScheduler -   -> 10061 reads (2.05% of total) failing MappingQualityZeroFilter
[2015-09-30T14:38Z] INFO  15:38:00,376 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:38Z] INFO  15:38:00,376 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:38Z] INFO  15:38:00,376 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:38Z] INFO  15:38:01,502 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:38Z] GATK: realign ('4', 94005855, 125588163) : syn3-normal
[2015-09-30T14:38Z] INFO  15:38:03,378 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:03,380 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:38Z] INFO  15:38:03,381 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:38Z] INFO  15:38:03,381 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:38Z] INFO  15:38:03,384 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign-realign.intervals -L 4:94005856-125588163 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmp6SiZut/1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam
[2015-09-30T14:38Z] INFO  15:38:03,390 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:38Z] INFO  15:38:03,390 HelpFormatter - Date/Time: 2015/09/30 15:38:03
[2015-09-30T14:38Z] INFO  15:38:03,390 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:03,390 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:03,515 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:38Z] INFO  15:38:03,581 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:38Z] INFO  15:38:03,589 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:38Z] INFO  15:38:03,603 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:38Z] INFO  15:38:03,822 IntervalUtils - Processing 31582308 bp from intervals
[2015-09-30T14:38Z] WARN  15:38:03,826 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:38Z] INFO  15:38:03,876 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:38Z] INFO  15:38:04,014 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:38Z] INFO  15:38:04,015 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:38Z] INFO  15:38:04,015 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:38Z] INFO  15:38:04,015 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:38Z] INFO  15:38:04,159 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:38Z] INFO  15:38:04,346 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:38Z] INFO  15:38:09,303 ProgressMeter -      4:88053445    500010.0    30.0 s      60.0 s       82.5%    36.0 s       6.0 s
[2015-09-30T14:38Z] INFO  15:38:12,381 ProgressMeter -            done    627350.0    33.0 s      52.0 s      100.0%    33.0 s       0.0 s
[2015-09-30T14:38Z] INFO  15:38:12,381 ProgressMeter - Total runtime 33.08 secs, 0.55 min, 0.01 hours
[2015-09-30T14:38Z] INFO  15:38:12,385 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 627350 total reads (0.00%)
[2015-09-30T14:38Z] INFO  15:38:12,385 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:38Z] INFO  15:38:12,385 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:38Z] INFO  15:38:12,386 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:38Z] INFO  15:38:13,396 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:38Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam
[2015-09-30T14:38Z] GATK pre-alignment ('4', 156624795, 188926424) : syn3-normal
[2015-09-30T14:38Z] INFO  15:38:17,580 ProgressMeter -     4:151174302    200002.0    30.0 s       2.5 m       82.5%    36.0 s       6.0 s
[2015-09-30T14:38Z] INFO  15:38:17,606 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:17,608 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:38Z] INFO  15:38:17,608 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:38Z] INFO  15:38:17,608 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:38Z] INFO  15:38:17,612 HelpFormatter - Program Args: -T PrintReads -L 4:156624796-188926424 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpzetOh5/1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam
[2015-09-30T14:38Z] INFO  15:38:17,617 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:38Z] INFO  15:38:17,618 HelpFormatter - Date/Time: 2015/09/30 15:38:17
[2015-09-30T14:38Z] INFO  15:38:17,618 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:17,618 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:17,733 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:38Z] INFO  15:38:18,717 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:38Z] INFO  15:38:18,768 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:38Z] INFO  15:38:18,775 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:38Z] INFO  15:38:18,790 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:38Z] INFO  15:38:18,804 IntervalUtils - Processing 32301629 bp from intervals
[2015-09-30T14:38Z] INFO  15:38:18,862 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:38Z] INFO  15:38:19,051 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:38Z] INFO  15:38:19,052 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:38Z] INFO  15:38:19,052 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:38Z] INFO  15:38:19,052 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:38Z] INFO  15:38:19,064 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:38Z] INFO  15:38:19,257 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:38Z] INFO  15:38:28,811 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:38Z] INFO  15:38:28,896 ProgressMeter -            done    398767.0    41.0 s     103.0 s      100.0%    41.0 s       0.0 s
[2015-09-30T14:38Z] INFO  15:38:28,896 ProgressMeter - Total runtime 41.35 secs, 0.69 min, 0.01 hours
[2015-09-30T14:38Z] INFO  15:38:28,896 MicroScheduler - 1455 reads were filtered out during the traversal out of approximately 400222 total reads (0.36%)
[2015-09-30T14:38Z] INFO  15:38:28,897 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:38Z] INFO  15:38:28,897 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:38Z] INFO  15:38:28,897 MicroScheduler -   -> 1455 reads (0.36% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:38Z] INFO  15:38:29,972 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:38Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam
[2015-09-30T14:38Z] INFO  15:38:30,767 ProgressMeter -            done    487976.0    26.0 s      54.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T14:38Z] INFO  15:38:30,767 ProgressMeter - Total runtime 26.75 secs, 0.45 min, 0.01 hours
[2015-09-30T14:38Z] INFO  15:38:30,771 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 487976 total reads (0.00%)
[2015-09-30T14:38Z] INFO  15:38:30,771 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:38Z] INFO  15:38:30,771 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:38Z] INFO  15:38:30,771 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:38Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam 4:125589909-156618518
[2015-09-30T14:38Z] GATK: RealignerTargetCreator
[2015-09-30T14:38Z] INFO  15:38:31,933 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:38Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam
[2015-09-30T14:38Z] GATK pre-alignment ('4', 189012293, 191154276) : syn3-normal
[2015-09-30T14:38Z] INFO  15:38:35,619 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:35,621 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:38Z] INFO  15:38:35,621 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:38Z] INFO  15:38:35,622 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:38Z] INFO  15:38:35,625 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpnOHwK8/1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign-realign.intervals -l INFO -L 4:125589909-156618518 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:38Z] INFO  15:38:35,631 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:38Z] INFO  15:38:35,631 HelpFormatter - Date/Time: 2015/09/30 15:38:35
[2015-09-30T14:38Z] INFO  15:38:35,631 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:35,632 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:35,690 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:38Z] INFO  15:38:35,762 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:35,764 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:38Z] INFO  15:38:35,765 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:38Z] INFO  15:38:35,765 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:38Z] INFO  15:38:35,768 HelpFormatter - Program Args: -T PrintReads -L 4:189012294-191154276 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpJLvDJ3/1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam
[2015-09-30T14:38Z] INFO  15:38:35,774 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:38Z] INFO  15:38:35,774 HelpFormatter - Date/Time: 2015/09/30 15:38:35
[2015-09-30T14:38Z] INFO  15:38:35,774 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:35,775 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:35,797 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:38Z] INFO  15:38:35,804 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:38Z] INFO  15:38:35,821 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:38Z] INFO  15:38:35,886 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:38Z] INFO  15:38:36,067 IntervalUtils - Processing 31028610 bp from intervals
[2015-09-30T14:38Z] WARN  15:38:36,071 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:38Z] INFO  15:38:36,129 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:38Z] INFO  15:38:36,274 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:38Z] INFO  15:38:36,274 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:38Z] INFO  15:38:36,275 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:38Z] INFO  15:38:36,275 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:38Z] INFO  15:38:36,603 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:38Z] INFO  15:38:36,654 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:38Z] INFO  15:38:36,662 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:38Z] INFO  15:38:36,677 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:38Z] INFO  15:38:36,691 IntervalUtils - Processing 2141983 bp from intervals
[2015-09-30T14:38Z] INFO  15:38:36,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:38Z] INFO  15:38:36,861 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:38Z] INFO  15:38:36,861 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:38Z] INFO  15:38:36,861 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:38Z] INFO  15:38:36,862 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:38Z] INFO  15:38:36,873 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:38Z] INFO  15:38:36,889 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:38Z] INFO  15:38:40,680 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:38Z] INFO  15:38:40,736 ProgressMeter -            done     21296.0     3.0 s       3.0 m       93.4%     3.0 s       0.0 s
[2015-09-30T14:38Z] INFO  15:38:40,737 ProgressMeter - Total runtime 3.88 secs, 0.06 min, 0.00 hours
[2015-09-30T14:38Z] INFO  15:38:40,737 MicroScheduler - 133 reads were filtered out during the traversal out of approximately 21429 total reads (0.62%)
[2015-09-30T14:38Z] INFO  15:38:40,737 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:38Z] INFO  15:38:40,738 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:38Z] INFO  15:38:40,738 MicroScheduler -   -> 133 reads (0.62% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:38Z] INFO  15:38:41,823 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:38Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam
[2015-09-30T14:38Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam 4:189012294-191154276
[2015-09-30T14:38Z] GATK: RealignerTargetCreator
[2015-09-30T14:38Z] INFO  15:38:44,064 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:44,066 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:38Z] INFO  15:38:44,066 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:38Z] INFO  15:38:44,066 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:38Z] INFO  15:38:44,070 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpjvqTAk/1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign-realign.intervals -l INFO -L 4:189012294-191154276 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:38Z] INFO  15:38:44,075 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:38Z] INFO  15:38:44,076 HelpFormatter - Date/Time: 2015/09/30 15:38:44
[2015-09-30T14:38Z] INFO  15:38:44,076 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:44,076 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:44,144 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:38Z] INFO  15:38:45,163 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:38Z] INFO  15:38:45,171 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:38Z] INFO  15:38:45,188 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:38Z] INFO  15:38:45,444 IntervalUtils - Processing 2141983 bp from intervals
[2015-09-30T14:38Z] WARN  15:38:45,448 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:38Z] INFO  15:38:45,508 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:38Z] INFO  15:38:45,547 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:38Z] INFO  15:38:45,548 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:38Z] INFO  15:38:45,548 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:38Z] INFO  15:38:45,548 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:38Z] INFO  15:38:48,134 ProgressMeter -            done   2141983.0     2.0 s       1.0 s      100.0%     2.0 s       0.0 s
[2015-09-30T14:38Z] INFO  15:38:48,135 ProgressMeter - Total runtime 2.59 secs, 0.04 min, 0.00 hours
[2015-09-30T14:38Z] INFO  15:38:48,138 MicroScheduler - 5657 reads were filtered out during the traversal out of approximately 21482 total reads (26.33%)
[2015-09-30T14:38Z] INFO  15:38:48,138 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:38Z] INFO  15:38:48,138 MicroScheduler -   -> 715 reads (3.33% of total) failing BadMateFilter
[2015-09-30T14:38Z] INFO  15:38:48,138 MicroScheduler -   -> 1012 reads (4.71% of total) failing DuplicateReadFilter
[2015-09-30T14:38Z] INFO  15:38:48,139 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:38Z] INFO  15:38:48,139 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:38Z] INFO  15:38:48,139 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:38Z] INFO  15:38:48,139 MicroScheduler -   -> 3930 reads (18.29% of total) failing MappingQualityZeroFilter
[2015-09-30T14:38Z] INFO  15:38:48,140 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:38Z] INFO  15:38:48,140 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:38Z] INFO  15:38:48,140 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:38Z] INFO  15:38:49,054 ProgressMeter -     4:177608042    200004.0    30.0 s       2.5 m       65.0%    46.0 s      16.0 s
[2015-09-30T14:38Z] INFO  15:38:49,077 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:38Z] GATK: realign ('4', 189012293, 191154276) : syn3-normal
[2015-09-30T14:38Z] INFO  15:38:51,343 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:51,345 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:38Z] INFO  15:38:51,345 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:38Z] INFO  15:38:51,346 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:38Z] INFO  15:38:51,349 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign-realign.intervals -L 4:189012294-191154276 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpBRysxO/1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam
[2015-09-30T14:38Z] INFO  15:38:51,354 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:38Z] INFO  15:38:51,355 HelpFormatter - Date/Time: 2015/09/30 15:38:51
[2015-09-30T14:38Z] INFO  15:38:51,355 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:51,355 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:38Z] INFO  15:38:51,998 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:38Z] INFO  15:38:52,064 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:38Z] INFO  15:38:52,071 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:38Z] INFO  15:38:52,088 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:38Z] INFO  15:38:52,316 IntervalUtils - Processing 2141983 bp from intervals
[2015-09-30T14:38Z] WARN  15:38:52,320 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:38Z] INFO  15:38:52,377 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:38Z] INFO  15:38:52,415 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:38Z] INFO  15:38:52,415 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:38Z] INFO  15:38:52,415 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:38Z] INFO  15:38:52,416 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:38Z] INFO  15:38:52,481 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:38Z] INFO  15:38:52,498 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:38Z] INFO  15:38:55,285 ProgressMeter -            done     21296.0     2.0 s       2.2 m       93.4%     2.0 s       0.0 s
[2015-09-30T14:38Z] INFO  15:38:55,286 ProgressMeter - Total runtime 2.87 secs, 0.05 min, 0.00 hours
[2015-09-30T14:38Z] INFO  15:38:55,289 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 21296 total reads (0.00%)
[2015-09-30T14:38Z] INFO  15:38:55,289 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:38Z] INFO  15:38:55,289 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:38Z] INFO  15:38:55,290 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:38Z] INFO  15:38:56,264 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:38Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam
[2015-09-30T14:38Z] INFO  15:38:58,265 ProgressMeter -            done   3.102861E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T14:38Z] INFO  15:38:58,265 ProgressMeter - Total runtime 21.99 secs, 0.37 min, 0.01 hours
[2015-09-30T14:38Z] INFO  15:38:58,268 MicroScheduler - 30879 reads were filtered out during the traversal out of approximately 401147 total reads (7.70%)
[2015-09-30T14:38Z] INFO  15:38:58,268 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:38Z] INFO  15:38:58,269 MicroScheduler -   -> 7289 reads (1.82% of total) failing BadMateFilter
[2015-09-30T14:38Z] INFO  15:38:58,269 MicroScheduler -   -> 15766 reads (3.93% of total) failing DuplicateReadFilter
[2015-09-30T14:38Z] INFO  15:38:58,269 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:38Z] INFO  15:38:58,269 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:38Z] INFO  15:38:58,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:38Z] INFO  15:38:58,270 MicroScheduler -   -> 7824 reads (1.95% of total) failing MappingQualityZeroFilter
[2015-09-30T14:38Z] INFO  15:38:58,270 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:38Z] INFO  15:38:58,270 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:38Z] INFO  15:38:58,270 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:38Z] GATK pre-alignment ('5', 0, 31268043) : syn3-normal
[2015-09-30T14:38Z] INFO  15:38:59,232 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:38Z] GATK: realign ('4', 125589908, 156618518) : syn3-normal
[2015-09-30T14:39Z] INFO  15:39:01,077 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:01,080 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:39Z] INFO  15:39:01,080 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:39Z] INFO  15:39:01,080 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:39Z] INFO  15:39:01,083 HelpFormatter - Program Args: -T PrintReads -L 5:1-31268043 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpyTo9MP/1_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam
[2015-09-30T14:39Z] INFO  15:39:01,089 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:39Z] INFO  15:39:01,089 HelpFormatter - Date/Time: 2015/09/30 15:39:01
[2015-09-30T14:39Z] INFO  15:39:01,089 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:01,089 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:01,500 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:01,502 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:39Z] INFO  15:39:01,502 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:39Z] INFO  15:39:01,502 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:39Z] INFO  15:39:01,506 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign-realign.intervals -L 4:125589909-156618518 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpO0xjRA/1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam
[2015-09-30T14:39Z] INFO  15:39:01,511 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:39Z] INFO  15:39:01,512 HelpFormatter - Date/Time: 2015/09/30 15:39:01
[2015-09-30T14:39Z] INFO  15:39:01,512 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:01,512 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:01,802 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:39Z] INFO  15:39:01,962 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:39Z] INFO  15:39:02,027 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:39Z] INFO  15:39:02,035 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:39Z] INFO  15:39:02,052 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:39Z] INFO  15:39:02,282 IntervalUtils - Processing 31028610 bp from intervals
[2015-09-30T14:39Z] WARN  15:39:02,286 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:39Z] INFO  15:39:02,344 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:39Z] INFO  15:39:02,488 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:39Z] INFO  15:39:02,489 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:39Z] INFO  15:39:02,489 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:39Z] INFO  15:39:02,490 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:39Z] INFO  15:39:02,540 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:39Z] INFO  15:39:02,592 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:39Z] INFO  15:39:02,600 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:39Z] INFO  15:39:02,616 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:39Z] INFO  15:39:02,629 IntervalUtils - Processing 31268043 bp from intervals
[2015-09-30T14:39Z] INFO  15:39:02,636 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:39Z] INFO  15:39:02,688 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:39Z] INFO  15:39:02,828 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:39Z] INFO  15:39:02,879 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:39Z] INFO  15:39:02,880 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:39Z] INFO  15:39:02,880 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:39Z] INFO  15:39:02,880 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:39Z] INFO  15:39:02,892 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:39Z] INFO  15:39:03,094 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:39Z] INFO  15:39:04,599 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:39Z] INFO  15:39:04,691 ProgressMeter -            done    411523.0    45.0 s     110.0 s      100.0%    45.0 s       0.0 s
[2015-09-30T14:39Z] INFO  15:39:04,691 ProgressMeter - Total runtime 45.64 secs, 0.76 min, 0.01 hours
[2015-09-30T14:39Z] INFO  15:39:04,692 MicroScheduler - 1443 reads were filtered out during the traversal out of approximately 412966 total reads (0.35%)
[2015-09-30T14:39Z] INFO  15:39:04,692 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:39Z] INFO  15:39:04,692 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:39Z] INFO  15:39:04,692 MicroScheduler -   -> 1443 reads (0.35% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:39Z] INFO  15:39:05,829 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:39Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam
[2015-09-30T14:39Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam 4:156624796-188926424
[2015-09-30T14:39Z] GATK: RealignerTargetCreator
[2015-09-30T14:39Z] INFO  15:39:09,249 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:09,251 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:39Z] INFO  15:39:09,251 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:39Z] INFO  15:39:09,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:39Z] INFO  15:39:09,255 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpsYfDUk/1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign-realign.intervals -l INFO -L 4:156624796-188926424 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:39Z] INFO  15:39:09,260 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:39Z] INFO  15:39:09,261 HelpFormatter - Date/Time: 2015/09/30 15:39:09
[2015-09-30T14:39Z] INFO  15:39:09,261 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:09,261 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:09,330 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:39Z] INFO  15:39:09,443 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:39Z] INFO  15:39:09,451 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:39Z] INFO  15:39:09,467 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:39Z] INFO  15:39:09,706 IntervalUtils - Processing 32301629 bp from intervals
[2015-09-30T14:39Z] WARN  15:39:09,710 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:39Z] INFO  15:39:09,766 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:39Z] INFO  15:39:09,905 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:39Z] INFO  15:39:09,905 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:39Z] INFO  15:39:09,905 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:39Z] INFO  15:39:09,906 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:39Z] INFO  15:39:23,961 ProgressMeter -            done    398767.0    21.0 s      53.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T14:39Z] INFO  15:39:23,962 ProgressMeter - Total runtime 21.47 secs, 0.36 min, 0.01 hours
[2015-09-30T14:39Z] INFO  15:39:23,965 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 398767 total reads (0.00%)
[2015-09-30T14:39Z] INFO  15:39:23,965 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:39Z] INFO  15:39:23,965 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:39Z] INFO  15:39:23,965 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:39Z] INFO  15:39:25,133 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:39Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam
[2015-09-30T14:39Z] GATK pre-alignment ('5', 31293868, 62597714) : syn3-normal
[2015-09-30T14:39Z] INFO  15:39:28,835 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:28,837 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:39Z] INFO  15:39:28,837 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:39Z] INFO  15:39:28,838 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:39Z] INFO  15:39:28,841 HelpFormatter - Program Args: -T PrintReads -L 5:31293869-62597714 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmphan_ln/1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam
[2015-09-30T14:39Z] INFO  15:39:28,847 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:39Z] INFO  15:39:28,847 HelpFormatter - Date/Time: 2015/09/30 15:39:28
[2015-09-30T14:39Z] INFO  15:39:28,847 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:28,847 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:28,963 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:39Z] INFO  15:39:29,642 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:39Z] INFO  15:39:29,689 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:39Z] INFO  15:39:29,696 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:39Z] INFO  15:39:29,710 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:39Z] INFO  15:39:29,722 IntervalUtils - Processing 31303846 bp from intervals
[2015-09-30T14:39Z] INFO  15:39:29,777 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:39Z] INFO  15:39:29,960 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:39Z] INFO  15:39:29,960 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:39Z] INFO  15:39:29,961 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:39Z] INFO  15:39:29,961 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:39Z] INFO  15:39:29,972 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:39Z] INFO  15:39:30,156 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:39Z] INFO  15:39:31,736 ProgressMeter -            done   3.2301629E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T14:39Z] INFO  15:39:31,737 ProgressMeter - Total runtime 21.83 secs, 0.36 min, 0.01 hours
[2015-09-30T14:39Z] INFO  15:39:31,740 MicroScheduler - 32851 reads were filtered out during the traversal out of approximately 414215 total reads (7.93%)
[2015-09-30T14:39Z] INFO  15:39:31,740 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:39Z] INFO  15:39:31,740 MicroScheduler -   -> 7924 reads (1.91% of total) failing BadMateFilter
[2015-09-30T14:39Z] INFO  15:39:31,741 MicroScheduler -   -> 16747 reads (4.04% of total) failing DuplicateReadFilter
[2015-09-30T14:39Z] INFO  15:39:31,741 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:39Z] INFO  15:39:31,741 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:39Z] INFO  15:39:31,741 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:39Z] INFO  15:39:31,742 MicroScheduler -   -> 8180 reads (1.97% of total) failing MappingQualityZeroFilter
[2015-09-30T14:39Z] INFO  15:39:31,742 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:39Z] INFO  15:39:31,742 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:39Z] INFO  15:39:31,742 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:39Z] INFO  15:39:32,712 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:39Z] GATK: realign ('4', 156624795, 188926424) : syn3-normal
[2015-09-30T14:39Z] INFO  15:39:32,883 ProgressMeter -       5:7709344    200002.0    30.0 s       2.5 m       24.7%     2.0 m      91.0 s
[2015-09-30T14:39Z] INFO  15:39:36,123 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:36,125 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:39Z] INFO  15:39:36,125 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:39Z] INFO  15:39:36,125 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:39Z] INFO  15:39:36,128 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign-realign.intervals -L 4:156624796-188926424 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/tx/tmpfxns48/1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam
[2015-09-30T14:39Z] INFO  15:39:36,134 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:39Z] INFO  15:39:36,135 HelpFormatter - Date/Time: 2015/09/30 15:39:36
[2015-09-30T14:39Z] INFO  15:39:36,135 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:36,135 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:39Z] INFO  15:39:36,264 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:39Z] INFO  15:39:36,328 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:39Z] INFO  15:39:36,335 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:39Z] INFO  15:39:36,351 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:39Z] INFO  15:39:37,018 IntervalUtils - Processing 32301629 bp from intervals
[2015-09-30T14:39Z] WARN  15:39:37,022 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:39Z] INFO  15:39:37,080 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:39Z] INFO  15:39:37,224 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:39Z] INFO  15:39:37,225 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:39Z] INFO  15:39:37,225 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:39Z] INFO  15:39:37,226 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:39Z] INFO  15:39:37,380 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:39Z] INFO  15:39:37,572 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:39Z] INFO  15:39:56,532 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:39Z] INFO  15:39:56,718 ProgressMeter -            done    502811.0    53.0 s     107.0 s      100.0%    53.0 s       0.0 s
[2015-09-30T14:39Z] INFO  15:39:56,718 ProgressMeter - Total runtime 53.84 secs, 0.90 min, 0.01 hours
[2015-09-30T14:39Z] INFO  15:39:56,718 MicroScheduler - 1216 reads were filtered out during the traversal out of approximately 504027 total reads (0.24%)
[2015-09-30T14:39Z] INFO  15:39:56,719 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:39Z] INFO  15:39:56,719 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:39Z] INFO  15:39:56,719 MicroScheduler -   -> 1216 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:39Z] INFO  15:39:57,805 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:39Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam
[2015-09-30T14:39Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam 5:1-31268043
[2015-09-30T14:39Z] GATK: RealignerTargetCreator
[2015-09-30T14:39Z] INFO  15:39:59,963 ProgressMeter -      5:37298861    200002.0    30.0 s       2.5 m       19.2%     2.6 m       2.1 m
[2015-09-30T14:40Z] INFO  15:40:01,239 ProgressMeter -            done    411523.0    24.0 s      58.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T14:40Z] INFO  15:40:01,239 ProgressMeter - Total runtime 24.01 secs, 0.40 min, 0.01 hours
[2015-09-30T14:40Z] INFO  15:40:01,243 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 411523 total reads (0.00%)
[2015-09-30T14:40Z] INFO  15:40:01,243 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:40Z] INFO  15:40:01,243 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:40Z] INFO  15:40:01,243 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:40Z] INFO  15:40:01,306 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:01,308 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:40Z] INFO  15:40:01,308 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:40Z] INFO  15:40:01,308 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:40Z] INFO  15:40:01,312 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpswYWIP/1_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign-realign.intervals -l INFO -L 5:1-31268043 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:40Z] INFO  15:40:01,317 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:40Z] INFO  15:40:01,318 HelpFormatter - Date/Time: 2015/09/30 15:40:01
[2015-09-30T14:40Z] INFO  15:40:01,318 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:01,318 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:01,381 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:40Z] INFO  15:40:01,506 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:40Z] INFO  15:40:01,514 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:40Z] INFO  15:40:01,530 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:40Z] INFO  15:40:01,786 IntervalUtils - Processing 31268043 bp from intervals
[2015-09-30T14:40Z] WARN  15:40:01,790 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:40Z] INFO  15:40:01,848 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:40Z] INFO  15:40:01,982 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:40Z] INFO  15:40:01,983 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:40Z] INFO  15:40:01,983 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:40Z] INFO  15:40:01,983 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:40Z] INFO  15:40:02,387 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:40Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam
[2015-09-30T14:40Z] GATK pre-alignment ('5', 63256014, 94276127) : syn3-normal
[2015-09-30T14:40Z] INFO  15:40:06,095 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:06,097 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:40Z] INFO  15:40:06,097 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:40Z] INFO  15:40:06,097 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:40Z] INFO  15:40:06,101 HelpFormatter - Program Args: -T PrintReads -L 5:63256015-94276127 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpKSj6Uo/1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam
[2015-09-30T14:40Z] INFO  15:40:06,106 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:40Z] INFO  15:40:06,106 HelpFormatter - Date/Time: 2015/09/30 15:40:06
[2015-09-30T14:40Z] INFO  15:40:06,107 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:06,107 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:06,213 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:40Z] INFO  15:40:06,974 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:40Z] INFO  15:40:07,026 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:40Z] INFO  15:40:07,034 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:40Z] INFO  15:40:07,050 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:40Z] INFO  15:40:07,064 IntervalUtils - Processing 31020113 bp from intervals
[2015-09-30T14:40Z] INFO  15:40:07,126 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:40Z] INFO  15:40:07,519 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:40Z] INFO  15:40:07,519 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:40Z] INFO  15:40:07,519 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:40Z] INFO  15:40:07,519 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:40Z] INFO  15:40:07,531 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:40Z] INFO  15:40:07,740 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:40Z] INFO  15:40:24,618 ProgressMeter -            done   3.1268043E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T14:40Z] INFO  15:40:24,619 ProgressMeter - Total runtime 22.64 secs, 0.38 min, 0.01 hours
[2015-09-30T14:40Z] INFO  15:40:24,622 MicroScheduler - 90580 reads were filtered out during the traversal out of approximately 505662 total reads (17.91%)
[2015-09-30T14:40Z] INFO  15:40:24,622 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:40Z] INFO  15:40:24,622 MicroScheduler -   -> 7392 reads (1.46% of total) failing BadMateFilter
[2015-09-30T14:40Z] INFO  15:40:24,623 MicroScheduler -   -> 21938 reads (4.34% of total) failing DuplicateReadFilter
[2015-09-30T14:40Z] INFO  15:40:24,623 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:40Z] INFO  15:40:24,623 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:40Z] INFO  15:40:24,623 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:40Z] INFO  15:40:24,623 MicroScheduler -   -> 61250 reads (12.11% of total) failing MappingQualityZeroFilter
[2015-09-30T14:40Z] INFO  15:40:24,624 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:40Z] INFO  15:40:24,624 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:40Z] INFO  15:40:24,624 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:40Z] INFO  15:40:25,634 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:40Z] GATK: realign ('5', 0, 31268043) : syn3-normal
[2015-09-30T14:40Z] INFO  15:40:27,428 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:27,430 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:40Z] INFO  15:40:27,430 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:40Z] INFO  15:40:27,431 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:40Z] INFO  15:40:27,434 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign-realign.intervals -L 5:1-31268043 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpA3F2f4/1_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam
[2015-09-30T14:40Z] INFO  15:40:27,439 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:40Z] INFO  15:40:27,440 HelpFormatter - Date/Time: 2015/09/30 15:40:27
[2015-09-30T14:40Z] INFO  15:40:27,440 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:27,440 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:27,565 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:40Z] INFO  15:40:27,627 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:40Z] INFO  15:40:27,634 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:40Z] INFO  15:40:27,649 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:40Z] INFO  15:40:28,318 IntervalUtils - Processing 31268043 bp from intervals
[2015-09-30T14:40Z] WARN  15:40:28,322 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:40Z] INFO  15:40:28,379 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:40Z] INFO  15:40:28,516 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:40Z] INFO  15:40:28,517 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:40Z] INFO  15:40:28,517 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:40Z] INFO  15:40:28,518 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:40Z] INFO  15:40:28,664 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:40Z] INFO  15:40:28,856 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:40Z] INFO  15:40:29,997 ProgressMeter -      5:58854008    500006.0    60.0 s     120.0 s       88.0%    68.0 s       8.0 s
[2015-09-30T14:40Z] INFO  15:40:34,410 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:40Z] INFO  15:40:34,576 ProgressMeter -            done    594527.0    64.0 s     108.0 s      100.0%    64.0 s       0.0 s
[2015-09-30T14:40Z] INFO  15:40:34,577 ProgressMeter - Total runtime 64.62 secs, 1.08 min, 0.02 hours
[2015-09-30T14:40Z] INFO  15:40:34,577 MicroScheduler - 1743 reads were filtered out during the traversal out of approximately 596270 total reads (0.29%)
[2015-09-30T14:40Z] INFO  15:40:34,577 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:40Z] INFO  15:40:34,578 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:40Z] INFO  15:40:34,578 MicroScheduler -   -> 1743 reads (0.29% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:40Z] INFO  15:40:35,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:40Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam
[2015-09-30T14:40Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam 5:31293869-62597714
[2015-09-30T14:40Z] GATK: RealignerTargetCreator
[2015-09-30T14:40Z] INFO  15:40:37,522 ProgressMeter -      5:71411489    200002.0    30.0 s       2.5 m       26.3%   114.0 s      84.0 s
[2015-09-30T14:40Z] INFO  15:40:38,807 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:38,810 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:40Z] INFO  15:40:38,810 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:40Z] INFO  15:40:38,810 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:40Z] INFO  15:40:38,814 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpYHoQOT/1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign-realign.intervals -l INFO -L 5:31293869-62597714 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:40Z] INFO  15:40:38,818 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:40Z] INFO  15:40:38,819 HelpFormatter - Date/Time: 2015/09/30 15:40:38
[2015-09-30T14:40Z] INFO  15:40:38,819 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:38,819 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:40Z] INFO  15:40:38,877 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:40Z] INFO  15:40:38,993 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:40Z] INFO  15:40:39,001 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:40Z] INFO  15:40:39,017 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:40Z] INFO  15:40:39,565 IntervalUtils - Processing 31303846 bp from intervals
[2015-09-30T14:40Z] WARN  15:40:39,569 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:40Z] INFO  15:40:39,625 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:40Z] INFO  15:40:39,755 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:40Z] INFO  15:40:39,755 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:40Z] INFO  15:40:39,755 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:40Z] INFO  15:40:39,756 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:40Z] INFO  15:40:55,289 ProgressMeter -            done    502811.0    26.0 s      53.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T14:40Z] INFO  15:40:55,289 ProgressMeter - Total runtime 26.77 secs, 0.45 min, 0.01 hours
[2015-09-30T14:40Z] INFO  15:40:55,292 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 502811 total reads (0.00%)
[2015-09-30T14:40Z] INFO  15:40:55,293 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:40Z] INFO  15:40:55,293 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:40Z] INFO  15:40:55,293 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:40Z] INFO  15:40:56,383 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:40Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam
[2015-09-30T14:40Z] GATK pre-alignment ('5', 94277739, 125696417) : syn3-normal
[2015-09-30T14:41Z] INFO  15:41:00,555 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:00,557 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:41Z] INFO  15:41:00,557 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:41Z] INFO  15:41:00,557 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:41Z] INFO  15:41:00,560 HelpFormatter - Program Args: -T PrintReads -L 5:94277740-125696417 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmp1ilPBV/1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam
[2015-09-30T14:41Z] INFO  15:41:00,566 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:41Z] INFO  15:41:00,566 HelpFormatter - Date/Time: 2015/09/30 15:41:00
[2015-09-30T14:41Z] INFO  15:41:00,566 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:00,567 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:01,267 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:41Z] INFO  15:41:01,976 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:41Z] INFO  15:41:02,026 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:41Z] INFO  15:41:02,034 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:41Z] INFO  15:41:02,048 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:41Z] INFO  15:41:02,061 IntervalUtils - Processing 31418678 bp from intervals
[2015-09-30T14:41Z] INFO  15:41:02,118 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:41Z] INFO  15:41:02,319 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:41Z] INFO  15:41:02,320 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:41Z] INFO  15:41:02,320 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:41Z] INFO  15:41:02,320 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:41Z] INFO  15:41:02,331 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:41Z] INFO  15:41:02,535 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:41Z] INFO  15:41:04,550 ProgressMeter -            done   3.1303846E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T14:41Z] INFO  15:41:04,551 ProgressMeter - Total runtime 24.80 secs, 0.41 min, 0.01 hours
[2015-09-30T14:41Z] INFO  15:41:04,554 MicroScheduler - 47210 reads were filtered out during the traversal out of approximately 597882 total reads (7.90%)
[2015-09-30T14:41Z] INFO  15:41:04,554 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:41Z] INFO  15:41:04,554 MicroScheduler -   -> 8722 reads (1.46% of total) failing BadMateFilter
[2015-09-30T14:41Z] INFO  15:41:04,554 MicroScheduler -   -> 24627 reads (4.12% of total) failing DuplicateReadFilter
[2015-09-30T14:41Z] INFO  15:41:04,555 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:41Z] INFO  15:41:04,555 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:41Z] INFO  15:41:04,555 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:41Z] INFO  15:41:04,555 MicroScheduler -   -> 13861 reads (2.32% of total) failing MappingQualityZeroFilter
[2015-09-30T14:41Z] INFO  15:41:04,556 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:41Z] INFO  15:41:04,556 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:41Z] INFO  15:41:04,556 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:41Z] INFO  15:41:06,183 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:41Z] GATK: realign ('5', 31293868, 62597714) : syn3-normal
[2015-09-30T14:41Z] INFO  15:41:08,029 ProgressMeter -      5:86673919    500006.0    60.0 s       2.0 m       75.5%    79.0 s      19.0 s
[2015-09-30T14:41Z] INFO  15:41:08,166 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:08,168 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:41Z] INFO  15:41:08,168 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:41Z] INFO  15:41:08,169 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:41Z] INFO  15:41:08,172 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign-realign.intervals -L 5:31293869-62597714 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpvRWYhF/1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam
[2015-09-30T14:41Z] INFO  15:41:08,177 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:41Z] INFO  15:41:08,178 HelpFormatter - Date/Time: 2015/09/30 15:41:08
[2015-09-30T14:41Z] INFO  15:41:08,178 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:08,178 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:08,304 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:41Z] INFO  15:41:08,367 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:41Z] INFO  15:41:08,374 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:41Z] INFO  15:41:08,390 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:41Z] INFO  15:41:08,859 IntervalUtils - Processing 31303846 bp from intervals
[2015-09-30T14:41Z] WARN  15:41:08,863 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:41Z] INFO  15:41:08,919 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:41Z] INFO  15:41:09,053 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:41Z] INFO  15:41:09,053 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:41Z] INFO  15:41:09,054 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:41Z] INFO  15:41:09,054 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:41Z] INFO  15:41:09,191 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:41Z] INFO  15:41:09,376 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:41Z] INFO  15:41:14,842 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:41Z] INFO  15:41:15,020 ProgressMeter -            done    641715.0    67.0 s     105.0 s      100.0%    67.0 s       0.0 s
[2015-09-30T14:41Z] INFO  15:41:15,020 ProgressMeter - Total runtime 67.50 secs, 1.13 min, 0.02 hours
[2015-09-30T14:41Z] INFO  15:41:15,020 MicroScheduler - 2042 reads were filtered out during the traversal out of approximately 643757 total reads (0.32%)
[2015-09-30T14:41Z] INFO  15:41:15,021 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:41Z] INFO  15:41:15,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:41Z] INFO  15:41:15,021 MicroScheduler -   -> 2042 reads (0.32% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:41Z] INFO  15:41:16,086 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:41Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam
[2015-09-30T14:41Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam 5:63256015-94276127
[2015-09-30T14:41Z] GATK: RealignerTargetCreator
[2015-09-30T14:41Z] INFO  15:41:19,830 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:19,832 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:41Z] INFO  15:41:19,833 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:41Z] INFO  15:41:19,833 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:41Z] INFO  15:41:19,837 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpnJy8rX/1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign-realign.intervals -l INFO -L 5:63256015-94276127 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:41Z] INFO  15:41:19,842 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:41Z] INFO  15:41:19,842 HelpFormatter - Date/Time: 2015/09/30 15:41:19
[2015-09-30T14:41Z] INFO  15:41:19,842 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:19,842 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:19,902 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:41Z] INFO  15:41:20,020 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:41Z] INFO  15:41:20,028 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:41Z] INFO  15:41:20,045 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:41Z] INFO  15:41:20,305 IntervalUtils - Processing 31020113 bp from intervals
[2015-09-30T14:41Z] WARN  15:41:20,310 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:41Z] INFO  15:41:20,368 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:41Z] INFO  15:41:20,512 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:41Z] INFO  15:41:20,512 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:41Z] INFO  15:41:20,512 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:41Z] INFO  15:41:20,513 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:41Z] INFO  15:41:32,323 ProgressMeter -     5:114578465    200002.0    30.0 s       2.5 m       64.6%    46.0 s      16.0 s
[2015-09-30T14:41Z] INFO  15:41:37,707 ProgressMeter -            done    594527.0    28.0 s      48.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T14:41Z] INFO  15:41:37,707 ProgressMeter - Total runtime 28.65 secs, 0.48 min, 0.01 hours
[2015-09-30T14:41Z] INFO  15:41:37,710 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 594527 total reads (0.00%)
[2015-09-30T14:41Z] INFO  15:41:37,711 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:41Z] INFO  15:41:37,711 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:41Z] INFO  15:41:37,711 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:41Z] INFO  15:41:38,817 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:41Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam
[2015-09-30T14:41Z] GATK pre-alignment ('5', 125759062, 156781785) : syn3-normal
[2015-09-30T14:41Z] INFO  15:41:43,183 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:41Z] INFO  15:41:43,486 ProgressMeter -            done    354190.0    41.0 s     116.0 s      100.0%    41.0 s       0.0 s
[2015-09-30T14:41Z] INFO  15:41:43,487 ProgressMeter - Total runtime 41.17 secs, 0.69 min, 0.01 hours
[2015-09-30T14:41Z] INFO  15:41:43,487 MicroScheduler - 1277 reads were filtered out during the traversal out of approximately 355467 total reads (0.36%)
[2015-09-30T14:41Z] INFO  15:41:43,487 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:41Z] INFO  15:41:43,488 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:41Z] INFO  15:41:43,488 MicroScheduler -   -> 1277 reads (0.36% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:41Z] INFO  15:41:43,779 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:43,781 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:41Z] INFO  15:41:43,781 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:41Z] INFO  15:41:43,781 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:41Z] INFO  15:41:43,785 HelpFormatter - Program Args: -T PrintReads -L 5:125759063-156781785 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpWYWIXG/1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam
[2015-09-30T14:41Z] INFO  15:41:43,790 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:41Z] INFO  15:41:43,790 HelpFormatter - Date/Time: 2015/09/30 15:41:43
[2015-09-30T14:41Z] INFO  15:41:43,791 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:43,791 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:43,902 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:41Z] INFO  15:41:45,086 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:41Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam
[2015-09-30T14:41Z] INFO  15:41:45,314 ProgressMeter -            done   3.1020113E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T14:41Z] INFO  15:41:45,315 ProgressMeter - Total runtime 24.80 secs, 0.41 min, 0.01 hours
[2015-09-30T14:41Z] INFO  15:41:45,318 MicroScheduler - 117198 reads were filtered out during the traversal out of approximately 645149 total reads (18.17%)
[2015-09-30T14:41Z] INFO  15:41:45,318 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:41Z] INFO  15:41:45,319 MicroScheduler -   -> 8449 reads (1.31% of total) failing BadMateFilter
[2015-09-30T14:41Z] INFO  15:41:45,319 MicroScheduler -   -> 22274 reads (3.45% of total) failing DuplicateReadFilter
[2015-09-30T14:41Z] INFO  15:41:45,319 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:41Z] INFO  15:41:45,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:41Z] INFO  15:41:45,320 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:41Z] INFO  15:41:45,320 MicroScheduler -   -> 86475 reads (13.40% of total) failing MappingQualityZeroFilter
[2015-09-30T14:41Z] INFO  15:41:45,320 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:41Z] INFO  15:41:45,320 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:41Z] INFO  15:41:45,321 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:41Z] INFO  15:41:46,208 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:41Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam 5:94277740-125696417
[2015-09-30T14:41Z] GATK: RealignerTargetCreator
[2015-09-30T14:41Z] INFO  15:41:46,260 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:41Z] INFO  15:41:46,267 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:41Z] INFO  15:41:46,282 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:41Z] INFO  15:41:46,294 IntervalUtils - Processing 31022723 bp from intervals
[2015-09-30T14:41Z] INFO  15:41:46,350 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:41Z] INFO  15:41:46,400 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:41Z] GATK: realign ('5', 63256014, 94276127) : syn3-normal
[2015-09-30T14:41Z] INFO  15:41:46,658 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:41Z] INFO  15:41:46,659 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:41Z] INFO  15:41:46,659 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:41Z] INFO  15:41:46,659 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:41Z] INFO  15:41:46,671 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:41Z] INFO  15:41:46,872 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:41Z] INFO  15:41:50,297 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:50,299 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:41Z] INFO  15:41:50,299 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:41Z] INFO  15:41:50,299 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:41Z] INFO  15:41:50,303 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpteIwiN/1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign-realign.intervals -l INFO -L 5:94277740-125696417 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:41Z] INFO  15:41:50,308 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:41Z] INFO  15:41:50,309 HelpFormatter - Date/Time: 2015/09/30 15:41:50
[2015-09-30T14:41Z] INFO  15:41:50,309 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:50,309 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:50,365 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:41Z] INFO  15:41:51,209 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:51,212 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:41Z] INFO  15:41:51,212 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:41Z] INFO  15:41:51,212 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:41Z] INFO  15:41:51,216 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign-realign.intervals -L 5:63256015-94276127 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpfubCjr/1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam
[2015-09-30T14:41Z] INFO  15:41:51,222 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:41Z] INFO  15:41:51,223 HelpFormatter - Date/Time: 2015/09/30 15:41:51
[2015-09-30T14:41Z] INFO  15:41:51,223 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:51,223 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:41Z] INFO  15:41:51,346 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:41Z] INFO  15:41:51,409 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:41Z] INFO  15:41:51,416 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:41Z] INFO  15:41:51,433 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:41Z] INFO  15:41:51,566 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:41Z] INFO  15:41:51,574 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:41Z] INFO  15:41:51,590 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:41Z] INFO  15:41:51,694 IntervalUtils - Processing 31020113 bp from intervals
[2015-09-30T14:41Z] WARN  15:41:51,698 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:41Z] INFO  15:41:51,755 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:41Z] INFO  15:41:51,840 IntervalUtils - Processing 31418678 bp from intervals
[2015-09-30T14:41Z] WARN  15:41:51,844 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:41Z] INFO  15:41:51,898 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:41Z] INFO  15:41:51,898 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:41Z] INFO  15:41:51,899 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:41Z] INFO  15:41:51,899 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:41Z] INFO  15:41:51,905 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:41Z] INFO  15:41:52,041 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:41Z] INFO  15:41:52,050 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:41Z] INFO  15:41:52,050 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:41Z] INFO  15:41:52,051 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:41Z] INFO  15:41:52,051 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:41Z] INFO  15:41:52,228 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:42Z] INFO  15:42:14,618 ProgressMeter -            done   3.1418678E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T14:42Z] INFO  15:42:14,619 ProgressMeter - Total runtime 22.57 secs, 0.38 min, 0.01 hours
[2015-09-30T14:42Z] INFO  15:42:14,622 MicroScheduler - 29225 reads were filtered out during the traversal out of approximately 356394 total reads (8.20%)
[2015-09-30T14:42Z] INFO  15:42:14,622 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:42Z] INFO  15:42:14,622 MicroScheduler -   -> 6911 reads (1.94% of total) failing BadMateFilter
[2015-09-30T14:42Z] INFO  15:42:14,623 MicroScheduler -   -> 13750 reads (3.86% of total) failing DuplicateReadFilter
[2015-09-30T14:42Z] INFO  15:42:14,623 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:42Z] INFO  15:42:14,623 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:42Z] INFO  15:42:14,623 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:42Z] INFO  15:42:14,624 MicroScheduler -   -> 8564 reads (2.40% of total) failing MappingQualityZeroFilter
[2015-09-30T14:42Z] INFO  15:42:14,624 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:42Z] INFO  15:42:14,624 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:42Z] INFO  15:42:14,624 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:42Z] INFO  15:42:15,578 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:42Z] GATK: realign ('5', 94277739, 125696417) : syn3-normal
[2015-09-30T14:42Z] INFO  15:42:16,670 ProgressMeter -     5:133745339    200003.0    30.0 s       2.5 m       25.7%   116.0 s      86.0 s
[2015-09-30T14:42Z] INFO  15:42:17,499 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:42Z] INFO  15:42:17,501 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:42Z] INFO  15:42:17,501 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:42Z] INFO  15:42:17,501 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:42Z] INFO  15:42:17,505 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign-realign.intervals -L 5:94277740-125696417 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpkrpNbV/1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam
[2015-09-30T14:42Z] INFO  15:42:17,511 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:42Z] INFO  15:42:17,511 HelpFormatter - Date/Time: 2015/09/30 15:42:17
[2015-09-30T14:42Z] INFO  15:42:17,511 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:42Z] INFO  15:42:17,511 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:42Z] INFO  15:42:17,643 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:42Z] INFO  15:42:17,712 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:42Z] INFO  15:42:17,720 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:42Z] INFO  15:42:17,736 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:42Z] INFO  15:42:18,264 IntervalUtils - Processing 31418678 bp from intervals
[2015-09-30T14:42Z] WARN  15:42:18,268 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:42Z] INFO  15:42:18,325 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:42Z] INFO  15:42:18,472 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:42Z] INFO  15:42:18,472 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:42Z] INFO  15:42:18,473 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:42Z] INFO  15:42:18,473 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:42Z] INFO  15:42:18,622 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:42Z] INFO  15:42:18,814 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:42Z] INFO  15:42:21,902 ProgressMeter -      5:80040637    400005.0    30.0 s      75.0 s       54.1%    55.0 s      25.0 s
[2015-09-30T14:42Z] INFO  15:42:28,066 ProgressMeter -            done    641715.0    36.0 s      56.0 s      100.0%    36.0 s       0.0 s
[2015-09-30T14:42Z] INFO  15:42:28,066 ProgressMeter - Total runtime 36.17 secs, 0.60 min, 0.01 hours
[2015-09-30T14:42Z] INFO  15:42:28,070 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 641715 total reads (0.00%)
[2015-09-30T14:42Z] INFO  15:42:28,070 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:42Z] INFO  15:42:28,070 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:42Z] INFO  15:42:28,071 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:42Z] INFO  15:42:29,105 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:42Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam
[2015-09-30T14:42Z] GATK pre-alignment ('5', 156785743, 180915260) : syn3-normal
[2015-09-30T14:42Z] INFO  15:42:32,807 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:42Z] INFO  15:42:32,809 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:42Z] INFO  15:42:32,809 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:42Z] INFO  15:42:32,809 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:42Z] INFO  15:42:32,812 HelpFormatter - Program Args: -T PrintReads -L 5:156785744-180915260 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpK76mIU/1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam
[2015-09-30T14:42Z] INFO  15:42:32,818 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:42Z] INFO  15:42:32,818 HelpFormatter - Date/Time: 2015/09/30 15:42:32
[2015-09-30T14:42Z] INFO  15:42:32,818 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:42Z] INFO  15:42:32,818 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:42Z] INFO  15:42:32,938 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:42Z] INFO  15:42:34,668 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:42Z] INFO  15:42:34,717 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:42Z] INFO  15:42:34,725 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:42Z] INFO  15:42:34,739 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:42Z] INFO  15:42:34,752 IntervalUtils - Processing 24129517 bp from intervals
[2015-09-30T14:42Z] INFO  15:42:34,809 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:42Z] INFO  15:42:34,987 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:42Z] INFO  15:42:34,988 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:42Z] INFO  15:42:34,988 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:42Z] INFO  15:42:34,988 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:42Z] INFO  15:42:34,999 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:42Z] INFO  15:42:35,153 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:42Z] INFO  15:42:39,515 ProgressMeter -            done    354190.0    21.0 s      59.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T14:42Z] INFO  15:42:39,516 ProgressMeter - Total runtime 21.04 secs, 0.35 min, 0.01 hours
[2015-09-30T14:42Z] INFO  15:42:39,519 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 354190 total reads (0.00%)
[2015-09-30T14:42Z] INFO  15:42:39,519 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:42Z] INFO  15:42:39,519 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:42Z] INFO  15:42:39,520 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:42Z] INFO  15:42:40,640 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:42Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam
[2015-09-30T14:42Z] GATK pre-alignment ('6', 0, 31080572) : syn3-normal
[2015-09-30T14:42Z] INFO  15:42:43,283 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:42Z] INFO  15:42:43,285 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:42Z] INFO  15:42:43,285 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:42Z] INFO  15:42:43,285 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:42Z] INFO  15:42:43,289 HelpFormatter - Program Args: -T PrintReads -L 6:1-31080572 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpiB58o4/1_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam
[2015-09-30T14:42Z] INFO  15:42:43,294 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:42Z] INFO  15:42:43,295 HelpFormatter - Date/Time: 2015/09/30 15:42:43
[2015-09-30T14:42Z] INFO  15:42:43,295 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:42Z] INFO  15:42:43,295 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:42Z] INFO  15:42:43,402 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:42Z] INFO  15:42:46,295 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:42Z] INFO  15:42:46,347 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:42Z] INFO  15:42:46,354 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:42Z] INFO  15:42:46,370 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:42Z] INFO  15:42:46,383 IntervalUtils - Processing 31080572 bp from intervals
[2015-09-30T14:42Z] INFO  15:42:46,442 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:42Z] INFO  15:42:46,652 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:42Z] INFO  15:42:46,652 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:42Z] INFO  15:42:46,653 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:42Z] INFO  15:42:46,653 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:42Z] INFO  15:42:46,665 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:42Z] INFO  15:42:46,671 ProgressMeter -     5:140263661    600008.0    60.0 s     100.0 s       46.8%     2.1 m      68.0 s
[2015-09-30T14:42Z] INFO  15:42:46,869 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:43Z] INFO  15:43:04,990 ProgressMeter -     5:170381080    200003.0    30.0 s       2.5 m       56.3%    53.0 s      23.0 s
[2015-09-30T14:43Z] INFO  15:43:16,677 ProgressMeter -      6:11232643    200003.0    30.0 s       2.5 m       36.1%    83.0 s      53.0 s
[2015-09-30T14:43Z] INFO  15:43:16,880 ProgressMeter -     5:149450368    900011.0    90.0 s     100.0 s       76.4%   117.0 s      27.0 s
[2015-09-30T14:43Z] INFO  15:43:34,991 ProgressMeter -     5:177545688    500006.0    60.0 s     120.0 s       86.0%    69.0 s       9.0 s
[2015-09-30T14:43Z] INFO  15:43:38,898 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:43Z] INFO  15:43:39,307 ProgressMeter -            done   1285581.0   112.0 s      87.0 s      100.0%   112.0 s       0.0 s
[2015-09-30T14:43Z] INFO  15:43:39,307 ProgressMeter - Total runtime 112.65 secs, 1.88 min, 0.03 hours
[2015-09-30T14:43Z] INFO  15:43:39,307 MicroScheduler - 2623 reads were filtered out during the traversal out of approximately 1288204 total reads (0.20%)
[2015-09-30T14:43Z] INFO  15:43:39,308 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:43Z] INFO  15:43:39,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:43Z] INFO  15:43:39,308 MicroScheduler -   -> 2623 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:43Z] INFO  15:43:40,300 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:43Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam
[2015-09-30T14:43Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam 5:125759063-156781785
[2015-09-30T14:43Z] GATK: RealignerTargetCreator
[2015-09-30T14:43Z] INFO  15:43:45,902 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:43Z] INFO  15:43:45,904 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:43Z] INFO  15:43:45,904 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:43Z] INFO  15:43:45,904 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:43Z] INFO  15:43:45,908 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpeGHF78/1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign-realign.intervals -l INFO -L 5:125759063-156781785 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:43Z] INFO  15:43:45,914 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:43Z] INFO  15:43:45,914 HelpFormatter - Date/Time: 2015/09/30 15:43:45
[2015-09-30T14:43Z] INFO  15:43:45,914 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:43Z] INFO  15:43:45,914 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:43Z] INFO  15:43:45,972 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:43Z] INFO  15:43:46,080 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:43Z] INFO  15:43:46,088 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:43Z] INFO  15:43:46,104 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:43Z] INFO  15:43:46,565 IntervalUtils - Processing 31022723 bp from intervals
[2015-09-30T14:43Z] WARN  15:43:46,569 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:43Z] INFO  15:43:46,626 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:43Z] INFO  15:43:46,696 ProgressMeter -      6:28059442    600008.0    60.0 s     100.0 s       90.3%    66.0 s       6.0 s
[2015-09-30T14:43Z] INFO  15:43:46,775 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:43Z] INFO  15:43:46,776 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:43Z] INFO  15:43:46,776 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:43Z] INFO  15:43:46,777 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:43Z] INFO  15:43:56,551 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:43Z] INFO  15:43:56,677 ProgressMeter -            done    805272.0    81.0 s     101.0 s       99.9%    81.0 s       0.0 s
[2015-09-30T14:43Z] INFO  15:43:56,677 ProgressMeter - Total runtime 81.69 secs, 1.36 min, 0.02 hours
[2015-09-30T14:43Z] INFO  15:43:56,677 MicroScheduler - 1571 reads were filtered out during the traversal out of approximately 806843 total reads (0.19%)
[2015-09-30T14:43Z] INFO  15:43:56,678 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:43Z] INFO  15:43:56,678 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:43Z] INFO  15:43:56,678 MicroScheduler -   -> 1571 reads (0.19% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:43Z] INFO  15:43:57,673 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:43Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam
[2015-09-30T14:44Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam 5:156785744-180915260
[2015-09-30T14:44Z] GATK: RealignerTargetCreator
[2015-09-30T14:44Z] INFO  15:44:02,700 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:44Z] INFO  15:44:02,830 ProgressMeter -            done    870185.0    76.0 s      87.0 s      100.0%    76.0 s       0.0 s
[2015-09-30T14:44Z] INFO  15:44:02,831 ProgressMeter - Total runtime 76.18 secs, 1.27 min, 0.02 hours
[2015-09-30T14:44Z] INFO  15:44:02,831 MicroScheduler - 2199 reads were filtered out during the traversal out of approximately 872384 total reads (0.25%)
[2015-09-30T14:44Z] INFO  15:44:02,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:44Z] INFO  15:44:02,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:44Z] INFO  15:44:02,832 MicroScheduler -   -> 2199 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:44Z] INFO  15:44:03,301 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:03,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:44Z] INFO  15:44:03,303 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:44Z] INFO  15:44:03,303 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:44Z] INFO  15:44:03,307 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpAxClA7/1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign-realign.intervals -l INFO -L 5:156785744-180915260 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:44Z] INFO  15:44:03,312 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:44Z] INFO  15:44:03,312 HelpFormatter - Date/Time: 2015/09/30 15:44:03
[2015-09-30T14:44Z] INFO  15:44:03,313 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:03,313 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:03,369 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:44Z] INFO  15:44:03,479 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:44Z] INFO  15:44:03,487 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:44Z] INFO  15:44:03,503 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:44Z] INFO  15:44:03,873 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:44Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam
[2015-09-30T14:44Z] INFO  15:44:04,626 IntervalUtils - Processing 24129517 bp from intervals
[2015-09-30T14:44Z] WARN  15:44:04,630 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:44Z] INFO  15:44:04,702 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:44Z] INFO  15:44:04,836 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:44Z] INFO  15:44:04,837 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:44Z] INFO  15:44:04,837 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:44Z] INFO  15:44:04,838 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:44Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam 6:1-31080572
[2015-09-30T14:44Z] GATK: RealignerTargetCreator
[2015-09-30T14:44Z] INFO  15:44:07,769 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:07,771 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:44Z] INFO  15:44:07,772 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:44Z] INFO  15:44:07,772 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:44Z] INFO  15:44:07,775 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpIs_eG5/1_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign-realign.intervals -l INFO -L 6:1-31080572 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:44Z] INFO  15:44:07,781 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:44Z] INFO  15:44:07,781 HelpFormatter - Date/Time: 2015/09/30 15:44:07
[2015-09-30T14:44Z] INFO  15:44:07,781 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:07,781 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:07,840 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:44Z] INFO  15:44:07,951 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:44Z] INFO  15:44:07,959 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:44Z] INFO  15:44:07,975 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:44Z] INFO  15:44:08,234 IntervalUtils - Processing 31080572 bp from intervals
[2015-09-30T14:44Z] WARN  15:44:08,238 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:44Z] INFO  15:44:08,295 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:44Z] INFO  15:44:08,478 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:44Z] INFO  15:44:08,479 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:44Z] INFO  15:44:08,479 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:44Z] INFO  15:44:08,480 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:44Z] INFO  15:44:16,779 ProgressMeter -     5:150723417   2.4957354E7    30.0 s       1.0 s       80.5%    37.0 s       7.0 s
[2015-09-30T14:44Z] INFO  15:44:21,689 ProgressMeter -            done   3.1022723E7    34.0 s       1.0 s      100.0%    34.0 s       0.0 s
[2015-09-30T14:44Z] INFO  15:44:21,689 ProgressMeter - Total runtime 34.91 secs, 0.58 min, 0.01 hours
[2015-09-30T14:44Z] INFO  15:44:21,693 MicroScheduler - 97484 reads were filtered out during the traversal out of approximately 1293138 total reads (7.54%)
[2015-09-30T14:44Z] INFO  15:44:21,693 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:44Z] INFO  15:44:21,694 MicroScheduler -   -> 13268 reads (1.03% of total) failing BadMateFilter
[2015-09-30T14:44Z] INFO  15:44:21,694 MicroScheduler -   -> 60213 reads (4.66% of total) failing DuplicateReadFilter
[2015-09-30T14:44Z] INFO  15:44:21,694 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:44Z] INFO  15:44:21,694 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:44Z] INFO  15:44:21,695 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:44Z] INFO  15:44:21,695 MicroScheduler -   -> 24003 reads (1.86% of total) failing MappingQualityZeroFilter
[2015-09-30T14:44Z] INFO  15:44:21,695 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:44Z] INFO  15:44:21,695 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:44Z] INFO  15:44:21,695 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:44Z] INFO  15:44:22,660 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:44Z] GATK: realign ('5', 125759062, 156781785) : syn3-normal
[2015-09-30T14:44Z] INFO  15:44:26,874 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:26,876 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:44Z] INFO  15:44:26,876 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:44Z] INFO  15:44:26,876 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:44Z] INFO  15:44:26,880 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign-realign.intervals -L 5:125759063-156781785 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpqlyIIN/1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam
[2015-09-30T14:44Z] INFO  15:44:26,885 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:44Z] INFO  15:44:26,886 HelpFormatter - Date/Time: 2015/09/30 15:44:26
[2015-09-30T14:44Z] INFO  15:44:26,886 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:26,886 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:27,017 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:44Z] INFO  15:44:27,083 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:44Z] INFO  15:44:27,091 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:44Z] INFO  15:44:27,107 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:44Z] INFO  15:44:27,346 IntervalUtils - Processing 31022723 bp from intervals
[2015-09-30T14:44Z] WARN  15:44:27,351 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:44Z] INFO  15:44:27,408 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:44Z] INFO  15:44:27,555 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:44Z] INFO  15:44:27,556 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:44Z] INFO  15:44:27,556 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:44Z] INFO  15:44:27,557 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:44Z] INFO  15:44:27,695 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:44Z] INFO  15:44:27,882 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:44Z] INFO  15:44:28,683 ProgressMeter -            done   2.4129517E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T14:44Z] INFO  15:44:28,684 ProgressMeter - Total runtime 23.85 secs, 0.40 min, 0.01 hours
[2015-09-30T14:44Z] INFO  15:44:28,687 MicroScheduler - 80517 reads were filtered out during the traversal out of approximately 810088 total reads (9.94%)
[2015-09-30T14:44Z] INFO  15:44:28,687 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:44Z] INFO  15:44:28,687 MicroScheduler -   -> 9037 reads (1.12% of total) failing BadMateFilter
[2015-09-30T14:44Z] INFO  15:44:28,688 MicroScheduler -   -> 39116 reads (4.83% of total) failing DuplicateReadFilter
[2015-09-30T14:44Z] INFO  15:44:28,688 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:44Z] INFO  15:44:28,688 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:44Z] INFO  15:44:28,688 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:44Z] INFO  15:44:28,689 MicroScheduler -   -> 32364 reads (4.00% of total) failing MappingQualityZeroFilter
[2015-09-30T14:44Z] INFO  15:44:28,689 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:44Z] INFO  15:44:28,689 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:44Z] INFO  15:44:28,689 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:44Z] INFO  15:44:30,029 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:44Z] GATK: realign ('5', 156785743, 180915260) : syn3-normal
[2015-09-30T14:44Z] INFO  15:44:32,632 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:32,634 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:44Z] INFO  15:44:32,634 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:44Z] INFO  15:44:32,634 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:44Z] INFO  15:44:32,638 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign-realign.intervals -L 5:156785744-180915260 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/tx/tmpPtnwJo/1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam
[2015-09-30T14:44Z] INFO  15:44:32,644 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:44Z] INFO  15:44:32,644 HelpFormatter - Date/Time: 2015/09/30 15:44:32
[2015-09-30T14:44Z] INFO  15:44:32,645 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:32,645 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:32,773 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:44Z] INFO  15:44:32,839 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:44Z] INFO  15:44:32,846 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:44Z] INFO  15:44:32,863 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:44Z] INFO  15:44:33,192 IntervalUtils - Processing 24129517 bp from intervals
[2015-09-30T14:44Z] WARN  15:44:33,196 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:44Z] INFO  15:44:33,253 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:44Z] INFO  15:44:33,378 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:44Z] INFO  15:44:33,378 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:44Z] INFO  15:44:33,379 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:44Z] INFO  15:44:33,379 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:44Z] INFO  15:44:33,519 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:44Z] INFO  15:44:33,675 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:44Z] INFO  15:44:37,169 ProgressMeter -            done   3.1080572E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T14:44Z] INFO  15:44:37,169 ProgressMeter - Total runtime 28.69 secs, 0.48 min, 0.01 hours
[2015-09-30T14:44Z] INFO  15:44:37,172 MicroScheduler - 70256 reads were filtered out during the traversal out of approximately 874987 total reads (8.03%)
[2015-09-30T14:44Z] INFO  15:44:37,173 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:44Z] INFO  15:44:37,173 MicroScheduler -   -> 11417 reads (1.30% of total) failing BadMateFilter
[2015-09-30T14:44Z] INFO  15:44:37,173 MicroScheduler -   -> 40080 reads (4.58% of total) failing DuplicateReadFilter
[2015-09-30T14:44Z] INFO  15:44:37,173 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:44Z] INFO  15:44:37,174 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:44Z] INFO  15:44:37,174 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:44Z] INFO  15:44:37,174 MicroScheduler -   -> 18759 reads (2.14% of total) failing MappingQualityZeroFilter
[2015-09-30T14:44Z] INFO  15:44:37,174 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:44Z] INFO  15:44:37,175 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:44Z] INFO  15:44:37,175 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:44Z] INFO  15:44:38,198 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:44Z] GATK: realign ('6', 0, 31080572) : syn3-normal
[2015-09-30T14:44Z] INFO  15:44:40,283 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:40,285 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:44Z] INFO  15:44:40,285 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:44Z] INFO  15:44:40,285 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:44Z] INFO  15:44:40,289 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign-realign.intervals -L 6:1-31080572 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpuu9J_y/1_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam
[2015-09-30T14:44Z] INFO  15:44:40,294 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:44Z] INFO  15:44:40,294 HelpFormatter - Date/Time: 2015/09/30 15:44:40
[2015-09-30T14:44Z] INFO  15:44:40,295 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:40,295 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:44Z] INFO  15:44:40,420 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:44Z] INFO  15:44:40,483 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:44Z] INFO  15:44:40,491 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:44Z] INFO  15:44:40,506 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:44Z] INFO  15:44:40,738 IntervalUtils - Processing 31080572 bp from intervals
[2015-09-30T14:44Z] WARN  15:44:40,742 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:44Z] INFO  15:44:40,795 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:44Z] INFO  15:44:40,933 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:44Z] INFO  15:44:40,934 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:44Z] INFO  15:44:40,934 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:44Z] INFO  15:44:40,935 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:44Z] INFO  15:44:41,083 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:44Z] INFO  15:44:41,265 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:44Z] INFO  15:44:58,489 ProgressMeter -     5:140031182    500006.0    30.0 s      61.0 s       46.0%    65.0 s      35.0 s
[2015-09-30T14:45Z] INFO  15:45:04,073 ProgressMeter -     5:177547293    500006.0    30.0 s      61.0 s       86.0%    34.0 s       4.0 s
[2015-09-30T14:45Z] INFO  15:45:10,937 ProgressMeter -      6:24717182    500007.0    30.0 s      60.0 s       79.5%    37.0 s       7.0 s
[2015-09-30T14:45Z] INFO  15:45:12,608 ProgressMeter -            done    805272.0    39.0 s      48.0 s       99.9%    39.0 s       0.0 s
[2015-09-30T14:45Z] INFO  15:45:12,609 ProgressMeter - Total runtime 39.23 secs, 0.65 min, 0.01 hours
[2015-09-30T14:45Z] INFO  15:45:12,612 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 805272 total reads (0.00%)
[2015-09-30T14:45Z] INFO  15:45:12,612 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:45Z] INFO  15:45:12,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:45Z] INFO  15:45:12,612 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:45Z] INFO  15:45:13,711 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:45Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam
[2015-09-30T14:45Z] GATK pre-alignment ('6', 31082315, 62284583) : syn3-normal
[2015-09-30T14:45Z] INFO  15:45:18,292 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:45Z] INFO  15:45:18,294 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:45Z] INFO  15:45:18,295 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:45Z] INFO  15:45:18,295 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:45Z] INFO  15:45:18,298 HelpFormatter - Program Args: -T PrintReads -L 6:31082316-62284583 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpE8K09Z/1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam
[2015-09-30T14:45Z] INFO  15:45:18,304 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:45Z] INFO  15:45:18,304 HelpFormatter - Date/Time: 2015/09/30 15:45:18
[2015-09-30T14:45Z] INFO  15:45:18,304 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:45Z] INFO  15:45:18,304 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:45Z] INFO  15:45:18,416 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:45Z] INFO  15:45:19,752 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:45Z] INFO  15:45:19,801 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:45Z] INFO  15:45:19,809 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:45Z] INFO  15:45:19,877 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2015-09-30T14:45Z] INFO  15:45:19,897 IntervalUtils - Processing 31202268 bp from intervals
[2015-09-30T14:45Z] INFO  15:45:19,952 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:45Z] INFO  15:45:20,140 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:45Z] INFO  15:45:20,140 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:45Z] INFO  15:45:20,141 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:45Z] INFO  15:45:20,141 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:45Z] INFO  15:45:20,152 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:45Z] INFO  15:45:20,347 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:45Z] INFO  15:45:24,693 ProgressMeter -            done    870185.0    43.0 s      50.0 s      100.0%    43.0 s       0.0 s
[2015-09-30T14:45Z] INFO  15:45:24,693 ProgressMeter - Total runtime 43.76 secs, 0.73 min, 0.01 hours
[2015-09-30T14:45Z] INFO  15:45:24,697 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 870185 total reads (0.00%)
[2015-09-30T14:45Z] INFO  15:45:24,697 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:45Z] INFO  15:45:24,697 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:45Z] INFO  15:45:24,698 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:45Z] INFO  15:45:25,889 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:45Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam
[2015-09-30T14:45Z] INFO  15:45:27,734 ProgressMeter -            done   1285581.0    60.0 s      46.0 s      100.0%    60.0 s       0.0 s
[2015-09-30T14:45Z] INFO  15:45:27,735 ProgressMeter - Total runtime 60.18 secs, 1.00 min, 0.02 hours
[2015-09-30T14:45Z] INFO  15:45:27,738 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1285581 total reads (0.00%)
[2015-09-30T14:45Z] INFO  15:45:27,738 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:45Z] INFO  15:45:27,738 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:45Z] INFO  15:45:27,738 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:45Z] GATK pre-alignment ('6', 62389878, 93953543) : syn3-normal
[2015-09-30T14:45Z] INFO  15:45:28,895 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:45Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam
[2015-09-30T14:45Z] GATK pre-alignment ('6', 93954776, 124979769) : syn3-normal
[2015-09-30T14:45Z] INFO  15:45:34,191 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:45Z] INFO  15:45:34,193 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:45Z] INFO  15:45:34,193 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:45Z] INFO  15:45:34,193 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:45Z] INFO  15:45:34,196 HelpFormatter - Program Args: -T PrintReads -L 6:62389879-93953543 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpZf9m1O/1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam
[2015-09-30T14:45Z] INFO  15:45:34,202 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:45Z] INFO  15:45:34,203 HelpFormatter - Date/Time: 2015/09/30 15:45:34
[2015-09-30T14:45Z] INFO  15:45:34,203 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:45Z] INFO  15:45:34,203 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:45Z] INFO  15:45:34,304 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:45Z] INFO  15:45:35,625 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:45Z] INFO  15:45:35,627 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:45Z] INFO  15:45:35,627 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:45Z] INFO  15:45:35,627 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:45Z] INFO  15:45:35,630 HelpFormatter - Program Args: -T PrintReads -L 6:93954777-124979769 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmp6IvW8K/1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam
[2015-09-30T14:45Z] INFO  15:45:35,636 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:45Z] INFO  15:45:35,636 HelpFormatter - Date/Time: 2015/09/30 15:45:35
[2015-09-30T14:45Z] INFO  15:45:35,636 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:45Z] INFO  15:45:35,636 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:45Z] INFO  15:45:35,739 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:45Z] INFO  15:45:36,959 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:45Z] INFO  15:45:37,009 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:45Z] INFO  15:45:37,017 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:45Z] INFO  15:45:37,031 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:45Z] INFO  15:45:37,044 IntervalUtils - Processing 31563665 bp from intervals
[2015-09-30T14:45Z] INFO  15:45:37,102 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:45Z] INFO  15:45:37,121 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:45Z] INFO  15:45:37,170 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:45Z] INFO  15:45:37,177 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:45Z] INFO  15:45:37,191 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:45Z] INFO  15:45:37,204 IntervalUtils - Processing 31024993 bp from intervals
[2015-09-30T14:45Z] INFO  15:45:37,260 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:45Z] INFO  15:45:37,332 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:45Z] INFO  15:45:37,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:45Z] INFO  15:45:37,333 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:45Z] INFO  15:45:37,333 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:45Z] INFO  15:45:37,345 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:45Z] INFO  15:45:37,453 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:45Z] INFO  15:45:37,454 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:45Z] INFO  15:45:37,454 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:45Z] INFO  15:45:37,454 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:45Z] INFO  15:45:37,465 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:45Z] INFO  15:45:37,544 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:45Z] INFO  15:45:37,648 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:45Z] INFO  15:45:51,786 ProgressMeter -      6:32015324    200002.0    31.0 s       2.6 m        3.0%    17.3 m      16.8 m
[2015-09-30T14:46Z] INFO  15:46:07,336 ProgressMeter -      6:83963682    200002.0    30.0 s       2.5 m       68.4%    43.0 s      13.0 s
[2015-09-30T14:46Z] INFO  15:46:07,456 ProgressMeter -     6:109816545    200002.0    30.0 s       2.5 m       51.1%    58.0 s      28.0 s
[2015-09-30T14:46Z] INFO  15:46:19,892 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@3fe40c9f
[2015-09-30T14:46Z] INFO  15:46:20,104 ProgressMeter -            done    444391.0    42.0 s      96.0 s      100.0%    42.0 s       0.0 s
[2015-09-30T14:46Z] INFO  15:46:20,105 ProgressMeter - Total runtime 42.77 secs, 0.71 min, 0.01 hours
[2015-09-30T14:46Z] INFO  15:46:20,105 MicroScheduler - 1387 reads were filtered out during the traversal out of approximately 445778 total reads (0.31%)
[2015-09-30T14:46Z] INFO  15:46:20,105 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:46Z] INFO  15:46:20,106 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:46Z] INFO  15:46:20,106 MicroScheduler -   -> 1387 reads (0.31% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:46Z] INFO  15:46:21,097 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:46Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam
[2015-09-30T14:46Z] INFO  15:46:22,221 ProgressMeter -      6:34824600    500006.0    62.0 s       2.1 m       12.0%     8.6 m       7.6 m
[2015-09-30T14:46Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam 6:62389879-93953543
[2015-09-30T14:46Z] GATK: RealignerTargetCreator
[2015-09-30T14:46Z] INFO  15:46:24,209 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:46Z] INFO  15:46:24,211 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:46Z] INFO  15:46:24,211 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:46Z] INFO  15:46:24,211 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:46Z] INFO  15:46:24,215 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmp9_m1dy/1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign-realign.intervals -l INFO -L 6:62389879-93953543 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:46Z] INFO  15:46:24,220 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:46Z] INFO  15:46:24,220 HelpFormatter - Date/Time: 2015/09/30 15:46:24
[2015-09-30T14:46Z] INFO  15:46:24,220 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:46Z] INFO  15:46:24,221 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:46Z] INFO  15:46:24,278 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:46Z] INFO  15:46:25,184 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:46Z] INFO  15:46:25,192 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:46Z] INFO  15:46:25,271 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2015-09-30T14:46Z] INFO  15:46:26,129 IntervalUtils - Processing 31563665 bp from intervals
[2015-09-30T14:46Z] WARN  15:46:26,133 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:46Z] INFO  15:46:26,192 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:46Z] INFO  15:46:26,507 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:46Z] INFO  15:46:26,507 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:46Z] INFO  15:46:26,508 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:46Z] INFO  15:46:26,508 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:46Z] INFO  15:46:30,416 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:46Z] INFO  15:46:30,543 ProgressMeter -            done    488983.0    53.0 s     108.0 s      100.0%    53.0 s       0.0 s
[2015-09-30T14:46Z] INFO  15:46:30,543 ProgressMeter - Total runtime 53.09 secs, 0.88 min, 0.01 hours
[2015-09-30T14:46Z] INFO  15:46:30,544 MicroScheduler - 1480 reads were filtered out during the traversal out of approximately 490463 total reads (0.30%)
[2015-09-30T14:46Z] INFO  15:46:30,544 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:46Z] INFO  15:46:30,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:46Z] INFO  15:46:30,545 MicroScheduler -   -> 1480 reads (0.30% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:46Z] INFO  15:46:31,733 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:46Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam
[2015-09-30T14:46Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam 6:93954777-124979769
[2015-09-30T14:46Z] GATK: RealignerTargetCreator
[2015-09-30T14:46Z] INFO  15:46:35,592 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:46Z] INFO  15:46:35,594 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:46Z] INFO  15:46:35,594 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:46Z] INFO  15:46:35,594 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:46Z] INFO  15:46:35,597 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpwXIvFN/1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign-realign.intervals -l INFO -L 6:93954777-124979769 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:46Z] INFO  15:46:35,603 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:46Z] INFO  15:46:35,603 HelpFormatter - Date/Time: 2015/09/30 15:46:35
[2015-09-30T14:46Z] INFO  15:46:35,603 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:46Z] INFO  15:46:35,603 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:46Z] INFO  15:46:35,660 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:46Z] INFO  15:46:35,764 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:46Z] INFO  15:46:35,772 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:46Z] INFO  15:46:35,787 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:46Z] INFO  15:46:36,026 IntervalUtils - Processing 31024993 bp from intervals
[2015-09-30T14:46Z] WARN  15:46:36,030 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:46Z] INFO  15:46:36,085 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:46Z] INFO  15:46:36,216 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:46Z] INFO  15:46:36,217 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:46Z] INFO  15:46:36,217 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:46Z] INFO  15:46:36,217 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:46Z] INFO  15:46:49,282 ProgressMeter -            done   3.1563665E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T14:46Z] INFO  15:46:49,282 ProgressMeter - Total runtime 22.78 secs, 0.38 min, 0.01 hours
[2015-09-30T14:46Z] INFO  15:46:49,285 MicroScheduler - 33598 reads were filtered out during the traversal out of approximately 446854 total reads (7.52%)
[2015-09-30T14:46Z] INFO  15:46:49,286 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:46Z] INFO  15:46:49,286 MicroScheduler -   -> 7559 reads (1.69% of total) failing BadMateFilter
[2015-09-30T14:46Z] INFO  15:46:49,286 MicroScheduler -   -> 17573 reads (3.93% of total) failing DuplicateReadFilter
[2015-09-30T14:46Z] INFO  15:46:49,287 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:46Z] INFO  15:46:49,287 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:46Z] INFO  15:46:49,287 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:46Z] INFO  15:46:49,287 MicroScheduler -   -> 8466 reads (1.89% of total) failing MappingQualityZeroFilter
[2015-09-30T14:46Z] INFO  15:46:49,287 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:46Z] INFO  15:46:49,288 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:46Z] INFO  15:46:49,288 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:46Z] INFO  15:46:50,259 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:46Z] GATK: realign ('6', 62389878, 93953543) : syn3-normal
[2015-09-30T14:46Z] INFO  15:46:52,250 ProgressMeter -      6:39042051    800010.0    92.0 s     115.0 s       25.5%     6.0 m       4.5 m
[2015-09-30T14:46Z] INFO  15:46:52,370 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:46Z] INFO  15:46:52,372 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:46Z] INFO  15:46:52,372 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:46Z] INFO  15:46:52,373 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:46Z] INFO  15:46:52,376 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign-realign.intervals -L 6:62389879-93953543 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpL1bctY/1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam
[2015-09-30T14:46Z] INFO  15:46:52,381 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:46Z] INFO  15:46:52,381 HelpFormatter - Date/Time: 2015/09/30 15:46:52
[2015-09-30T14:46Z] INFO  15:46:52,382 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:46Z] INFO  15:46:52,382 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:46Z] INFO  15:46:52,500 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:46Z] INFO  15:46:52,563 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:46Z] INFO  15:46:52,570 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:46Z] INFO  15:46:52,585 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:46Z] INFO  15:46:52,808 IntervalUtils - Processing 31563665 bp from intervals
[2015-09-30T14:46Z] WARN  15:46:52,812 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:46Z] INFO  15:46:52,867 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:46Z] INFO  15:46:53,020 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:46Z] INFO  15:46:53,021 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:46Z] INFO  15:46:53,021 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:46Z] INFO  15:46:53,022 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:46Z] INFO  15:46:53,168 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:46Z] INFO  15:46:53,355 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:46Z] INFO  15:46:57,790 ProgressMeter -            done   3.1024993E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T14:46Z] INFO  15:46:57,790 ProgressMeter - Total runtime 21.57 secs, 0.36 min, 0.01 hours
[2015-09-30T14:46Z] INFO  15:46:57,794 MicroScheduler - 36372 reads were filtered out during the traversal out of approximately 491988 total reads (7.39%)
[2015-09-30T14:46Z] INFO  15:46:57,794 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:46Z] INFO  15:46:57,794 MicroScheduler -   -> 7871 reads (1.60% of total) failing BadMateFilter
[2015-09-30T14:46Z] INFO  15:46:57,794 MicroScheduler -   -> 19511 reads (3.97% of total) failing DuplicateReadFilter
[2015-09-30T14:46Z] INFO  15:46:57,795 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:46Z] INFO  15:46:57,795 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:46Z] INFO  15:46:57,795 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:46Z] INFO  15:46:57,795 MicroScheduler -   -> 8990 reads (1.83% of total) failing MappingQualityZeroFilter
[2015-09-30T14:46Z] INFO  15:46:57,796 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:46Z] INFO  15:46:57,796 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:46Z] INFO  15:46:57,796 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:46Z] INFO  15:46:58,770 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:47Z] GATK: realign ('6', 93954776, 124979769) : syn3-normal
[2015-09-30T14:47Z] INFO  15:47:04,259 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:47Z] INFO  15:47:04,261 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:47Z] INFO  15:47:04,261 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:47Z] INFO  15:47:04,261 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:47Z] INFO  15:47:04,265 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign-realign.intervals -L 6:93954777-124979769 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpx4SCdM/1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam
[2015-09-30T14:47Z] INFO  15:47:04,271 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:47Z] INFO  15:47:04,271 HelpFormatter - Date/Time: 2015/09/30 15:47:04
[2015-09-30T14:47Z] INFO  15:47:04,271 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:47Z] INFO  15:47:04,271 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:47Z] INFO  15:47:04,399 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:47Z] INFO  15:47:04,699 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:47Z] INFO  15:47:04,707 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:47Z] INFO  15:47:04,723 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:47Z] INFO  15:47:04,954 IntervalUtils - Processing 31024993 bp from intervals
[2015-09-30T14:47Z] WARN  15:47:04,958 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:47Z] INFO  15:47:05,014 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:47Z] INFO  15:47:05,146 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:47Z] INFO  15:47:05,146 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:47Z] INFO  15:47:05,147 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:47Z] INFO  15:47:05,147 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:47Z] INFO  15:47:05,298 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:47Z] INFO  15:47:05,479 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:47Z] INFO  15:47:19,741 ProgressMeter -            done    444391.0    26.0 s      60.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T14:47Z] INFO  15:47:19,741 ProgressMeter - Total runtime 26.72 secs, 0.45 min, 0.01 hours
[2015-09-30T14:47Z] INFO  15:47:19,744 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 444391 total reads (0.00%)
[2015-09-30T14:47Z] INFO  15:47:19,745 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:47Z] INFO  15:47:19,745 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:47Z] INFO  15:47:19,745 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:47Z] INFO  15:47:20,900 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:47Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam
[2015-09-30T14:47Z] GATK pre-alignment ('6', 125064552, 156268261) : syn3-normal
[2015-09-30T14:47Z] INFO  15:47:24,796 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:47Z] INFO  15:47:24,799 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:47Z] INFO  15:47:24,799 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:47Z] INFO  15:47:24,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:47Z] INFO  15:47:24,802 HelpFormatter - Program Args: -T PrintReads -L 6:125064553-156268261 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmp2sbUH6/1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam
[2015-09-30T14:47Z] INFO  15:47:24,808 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:47Z] INFO  15:47:24,809 HelpFormatter - Date/Time: 2015/09/30 15:47:24
[2015-09-30T14:47Z] INFO  15:47:24,809 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:47Z] INFO  15:47:24,809 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:47Z] INFO  15:47:24,913 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:47Z] INFO  15:47:26,251 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:47Z] INFO  15:47:26,303 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:47Z] INFO  15:47:26,311 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:47Z] INFO  15:47:26,464 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
[2015-09-30T14:47Z] INFO  15:47:26,529 IntervalUtils - Processing 31203709 bp from intervals
[2015-09-30T14:47Z] INFO  15:47:26,608 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:47Z] INFO  15:47:27,003 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:47Z] INFO  15:47:27,004 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:47Z] INFO  15:47:27,004 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:47Z] INFO  15:47:27,004 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:47Z] INFO  15:47:27,016 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:47Z] INFO  15:47:27,215 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:47Z] INFO  15:47:32,251 ProgressMeter -      6:44273916   1200016.0     2.2 m     110.0 s       42.3%     5.2 m       3.0 m
[2015-09-30T14:47Z] INFO  15:47:32,917 ProgressMeter -            done    488983.0    27.0 s      56.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T14:47Z] INFO  15:47:32,918 ProgressMeter - Total runtime 27.77 secs, 0.46 min, 0.01 hours
[2015-09-30T14:47Z] INFO  15:47:32,921 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 488983 total reads (0.00%)
[2015-09-30T14:47Z] INFO  15:47:32,921 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:47Z] INFO  15:47:32,921 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:47Z] INFO  15:47:32,922 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:47Z] INFO  15:47:34,044 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:47Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam
[2015-09-30T14:47Z] GATK pre-alignment ('6', 156275378, 171115067) : syn3-normal
[2015-09-30T14:47Z] INFO  15:47:37,072 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:47Z] INFO  15:47:37,074 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:47Z] INFO  15:47:37,074 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:47Z] INFO  15:47:37,074 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:47Z] INFO  15:47:37,078 HelpFormatter - Program Args: -T PrintReads -L 6:156275379-171115067 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpGH2bBq/1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam
[2015-09-30T14:47Z] INFO  15:47:37,083 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:47Z] INFO  15:47:37,084 HelpFormatter - Date/Time: 2015/09/30 15:47:37
[2015-09-30T14:47Z] INFO  15:47:37,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:47Z] INFO  15:47:37,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:47Z] INFO  15:47:37,193 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:47Z] INFO  15:47:38,749 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:47Z] INFO  15:47:38,801 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:47Z] INFO  15:47:38,809 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:47Z] INFO  15:47:38,824 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:47Z] INFO  15:47:38,837 IntervalUtils - Processing 14839689 bp from intervals
[2015-09-30T14:47Z] INFO  15:47:38,895 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:47Z] INFO  15:47:39,053 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:47Z] INFO  15:47:39,054 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:47Z] INFO  15:47:39,054 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:47Z] INFO  15:47:39,054 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:47Z] INFO  15:47:39,066 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:47Z] INFO  15:47:39,170 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:47Z] INFO  15:47:57,007 ProgressMeter -     6:136847254    200003.0    30.0 s       2.5 m       37.8%    79.0 s      49.0 s
[2015-09-30T14:48Z] INFO  15:48:03,043 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:48Z] INFO  15:48:03,104 ProgressMeter -            done   1554484.0     2.7 m     104.0 s      100.0%     2.7 m       0.0 s
[2015-09-30T14:48Z] INFO  15:48:03,105 ProgressMeter - Total runtime 162.96 secs, 2.72 min, 0.05 hours
[2015-09-30T14:48Z] INFO  15:48:03,105 MicroScheduler - 2660 reads were filtered out during the traversal out of approximately 1557144 total reads (0.17%)
[2015-09-30T14:48Z] INFO  15:48:03,105 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:48Z] INFO  15:48:03,106 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:48Z] INFO  15:48:03,106 MicroScheduler -   -> 2660 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:48Z] INFO  15:48:05,714 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:48Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam
[2015-09-30T14:48Z] INFO  15:48:09,057 ProgressMeter -     6:162621964    200002.0    30.0 s       2.5 m       42.8%    70.0 s      40.0 s
[2015-09-30T14:48Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam 6:31082316-62284583
[2015-09-30T14:48Z] GATK: RealignerTargetCreator
[2015-09-30T14:48Z] INFO  15:48:12,197 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:12,199 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:48Z] INFO  15:48:12,199 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:48Z] INFO  15:48:12,199 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:48Z] INFO  15:48:12,203 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpNru39x/1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign-realign.intervals -l INFO -L 6:31082316-62284583 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:48Z] INFO  15:48:12,208 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:48Z] INFO  15:48:12,209 HelpFormatter - Date/Time: 2015/09/30 15:48:12
[2015-09-30T14:48Z] INFO  15:48:12,209 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:12,209 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:12,267 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:48Z] INFO  15:48:13,230 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:48Z] INFO  15:48:13,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:48Z] INFO  15:48:13,254 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:48Z] INFO  15:48:13,503 IntervalUtils - Processing 31202268 bp from intervals
[2015-09-30T14:48Z] WARN  15:48:13,507 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:48Z] INFO  15:48:13,562 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:48Z] INFO  15:48:13,700 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:48Z] INFO  15:48:13,701 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:48Z] INFO  15:48:13,701 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:48Z] INFO  15:48:13,701 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:48Z] INFO  15:48:25,398 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:48Z] INFO  15:48:25,491 ProgressMeter -            done    448182.0    46.0 s     103.0 s       99.6%    46.0 s       0.0 s
[2015-09-30T14:48Z] INFO  15:48:25,492 ProgressMeter - Total runtime 46.44 secs, 0.77 min, 0.01 hours
[2015-09-30T14:48Z] INFO  15:48:25,492 MicroScheduler - 973 reads were filtered out during the traversal out of approximately 449155 total reads (0.22%)
[2015-09-30T14:48Z] INFO  15:48:25,492 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:48Z] INFO  15:48:25,493 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:48Z] INFO  15:48:25,493 MicroScheduler -   -> 973 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:48Z] INFO  15:48:26,547 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:48Z] INFO  15:48:27,008 ProgressMeter -     6:151686911    500010.0    60.0 s     120.0 s       85.3%    70.0 s      10.0 s
[2015-09-30T14:48Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam
[2015-09-30T14:48Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam 6:156275379-171115067
[2015-09-30T14:48Z] GATK: RealignerTargetCreator
[2015-09-30T14:48Z] INFO  15:48:30,305 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:30,307 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:48Z] INFO  15:48:30,307 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:48Z] INFO  15:48:30,307 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:48Z] INFO  15:48:30,311 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmphI1VxL/1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign-realign.intervals -l INFO -L 6:156275379-171115067 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:48Z] INFO  15:48:30,316 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:48Z] INFO  15:48:30,317 HelpFormatter - Date/Time: 2015/09/30 15:48:30
[2015-09-30T14:48Z] INFO  15:48:30,317 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:30,317 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:30,376 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:48Z] INFO  15:48:31,208 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:48Z] INFO  15:48:31,216 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:48Z] INFO  15:48:31,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:48Z] INFO  15:48:31,486 IntervalUtils - Processing 14839689 bp from intervals
[2015-09-30T14:48Z] WARN  15:48:31,490 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:48Z] INFO  15:48:31,548 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:48Z] INFO  15:48:31,645 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:48Z] INFO  15:48:31,646 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:48Z] INFO  15:48:31,646 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:48Z] INFO  15:48:31,647 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:48Z] INFO  15:48:38,117 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:48Z] INFO  15:48:38,192 ProgressMeter -            done    677914.0    71.0 s     105.0 s      100.0%    71.0 s       0.0 s
[2015-09-30T14:48Z] INFO  15:48:38,193 ProgressMeter - Total runtime 71.19 secs, 1.19 min, 0.02 hours
[2015-09-30T14:48Z] INFO  15:48:38,193 MicroScheduler - 1940 reads were filtered out during the traversal out of approximately 679854 total reads (0.29%)
[2015-09-30T14:48Z] INFO  15:48:38,194 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:48Z] INFO  15:48:38,194 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:48Z] INFO  15:48:38,194 MicroScheduler -   -> 1940 reads (0.29% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:48Z] INFO  15:48:39,194 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:48Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam
[2015-09-30T14:48Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam 6:125064553-156268261
[2015-09-30T14:48Z] GATK: RealignerTargetCreator
[2015-09-30T14:48Z] INFO  15:48:42,583 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:42,585 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:48Z] INFO  15:48:42,585 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:48Z] INFO  15:48:42,585 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:48Z] INFO  15:48:42,589 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpA7ZF0K/1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign-realign.intervals -l INFO -L 6:125064553-156268261 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:48Z] INFO  15:48:42,594 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:48Z] INFO  15:48:42,595 HelpFormatter - Date/Time: 2015/09/30 15:48:42
[2015-09-30T14:48Z] INFO  15:48:42,595 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:42,595 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:42,654 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:48Z] INFO  15:48:42,770 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:48Z] INFO  15:48:42,778 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:48Z] INFO  15:48:42,794 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:48Z] INFO  15:48:43,704 ProgressMeter -      6:52477169   2.1379253E7    30.0 s       1.0 s       68.6%    43.0 s      13.0 s
[2015-09-30T14:48Z] INFO  15:48:43,860 IntervalUtils - Processing 31203709 bp from intervals
[2015-09-30T14:48Z] WARN  15:48:43,864 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:48Z] INFO  15:48:43,921 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:48Z] INFO  15:48:44,064 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:48Z] INFO  15:48:44,064 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:48Z] INFO  15:48:44,065 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:48Z] INFO  15:48:44,065 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:48Z] INFO  15:48:46,469 ProgressMeter -            done   1.4839689E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2015-09-30T14:48Z] INFO  15:48:46,470 ProgressMeter - Total runtime 14.82 secs, 0.25 min, 0.00 hours
[2015-09-30T14:48Z] INFO  15:48:46,473 MicroScheduler - 61482 reads were filtered out during the traversal out of approximately 451096 total reads (13.63%)
[2015-09-30T14:48Z] INFO  15:48:46,473 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:48Z] INFO  15:48:46,473 MicroScheduler -   -> 5135 reads (1.14% of total) failing BadMateFilter
[2015-09-30T14:48Z] INFO  15:48:46,474 MicroScheduler -   -> 19972 reads (4.43% of total) failing DuplicateReadFilter
[2015-09-30T14:48Z] INFO  15:48:46,474 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:48Z] INFO  15:48:46,474 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:48Z] INFO  15:48:46,474 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:48Z] INFO  15:48:46,475 MicroScheduler -   -> 36375 reads (8.06% of total) failing MappingQualityZeroFilter
[2015-09-30T14:48Z] INFO  15:48:46,475 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:48Z] INFO  15:48:46,475 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:48Z] INFO  15:48:46,475 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:48Z] INFO  15:48:47,442 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:48Z] GATK: realign ('6', 156275378, 171115067) : syn3-normal
[2015-09-30T14:48Z] INFO  15:48:50,045 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:50,047 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:48Z] INFO  15:48:50,048 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:48Z] INFO  15:48:50,048 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:48Z] INFO  15:48:50,051 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign-realign.intervals -L 6:156275379-171115067 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpO9YbKg/1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam
[2015-09-30T14:48Z] INFO  15:48:50,057 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:48Z] INFO  15:48:50,057 HelpFormatter - Date/Time: 2015/09/30 15:48:50
[2015-09-30T14:48Z] INFO  15:48:50,057 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:50,058 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:50,069 ProgressMeter -            done   3.1202268E7    36.0 s       1.0 s      100.0%    36.0 s       0.0 s
[2015-09-30T14:48Z] INFO  15:48:50,070 ProgressMeter - Total runtime 36.37 secs, 0.61 min, 0.01 hours
[2015-09-30T14:48Z] INFO  15:48:50,073 MicroScheduler - 142282 reads were filtered out during the traversal out of approximately 1564091 total reads (9.10%)
[2015-09-30T14:48Z] INFO  15:48:50,073 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:48Z] INFO  15:48:50,073 MicroScheduler -   -> 14911 reads (0.95% of total) failing BadMateFilter
[2015-09-30T14:48Z] INFO  15:48:50,074 MicroScheduler -   -> 73565 reads (4.70% of total) failing DuplicateReadFilter
[2015-09-30T14:48Z] INFO  15:48:50,074 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:48Z] INFO  15:48:50,074 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:48Z] INFO  15:48:50,074 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:48Z] INFO  15:48:50,074 MicroScheduler -   -> 53806 reads (3.44% of total) failing MappingQualityZeroFilter
[2015-09-30T14:48Z] INFO  15:48:50,075 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:48Z] INFO  15:48:50,075 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:48Z] INFO  15:48:50,075 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:48Z] INFO  15:48:50,190 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:48Z] INFO  15:48:50,253 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:48Z] INFO  15:48:50,260 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:48Z] INFO  15:48:50,275 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:48Z] INFO  15:48:51,059 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:48Z] GATK: realign ('6', 31082315, 62284583) : syn3-normal
[2015-09-30T14:48Z] INFO  15:48:51,098 IntervalUtils - Processing 14839689 bp from intervals
[2015-09-30T14:48Z] WARN  15:48:51,102 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:48Z] INFO  15:48:51,159 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:48Z] INFO  15:48:51,249 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:48Z] INFO  15:48:51,249 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:48Z] INFO  15:48:51,250 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:48Z] INFO  15:48:51,250 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:48Z] INFO  15:48:51,381 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:48Z] INFO  15:48:51,488 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:48Z] INFO  15:48:53,055 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:53,057 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:48Z] INFO  15:48:53,057 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:48Z] INFO  15:48:53,057 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:48Z] INFO  15:48:53,061 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign-realign.intervals -L 6:31082316-62284583 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpLBBKwl/1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam
[2015-09-30T14:48Z] INFO  15:48:53,067 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:48Z] INFO  15:48:53,067 HelpFormatter - Date/Time: 2015/09/30 15:48:53
[2015-09-30T14:48Z] INFO  15:48:53,067 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:53,067 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:48Z] INFO  15:48:53,706 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:48Z] INFO  15:48:53,770 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:48Z] INFO  15:48:53,777 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:48Z] INFO  15:48:53,793 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:48Z] INFO  15:48:54,024 IntervalUtils - Processing 31202268 bp from intervals
[2015-09-30T14:48Z] WARN  15:48:54,028 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:48Z] INFO  15:48:54,081 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:48Z] INFO  15:48:54,212 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:48Z] INFO  15:48:54,212 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:48Z] INFO  15:48:54,213 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:48Z] INFO  15:48:54,213 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:48Z] INFO  15:48:54,372 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:48Z] INFO  15:48:54,548 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:49Z] INFO  15:49:09,941 ProgressMeter -            done   3.1203709E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T14:49Z] INFO  15:49:09,942 ProgressMeter - Total runtime 25.88 secs, 0.43 min, 0.01 hours
[2015-09-30T14:49Z] INFO  15:49:09,945 MicroScheduler - 52410 reads were filtered out during the traversal out of approximately 682719 total reads (7.68%)
[2015-09-30T14:49Z] INFO  15:49:09,945 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:49Z] INFO  15:49:09,946 MicroScheduler -   -> 9688 reads (1.42% of total) failing BadMateFilter
[2015-09-30T14:49Z] INFO  15:49:09,946 MicroScheduler -   -> 27608 reads (4.04% of total) failing DuplicateReadFilter
[2015-09-30T14:49Z] INFO  15:49:09,946 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:49Z] INFO  15:49:09,946 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:49Z] INFO  15:49:09,947 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:49Z] INFO  15:49:09,947 MicroScheduler -   -> 15114 reads (2.21% of total) failing MappingQualityZeroFilter
[2015-09-30T14:49Z] INFO  15:49:09,947 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:49Z] INFO  15:49:09,947 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:49Z] INFO  15:49:09,947 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:49Z] INFO  15:49:11,011 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:49Z] GATK: realign ('6', 125064552, 156268261) : syn3-normal
[2015-09-30T14:49Z] INFO  15:49:13,640 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:49Z] INFO  15:49:13,642 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:49Z] INFO  15:49:13,642 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:49Z] INFO  15:49:13,642 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:49Z] INFO  15:49:13,646 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign-realign.intervals -L 6:125064553-156268261 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/tx/tmpUvhQMz/1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam
[2015-09-30T14:49Z] INFO  15:49:13,652 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:49Z] INFO  15:49:13,652 HelpFormatter - Date/Time: 2015/09/30 15:49:13
[2015-09-30T14:49Z] INFO  15:49:13,652 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:49Z] INFO  15:49:13,653 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:49Z] INFO  15:49:14,318 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:49Z] INFO  15:49:14,386 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:49Z] INFO  15:49:14,393 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:49Z] INFO  15:49:14,410 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:49Z] INFO  15:49:14,637 IntervalUtils - Processing 31203709 bp from intervals
[2015-09-30T14:49Z] WARN  15:49:14,641 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:49Z] INFO  15:49:14,696 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:49Z] INFO  15:49:14,840 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:49Z] INFO  15:49:14,841 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:49Z] INFO  15:49:14,841 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:49Z] INFO  15:49:14,841 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:49Z] INFO  15:49:14,994 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:49Z] INFO  15:49:15,180 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:49Z] INFO  15:49:17,589 ProgressMeter -            done    448182.0    26.0 s      58.0 s       99.6%    26.0 s       0.0 s
[2015-09-30T14:49Z] INFO  15:49:17,590 ProgressMeter - Total runtime 26.34 secs, 0.44 min, 0.01 hours
[2015-09-30T14:49Z] INFO  15:49:17,593 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 448182 total reads (0.00%)
[2015-09-30T14:49Z] INFO  15:49:17,593 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:49Z] INFO  15:49:17,593 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:49Z] INFO  15:49:17,594 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:49Z] INFO  15:49:18,616 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:49Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam
[2015-09-30T14:49Z] GATK pre-alignment ('7', 0, 31019109) : syn3-normal
[2015-09-30T14:49Z] INFO  15:49:22,778 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:49Z] INFO  15:49:22,780 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:49Z] INFO  15:49:22,781 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:49Z] INFO  15:49:22,781 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:49Z] INFO  15:49:22,784 HelpFormatter - Program Args: -T PrintReads -L 7:1-31019109 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmp034BZz/1_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam
[2015-09-30T14:49Z] INFO  15:49:22,790 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:49Z] INFO  15:49:22,790 HelpFormatter - Date/Time: 2015/09/30 15:49:22
[2015-09-30T14:49Z] INFO  15:49:22,790 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:49Z] INFO  15:49:22,790 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:49Z] INFO  15:49:22,896 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:49Z] INFO  15:49:24,121 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:49Z] INFO  15:49:24,172 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:49Z] INFO  15:49:24,180 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:49Z] INFO  15:49:24,195 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:49Z] INFO  15:49:24,208 IntervalUtils - Processing 31019109 bp from intervals
[2015-09-30T14:49Z] INFO  15:49:24,215 ProgressMeter -      6:33412703    400005.0    30.0 s      75.0 s        7.5%     6.7 m       6.2 m
[2015-09-30T14:49Z] INFO  15:49:24,267 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:49Z] INFO  15:49:24,483 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:49Z] INFO  15:49:24,484 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:49Z] INFO  15:49:24,484 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:49Z] INFO  15:49:24,484 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:49Z] INFO  15:49:24,496 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:49Z] INFO  15:49:24,702 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:49Z] INFO  15:49:45,832 ProgressMeter -     6:152716529    600011.0    30.0 s      51.0 s       88.6%    33.0 s       3.0 s
[2015-09-30T14:49Z] INFO  15:49:49,092 ProgressMeter -            done    677914.0    34.0 s      50.0 s      100.0%    34.0 s       0.0 s
[2015-09-30T14:49Z] INFO  15:49:49,093 ProgressMeter - Total runtime 34.25 secs, 0.57 min, 0.01 hours
[2015-09-30T14:49Z] INFO  15:49:49,096 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 677914 total reads (0.00%)
[2015-09-30T14:49Z] INFO  15:49:49,096 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:49Z] INFO  15:49:49,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:49Z] INFO  15:49:49,097 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:49Z] INFO  15:49:50,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:49Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam
[2015-09-30T14:49Z] GATK pre-alignment ('7', 31022897, 62585293) : syn3-normal
[2015-09-30T14:49Z] INFO  15:49:53,646 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:49Z] INFO  15:49:53,648 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:49Z] INFO  15:49:53,648 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:49Z] INFO  15:49:53,649 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:49Z] INFO  15:49:53,652 HelpFormatter - Program Args: -T PrintReads -L 7:31022898-62585293 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmp8K_k_x/1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam
[2015-09-30T14:49Z] INFO  15:49:53,657 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:49Z] INFO  15:49:53,658 HelpFormatter - Date/Time: 2015/09/30 15:49:53
[2015-09-30T14:49Z] INFO  15:49:53,658 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:49Z] INFO  15:49:53,658 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:49Z] INFO  15:49:53,764 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:49Z] INFO  15:49:54,487 ProgressMeter -       7:4839561    200003.0    30.0 s       2.5 m       15.6%     3.2 m       2.7 m
[2015-09-30T14:49Z] INFO  15:49:54,908 ProgressMeter -      6:43517342   1100015.0    60.0 s      55.0 s       39.9%     2.5 m      90.0 s
[2015-09-30T14:49Z] INFO  15:49:55,350 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:49Z] INFO  15:49:55,398 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:49Z] INFO  15:49:55,406 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:49Z] INFO  15:49:55,420 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:49Z] INFO  15:49:55,433 IntervalUtils - Processing 31562396 bp from intervals
[2015-09-30T14:49Z] INFO  15:49:55,489 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:49Z] INFO  15:49:55,679 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:49Z] INFO  15:49:55,680 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:49Z] INFO  15:49:55,680 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:49Z] INFO  15:49:55,680 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:49Z] INFO  15:49:55,691 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:49Z] INFO  15:49:55,885 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:50Z] INFO  15:50:10,490 ProgressMeter -            done   1554484.0    76.0 s      49.0 s      100.0%    76.0 s       0.0 s
[2015-09-30T14:50Z] INFO  15:50:10,490 ProgressMeter - Total runtime 76.28 secs, 1.27 min, 0.02 hours
[2015-09-30T14:50Z] INFO  15:50:10,494 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1554484 total reads (0.00%)
[2015-09-30T14:50Z] INFO  15:50:10,494 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:50Z] INFO  15:50:10,494 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:50Z] INFO  15:50:10,494 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:50Z] INFO  15:50:11,684 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:50Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam
[2015-09-30T14:50Z] GATK pre-alignment ('7', 62708318, 93925745) : syn3-normal
[2015-09-30T14:50Z] INFO  15:50:17,277 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:50Z] INFO  15:50:17,280 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:50Z] INFO  15:50:17,280 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:50Z] INFO  15:50:17,280 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:50Z] INFO  15:50:17,284 HelpFormatter - Program Args: -T PrintReads -L 7:62708319-93925745 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmp7HOIJK/1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam
[2015-09-30T14:50Z] INFO  15:50:17,289 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:50Z] INFO  15:50:17,290 HelpFormatter - Date/Time: 2015/09/30 15:50:17
[2015-09-30T14:50Z] INFO  15:50:17,290 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:50Z] INFO  15:50:17,290 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:50Z] INFO  15:50:18,370 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:50Z] INFO  15:50:19,083 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:50Z] INFO  15:50:19,133 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:50Z] INFO  15:50:19,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:50Z] INFO  15:50:19,154 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:50Z] INFO  15:50:19,167 IntervalUtils - Processing 31217427 bp from intervals
[2015-09-30T14:50Z] INFO  15:50:19,222 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:50Z] INFO  15:50:19,421 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:50Z] INFO  15:50:19,421 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:50Z] INFO  15:50:19,422 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:50Z] INFO  15:50:19,422 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:50Z] INFO  15:50:19,432 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:50Z] INFO  15:50:19,638 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:50Z] INFO  15:50:24,488 ProgressMeter -      7:21550754    600009.0    60.0 s     100.0 s       69.5%    86.0 s      26.0 s
[2015-09-30T14:50Z] INFO  15:50:25,683 ProgressMeter -      7:40435920    200002.0    30.0 s       2.5 m       29.8%   100.0 s      70.0 s
[2015-09-30T14:50Z] INFO  15:50:46,624 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:50Z] INFO  15:50:46,807 ProgressMeter -            done    944787.0    82.0 s      87.0 s      100.0%    82.0 s       0.0 s
[2015-09-30T14:50Z] INFO  15:50:46,808 ProgressMeter - Total runtime 82.32 secs, 1.37 min, 0.02 hours
[2015-09-30T14:50Z] INFO  15:50:46,808 MicroScheduler - 2107 reads were filtered out during the traversal out of approximately 946894 total reads (0.22%)
[2015-09-30T14:50Z] INFO  15:50:46,808 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:50Z] INFO  15:50:46,808 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:50Z] INFO  15:50:46,809 MicroScheduler -   -> 2107 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:50Z] INFO  15:50:47,818 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:50Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam
[2015-09-30T14:50Z] INFO  15:50:49,424 ProgressMeter -      7:72496208    200002.0    30.0 s       2.5 m       31.4%    95.0 s      65.0 s
[2015-09-30T14:50Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam 7:1-31019109
[2015-09-30T14:50Z] GATK: RealignerTargetCreator
[2015-09-30T14:50Z] INFO  15:50:55,006 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:50Z] INFO  15:50:55,008 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:50Z] INFO  15:50:55,008 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:50Z] INFO  15:50:55,008 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:50Z] INFO  15:50:55,011 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpeK_eMD/1_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign-realign.intervals -l INFO -L 7:1-31019109 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:50Z] INFO  15:50:55,018 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:50Z] INFO  15:50:55,018 HelpFormatter - Date/Time: 2015/09/30 15:50:55
[2015-09-30T14:50Z] INFO  15:50:55,018 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:50Z] INFO  15:50:55,018 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:50Z] INFO  15:50:55,075 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:50Z] INFO  15:50:55,658 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:50Z] INFO  15:50:55,666 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:50Z] INFO  15:50:55,682 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:50Z] INFO  15:50:55,926 ProgressMeter -      7:48279219    500006.0    60.0 s     120.0 s       54.7%   109.0 s      49.0 s
[2015-09-30T14:50Z] INFO  15:50:56,379 IntervalUtils - Processing 31019109 bp from intervals
[2015-09-30T14:50Z] WARN  15:50:56,383 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:50Z] INFO  15:50:56,446 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:50Z] INFO  15:50:56,968 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:50Z] INFO  15:50:56,969 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:50Z] INFO  15:50:56,969 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:50Z] INFO  15:50:56,970 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:51Z] INFO  15:51:12,023 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:51Z] INFO  15:51:12,095 ProgressMeter -            done    701450.0    76.0 s     108.0 s      100.0%    76.0 s       0.0 s
[2015-09-30T14:51Z] INFO  15:51:12,096 ProgressMeter - Total runtime 76.42 secs, 1.27 min, 0.02 hours
[2015-09-30T14:51Z] INFO  15:51:12,096 MicroScheduler - 1799 reads were filtered out during the traversal out of approximately 703249 total reads (0.26%)
[2015-09-30T14:51Z] INFO  15:51:12,096 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:51Z] INFO  15:51:12,097 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:51Z] INFO  15:51:12,097 MicroScheduler -   -> 1799 reads (0.26% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:51Z] INFO  15:51:13,067 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:51Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam
[2015-09-30T14:51Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam 7:31022898-62585293
[2015-09-30T14:51Z] GATK: RealignerTargetCreator
[2015-09-30T14:51Z] INFO  15:51:17,093 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:51Z] INFO  15:51:17,095 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:51Z] INFO  15:51:17,095 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:51Z] INFO  15:51:17,096 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:51Z] INFO  15:51:17,099 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpdks7kI/1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign-realign.intervals -l INFO -L 7:31022898-62585293 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:51Z] INFO  15:51:17,105 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:51Z] INFO  15:51:17,105 HelpFormatter - Date/Time: 2015/09/30 15:51:17
[2015-09-30T14:51Z] INFO  15:51:17,105 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:51Z] INFO  15:51:17,105 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:51Z] INFO  15:51:17,162 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:51Z] INFO  15:51:17,273 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:51Z] INFO  15:51:17,281 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:51Z] INFO  15:51:17,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:51Z] INFO  15:51:17,552 IntervalUtils - Processing 31562396 bp from intervals
[2015-09-30T14:51Z] WARN  15:51:17,556 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:51Z] INFO  15:51:17,611 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:51Z] INFO  15:51:17,741 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:51Z] INFO  15:51:17,742 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:51Z] INFO  15:51:17,742 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:51Z] INFO  15:51:17,742 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:51Z] INFO  15:51:19,425 ProgressMeter -      7:75614302    500006.0    60.0 s     120.0 s       41.3%     2.4 m      85.0 s
[2015-09-30T14:51Z] INFO  15:51:26,973 ProgressMeter -      7:31019013   3.1014912E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T14:51Z] INFO  15:51:27,090 ProgressMeter -            done   3.1019109E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T14:51Z] INFO  15:51:27,090 ProgressMeter - Total runtime 30.12 secs, 0.50 min, 0.01 hours
[2015-09-30T14:51Z] INFO  15:51:27,096 MicroScheduler - 90876 reads were filtered out during the traversal out of approximately 950010 total reads (9.57%)
[2015-09-30T14:51Z] INFO  15:51:27,097 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:51Z] INFO  15:51:27,097 MicroScheduler -   -> 11071 reads (1.17% of total) failing BadMateFilter
[2015-09-30T14:51Z] INFO  15:51:27,098 MicroScheduler -   -> 44368 reads (4.67% of total) failing DuplicateReadFilter
[2015-09-30T14:51Z] INFO  15:51:27,098 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:51Z] INFO  15:51:27,099 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:51Z] INFO  15:51:27,099 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:51Z] INFO  15:51:27,100 MicroScheduler -   -> 35437 reads (3.73% of total) failing MappingQualityZeroFilter
[2015-09-30T14:51Z] INFO  15:51:27,100 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:51Z] INFO  15:51:27,100 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:51Z] INFO  15:51:27,101 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:51Z] INFO  15:51:28,078 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:51Z] GATK: realign ('7', 0, 31019109) : syn3-normal
[2015-09-30T14:51Z] INFO  15:51:30,536 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:51Z] INFO  15:51:30,538 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:51Z] INFO  15:51:30,538 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:51Z] INFO  15:51:30,538 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:51Z] INFO  15:51:30,542 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign-realign.intervals -L 7:1-31019109 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpXAQZkO/1_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam
[2015-09-30T14:51Z] INFO  15:51:30,547 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:51Z] INFO  15:51:30,548 HelpFormatter - Date/Time: 2015/09/30 15:51:30
[2015-09-30T14:51Z] INFO  15:51:30,548 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:51Z] INFO  15:51:30,548 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:51Z] INFO  15:51:30,672 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:51Z] INFO  15:51:30,734 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:51Z] INFO  15:51:30,741 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:51Z] INFO  15:51:30,757 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:51Z] INFO  15:51:31,415 IntervalUtils - Processing 31019109 bp from intervals
[2015-09-30T14:51Z] WARN  15:51:31,419 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:51Z] INFO  15:51:31,495 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:51Z] INFO  15:51:31,757 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:51Z] INFO  15:51:31,758 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:51Z] INFO  15:51:31,758 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:51Z] INFO  15:51:31,758 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:51Z] INFO  15:51:31,907 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:51Z] INFO  15:51:32,084 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:51Z] INFO  15:51:42,262 ProgressMeter -            done   3.1562396E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T14:51Z] INFO  15:51:42,263 ProgressMeter - Total runtime 24.52 secs, 0.41 min, 0.01 hours
[2015-09-30T14:51Z] INFO  15:51:42,266 MicroScheduler - 74819 reads were filtered out during the traversal out of approximately 705365 total reads (10.61%)
[2015-09-30T14:51Z] INFO  15:51:42,266 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:51Z] INFO  15:51:42,266 MicroScheduler -   -> 9521 reads (1.35% of total) failing BadMateFilter
[2015-09-30T14:51Z] INFO  15:51:42,266 MicroScheduler -   -> 32606 reads (4.62% of total) failing DuplicateReadFilter
[2015-09-30T14:51Z] INFO  15:51:42,267 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:51Z] INFO  15:51:42,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:51Z] INFO  15:51:42,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:51Z] INFO  15:51:42,267 MicroScheduler -   -> 32692 reads (4.63% of total) failing MappingQualityZeroFilter
[2015-09-30T14:51Z] INFO  15:51:42,268 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:51Z] INFO  15:51:42,268 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:51Z] INFO  15:51:42,268 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:51Z] INFO  15:51:43,764 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:51Z] GATK: realign ('7', 31022897, 62585293) : syn3-normal
[2015-09-30T14:51Z] INFO  15:51:45,854 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:51Z] INFO  15:51:45,856 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:51Z] INFO  15:51:45,856 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:51Z] INFO  15:51:45,856 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:51Z] INFO  15:51:45,859 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign-realign.intervals -L 7:31022898-62585293 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmp4z25XK/1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam
[2015-09-30T14:51Z] INFO  15:51:45,865 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:51Z] INFO  15:51:45,866 HelpFormatter - Date/Time: 2015/09/30 15:51:45
[2015-09-30T14:51Z] INFO  15:51:45,866 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:51Z] INFO  15:51:45,866 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:51Z] INFO  15:51:45,997 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:51Z] INFO  15:51:46,060 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:51Z] INFO  15:51:46,067 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:51Z] INFO  15:51:46,083 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:51Z] INFO  15:51:46,918 IntervalUtils - Processing 31562396 bp from intervals
[2015-09-30T14:51Z] WARN  15:51:46,922 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:51Z] INFO  15:51:46,976 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:51Z] INFO  15:51:47,109 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:51Z] INFO  15:51:47,110 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:51Z] INFO  15:51:47,110 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:51Z] INFO  15:51:47,111 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:51Z] INFO  15:51:47,249 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:51Z] INFO  15:51:47,434 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:51Z] INFO  15:51:53,564 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:51Z] INFO  15:51:53,702 ProgressMeter -            done    884995.0    94.0 s     106.0 s      100.0%    94.0 s       0.0 s
[2015-09-30T14:51Z] INFO  15:51:53,702 ProgressMeter - Total runtime 94.28 secs, 1.57 min, 0.03 hours
[2015-09-30T14:51Z] INFO  15:51:53,702 MicroScheduler - 2434 reads were filtered out during the traversal out of approximately 887429 total reads (0.27%)
[2015-09-30T14:51Z] INFO  15:51:53,703 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:51Z] INFO  15:51:53,703 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:51Z] INFO  15:51:53,703 MicroScheduler -   -> 2434 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:51Z] INFO  15:51:54,710 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:51Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam
[2015-09-30T14:51Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam 7:62708319-93925745
[2015-09-30T14:51Z] GATK: RealignerTargetCreator
[2015-09-30T14:52Z] INFO  15:52:00,147 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:00,149 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:52Z] INFO  15:52:00,150 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:52Z] INFO  15:52:00,150 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:52Z] INFO  15:52:00,154 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpiVDrQq/1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign-realign.intervals -l INFO -L 7:62708319-93925745 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:52Z] INFO  15:52:00,159 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:52Z] INFO  15:52:00,160 HelpFormatter - Date/Time: 2015/09/30 15:52:00
[2015-09-30T14:52Z] INFO  15:52:00,160 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:00,160 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:00,218 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:52Z] INFO  15:52:01,023 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:52Z] INFO  15:52:01,030 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:52Z] INFO  15:52:01,047 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:52Z] INFO  15:52:01,971 IntervalUtils - Processing 31217427 bp from intervals
[2015-09-30T14:52Z] WARN  15:52:01,977 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:52Z] INFO  15:52:02,083 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:52Z] INFO  15:52:02,471 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:52Z] INFO  15:52:02,471 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:52Z] INFO  15:52:02,472 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:52Z] INFO  15:52:02,473 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:52Z] INFO  15:52:04,098 ProgressMeter -      7:12683328    500008.0    32.0 s      64.0 s       40.9%    78.0 s      46.0 s
[2015-09-30T14:52Z] INFO  15:52:18,368 ProgressMeter -            done    944787.0    46.0 s      49.0 s      100.0%    46.0 s       0.0 s
[2015-09-30T14:52Z] INFO  15:52:18,369 ProgressMeter - Total runtime 46.61 secs, 0.78 min, 0.01 hours
[2015-09-30T14:52Z] INFO  15:52:18,372 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 944787 total reads (0.00%)
[2015-09-30T14:52Z] INFO  15:52:18,372 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:52Z] INFO  15:52:18,372 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:52Z] INFO  15:52:18,373 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:52Z] INFO  15:52:19,447 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:52Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam
[2015-09-30T14:52Z] INFO  15:52:20,785 ProgressMeter -      7:47954941    400005.0    33.0 s      84.0 s       53.6%    61.0 s      28.0 s
[2015-09-30T14:52Z] GATK pre-alignment ('7', 94024041, 125680568) : syn3-normal
[2015-09-30T14:52Z] INFO  15:52:25,909 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:25,911 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:52Z] INFO  15:52:25,912 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:52Z] INFO  15:52:25,912 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:52Z] INFO  15:52:25,915 HelpFormatter - Program Args: -T PrintReads -L 7:94024042-125680568 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpV7Ebgo/1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam
[2015-09-30T14:52Z] INFO  15:52:25,921 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:52Z] INFO  15:52:25,922 HelpFormatter - Date/Time: 2015/09/30 15:52:25
[2015-09-30T14:52Z] INFO  15:52:25,922 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:25,922 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:27,589 ProgressMeter -            done    701450.0    40.0 s      57.0 s      100.0%    40.0 s       0.0 s
[2015-09-30T14:52Z] INFO  15:52:27,590 ProgressMeter - Total runtime 40.48 secs, 0.67 min, 0.01 hours
[2015-09-30T14:52Z] INFO  15:52:27,593 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 701450 total reads (0.00%)
[2015-09-30T14:52Z] INFO  15:52:27,593 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:52Z] INFO  15:52:27,594 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:52Z] INFO  15:52:27,594 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:52Z] INFO  15:52:27,960 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:52Z] INFO  15:52:28,709 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:52Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam
[2015-09-30T14:52Z] INFO  15:52:30,162 ProgressMeter -            done   3.1217427E7    27.0 s       0.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T14:52Z] INFO  15:52:30,163 ProgressMeter - Total runtime 27.69 secs, 0.46 min, 0.01 hours
[2015-09-30T14:52Z] INFO  15:52:30,166 MicroScheduler - 204378 reads were filtered out during the traversal out of approximately 889703 total reads (22.97%)
[2015-09-30T14:52Z] INFO  15:52:30,166 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:52Z] INFO  15:52:30,167 MicroScheduler -   -> 10315 reads (1.16% of total) failing BadMateFilter
[2015-09-30T14:52Z] INFO  15:52:30,167 MicroScheduler -   -> 33332 reads (3.75% of total) failing DuplicateReadFilter
[2015-09-30T14:52Z] INFO  15:52:30,167 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:52Z] INFO  15:52:30,168 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:52Z] INFO  15:52:30,168 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:52Z] INFO  15:52:30,168 MicroScheduler -   -> 160731 reads (18.07% of total) failing MappingQualityZeroFilter
[2015-09-30T14:52Z] INFO  15:52:30,168 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:52Z] INFO  15:52:30,168 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:52Z] INFO  15:52:30,169 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:52Z] GATK pre-alignment ('7', 126078434, 157151579) : syn3-normal
[2015-09-30T14:52Z] INFO  15:52:32,071 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:52Z] GATK: realign ('7', 62708318, 93925745) : syn3-normal
[2015-09-30T14:52Z] INFO  15:52:34,774 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:52Z] INFO  15:52:34,825 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:52Z] INFO  15:52:34,832 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:52Z] INFO  15:52:34,847 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:52Z] INFO  15:52:34,860 IntervalUtils - Processing 31656527 bp from intervals
[2015-09-30T14:52Z] INFO  15:52:34,918 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:52Z] INFO  15:52:34,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:34,952 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:52Z] INFO  15:52:34,952 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:52Z] INFO  15:52:34,952 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:52Z] INFO  15:52:34,956 HelpFormatter - Program Args: -T PrintReads -L 7:126078435-157151579 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpp1SRPP/1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam
[2015-09-30T14:52Z] INFO  15:52:34,961 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:52Z] INFO  15:52:34,961 HelpFormatter - Date/Time: 2015/09/30 15:52:34
[2015-09-30T14:52Z] INFO  15:52:34,961 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:34,961 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:35,123 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:52Z] INFO  15:52:35,123 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:52Z] INFO  15:52:35,123 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:52Z] INFO  15:52:35,124 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:52Z] INFO  15:52:35,135 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:52Z] INFO  15:52:35,342 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:52Z] INFO  15:52:36,115 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:36,117 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:52Z] INFO  15:52:36,117 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:52Z] INFO  15:52:36,117 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:52Z] INFO  15:52:36,120 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign-realign.intervals -L 7:62708319-93925745 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpZ4Cu6m/1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam
[2015-09-30T14:52Z] INFO  15:52:36,126 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:52Z] INFO  15:52:36,127 HelpFormatter - Date/Time: 2015/09/30 15:52:36
[2015-09-30T14:52Z] INFO  15:52:36,127 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:36,127 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:52Z] INFO  15:52:36,254 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:52Z] INFO  15:52:36,319 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:52Z] INFO  15:52:36,326 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:52Z] INFO  15:52:36,343 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:52Z] INFO  15:52:36,569 IntervalUtils - Processing 31217427 bp from intervals
[2015-09-30T14:52Z] WARN  15:52:36,574 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:52Z] INFO  15:52:36,594 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:52Z] INFO  15:52:36,630 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:52Z] INFO  15:52:37,290 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:52Z] INFO  15:52:37,341 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:52Z] INFO  15:52:37,349 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:52Z] INFO  15:52:37,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:52Z] INFO  15:52:37,377 IntervalUtils - Processing 31073145 bp from intervals
[2015-09-30T14:52Z] INFO  15:52:37,435 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:52Z] INFO  15:52:38,062 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:52Z] INFO  15:52:38,062 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:52Z] INFO  15:52:38,063 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:52Z] INFO  15:52:38,063 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:52Z] INFO  15:52:38,210 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:52Z] INFO  15:52:38,222 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:52Z] INFO  15:52:38,222 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:52Z] INFO  15:52:38,223 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:52Z] INFO  15:52:38,223 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:52Z] INFO  15:52:38,235 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:52Z] INFO  15:52:38,404 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:52Z] INFO  15:52:38,443 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:53Z] INFO  15:53:05,126 ProgressMeter -      7:99221858    200003.0    30.0 s       2.5 m       16.4%     3.0 m       2.5 m
[2015-09-30T14:53Z] INFO  15:53:08,226 ProgressMeter -     7:131185600    200002.0    30.0 s       2.5 m       16.4%     3.0 m       2.5 m
[2015-09-30T14:53Z] INFO  15:53:09,039 ProgressMeter -      7:75615763    500006.0    30.0 s      61.0 s       41.3%    72.0 s      42.0 s
[2015-09-30T14:53Z] INFO  15:53:22,499 ProgressMeter -            done    884995.0    44.0 s      50.0 s      100.0%    44.0 s       0.0 s
[2015-09-30T14:53Z] INFO  15:53:22,499 ProgressMeter - Total runtime 44.44 secs, 0.74 min, 0.01 hours
[2015-09-30T14:53Z] INFO  15:53:22,502 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 884995 total reads (0.00%)
[2015-09-30T14:53Z] INFO  15:53:22,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:53Z] INFO  15:53:22,503 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:53Z] INFO  15:53:22,503 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:53Z] INFO  15:53:23,489 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:53Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam
[2015-09-30T14:53Z] GATK pre-alignment ('7', 157155595, 159138663) : syn3-normal
[2015-09-30T14:53Z] INFO  15:53:28,312 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:53Z] INFO  15:53:28,314 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:53Z] INFO  15:53:28,314 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:53Z] INFO  15:53:28,315 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:53Z] INFO  15:53:28,318 HelpFormatter - Program Args: -T PrintReads -L 7:157155596-159138663 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmp9zT5PY/1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam
[2015-09-30T14:53Z] INFO  15:53:28,324 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:53Z] INFO  15:53:28,324 HelpFormatter - Date/Time: 2015/09/30 15:53:28
[2015-09-30T14:53Z] INFO  15:53:28,324 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:53Z] INFO  15:53:28,324 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:53Z] INFO  15:53:28,431 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:53Z] INFO  15:53:30,166 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:53Z] INFO  15:53:30,218 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:53Z] INFO  15:53:30,225 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:53Z] INFO  15:53:30,240 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:53Z] INFO  15:53:30,254 IntervalUtils - Processing 1983068 bp from intervals
[2015-09-30T14:53Z] INFO  15:53:30,311 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:53Z] INFO  15:53:30,423 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:53Z] INFO  15:53:30,423 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:53Z] INFO  15:53:30,424 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:53Z] INFO  15:53:30,424 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:53Z] INFO  15:53:30,435 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:53Z] INFO  15:53:30,452 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:53Z] INFO  15:53:35,957 ProgressMeter -     7:101923769    600009.0    60.0 s     101.0 s       25.0%     4.0 m       3.0 m
[2015-09-30T14:53Z] INFO  15:53:38,731 ProgressMeter -     7:141731063    500008.0    60.0 s       2.0 m       50.4%   119.0 s      59.0 s
[2015-09-30T14:53Z] INFO  15:53:39,679 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@627346b4
[2015-09-30T14:53Z] INFO  15:53:39,772 ProgressMeter -            done     77248.0     9.0 s       2.0 m       90.3%     9.0 s       0.0 s
[2015-09-30T14:53Z] INFO  15:53:39,772 ProgressMeter - Total runtime 9.35 secs, 0.16 min, 0.00 hours
[2015-09-30T14:53Z] INFO  15:53:39,773 MicroScheduler - 209 reads were filtered out during the traversal out of approximately 77457 total reads (0.27%)
[2015-09-30T14:53Z] INFO  15:53:39,773 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:53Z] INFO  15:53:39,773 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:53Z] INFO  15:53:39,773 MicroScheduler -   -> 209 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:53Z] INFO  15:53:40,752 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:53Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam
[2015-09-30T14:53Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam 7:157155596-159138663
[2015-09-30T14:53Z] GATK: RealignerTargetCreator
[2015-09-30T14:53Z] INFO  15:53:43,241 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:53Z] INFO  15:53:43,243 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:53Z] INFO  15:53:43,243 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:53Z] INFO  15:53:43,243 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:53Z] INFO  15:53:43,247 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpZ5p7tR/1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign-realign.intervals -l INFO -L 7:157155596-159138663 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:53Z] INFO  15:53:43,252 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:53Z] INFO  15:53:43,252 HelpFormatter - Date/Time: 2015/09/30 15:53:43
[2015-09-30T14:53Z] INFO  15:53:43,252 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:53Z] INFO  15:53:43,253 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:53Z] INFO  15:53:43,309 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:53Z] INFO  15:53:43,420 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:53Z] INFO  15:53:43,427 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:53Z] INFO  15:53:43,442 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:53Z] INFO  15:53:44,129 IntervalUtils - Processing 1983068 bp from intervals
[2015-09-30T14:53Z] WARN  15:53:44,133 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:53Z] INFO  15:53:44,191 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:53Z] INFO  15:53:44,227 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:53Z] INFO  15:53:44,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:53Z] INFO  15:53:44,228 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:53Z] INFO  15:53:44,229 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:53Z] INFO  15:53:47,722 ProgressMeter -            done   1983068.0     3.0 s       1.0 s      100.0%     3.0 s       0.0 s
[2015-09-30T14:53Z] INFO  15:53:47,723 ProgressMeter - Total runtime 3.49 secs, 0.06 min, 0.00 hours
[2015-09-30T14:53Z] INFO  15:53:47,726 MicroScheduler - 6778 reads were filtered out during the traversal out of approximately 77568 total reads (8.74%)
[2015-09-30T14:53Z] INFO  15:53:47,726 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:53Z] INFO  15:53:47,726 MicroScheduler -   -> 885 reads (1.14% of total) failing BadMateFilter
[2015-09-30T14:53Z] INFO  15:53:47,727 MicroScheduler -   -> 3682 reads (4.75% of total) failing DuplicateReadFilter
[2015-09-30T14:53Z] INFO  15:53:47,727 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:53Z] INFO  15:53:47,727 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:53Z] INFO  15:53:47,727 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:53Z] INFO  15:53:47,728 MicroScheduler -   -> 2211 reads (2.85% of total) failing MappingQualityZeroFilter
[2015-09-30T14:53Z] INFO  15:53:47,728 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:53Z] INFO  15:53:47,728 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:53Z] INFO  15:53:47,728 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:53Z] INFO  15:53:48,709 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:53Z] GATK: realign ('7', 157155595, 159138663) : syn3-normal
[2015-09-30T14:53Z] INFO  15:53:50,915 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:53Z] INFO  15:53:50,917 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:53Z] INFO  15:53:50,917 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:53Z] INFO  15:53:50,918 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:53Z] INFO  15:53:50,921 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign-realign.intervals -L 7:157155596-159138663 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpGdhtYY/1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam
[2015-09-30T14:53Z] INFO  15:53:50,927 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:53Z] INFO  15:53:50,927 HelpFormatter - Date/Time: 2015/09/30 15:53:50
[2015-09-30T14:53Z] INFO  15:53:50,927 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:53Z] INFO  15:53:50,928 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:53Z] INFO  15:53:51,056 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:53Z] INFO  15:53:51,125 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:53Z] INFO  15:53:51,133 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:53Z] INFO  15:53:51,149 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:53Z] INFO  15:53:51,382 IntervalUtils - Processing 1983068 bp from intervals
[2015-09-30T14:53Z] WARN  15:53:51,386 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:53Z] INFO  15:53:51,444 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:53Z] INFO  15:53:51,487 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:53Z] INFO  15:53:51,488 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:53Z] INFO  15:53:51,488 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:53Z] INFO  15:53:51,488 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:53Z] INFO  15:53:51,547 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:53Z] INFO  15:53:51,565 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:53Z] INFO  15:53:57,959 ProgressMeter -            done     77248.0     6.0 s      83.0 s       90.3%     6.0 s       0.0 s
[2015-09-30T14:53Z] INFO  15:53:57,960 ProgressMeter - Total runtime 6.47 secs, 0.11 min, 0.00 hours
[2015-09-30T14:53Z] INFO  15:53:57,963 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 77248 total reads (0.00%)
[2015-09-30T14:53Z] INFO  15:53:57,963 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:53Z] INFO  15:53:57,963 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:53Z] INFO  15:53:57,963 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:53Z] INFO  15:53:58,960 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:53Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam
[2015-09-30T14:53Z] GATK pre-alignment ('8', 0, 31024990) : syn3-normal
[2015-09-30T14:54Z] INFO  15:54:00,877 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:54Z] INFO  15:54:00,878 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:54Z] INFO  15:54:00,879 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:54Z] INFO  15:54:00,879 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:54Z] INFO  15:54:00,882 HelpFormatter - Program Args: -T PrintReads -L 8:1-31024990 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpKZ5zj7/1_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam
[2015-09-30T14:54Z] INFO  15:54:00,887 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:54Z] INFO  15:54:00,888 HelpFormatter - Date/Time: 2015/09/30 15:54:00
[2015-09-30T14:54Z] INFO  15:54:00,888 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:54Z] INFO  15:54:00,888 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:54Z] INFO  15:54:01,468 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:54Z] INFO  15:54:02,241 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:54Z] INFO  15:54:02,293 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:54Z] INFO  15:54:02,301 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:54Z] INFO  15:54:02,365 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T14:54Z] INFO  15:54:02,431 IntervalUtils - Processing 31024990 bp from intervals
[2015-09-30T14:54Z] INFO  15:54:02,491 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:54Z] INFO  15:54:03,012 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:54Z] INFO  15:54:03,012 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:54Z] INFO  15:54:03,012 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:54Z] INFO  15:54:03,013 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:54Z] INFO  15:54:03,024 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:54Z] INFO  15:54:03,233 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:54Z] INFO  15:54:05,958 ProgressMeter -     7:112112065    900013.0    90.0 s     100.0 s       57.1%     2.6 m      67.0 s
[2015-09-30T14:54Z] INFO  15:54:08,749 ProgressMeter -     7:150002623    900015.0    90.0 s     100.0 s       77.0%   116.0 s      26.0 s
[2015-09-30T14:54Z] INFO  15:54:19,581 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:54Z] INFO  15:54:19,631 ProgressMeter -            done   1177999.0   104.0 s      88.0 s      100.0%   104.0 s       0.0 s
[2015-09-30T14:54Z] INFO  15:54:19,632 ProgressMeter - Total runtime 104.51 secs, 1.74 min, 0.03 hours
[2015-09-30T14:54Z] INFO  15:54:19,632 MicroScheduler - 2987 reads were filtered out during the traversal out of approximately 1180986 total reads (0.25%)
[2015-09-30T14:54Z] INFO  15:54:19,632 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:54Z] INFO  15:54:19,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:54Z] INFO  15:54:19,633 MicroScheduler -   -> 2987 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:54Z] INFO  15:54:20,614 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:54Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam
[2015-09-30T14:54Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam 7:94024042-125680568
[2015-09-30T14:54Z] GATK: RealignerTargetCreator
[2015-09-30T14:54Z] INFO  15:54:26,055 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:54Z] INFO  15:54:26,056 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:54Z] INFO  15:54:26,057 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:54Z] INFO  15:54:26,057 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:54Z] INFO  15:54:26,060 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpOmwuGG/1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign-realign.intervals -l INFO -L 7:94024042-125680568 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:54Z] INFO  15:54:26,065 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:54Z] INFO  15:54:26,066 HelpFormatter - Date/Time: 2015/09/30 15:54:26
[2015-09-30T14:54Z] INFO  15:54:26,066 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:54Z] INFO  15:54:26,066 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:54Z] INFO  15:54:26,119 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:54Z] INFO  15:54:26,216 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:54Z] INFO  15:54:26,224 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:54Z] INFO  15:54:26,238 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:54Z] INFO  15:54:26,467 IntervalUtils - Processing 31656527 bp from intervals
[2015-09-30T14:54Z] WARN  15:54:26,470 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:54Z] INFO  15:54:26,523 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:54Z] INFO  15:54:26,665 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:54Z] INFO  15:54:26,665 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:54Z] INFO  15:54:26,666 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:54Z] INFO  15:54:26,666 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:54Z] INFO  15:54:32,843 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7e2705ea
[2015-09-30T14:54Z] INFO  15:54:33,295 ProgressMeter -      8:10532430    200003.0    30.0 s       2.5 m       33.9%    88.0 s      58.0 s
[2015-09-30T14:54Z] INFO  15:54:33,467 ProgressMeter -            done   1298986.0   115.0 s      88.0 s      100.0%   115.0 s       0.0 s
[2015-09-30T14:54Z] INFO  15:54:33,468 ProgressMeter - Total runtime 115.25 secs, 1.92 min, 0.03 hours
[2015-09-30T14:54Z] INFO  15:54:33,468 MicroScheduler - 2509 reads were filtered out during the traversal out of approximately 1301495 total reads (0.19%)
[2015-09-30T14:54Z] INFO  15:54:33,468 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:54Z] INFO  15:54:33,469 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:54Z] INFO  15:54:33,469 MicroScheduler -   -> 2509 reads (0.19% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:54Z] INFO  15:54:34,483 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:54Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam
[2015-09-30T14:54Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam 7:126078435-157151579
[2015-09-30T14:54Z] GATK: RealignerTargetCreator
[2015-09-30T14:54Z] INFO  15:54:42,667 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:54Z] INFO  15:54:42,670 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:54Z] INFO  15:54:42,670 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:54Z] INFO  15:54:42,670 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:54Z] INFO  15:54:42,674 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpfhefWb/1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign-realign.intervals -l INFO -L 7:126078435-157151579 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:54Z] INFO  15:54:42,680 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:54Z] INFO  15:54:42,680 HelpFormatter - Date/Time: 2015/09/30 15:54:42
[2015-09-30T14:54Z] INFO  15:54:42,680 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:54Z] INFO  15:54:42,680 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:54Z] INFO  15:54:42,749 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:54Z] INFO  15:54:42,875 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:54Z] INFO  15:54:42,884 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:54Z] INFO  15:54:42,900 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:54Z] INFO  15:54:43,144 IntervalUtils - Processing 31073145 bp from intervals
[2015-09-30T14:54Z] WARN  15:54:43,149 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:54Z] INFO  15:54:43,207 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:54Z] INFO  15:54:43,366 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:54Z] INFO  15:54:43,367 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:54Z] INFO  15:54:43,367 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:54Z] INFO  15:54:43,368 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:54Z] INFO  15:54:56,669 ProgressMeter -     7:124304925   3.0264983E7    30.0 s       0.0 s       95.7%    31.0 s       1.0 s
[2015-09-30T14:54Z] INFO  15:54:57,592 ProgressMeter -            done   3.1656527E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T14:54Z] INFO  15:54:57,593 ProgressMeter - Total runtime 30.93 secs, 0.52 min, 0.01 hours
[2015-09-30T14:54Z] INFO  15:54:57,593 MicroScheduler - 187028 reads were filtered out during the traversal out of approximately 1184770 total reads (15.79%)
[2015-09-30T14:54Z] INFO  15:54:57,594 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:54Z] INFO  15:54:57,594 MicroScheduler -   -> 12646 reads (1.07% of total) failing BadMateFilter
[2015-09-30T14:54Z] INFO  15:54:57,594 MicroScheduler -   -> 52394 reads (4.42% of total) failing DuplicateReadFilter
[2015-09-30T14:54Z] INFO  15:54:57,594 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:54Z] INFO  15:54:57,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:54Z] INFO  15:54:57,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:54Z] INFO  15:54:57,595 MicroScheduler -   -> 121988 reads (10.30% of total) failing MappingQualityZeroFilter
[2015-09-30T14:54Z] INFO  15:54:57,595 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:54Z] INFO  15:54:57,595 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:54Z] INFO  15:54:57,596 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:54Z] INFO  15:54:58,623 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:54Z] GATK: realign ('7', 94024041, 125680568) : syn3-normal
[2015-09-30T14:55Z] INFO  15:55:01,075 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:55Z] INFO  15:55:01,077 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:55Z] INFO  15:55:01,077 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:55Z] INFO  15:55:01,077 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:55Z] INFO  15:55:01,081 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign-realign.intervals -L 7:94024042-125680568 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmp1v97FS/1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam
[2015-09-30T14:55Z] INFO  15:55:01,087 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:55Z] INFO  15:55:01,087 HelpFormatter - Date/Time: 2015/09/30 15:55:01
[2015-09-30T14:55Z] INFO  15:55:01,088 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:55Z] INFO  15:55:01,088 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:55Z] INFO  15:55:01,208 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:55Z] INFO  15:55:01,270 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:55Z] INFO  15:55:01,278 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:55Z] INFO  15:55:01,293 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:55Z] INFO  15:55:01,745 IntervalUtils - Processing 31656527 bp from intervals
[2015-09-30T14:55Z] WARN  15:55:01,749 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:55Z] INFO  15:55:01,804 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:55Z] INFO  15:55:01,951 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:55Z] INFO  15:55:01,952 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:55Z] INFO  15:55:01,952 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:55Z] INFO  15:55:01,953 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:55Z] INFO  15:55:02,102 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:55Z] INFO  15:55:02,284 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:55Z] INFO  15:55:03,301 ProgressMeter -      8:22035828    500007.0    60.0 s     120.0 s       71.0%    84.0 s      24.0 s
[2015-09-30T14:55Z] INFO  15:55:13,370 ProgressMeter -     7:151053497   2.4965662E7    30.0 s       1.0 s       80.4%    37.0 s       7.0 s
[2015-09-30T14:55Z] INFO  15:55:18,704 ProgressMeter -            done   3.1073145E7    35.0 s       1.0 s      100.0%    35.0 s       0.0 s
[2015-09-30T14:55Z] INFO  15:55:18,704 ProgressMeter - Total runtime 35.34 secs, 0.59 min, 0.01 hours
[2015-09-30T14:55Z] INFO  15:55:18,708 MicroScheduler - 153098 reads were filtered out during the traversal out of approximately 1307303 total reads (11.71%)
[2015-09-30T14:55Z] INFO  15:55:18,708 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:55Z] INFO  15:55:18,708 MicroScheduler -   -> 13306 reads (1.02% of total) failing BadMateFilter
[2015-09-30T14:55Z] INFO  15:55:18,709 MicroScheduler -   -> 60137 reads (4.60% of total) failing DuplicateReadFilter
[2015-09-30T14:55Z] INFO  15:55:18,709 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:55Z] INFO  15:55:18,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:55Z] INFO  15:55:18,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:55Z] INFO  15:55:18,710 MicroScheduler -   -> 79655 reads (6.09% of total) failing MappingQualityZeroFilter
[2015-09-30T14:55Z] INFO  15:55:18,710 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:55Z] INFO  15:55:18,710 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:55Z] INFO  15:55:18,710 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:55Z] INFO  15:55:19,707 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:55Z] GATK: realign ('7', 126078434, 157151579) : syn3-normal
[2015-09-30T14:55Z] INFO  15:55:21,802 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:55Z] INFO  15:55:21,804 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:55Z] INFO  15:55:21,804 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:55Z] INFO  15:55:21,805 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:55Z] INFO  15:55:21,808 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign-realign.intervals -L 7:126078435-157151579 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/tx/tmpqOn5dQ/1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam
[2015-09-30T14:55Z] INFO  15:55:21,814 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:55Z] INFO  15:55:21,814 HelpFormatter - Date/Time: 2015/09/30 15:55:21
[2015-09-30T14:55Z] INFO  15:55:21,814 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:55Z] INFO  15:55:21,814 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:55Z] INFO  15:55:21,922 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:55Z] INFO  15:55:21,988 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:55Z] INFO  15:55:21,996 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:55Z] INFO  15:55:22,011 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:55Z] INFO  15:55:22,787 IntervalUtils - Processing 31073145 bp from intervals
[2015-09-30T14:55Z] WARN  15:55:22,791 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:55Z] INFO  15:55:22,845 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:55Z] INFO  15:55:23,004 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:55Z] INFO  15:55:23,005 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:55Z] INFO  15:55:23,005 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:55Z] INFO  15:55:23,005 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:55Z] INFO  15:55:23,151 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:55Z] INFO  15:55:23,343 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:55Z] INFO  15:55:31,955 ProgressMeter -     7:100888615    500007.0    30.0 s      60.0 s       21.7%     2.3 m     108.0 s
[2015-09-30T14:55Z] INFO  15:55:33,301 ProgressMeter -      8:28413535    800010.0    90.0 s     112.0 s       91.6%    98.0 s       8.0 s
[2015-09-30T14:55Z] INFO  15:55:40,950 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:55Z] INFO  15:55:41,208 ProgressMeter -            done    931394.0    98.0 s     105.0 s      100.0%    98.0 s       0.0 s
[2015-09-30T14:55Z] INFO  15:55:41,209 ProgressMeter - Total runtime 98.20 secs, 1.64 min, 0.03 hours
[2015-09-30T14:55Z] INFO  15:55:41,209 MicroScheduler - 2016 reads were filtered out during the traversal out of approximately 933410 total reads (0.22%)
[2015-09-30T14:55Z] INFO  15:55:41,209 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:55Z] INFO  15:55:41,209 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:55Z] INFO  15:55:41,209 MicroScheduler -   -> 2016 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:55Z] INFO  15:55:42,205 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:55Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam
[2015-09-30T14:55Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam 8:1-31024990
[2015-09-30T14:55Z] GATK: RealignerTargetCreator
[2015-09-30T14:55Z] INFO  15:55:46,965 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:55Z] INFO  15:55:46,967 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:55Z] INFO  15:55:46,968 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:55Z] INFO  15:55:46,968 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:55Z] INFO  15:55:46,971 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpmfNvV3/1_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign-realign.intervals -l INFO -L 8:1-31024990 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:55Z] INFO  15:55:46,977 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:55Z] INFO  15:55:46,977 HelpFormatter - Date/Time: 2015/09/30 15:55:46
[2015-09-30T14:55Z] INFO  15:55:46,977 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:55Z] INFO  15:55:46,977 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:55Z] INFO  15:55:47,034 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:55Z] INFO  15:55:47,138 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:55Z] INFO  15:55:47,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:55Z] INFO  15:55:47,161 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:55Z] INFO  15:55:47,879 IntervalUtils - Processing 31024990 bp from intervals
[2015-09-30T14:55Z] WARN  15:55:47,883 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:55Z] INFO  15:55:47,943 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:55Z] INFO  15:55:48,092 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:55Z] INFO  15:55:48,092 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:55Z] INFO  15:55:48,093 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:55Z] INFO  15:55:48,093 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:55Z] INFO  15:55:53,511 ProgressMeter -     7:139826751    500008.0    30.0 s      61.0 s       44.2%    67.0 s      37.0 s
[2015-09-30T14:55Z] INFO  15:55:56,473 ProgressMeter -            done   1177999.0    54.0 s      46.0 s      100.0%    54.0 s       0.0 s
[2015-09-30T14:55Z] INFO  15:55:56,474 ProgressMeter - Total runtime 54.52 secs, 0.91 min, 0.02 hours
[2015-09-30T14:55Z] INFO  15:55:56,477 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1177999 total reads (0.00%)
[2015-09-30T14:55Z] INFO  15:55:56,477 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:55Z] INFO  15:55:56,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:55Z] INFO  15:55:56,478 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:55Z] INFO  15:55:57,593 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:55Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam
[2015-09-30T14:56Z] GATK pre-alignment ('8', 31030285, 62213090) : syn3-normal
[2015-09-30T14:56Z] INFO  15:56:02,224 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:56Z] INFO  15:56:02,226 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:56Z] INFO  15:56:02,226 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:56Z] INFO  15:56:02,226 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:56Z] INFO  15:56:02,230 HelpFormatter - Program Args: -T PrintReads -L 8:31030286-62213090 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmp5GglAz/1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam
[2015-09-30T14:56Z] INFO  15:56:02,235 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:56Z] INFO  15:56:02,236 HelpFormatter - Date/Time: 2015/09/30 15:56:02
[2015-09-30T14:56Z] INFO  15:56:02,236 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:56Z] INFO  15:56:02,236 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:56Z] INFO  15:56:02,347 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:56Z] INFO  15:56:03,913 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:56Z] INFO  15:56:03,962 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:56Z] INFO  15:56:03,969 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:56Z] INFO  15:56:04,070 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2015-09-30T14:56Z] INFO  15:56:04,112 IntervalUtils - Processing 31182805 bp from intervals
[2015-09-30T14:56Z] INFO  15:56:04,171 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:56Z] INFO  15:56:04,750 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:56Z] INFO  15:56:04,750 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:56Z] INFO  15:56:04,751 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:56Z] INFO  15:56:04,751 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:56Z] INFO  15:56:04,762 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:56Z] INFO  15:56:04,963 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:56Z] INFO  15:56:16,910 ProgressMeter -            done   3.102499E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T14:56Z] INFO  15:56:16,911 ProgressMeter - Total runtime 28.82 secs, 0.48 min, 0.01 hours
[2015-09-30T14:56Z] INFO  15:56:16,914 MicroScheduler - 135882 reads were filtered out during the traversal out of approximately 938070 total reads (14.49%)
[2015-09-30T14:56Z] INFO  15:56:16,914 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:56Z] INFO  15:56:16,914 MicroScheduler -   -> 10682 reads (1.14% of total) failing BadMateFilter
[2015-09-30T14:56Z] INFO  15:56:16,915 MicroScheduler -   -> 40211 reads (4.29% of total) failing DuplicateReadFilter
[2015-09-30T14:56Z] INFO  15:56:16,915 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:56Z] INFO  15:56:16,915 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:56Z] INFO  15:56:16,915 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:56Z] INFO  15:56:16,916 MicroScheduler -   -> 84989 reads (9.06% of total) failing MappingQualityZeroFilter
[2015-09-30T14:56Z] INFO  15:56:16,916 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:56Z] INFO  15:56:16,916 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:56Z] INFO  15:56:16,916 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:56Z] INFO  15:56:17,907 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:56Z] GATK: realign ('8', 0, 31024990) : syn3-normal
[2015-09-30T14:56Z] INFO  15:56:20,037 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:56Z] INFO  15:56:20,039 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:56Z] INFO  15:56:20,039 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:56Z] INFO  15:56:20,040 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:56Z] INFO  15:56:20,043 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign-realign.intervals -L 8:1-31024990 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpcPOiCR/1_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam
[2015-09-30T14:56Z] INFO  15:56:20,049 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:56Z] INFO  15:56:20,049 HelpFormatter - Date/Time: 2015/09/30 15:56:20
[2015-09-30T14:56Z] INFO  15:56:20,050 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:56Z] INFO  15:56:20,050 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:56Z] INFO  15:56:20,156 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:56Z] INFO  15:56:20,798 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:56Z] INFO  15:56:20,805 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:56Z] INFO  15:56:20,820 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:56Z] INFO  15:56:21,045 IntervalUtils - Processing 31024990 bp from intervals
[2015-09-30T14:56Z] WARN  15:56:21,049 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:56Z] INFO  15:56:21,100 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:56Z] INFO  15:56:21,241 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:56Z] INFO  15:56:21,242 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:56Z] INFO  15:56:21,242 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:56Z] INFO  15:56:21,242 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:56Z] INFO  15:56:21,383 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:56Z] INFO  15:56:21,568 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:56Z] INFO  15:56:23,512 ProgressMeter -     7:155256075   1200019.0    60.0 s      50.0 s       93.9%    63.0 s       3.0 s
[2015-09-30T14:56Z] INFO  15:56:25,211 ProgressMeter -            done   1298986.0    62.0 s      47.0 s      100.0%    62.0 s       0.0 s
[2015-09-30T14:56Z] INFO  15:56:25,211 ProgressMeter - Total runtime 62.21 secs, 1.04 min, 0.02 hours
[2015-09-30T14:56Z] INFO  15:56:25,214 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1298986 total reads (0.00%)
[2015-09-30T14:56Z] INFO  15:56:25,215 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:56Z] INFO  15:56:25,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:56Z] INFO  15:56:25,215 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:56Z] INFO  15:56:26,360 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:56Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam
[2015-09-30T14:56Z] GATK pre-alignment ('8', 62288979, 93648031) : syn3-normal
[2015-09-30T14:56Z] INFO  15:56:32,260 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:56Z] INFO  15:56:32,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:56Z] INFO  15:56:32,262 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:56Z] INFO  15:56:32,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:56Z] INFO  15:56:32,266 HelpFormatter - Program Args: -T PrintReads -L 8:62288980-93648031 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmp7U_mnQ/1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam
[2015-09-30T14:56Z] INFO  15:56:32,272 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:56Z] INFO  15:56:32,272 HelpFormatter - Date/Time: 2015/09/30 15:56:32
[2015-09-30T14:56Z] INFO  15:56:32,272 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:56Z] INFO  15:56:32,272 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:56Z] INFO  15:56:32,388 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:56Z] INFO  15:56:33,740 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:56Z] INFO  15:56:33,789 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:56Z] INFO  15:56:33,796 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:56Z] INFO  15:56:33,912 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2015-09-30T14:56Z] INFO  15:56:33,947 IntervalUtils - Processing 31359052 bp from intervals
[2015-09-30T14:56Z] INFO  15:56:34,005 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:56Z] INFO  15:56:34,612 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:56Z] INFO  15:56:34,613 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:56Z] INFO  15:56:34,613 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:56Z] INFO  15:56:34,613 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:56Z] INFO  15:56:34,624 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:56Z] INFO  15:56:34,753 ProgressMeter -      8:41518491    200002.0    30.0 s       2.5 m       33.6%    89.0 s      59.0 s
[2015-09-30T14:56Z] INFO  15:56:34,804 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:56Z] INFO  15:56:52,232 ProgressMeter -      8:21840219    400006.0    30.0 s      77.0 s       70.4%    42.0 s      12.0 s
[2015-09-30T14:57Z] INFO  15:57:02,580 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:57Z] INFO  15:57:02,740 ProgressMeter -            done    522059.0    57.0 s     111.0 s      100.0%    57.0 s       0.0 s
[2015-09-30T14:57Z] INFO  15:57:02,740 ProgressMeter - Total runtime 57.99 secs, 0.97 min, 0.02 hours
[2015-09-30T14:57Z] INFO  15:57:02,741 MicroScheduler - 1552 reads were filtered out during the traversal out of approximately 523611 total reads (0.30%)
[2015-09-30T14:57Z] INFO  15:57:02,741 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:57Z] INFO  15:57:02,741 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:57Z] INFO  15:57:02,741 MicroScheduler -   -> 1552 reads (0.30% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:57Z] INFO  15:57:03,842 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:57Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam
[2015-09-30T14:57Z] INFO  15:57:04,617 ProgressMeter -      8:75941963    200002.0    30.0 s       2.5 m       43.5%    68.0 s      38.0 s
[2015-09-30T14:57Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam 8:31030286-62213090
[2015-09-30T14:57Z] GATK: RealignerTargetCreator
[2015-09-30T14:57Z] INFO  15:57:07,346 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:07,348 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:57Z] INFO  15:57:07,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:57Z] INFO  15:57:07,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:57Z] INFO  15:57:07,352 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpA_enq6/1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign-realign.intervals -l INFO -L 8:31030286-62213090 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:57Z] INFO  15:57:07,358 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:57Z] INFO  15:57:07,358 HelpFormatter - Date/Time: 2015/09/30 15:57:07
[2015-09-30T14:57Z] INFO  15:57:07,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:07,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:07,414 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:57Z] INFO  15:57:07,523 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:57Z] INFO  15:57:07,530 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:57Z] INFO  15:57:07,546 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:57Z] INFO  15:57:07,805 IntervalUtils - Processing 31182805 bp from intervals
[2015-09-30T14:57Z] WARN  15:57:07,809 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:57Z] INFO  15:57:07,866 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:57Z] INFO  15:57:08,011 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:57Z] INFO  15:57:08,012 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:57Z] INFO  15:57:08,012 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:57Z] INFO  15:57:08,012 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:57Z] INFO  15:57:09,530 ProgressMeter -            done    931394.0    48.0 s      51.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T14:57Z] INFO  15:57:09,530 ProgressMeter - Total runtime 48.29 secs, 0.80 min, 0.01 hours
[2015-09-30T14:57Z] INFO  15:57:09,533 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 931394 total reads (0.00%)
[2015-09-30T14:57Z] INFO  15:57:09,534 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:57Z] INFO  15:57:09,534 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:57Z] INFO  15:57:09,534 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:57Z] INFO  15:57:11,191 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:57Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam
[2015-09-30T14:57Z] GATK pre-alignment ('8', 93896832, 124968568) : syn3-normal
[2015-09-30T14:57Z] INFO  15:57:15,241 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:15,243 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:57Z] INFO  15:57:15,243 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:57Z] INFO  15:57:15,243 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:57Z] INFO  15:57:15,246 HelpFormatter - Program Args: -T PrintReads -L 8:93896833-124968568 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpaLtdfV/1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam
[2015-09-30T14:57Z] INFO  15:57:15,252 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:57Z] INFO  15:57:15,253 HelpFormatter - Date/Time: 2015/09/30 15:57:15
[2015-09-30T14:57Z] INFO  15:57:15,253 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:15,253 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:15,363 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:57Z] INFO  15:57:16,890 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:57Z] INFO  15:57:16,942 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:57Z] INFO  15:57:16,949 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:57Z] INFO  15:57:16,965 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:57Z] INFO  15:57:16,979 IntervalUtils - Processing 31071736 bp from intervals
[2015-09-30T14:57Z] INFO  15:57:17,040 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:57Z] INFO  15:57:17,242 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:57Z] INFO  15:57:17,242 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:57Z] INFO  15:57:17,243 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:57Z] INFO  15:57:17,243 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:57Z] INFO  15:57:17,254 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:57Z] INFO  15:57:17,455 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:57Z] INFO  15:57:32,308 ProgressMeter -            done   3.1182805E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T14:57Z] INFO  15:57:32,309 ProgressMeter - Total runtime 24.30 secs, 0.40 min, 0.01 hours
[2015-09-30T14:57Z] INFO  15:57:32,312 MicroScheduler - 41381 reads were filtered out during the traversal out of approximately 525001 total reads (7.88%)
[2015-09-30T14:57Z] INFO  15:57:32,312 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:57Z] INFO  15:57:32,312 MicroScheduler -   -> 8699 reads (1.66% of total) failing BadMateFilter
[2015-09-30T14:57Z] INFO  15:57:32,313 MicroScheduler -   -> 22684 reads (4.32% of total) failing DuplicateReadFilter
[2015-09-30T14:57Z] INFO  15:57:32,313 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:57Z] INFO  15:57:32,313 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:57Z] INFO  15:57:32,313 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:57Z] INFO  15:57:32,314 MicroScheduler -   -> 9998 reads (1.90% of total) failing MappingQualityZeroFilter
[2015-09-30T14:57Z] INFO  15:57:32,314 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:57Z] INFO  15:57:32,314 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:57Z] INFO  15:57:32,314 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:57Z] INFO  15:57:33,358 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:57Z] GATK: realign ('8', 31030285, 62213090) : syn3-normal
[2015-09-30T14:57Z] INFO  15:57:34,635 ProgressMeter -      8:90955734    500005.0    60.0 s     120.0 s       91.4%    65.0 s       5.0 s
[2015-09-30T14:57Z] INFO  15:57:37,379 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:37,382 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:57Z] INFO  15:57:37,382 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:57Z] INFO  15:57:37,382 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:57Z] INFO  15:57:37,385 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign-realign.intervals -L 8:31030286-62213090 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpsF4h1b/1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam
[2015-09-30T14:57Z] INFO  15:57:37,391 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:57Z] INFO  15:57:37,391 HelpFormatter - Date/Time: 2015/09/30 15:57:37
[2015-09-30T14:57Z] INFO  15:57:37,392 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:37,392 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:37,520 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:57Z] INFO  15:57:37,585 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:57Z] INFO  15:57:37,592 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:57Z] INFO  15:57:37,608 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:57Z] INFO  15:57:37,847 IntervalUtils - Processing 31182805 bp from intervals
[2015-09-30T14:57Z] WARN  15:57:37,851 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:57Z] INFO  15:57:37,907 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:57Z] INFO  15:57:38,082 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T14:57Z] INFO  15:57:38,304 ProgressMeter -            done    571980.0    63.0 s     111.0 s      100.0%    63.0 s       0.0 s
[2015-09-30T14:57Z] INFO  15:57:38,305 ProgressMeter - Total runtime 63.69 secs, 1.06 min, 0.02 hours
[2015-09-30T14:57Z] INFO  15:57:38,305 MicroScheduler - 1559 reads were filtered out during the traversal out of approximately 573539 total reads (0.27%)
[2015-09-30T14:57Z] INFO  15:57:38,305 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:57Z] INFO  15:57:38,305 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:57Z] INFO  15:57:38,306 MicroScheduler -   -> 1559 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:57Z] INFO  15:57:38,549 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:57Z] INFO  15:57:38,550 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:57Z] INFO  15:57:38,550 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:57Z] INFO  15:57:38,551 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:57Z] INFO  15:57:38,676 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:57Z] INFO  15:57:38,864 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:57Z] INFO  15:57:39,331 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:57Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam
[2015-09-30T14:57Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam 8:62288980-93648031
[2015-09-30T14:57Z] GATK: RealignerTargetCreator
[2015-09-30T14:57Z] INFO  15:57:43,118 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:43,120 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:57Z] INFO  15:57:43,120 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:57Z] INFO  15:57:43,120 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:57Z] INFO  15:57:43,124 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpzlyLd1/1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign-realign.intervals -l INFO -L 8:62288980-93648031 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:57Z] INFO  15:57:43,130 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:57Z] INFO  15:57:43,130 HelpFormatter - Date/Time: 2015/09/30 15:57:43
[2015-09-30T14:57Z] INFO  15:57:43,130 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:43,130 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:57Z] INFO  15:57:43,189 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:57Z] INFO  15:57:43,989 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:57Z] INFO  15:57:43,996 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:57Z] INFO  15:57:44,012 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:57Z] INFO  15:57:44,700 IntervalUtils - Processing 31359052 bp from intervals
[2015-09-30T14:57Z] WARN  15:57:44,704 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:57Z] INFO  15:57:44,759 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:57Z] INFO  15:57:44,903 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:57Z] INFO  15:57:44,904 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:57Z] INFO  15:57:44,904 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:57Z] INFO  15:57:44,905 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:57Z] INFO  15:57:47,414 ProgressMeter -     8:102381472    200003.0    30.0 s       2.5 m       27.3%   109.0 s      79.0 s
[2015-09-30T14:58Z] INFO  15:58:06,217 ProgressMeter -            done   3.1359052E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T14:58Z] INFO  15:58:06,218 ProgressMeter - Total runtime 21.31 secs, 0.36 min, 0.01 hours
[2015-09-30T14:58Z] INFO  15:58:06,218 MicroScheduler - 207315 reads were filtered out during the traversal out of approximately 575278 total reads (36.04%)
[2015-09-30T14:58Z] INFO  15:58:06,219 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:58Z] INFO  15:58:06,219 MicroScheduler -   -> 7380 reads (1.28% of total) failing BadMateFilter
[2015-09-30T14:58Z] INFO  15:58:06,219 MicroScheduler -   -> 15735 reads (2.74% of total) failing DuplicateReadFilter
[2015-09-30T14:58Z] INFO  15:58:06,219 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:58Z] INFO  15:58:06,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:58Z] INFO  15:58:06,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:58Z] INFO  15:58:06,220 MicroScheduler -   -> 184200 reads (32.02% of total) failing MappingQualityZeroFilter
[2015-09-30T14:58Z] INFO  15:58:06,220 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:58Z] INFO  15:58:06,221 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:58Z] INFO  15:58:06,221 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:58Z] INFO  15:58:07,206 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:58Z] GATK: realign ('8', 62288979, 93648031) : syn3-normal
[2015-09-30T14:58Z] INFO  15:58:08,810 ProgressMeter -            done    522059.0    30.0 s      57.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T14:58Z] INFO  15:58:08,811 ProgressMeter - Total runtime 30.26 secs, 0.50 min, 0.01 hours
[2015-09-30T14:58Z] INFO  15:58:08,813 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 522059 total reads (0.00%)
[2015-09-30T14:58Z] INFO  15:58:08,814 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:58Z] INFO  15:58:08,814 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:58Z] INFO  15:58:08,814 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:58Z] INFO  15:58:09,416 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:09,418 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:58Z] INFO  15:58:09,418 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:58Z] INFO  15:58:09,419 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:58Z] INFO  15:58:09,422 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign-realign.intervals -L 8:62288980-93648031 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpWbc1hE/1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam
[2015-09-30T14:58Z] INFO  15:58:09,429 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:58Z] INFO  15:58:09,429 HelpFormatter - Date/Time: 2015/09/30 15:58:09
[2015-09-30T14:58Z] INFO  15:58:09,429 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:09,429 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:09,531 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:58Z] INFO  15:58:09,595 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:58Z] INFO  15:58:09,603 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:58Z] INFO  15:58:09,618 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:58Z] INFO  15:58:09,838 IntervalUtils - Processing 31359052 bp from intervals
[2015-09-30T14:58Z] WARN  15:58:09,842 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:58Z] INFO  15:58:09,895 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:58Z] INFO  15:58:09,957 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:58Z] INFO  15:58:10,031 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:58Z] INFO  15:58:10,031 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:58Z] INFO  15:58:10,032 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:58Z] INFO  15:58:10,032 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:58Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam
[2015-09-30T14:58Z] INFO  15:58:10,191 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:58Z] INFO  15:58:10,377 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:58Z] GATK pre-alignment ('8', 124975213, 146364022) : syn3-normal
[2015-09-30T14:58Z] INFO  15:58:13,424 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:13,426 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:58Z] INFO  15:58:13,426 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:58Z] INFO  15:58:13,426 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:58Z] INFO  15:58:13,430 HelpFormatter - Program Args: -T PrintReads -L 8:124975214-146364022 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpeTyZZd/1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam
[2015-09-30T14:58Z] INFO  15:58:13,436 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:58Z] INFO  15:58:13,436 HelpFormatter - Date/Time: 2015/09/30 15:58:13
[2015-09-30T14:58Z] INFO  15:58:13,436 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:13,436 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:13,539 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:58Z] INFO  15:58:14,675 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:58Z] INFO  15:58:14,725 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:58Z] INFO  15:58:14,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:58Z] INFO  15:58:14,747 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T14:58Z] INFO  15:58:14,759 IntervalUtils - Processing 21388809 bp from intervals
[2015-09-30T14:58Z] INFO  15:58:14,816 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:58Z] INFO  15:58:14,982 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:58Z] INFO  15:58:14,983 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:58Z] INFO  15:58:14,983 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:58Z] INFO  15:58:14,983 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:58Z] INFO  15:58:14,994 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:58Z] INFO  15:58:15,128 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:58Z] INFO  15:58:16,530 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:58Z] INFO  15:58:16,754 ProgressMeter -            done    515882.0    59.0 s     115.0 s      100.0%    59.0 s       0.0 s
[2015-09-30T14:58Z] INFO  15:58:16,754 ProgressMeter - Total runtime 59.51 secs, 0.99 min, 0.02 hours
[2015-09-30T14:58Z] INFO  15:58:16,755 MicroScheduler - 1618 reads were filtered out during the traversal out of approximately 517500 total reads (0.31%)
[2015-09-30T14:58Z] INFO  15:58:16,755 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:58Z] INFO  15:58:16,755 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:58Z] INFO  15:58:16,755 MicroScheduler -   -> 1618 reads (0.31% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:58Z] INFO  15:58:18,151 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:58Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam
[2015-09-30T14:58Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam 8:93896833-124968568
[2015-09-30T14:58Z] GATK: RealignerTargetCreator
[2015-09-30T14:58Z] INFO  15:58:23,066 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:23,068 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:58Z] INFO  15:58:23,068 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:58Z] INFO  15:58:23,068 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:58Z] INFO  15:58:23,072 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmp00oAHD/1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign-realign.intervals -l INFO -L 8:93896833-124968568 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:58Z] INFO  15:58:23,077 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:58Z] INFO  15:58:23,078 HelpFormatter - Date/Time: 2015/09/30 15:58:23
[2015-09-30T14:58Z] INFO  15:58:23,078 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:23,078 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:23,139 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:58Z] INFO  15:58:23,248 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:58Z] INFO  15:58:23,256 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:58Z] INFO  15:58:23,271 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:58Z] INFO  15:58:23,832 IntervalUtils - Processing 31071736 bp from intervals
[2015-09-30T14:58Z] WARN  15:58:23,836 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:58Z] INFO  15:58:23,894 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:58Z] INFO  15:58:24,033 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:58Z] INFO  15:58:24,033 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:58Z] INFO  15:58:24,033 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:58Z] INFO  15:58:24,034 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:58Z] INFO  15:58:40,285 ProgressMeter -      8:89059085    500005.0    30.0 s      60.0 s       85.4%    35.0 s       5.0 s
[2015-09-30T14:58Z] INFO  15:58:42,987 ProgressMeter -            done    571980.0    32.0 s      57.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T14:58Z] INFO  15:58:42,988 ProgressMeter - Total runtime 32.96 secs, 0.55 min, 0.01 hours
[2015-09-30T14:58Z] INFO  15:58:42,991 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 571980 total reads (0.00%)
[2015-09-30T14:58Z] INFO  15:58:42,991 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:58Z] INFO  15:58:42,992 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:58Z] INFO  15:58:42,992 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:58Z] INFO  15:58:44,066 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:58Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam
[2015-09-30T14:58Z] INFO  15:58:44,985 ProgressMeter -     8:139833300    200004.0    30.0 s       2.5 m       69.5%    43.0 s      13.0 s
[2015-09-30T14:58Z] GATK pre-alignment ('9', 0, 32405837) : syn3-normal
[2015-09-30T14:58Z] INFO  15:58:47,120 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:47,122 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:58Z] INFO  15:58:47,122 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:58Z] INFO  15:58:47,122 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:58Z] INFO  15:58:47,125 HelpFormatter - Program Args: -T PrintReads -L 9:1-32405837 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpDzoqMb/1_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam
[2015-09-30T14:58Z] INFO  15:58:47,131 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:58Z] INFO  15:58:47,131 HelpFormatter - Date/Time: 2015/09/30 15:58:47
[2015-09-30T14:58Z] INFO  15:58:47,131 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:47,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:47,233 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:58Z] INFO  15:58:47,846 ProgressMeter -            done   3.1071736E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T14:58Z] INFO  15:58:47,847 ProgressMeter - Total runtime 23.81 secs, 0.40 min, 0.01 hours
[2015-09-30T14:58Z] INFO  15:58:47,850 MicroScheduler - 38426 reads were filtered out during the traversal out of approximately 519445 total reads (7.40%)
[2015-09-30T14:58Z] INFO  15:58:47,850 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:58Z] INFO  15:58:47,851 MicroScheduler -   -> 8581 reads (1.65% of total) failing BadMateFilter
[2015-09-30T14:58Z] INFO  15:58:47,851 MicroScheduler -   -> 20747 reads (3.99% of total) failing DuplicateReadFilter
[2015-09-30T14:58Z] INFO  15:58:47,851 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T14:58Z] INFO  15:58:47,851 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:58Z] INFO  15:58:47,852 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T14:58Z] INFO  15:58:47,852 MicroScheduler -   -> 9098 reads (1.75% of total) failing MappingQualityZeroFilter
[2015-09-30T14:58Z] INFO  15:58:47,852 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:58Z] INFO  15:58:47,852 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T14:58Z] INFO  15:58:47,852 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T14:58Z] INFO  15:58:48,421 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:58Z] INFO  15:58:48,472 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:58Z] INFO  15:58:48,479 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:58Z] INFO  15:58:48,494 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:58Z] INFO  15:58:48,508 IntervalUtils - Processing 32405837 bp from intervals
[2015-09-30T14:58Z] INFO  15:58:48,565 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:58Z] INFO  15:58:48,763 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:58Z] INFO  15:58:48,763 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:58Z] INFO  15:58:48,763 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:58Z] INFO  15:58:48,764 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:58Z] INFO  15:58:48,775 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:58Z] INFO  15:58:48,821 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:58Z] GATK: realign ('8', 93896832, 124968568) : syn3-normal
[2015-09-30T14:58Z] INFO  15:58:48,980 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:58Z] INFO  15:58:50,890 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:50,892 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:58Z] INFO  15:58:50,892 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:58Z] INFO  15:58:50,892 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:58Z] INFO  15:58:50,895 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign-realign.intervals -L 8:93896833-124968568 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpNeXh2a/1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam
[2015-09-30T14:58Z] INFO  15:58:50,900 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:58Z] INFO  15:58:50,901 HelpFormatter - Date/Time: 2015/09/30 15:58:50
[2015-09-30T14:58Z] INFO  15:58:50,901 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:50,901 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:58Z] INFO  15:58:51,816 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:58Z] INFO  15:58:51,882 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T14:58Z] INFO  15:58:51,890 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:58Z] INFO  15:58:51,906 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:58Z] INFO  15:58:52,143 IntervalUtils - Processing 31071736 bp from intervals
[2015-09-30T14:58Z] WARN  15:58:52,147 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:58Z] INFO  15:58:52,472 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:58Z] INFO  15:58:52,615 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:58Z] INFO  15:58:52,615 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:58Z] INFO  15:58:52,616 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:58Z] INFO  15:58:52,616 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:58Z] INFO  15:58:52,758 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:58Z] INFO  15:58:52,947 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:59Z] INFO  15:59:14,997 ProgressMeter -     8:145111223    500009.0    60.0 s     120.0 s       94.1%    63.0 s       3.0 s
[2015-09-30T14:59Z] INFO  15:59:18,766 ProgressMeter -      9:12701847    200002.0    30.0 s       2.5 m       39.2%    76.0 s      46.0 s
[2015-09-30T14:59Z] INFO  15:59:21,884 ProgressMeter -            done    515882.0    29.0 s      56.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T14:59Z] INFO  15:59:21,884 ProgressMeter - Total runtime 29.27 secs, 0.49 min, 0.01 hours
[2015-09-30T14:59Z] INFO  15:59:21,887 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 515882 total reads (0.00%)
[2015-09-30T14:59Z] INFO  15:59:21,887 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:59Z] INFO  15:59:21,887 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:59Z] INFO  15:59:21,888 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:59Z] INFO  15:59:23,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:59Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam
[2015-09-30T14:59Z] GATK pre-alignment ('9', 32406980, 65488652) : syn3-normal
[2015-09-30T14:59Z] INFO  15:59:26,322 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:59Z] INFO  15:59:26,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:59Z] INFO  15:59:26,324 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:59Z] INFO  15:59:26,325 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:59Z] INFO  15:59:26,328 HelpFormatter - Program Args: -T PrintReads -L 9:32406981-65488652 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpkYLIuU/1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam
[2015-09-30T14:59Z] INFO  15:59:26,334 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:59Z] INFO  15:59:26,334 HelpFormatter - Date/Time: 2015/09/30 15:59:26
[2015-09-30T14:59Z] INFO  15:59:26,334 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:59Z] INFO  15:59:26,334 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:59Z] INFO  15:59:26,441 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:59Z] INFO  15:59:28,653 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T14:59Z] INFO  15:59:28,705 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T14:59Z] INFO  15:59:28,713 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:59Z] INFO  15:59:28,728 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:59Z] INFO  15:59:28,741 IntervalUtils - Processing 33081672 bp from intervals
[2015-09-30T14:59Z] INFO  15:59:28,797 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:59Z] INFO  15:59:28,959 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:59Z] INFO  15:59:28,959 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:59Z] INFO  15:59:28,960 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:59Z] INFO  15:59:28,960 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T14:59Z] INFO  15:59:28,971 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T14:59Z] INFO  15:59:29,136 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T14:59Z] INFO  15:59:30,130 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T14:59Z] INFO  15:59:30,211 ProgressMeter -            done    710574.0    75.0 s     105.0 s       99.6%    75.0 s       0.0 s
[2015-09-30T14:59Z] INFO  15:59:30,211 ProgressMeter - Total runtime 75.23 secs, 1.25 min, 0.02 hours
[2015-09-30T14:59Z] INFO  15:59:30,211 MicroScheduler - 1327 reads were filtered out during the traversal out of approximately 711901 total reads (0.19%)
[2015-09-30T14:59Z] INFO  15:59:30,212 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:59Z] INFO  15:59:30,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:59Z] INFO  15:59:30,212 MicroScheduler -   -> 1327 reads (0.19% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:59Z] INFO  15:59:31,362 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:59Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam
[2015-09-30T14:59Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam 8:124975214-146364022
[2015-09-30T14:59Z] GATK: RealignerTargetCreator
[2015-09-30T14:59Z] INFO  15:59:38,457 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:59Z] INFO  15:59:38,459 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:59Z] INFO  15:59:38,459 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:59Z] INFO  15:59:38,459 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:59Z] INFO  15:59:38,463 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmpTs21M4/1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign-realign.intervals -l INFO -L 8:124975214-146364022 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:59Z] INFO  15:59:38,469 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:59Z] INFO  15:59:38,470 HelpFormatter - Date/Time: 2015/09/30 15:59:38
[2015-09-30T14:59Z] INFO  15:59:38,470 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:59Z] INFO  15:59:38,470 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:59Z] INFO  15:59:38,529 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:59Z] INFO  15:59:38,637 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:59Z] INFO  15:59:38,645 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:59Z] INFO  15:59:38,661 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:59Z] INFO  15:59:39,502 IntervalUtils - Processing 21388809 bp from intervals
[2015-09-30T14:59Z] WARN  15:59:39,507 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:59Z] INFO  15:59:39,566 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:59Z] INFO  15:59:40,804 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T14:59Z] INFO  15:59:40,901 ProgressMeter -            done    473124.0    52.0 s     110.0 s      100.0%    52.0 s       0.0 s
[2015-09-30T14:59Z] INFO  15:59:40,901 ProgressMeter - Total runtime 52.14 secs, 0.87 min, 0.01 hours
[2015-09-30T14:59Z] INFO  15:59:40,901 MicroScheduler - 1545 reads were filtered out during the traversal out of approximately 474669 total reads (0.33%)
[2015-09-30T14:59Z] INFO  15:59:40,902 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T14:59Z] INFO  15:59:40,902 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T14:59Z] INFO  15:59:40,902 MicroScheduler -   -> 1545 reads (0.33% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T14:59Z] INFO  15:59:40,963 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:59Z] INFO  15:59:40,964 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:59Z] INFO  15:59:40,964 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:59Z] INFO  15:59:40,965 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:59Z] INFO  15:59:41,955 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T14:59Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam
[2015-09-30T14:59Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam 9:1-32405837
[2015-09-30T14:59Z] GATK: RealignerTargetCreator
[2015-09-30T14:59Z] INFO  15:59:47,168 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:59Z] INFO  15:59:47,170 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T14:59Z] INFO  15:59:47,171 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T14:59Z] INFO  15:59:47,171 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T14:59Z] INFO  15:59:47,174 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpCSNwwj/1_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign-realign.intervals -l INFO -L 9:1-32405837 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T14:59Z] INFO  15:59:47,180 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T14:59Z] INFO  15:59:47,181 HelpFormatter - Date/Time: 2015/09/30 15:59:47
[2015-09-30T14:59Z] INFO  15:59:47,181 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:59Z] INFO  15:59:47,181 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T14:59Z] INFO  15:59:47,238 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T14:59Z] INFO  15:59:48,188 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T14:59Z] INFO  15:59:48,196 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T14:59Z] INFO  15:59:48,213 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T14:59Z] INFO  15:59:48,474 IntervalUtils - Processing 32405837 bp from intervals
[2015-09-30T14:59Z] WARN  15:59:48,478 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T14:59Z] INFO  15:59:48,539 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T14:59Z] INFO  15:59:48,684 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T14:59Z] INFO  15:59:48,685 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T14:59Z] INFO  15:59:48,685 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T14:59Z] INFO  15:59:48,686 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T14:59Z] INFO  15:59:58,962 ProgressMeter -      9:34652118    100001.0    30.0 s       5.0 m        6.8%     7.4 m       6.9 m
[2015-09-30T15:00Z] INFO  16:00:02,480 ProgressMeter -            done   2.1388809E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T15:00Z] INFO  16:00:02,480 ProgressMeter - Total runtime 21.52 secs, 0.36 min, 0.01 hours
[2015-09-30T15:00Z] INFO  16:00:02,483 MicroScheduler - 76651 reads were filtered out during the traversal out of approximately 714294 total reads (10.73%)
[2015-09-30T15:00Z] INFO  16:00:02,484 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:00Z] INFO  16:00:02,484 MicroScheduler -   -> 7630 reads (1.07% of total) failing BadMateFilter
[2015-09-30T15:00Z] INFO  16:00:02,484 MicroScheduler -   -> 37567 reads (5.26% of total) failing DuplicateReadFilter
[2015-09-30T15:00Z] INFO  16:00:02,484 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:00Z] INFO  16:00:02,485 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:00Z] INFO  16:00:02,485 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:00Z] INFO  16:00:02,485 MicroScheduler -   -> 31454 reads (4.40% of total) failing MappingQualityZeroFilter
[2015-09-30T15:00Z] INFO  16:00:02,485 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:00Z] INFO  16:00:02,486 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:00Z] INFO  16:00:02,486 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:00Z] INFO  16:00:04,472 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:00Z] GATK: realign ('8', 124975213, 146364022) : syn3-normal
[2015-09-30T15:00Z] INFO  16:00:07,269 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:07,272 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:00Z] INFO  16:00:07,272 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:00Z] INFO  16:00:07,272 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:00Z] INFO  16:00:07,275 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign-realign.intervals -L 8:124975214-146364022 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/tx/tmp0B5GnD/1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam
[2015-09-30T15:00Z] INFO  16:00:07,281 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:00Z] INFO  16:00:07,281 HelpFormatter - Date/Time: 2015/09/30 16:00:07
[2015-09-30T15:00Z] INFO  16:00:07,281 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:07,281 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:07,410 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:00Z] INFO  16:00:07,475 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:00Z] INFO  16:00:07,483 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:00Z] INFO  16:00:07,499 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:00Z] INFO  16:00:07,740 IntervalUtils - Processing 21388809 bp from intervals
[2015-09-30T15:00Z] WARN  16:00:07,745 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:00Z] INFO  16:00:07,823 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:00Z] INFO  16:00:07,933 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:00Z] INFO  16:00:07,934 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:00Z] INFO  16:00:07,934 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:00Z] INFO  16:00:07,935 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:00Z] INFO  16:00:08,076 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:00Z] INFO  16:00:08,224 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:00Z] INFO  16:00:11,102 ProgressMeter -            done   3.2405837E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T15:00Z] INFO  16:00:11,102 ProgressMeter - Total runtime 22.42 secs, 0.37 min, 0.01 hours
[2015-09-30T15:00Z] INFO  16:00:11,105 MicroScheduler - 44218 reads were filtered out during the traversal out of approximately 476367 total reads (9.28%)
[2015-09-30T15:00Z] INFO  16:00:11,106 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:00Z] INFO  16:00:11,106 MicroScheduler -   -> 7890 reads (1.66% of total) failing BadMateFilter
[2015-09-30T15:00Z] INFO  16:00:11,106 MicroScheduler -   -> 19253 reads (4.04% of total) failing DuplicateReadFilter
[2015-09-30T15:00Z] INFO  16:00:11,106 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:00Z] INFO  16:00:11,107 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:00Z] INFO  16:00:11,107 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:00Z] INFO  16:00:11,107 MicroScheduler -   -> 17075 reads (3.58% of total) failing MappingQualityZeroFilter
[2015-09-30T15:00Z] INFO  16:00:11,107 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:00Z] INFO  16:00:11,108 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:00Z] INFO  16:00:11,108 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:00Z] INFO  16:00:12,041 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:00Z] GATK: realign ('9', 0, 32405837) : syn3-normal
[2015-09-30T15:00Z] INFO  16:00:14,765 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:14,767 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:00Z] INFO  16:00:14,767 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:00Z] INFO  16:00:14,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:00Z] INFO  16:00:14,771 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign-realign.intervals -L 9:1-32405837 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpZQ9oGB/1_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam
[2015-09-30T15:00Z] INFO  16:00:14,776 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:00Z] INFO  16:00:14,776 HelpFormatter - Date/Time: 2015/09/30 16:00:14
[2015-09-30T15:00Z] INFO  16:00:14,777 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:14,777 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:14,885 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:00Z] INFO  16:00:14,952 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:00Z] INFO  16:00:14,960 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:00Z] INFO  16:00:14,975 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:00Z] INFO  16:00:15,197 IntervalUtils - Processing 32405837 bp from intervals
[2015-09-30T15:00Z] WARN  16:00:15,201 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:00Z] INFO  16:00:15,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:00Z] INFO  16:00:15,401 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:00Z] INFO  16:00:15,401 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:00Z] INFO  16:00:15,402 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:00Z] INFO  16:00:15,402 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:00Z] INFO  16:00:15,537 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:00Z] INFO  16:00:15,728 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:00Z] INFO  16:00:29,359 ProgressMeter -      9:39890936    400004.0    60.0 s       2.5 m       22.6%     4.4 m       3.4 m
[2015-09-30T15:00Z] INFO  16:00:38,502 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:00Z] INFO  16:00:38,776 ProgressMeter -            done    572397.0    69.0 s       2.0 m      100.0%    69.0 s       0.0 s
[2015-09-30T15:00Z] INFO  16:00:38,776 ProgressMeter - Total runtime 69.82 secs, 1.16 min, 0.02 hours
[2015-09-30T15:00Z] INFO  16:00:38,776 MicroScheduler - 1145 reads were filtered out during the traversal out of approximately 573542 total reads (0.20%)
[2015-09-30T15:00Z] INFO  16:00:38,777 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:00Z] INFO  16:00:38,777 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:00Z] INFO  16:00:38,777 MicroScheduler -   -> 1145 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:00Z] INFO  16:00:39,042 ProgressMeter -     8:144911820    400006.0    31.0 s      77.0 s       93.2%    33.0 s       2.0 s
[2015-09-30T15:00Z] INFO  16:00:39,800 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:00Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam
[2015-09-30T15:00Z] INFO  16:00:42,107 ProgressMeter -            done    473124.0    26.0 s      56.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T15:00Z] INFO  16:00:42,108 ProgressMeter - Total runtime 26.71 secs, 0.45 min, 0.01 hours
[2015-09-30T15:00Z] INFO  16:00:42,111 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 473124 total reads (0.00%)
[2015-09-30T15:00Z] INFO  16:00:42,111 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:00Z] INFO  16:00:42,111 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:00Z] INFO  16:00:42,112 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:00Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam 9:32406981-65488652
[2015-09-30T15:00Z] GATK: RealignerTargetCreator
[2015-09-30T15:00Z] INFO  16:00:43,218 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:00Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam
[2015-09-30T15:00Z] GATK pre-alignment ('9', 65505265, 96581951) : syn3-normal
[2015-09-30T15:00Z] INFO  16:00:45,990 ProgressMeter -            done    710574.0    38.0 s      53.0 s       99.6%    38.0 s       0.0 s
[2015-09-30T15:00Z] INFO  16:00:45,991 ProgressMeter - Total runtime 38.06 secs, 0.63 min, 0.01 hours
[2015-09-30T15:00Z] INFO  16:00:45,994 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 710574 total reads (0.00%)
[2015-09-30T15:00Z] INFO  16:00:45,994 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:00Z] INFO  16:00:45,995 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:00Z] INFO  16:00:45,995 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:00Z] INFO  16:00:47,332 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:47,334 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:00Z] INFO  16:00:47,334 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:00Z] INFO  16:00:47,334 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:00Z] INFO  16:00:47,338 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpwvq53T/1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign-realign.intervals -l INFO -L 9:32406981-65488652 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:00Z] INFO  16:00:47,344 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:00Z] INFO  16:00:47,344 HelpFormatter - Date/Time: 2015/09/30 16:00:47
[2015-09-30T15:00Z] INFO  16:00:47,344 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:47,344 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:47,399 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:00Z] INFO  16:00:47,503 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:00Z] INFO  16:00:47,511 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:00Z] INFO  16:00:47,527 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:00Z] INFO  16:00:47,871 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:00Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam
[2015-09-30T15:00Z] GATK pre-alignment ('9', 96714155, 127734373) : syn3-normal
[2015-09-30T15:00Z] INFO  16:00:51,337 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:51,339 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:00Z] INFO  16:00:51,339 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:00Z] INFO  16:00:51,340 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:00Z] INFO  16:00:51,343 HelpFormatter - Program Args: -T PrintReads -L 9:65505266-96581951 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpMxrfEi/1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam
[2015-09-30T15:00Z] INFO  16:00:51,349 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:00Z] INFO  16:00:51,350 HelpFormatter - Date/Time: 2015/09/30 16:00:51
[2015-09-30T15:00Z] INFO  16:00:51,350 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:51,350 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:51,569 IntervalUtils - Processing 33081672 bp from intervals
[2015-09-30T15:00Z] WARN  16:00:51,573 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:00Z] INFO  16:00:51,630 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:00Z] INFO  16:00:51,735 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:00Z] INFO  16:00:51,736 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:00Z] INFO  16:00:51,736 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:00Z] INFO  16:00:51,736 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:00Z] INFO  16:00:52,536 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:00Z] INFO  16:00:53,243 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:00Z] INFO  16:00:53,292 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:00Z] INFO  16:00:53,300 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:00Z] INFO  16:00:53,315 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:00Z] INFO  16:00:53,328 IntervalUtils - Processing 31076686 bp from intervals
[2015-09-30T15:00Z] INFO  16:00:53,386 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:00Z] INFO  16:00:53,578 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:00Z] INFO  16:00:53,578 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:00Z] INFO  16:00:53,578 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:00Z] INFO  16:00:53,579 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:00Z] INFO  16:00:53,590 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:00Z] INFO  16:00:53,777 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:00Z] INFO  16:00:53,819 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:53,821 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:00Z] INFO  16:00:53,821 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:00Z] INFO  16:00:53,822 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:00Z] INFO  16:00:53,825 HelpFormatter - Program Args: -T PrintReads -L 9:96714156-127734373 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmp3FJeL3/1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam
[2015-09-30T15:00Z] INFO  16:00:53,830 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:00Z] INFO  16:00:53,830 HelpFormatter - Date/Time: 2015/09/30 16:00:53
[2015-09-30T15:00Z] INFO  16:00:53,830 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:53,831 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:00Z] INFO  16:00:53,933 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:00Z] INFO  16:00:56,386 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:00Z] INFO  16:00:56,438 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:00Z] INFO  16:00:56,446 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:00Z] INFO  16:00:56,461 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:00Z] INFO  16:00:56,475 IntervalUtils - Processing 31020218 bp from intervals
[2015-09-30T15:00Z] INFO  16:00:56,532 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:00Z] INFO  16:00:56,736 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:00Z] INFO  16:00:56,736 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:00Z] INFO  16:00:56,737 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:00Z] INFO  16:00:56,737 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:00Z] INFO  16:00:56,748 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:00Z] INFO  16:00:56,945 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:01Z] INFO  16:01:14,110 ProgressMeter -            done   3.3081672E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T15:01Z] INFO  16:01:14,110 ProgressMeter - Total runtime 22.37 secs, 0.37 min, 0.01 hours
[2015-09-30T15:01Z] INFO  16:01:14,113 MicroScheduler - 113882 reads were filtered out during the traversal out of approximately 575395 total reads (19.79%)
[2015-09-30T15:01Z] INFO  16:01:14,113 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:01Z] INFO  16:01:14,114 MicroScheduler -   -> 4672 reads (0.81% of total) failing BadMateFilter
[2015-09-30T15:01Z] INFO  16:01:14,114 MicroScheduler -   -> 23753 reads (4.13% of total) failing DuplicateReadFilter
[2015-09-30T15:01Z] INFO  16:01:14,114 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:01Z] INFO  16:01:14,115 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:01Z] INFO  16:01:14,115 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:01Z] INFO  16:01:14,115 MicroScheduler -   -> 85457 reads (14.85% of total) failing MappingQualityZeroFilter
[2015-09-30T15:01Z] INFO  16:01:14,115 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:01Z] INFO  16:01:14,115 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:01Z] INFO  16:01:14,116 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:01Z] INFO  16:01:15,408 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:01Z] GATK: realign ('9', 32406980, 65488652) : syn3-normal
[2015-09-30T15:01Z] INFO  16:01:17,339 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:01Z] INFO  16:01:17,341 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:01Z] INFO  16:01:17,341 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:01Z] INFO  16:01:17,341 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:01Z] INFO  16:01:17,344 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign-realign.intervals -L 9:32406981-65488652 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmprOtwZx/1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam
[2015-09-30T15:01Z] INFO  16:01:17,350 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:01Z] INFO  16:01:17,350 HelpFormatter - Date/Time: 2015/09/30 16:01:17
[2015-09-30T15:01Z] INFO  16:01:17,350 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:01Z] INFO  16:01:17,350 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:01Z] INFO  16:01:17,474 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:01Z] INFO  16:01:17,536 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:01Z] INFO  16:01:17,543 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:01Z] INFO  16:01:17,559 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:01Z] INFO  16:01:17,796 IntervalUtils - Processing 33081672 bp from intervals
[2015-09-30T15:01Z] WARN  16:01:17,799 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:01Z] INFO  16:01:17,854 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:01Z] INFO  16:01:17,946 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:01Z] INFO  16:01:17,947 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:01Z] INFO  16:01:17,947 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:01Z] INFO  16:01:17,947 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:01Z] INFO  16:01:18,043 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:01Z] INFO  16:01:18,209 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:01Z] INFO  16:01:24,669 ProgressMeter -      9:74061891    200003.0    31.0 s       2.6 m       27.5%   112.0 s      81.0 s
[2015-09-30T15:01Z] INFO  16:01:27,280 ProgressMeter -     9:101552972    200002.0    30.0 s       2.5 m       15.6%     3.2 m       2.7 m
[2015-09-30T15:01Z] INFO  16:01:48,837 ProgressMeter -            done    572397.0    30.0 s      53.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T15:01Z] INFO  16:01:48,837 ProgressMeter - Total runtime 30.89 secs, 0.51 min, 0.01 hours
[2015-09-30T15:01Z] INFO  16:01:48,840 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 572397 total reads (0.00%)
[2015-09-30T15:01Z] INFO  16:01:48,840 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:01Z] INFO  16:01:48,841 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:01Z] INFO  16:01:48,841 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:01Z] INFO  16:01:49,986 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:01Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam
[2015-09-30T15:01Z] GATK pre-alignment ('9', 127737328, 141213431) : syn3-normal
[2015-09-30T15:01Z] INFO  16:01:53,973 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:01Z] INFO  16:01:53,975 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:01Z] INFO  16:01:53,975 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:01Z] INFO  16:01:53,975 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:01Z] INFO  16:01:53,978 HelpFormatter - Program Args: -T PrintReads -L 9:127737329-141213431 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpEO4usR/1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam
[2015-09-30T15:01Z] INFO  16:01:53,985 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:01Z] INFO  16:01:53,985 HelpFormatter - Date/Time: 2015/09/30 16:01:53
[2015-09-30T15:01Z] INFO  16:01:53,985 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:01Z] INFO  16:01:53,985 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:01Z] INFO  16:01:54,094 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:01Z] INFO  16:01:55,048 ProgressMeter -      9:93983606    500006.0    61.0 s       2.0 m       91.6%    66.0 s       5.0 s
[2015-09-30T15:01Z] INFO  16:01:55,782 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:01Z] INFO  16:01:55,834 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:01Z] INFO  16:01:55,841 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:01Z] INFO  16:01:55,857 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:01Z] INFO  16:01:55,871 IntervalUtils - Processing 13476103 bp from intervals
[2015-09-30T15:01Z] INFO  16:01:55,932 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:01Z] INFO  16:01:56,095 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:01Z] INFO  16:01:56,096 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:01Z] INFO  16:01:56,096 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:01Z] INFO  16:01:56,096 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:01Z] INFO  16:01:56,108 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:01Z] INFO  16:01:56,203 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:01Z] INFO  16:01:57,281 ProgressMeter -     9:115648695    500005.0    60.0 s       2.0 m       61.0%    98.0 s      38.0 s
[2015-09-30T15:02Z] INFO  16:02:06,351 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@a585ef
[2015-09-30T15:02Z] INFO  16:02:06,466 ProgressMeter -            done    750752.0    72.0 s      97.0 s      100.0%    72.0 s       0.0 s
[2015-09-30T15:02Z] INFO  16:02:06,466 ProgressMeter - Total runtime 72.89 secs, 1.21 min, 0.02 hours
[2015-09-30T15:02Z] INFO  16:02:06,466 MicroScheduler - 2391 reads were filtered out during the traversal out of approximately 753143 total reads (0.32%)
[2015-09-30T15:02Z] INFO  16:02:06,467 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:02Z] INFO  16:02:06,467 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:02Z] INFO  16:02:06,467 MicroScheduler -   -> 2391 reads (0.32% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:02Z] INFO  16:02:07,512 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:02Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam
[2015-09-30T15:02Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam 9:65505266-96581951
[2015-09-30T15:02Z] GATK: RealignerTargetCreator
[2015-09-30T15:02Z] INFO  16:02:14,019 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:02Z] INFO  16:02:14,022 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:02Z] INFO  16:02:14,022 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:02Z] INFO  16:02:14,022 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:02Z] INFO  16:02:14,026 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpU5fSxb/1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign-realign.intervals -l INFO -L 9:65505266-96581951 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:02Z] INFO  16:02:14,032 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:02Z] INFO  16:02:14,032 HelpFormatter - Date/Time: 2015/09/30 16:02:14
[2015-09-30T15:02Z] INFO  16:02:14,032 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:02Z] INFO  16:02:14,032 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:02Z] INFO  16:02:14,092 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:02Z] INFO  16:02:14,207 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:02Z] INFO  16:02:14,215 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:02Z] INFO  16:02:14,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:02Z] INFO  16:02:14,496 IntervalUtils - Processing 31076686 bp from intervals
[2015-09-30T15:02Z] WARN  16:02:14,500 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:02Z] INFO  16:02:14,557 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:02Z] INFO  16:02:14,710 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:02Z] INFO  16:02:14,711 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:02Z] INFO  16:02:14,711 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:02Z] INFO  16:02:14,711 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:02Z] INFO  16:02:26,098 ProgressMeter -     9:130898410    200004.0    30.0 s       2.5 m       23.5%     2.1 m      97.0 s
[2015-09-30T15:02Z] INFO  16:02:27,282 ProgressMeter -     9:125274388    900009.0    90.0 s     100.0 s       92.1%    97.0 s       7.0 s
[2015-09-30T15:02Z] INFO  16:02:37,265 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:02Z] INFO  16:02:37,473 ProgressMeter -            done   1073849.0   100.0 s      93.0 s      100.0%   100.0 s       0.0 s
[2015-09-30T15:02Z] INFO  16:02:37,474 ProgressMeter - Total runtime 100.74 secs, 1.68 min, 0.03 hours
[2015-09-30T15:02Z] INFO  16:02:37,474 MicroScheduler - 2146 reads were filtered out during the traversal out of approximately 1075995 total reads (0.20%)
[2015-09-30T15:02Z] INFO  16:02:37,474 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:02Z] INFO  16:02:37,474 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:02Z] INFO  16:02:37,475 MicroScheduler -   -> 2146 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:02Z] INFO  16:02:38,607 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:02Z] INFO  16:02:40,068 ProgressMeter -            done   3.1076686E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T15:02Z] INFO  16:02:40,068 ProgressMeter - Total runtime 25.36 secs, 0.42 min, 0.01 hours
[2015-09-30T15:02Z] INFO  16:02:40,072 MicroScheduler - 135058 reads were filtered out during the traversal out of approximately 754538 total reads (17.90%)
[2015-09-30T15:02Z] INFO  16:02:40,072 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:02Z] INFO  16:02:40,072 MicroScheduler -   -> 10832 reads (1.44% of total) failing BadMateFilter
[2015-09-30T15:02Z] INFO  16:02:40,072 MicroScheduler -   -> 30824 reads (4.09% of total) failing DuplicateReadFilter
[2015-09-30T15:02Z] INFO  16:02:40,073 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:02Z] INFO  16:02:40,073 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:02Z] INFO  16:02:40,073 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:02Z] INFO  16:02:40,073 MicroScheduler -   -> 93402 reads (12.38% of total) failing MappingQualityZeroFilter
[2015-09-30T15:02Z] INFO  16:02:40,074 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:02Z] INFO  16:02:40,074 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:02Z] INFO  16:02:40,074 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:02Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam
[2015-09-30T15:02Z] INFO  16:02:41,057 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:02Z] GATK: realign ('9', 65505265, 96581951) : syn3-normal
[2015-09-30T15:02Z] INFO  16:02:43,022 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:02Z] INFO  16:02:43,024 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:02Z] INFO  16:02:43,024 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:02Z] INFO  16:02:43,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:02Z] INFO  16:02:43,028 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign-realign.intervals -L 9:65505266-96581951 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpzgc8C8/1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam
[2015-09-30T15:02Z] INFO  16:02:43,034 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:02Z] INFO  16:02:43,034 HelpFormatter - Date/Time: 2015/09/30 16:02:43
[2015-09-30T15:02Z] INFO  16:02:43,034 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:02Z] INFO  16:02:43,034 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:02Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam 9:96714156-127734373
[2015-09-30T15:02Z] GATK: RealignerTargetCreator
[2015-09-30T15:02Z] INFO  16:02:44,245 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:02Z] INFO  16:02:44,313 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:02Z] INFO  16:02:44,321 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:02Z] INFO  16:02:44,337 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:02Z] INFO  16:02:44,567 IntervalUtils - Processing 31076686 bp from intervals
[2015-09-30T15:02Z] WARN  16:02:44,571 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:02Z] INFO  16:02:45,267 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:02Z] INFO  16:02:45,399 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:02Z] INFO  16:02:45,399 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:02Z] INFO  16:02:45,400 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:02Z] INFO  16:02:45,400 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:02Z] INFO  16:02:45,540 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:02Z] INFO  16:02:45,721 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:02Z] INFO  16:02:45,735 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:02Z] INFO  16:02:45,737 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:02Z] INFO  16:02:45,737 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:02Z] INFO  16:02:45,737 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:02Z] INFO  16:02:45,741 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpQb35uY/1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign-realign.intervals -l INFO -L 9:96714156-127734373 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:02Z] INFO  16:02:45,746 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:02Z] INFO  16:02:45,746 HelpFormatter - Date/Time: 2015/09/30 16:02:45
[2015-09-30T15:02Z] INFO  16:02:45,747 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:02Z] INFO  16:02:45,747 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:02Z] INFO  16:02:45,802 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:02Z] INFO  16:02:45,909 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:02Z] INFO  16:02:45,916 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:02Z] INFO  16:02:45,932 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:02Z] INFO  16:02:46,192 IntervalUtils - Processing 31020218 bp from intervals
[2015-09-30T15:02Z] WARN  16:02:46,196 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:02Z] INFO  16:02:46,253 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:02Z] INFO  16:02:46,399 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:02Z] INFO  16:02:46,400 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:02Z] INFO  16:02:46,400 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:02Z] INFO  16:02:46,400 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:02Z] INFO  16:02:56,101 ProgressMeter -     9:133240827    500007.0    60.0 s     120.0 s       40.8%     2.4 m      86.0 s
[2015-09-30T15:03Z] INFO  16:03:15,632 ProgressMeter -      9:72741713    100001.0    30.0 s       5.0 m       23.3%     2.1 m      98.0 s
[2015-09-30T15:03Z] INFO  16:03:16,403 ProgressMeter -     9:127284413   3.0556757E7    30.0 s       0.0 s       98.5%    30.0 s       0.0 s
[2015-09-30T15:03Z] INFO  16:03:17,231 ProgressMeter -            done   3.1020218E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T15:03Z] INFO  16:03:17,232 ProgressMeter - Total runtime 30.83 secs, 0.51 min, 0.01 hours
[2015-09-30T15:03Z] INFO  16:03:17,235 MicroScheduler - 86112 reads were filtered out during the traversal out of approximately 1079940 total reads (7.97%)
[2015-09-30T15:03Z] INFO  16:03:17,235 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:03Z] INFO  16:03:17,235 MicroScheduler -   -> 11987 reads (1.11% of total) failing BadMateFilter
[2015-09-30T15:03Z] INFO  16:03:17,236 MicroScheduler -   -> 48699 reads (4.51% of total) failing DuplicateReadFilter
[2015-09-30T15:03Z] INFO  16:03:17,236 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:03Z] INFO  16:03:17,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:03Z] INFO  16:03:17,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:03Z] INFO  16:03:17,236 MicroScheduler -   -> 25426 reads (2.35% of total) failing MappingQualityZeroFilter
[2015-09-30T15:03Z] INFO  16:03:17,237 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:03Z] INFO  16:03:17,237 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:03Z] INFO  16:03:17,237 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:03Z] INFO  16:03:18,460 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:03Z] GATK: realign ('9', 96714155, 127734373) : syn3-normal
[2015-09-30T15:03Z] INFO  16:03:21,049 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:03Z] INFO  16:03:21,051 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:03Z] INFO  16:03:21,051 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:03Z] INFO  16:03:21,052 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:03Z] INFO  16:03:21,055 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign-realign.intervals -L 9:96714156-127734373 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpVnOL7_/1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam
[2015-09-30T15:03Z] INFO  16:03:21,061 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:03Z] INFO  16:03:21,061 HelpFormatter - Date/Time: 2015/09/30 16:03:21
[2015-09-30T15:03Z] INFO  16:03:21,061 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:03Z] INFO  16:03:21,061 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:03Z] INFO  16:03:21,186 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:03Z] INFO  16:03:21,250 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:03Z] INFO  16:03:21,257 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:03Z] INFO  16:03:21,273 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:03Z] INFO  16:03:21,507 IntervalUtils - Processing 31020218 bp from intervals
[2015-09-30T15:03Z] WARN  16:03:21,511 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:03Z] INFO  16:03:21,567 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:03Z] INFO  16:03:21,715 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:03Z] INFO  16:03:21,715 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:03Z] INFO  16:03:21,715 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:03Z] INFO  16:03:21,716 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:03Z] INFO  16:03:21,857 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:03Z] INFO  16:03:22,036 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:03Z] INFO  16:03:26,102 ProgressMeter -     9:136245984    800010.0    90.0 s     112.0 s       63.1%     2.4 m      52.0 s
[2015-09-30T15:03Z] INFO  16:03:36,418 ProgressMeter -            done    750752.0    51.0 s      67.0 s      100.0%    51.0 s       0.0 s
[2015-09-30T15:03Z] INFO  16:03:36,418 ProgressMeter - Total runtime 51.02 secs, 0.85 min, 0.01 hours
[2015-09-30T15:03Z] INFO  16:03:36,421 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 750752 total reads (0.00%)
[2015-09-30T15:03Z] INFO  16:03:36,421 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:03Z] INFO  16:03:36,422 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:03Z] INFO  16:03:36,422 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:03Z] INFO  16:03:37,559 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:03Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam
[2015-09-30T15:03Z] GATK pre-alignment ('10', 0, 31134673) : syn3-normal
[2015-09-30T15:03Z] INFO  16:03:44,115 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:03Z] INFO  16:03:44,117 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:03Z] INFO  16:03:44,117 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:03Z] INFO  16:03:44,117 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:03Z] INFO  16:03:44,120 HelpFormatter - Program Args: -T PrintReads -L 10:1-31134673 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpz13IL1/1_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam
[2015-09-30T15:03Z] INFO  16:03:44,126 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:03Z] INFO  16:03:44,126 HelpFormatter - Date/Time: 2015/09/30 16:03:44
[2015-09-30T15:03Z] INFO  16:03:44,126 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:03Z] INFO  16:03:44,126 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:03Z] INFO  16:03:44,713 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:03Z] INFO  16:03:45,372 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:03Z] INFO  16:03:45,419 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:03Z] INFO  16:03:45,426 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:03Z] INFO  16:03:45,439 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:03Z] INFO  16:03:45,451 IntervalUtils - Processing 31134673 bp from intervals
[2015-09-30T15:03Z] INFO  16:03:45,505 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:03Z] INFO  16:03:45,719 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:03Z] INFO  16:03:45,720 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:03Z] INFO  16:03:45,720 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:03Z] INFO  16:03:45,720 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:03Z] INFO  16:03:45,731 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:03Z] INFO  16:03:45,915 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:03Z] INFO  16:03:51,718 ProgressMeter -     9:114293412    500005.0    30.0 s      60.0 s       56.7%    52.0 s      22.0 s
[2015-09-30T15:03Z] INFO  16:03:56,330 ProgressMeter -     9:139299111   1000012.0   120.0 s     120.0 s       85.8%     2.3 m      19.0 s
[2015-09-30T15:04Z] INFO  16:04:12,875 ProgressMeter -            done   1073849.0    51.0 s      47.0 s      100.0%    51.0 s       0.0 s
[2015-09-30T15:04Z] INFO  16:04:12,875 ProgressMeter - Total runtime 51.16 secs, 0.85 min, 0.01 hours
[2015-09-30T15:04Z] INFO  16:04:12,878 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1073849 total reads (0.00%)
[2015-09-30T15:04Z] INFO  16:04:12,879 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:04Z] INFO  16:04:12,879 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:04Z] INFO  16:04:12,879 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:04Z] INFO  16:04:13,883 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:04Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam
[2015-09-30T15:04Z] INFO  16:04:15,797 ProgressMeter -     10:12162863    200002.0    30.0 s       2.5 m       39.1%    76.0 s      46.0 s
[2015-09-30T15:04Z] GATK pre-alignment ('10', 31137165, 62208748) : syn3-normal
[2015-09-30T15:04Z] INFO  16:04:18,405 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:04Z] INFO  16:04:18,407 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:04Z] INFO  16:04:18,407 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:04Z] INFO  16:04:18,407 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:04Z] INFO  16:04:18,410 HelpFormatter - Program Args: -T PrintReads -L 10:31137166-62208748 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpdm1iAf/1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam
[2015-09-30T15:04Z] INFO  16:04:18,416 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:04Z] INFO  16:04:18,416 HelpFormatter - Date/Time: 2015/09/30 16:04:18
[2015-09-30T15:04Z] INFO  16:04:18,416 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:04Z] INFO  16:04:18,416 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:04Z] INFO  16:04:18,517 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:04Z] INFO  16:04:19,906 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:04Z] INFO  16:04:19,953 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:04Z] INFO  16:04:19,960 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:04Z] INFO  16:04:19,975 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:04Z] INFO  16:04:19,987 IntervalUtils - Processing 31071583 bp from intervals
[2015-09-30T15:04Z] INFO  16:04:20,043 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:04Z] INFO  16:04:20,238 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:04Z] INFO  16:04:20,238 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:04Z] INFO  16:04:20,239 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:04Z] INFO  16:04:20,239 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:04Z] INFO  16:04:20,249 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:04Z] INFO  16:04:20,443 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:04Z] INFO  16:04:26,801 ProgressMeter -     9:140912161   1400018.0     2.5 m     107.0 s       97.8%     2.6 m       3.0 s
[2015-09-30T15:04Z] INFO  16:04:28,899 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:04Z] INFO  16:04:29,030 ProgressMeter -            done   1443569.0     2.5 m     105.0 s       99.5%     2.5 m       0.0 s
[2015-09-30T15:04Z] INFO  16:04:29,030 ProgressMeter - Total runtime 152.93 secs, 2.55 min, 0.04 hours
[2015-09-30T15:04Z] INFO  16:04:29,031 MicroScheduler - 1796 reads were filtered out during the traversal out of approximately 1445365 total reads (0.12%)
[2015-09-30T15:04Z] INFO  16:04:29,031 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:04Z] INFO  16:04:29,031 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:04Z] INFO  16:04:29,031 MicroScheduler -   -> 1796 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:04Z] INFO  16:04:30,144 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:04Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam
[2015-09-30T15:04Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam 9:127737329-141213431
[2015-09-30T15:04Z] GATK: RealignerTargetCreator
[2015-09-30T15:04Z] INFO  16:04:36,221 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:04Z] INFO  16:04:36,224 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:04Z] INFO  16:04:36,224 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:04Z] INFO  16:04:36,224 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:04Z] INFO  16:04:36,228 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpKWSeSH/1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign-realign.intervals -l INFO -L 9:127737329-141213431 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:04Z] INFO  16:04:36,233 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:04Z] INFO  16:04:36,234 HelpFormatter - Date/Time: 2015/09/30 16:04:36
[2015-09-30T15:04Z] INFO  16:04:36,234 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:04Z] INFO  16:04:36,234 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:04Z] INFO  16:04:36,650 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:04Z] INFO  16:04:36,825 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:04Z] INFO  16:04:36,833 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:04Z] INFO  16:04:36,848 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:04Z] INFO  16:04:37,099 IntervalUtils - Processing 13476103 bp from intervals
[2015-09-30T15:04Z] WARN  16:04:37,103 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:04Z] INFO  16:04:37,157 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:04Z] INFO  16:04:37,247 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:04Z] INFO  16:04:37,247 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:04Z] INFO  16:04:37,248 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:04Z] INFO  16:04:37,248 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:04Z] INFO  16:04:45,799 ProgressMeter -     10:27389407    600006.0    60.0 s     100.0 s       88.0%    68.0 s       8.0 s
[2015-09-30T15:04Z] INFO  16:04:50,241 ProgressMeter -     10:46336593    200003.0    30.0 s       2.5 m       48.9%    61.0 s      31.0 s
[2015-09-30T15:04Z] INFO  16:04:52,554 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:04Z] INFO  16:04:52,750 ProgressMeter -            done    760870.0    67.0 s      88.0 s      100.0%    67.0 s       0.0 s
[2015-09-30T15:04Z] INFO  16:04:52,750 ProgressMeter - Total runtime 67.03 secs, 1.12 min, 0.02 hours
[2015-09-30T15:04Z] INFO  16:04:52,751 MicroScheduler - 2164 reads were filtered out during the traversal out of approximately 763034 total reads (0.28%)
[2015-09-30T15:04Z] INFO  16:04:52,751 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:04Z] INFO  16:04:52,751 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:04Z] INFO  16:04:52,751 MicroScheduler -   -> 2164 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:04Z] INFO  16:04:53,784 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:04Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam
[2015-09-30T15:04Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam 10:1-31134673
[2015-09-30T15:04Z] GATK: RealignerTargetCreator
[2015-09-30T15:05Z] INFO  16:05:00,090 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:00,092 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:05Z] INFO  16:05:00,092 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:05Z] INFO  16:05:00,093 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:05Z] INFO  16:05:00,096 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpAxn6o5/1_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign-realign.intervals -l INFO -L 10:1-31134673 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:05Z] INFO  16:05:00,101 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:05Z] INFO  16:05:00,102 HelpFormatter - Date/Time: 2015/09/30 16:05:00
[2015-09-30T15:05Z] INFO  16:05:00,102 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:00,102 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:00,157 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:05Z] INFO  16:05:00,265 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:05Z] INFO  16:05:00,414 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:05Z] INFO  16:05:00,429 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:05Z] INFO  16:05:00,689 IntervalUtils - Processing 31134673 bp from intervals
[2015-09-30T15:05Z] WARN  16:05:00,693 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:05Z] INFO  16:05:01,540 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:05Z] INFO  16:05:01,678 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:05Z] INFO  16:05:01,678 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:05Z] INFO  16:05:01,678 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:05Z] INFO  16:05:01,679 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:05Z] INFO  16:05:06,404 ProgressMeter -            done   1.3476103E7    29.0 s       2.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T15:05Z] INFO  16:05:06,405 ProgressMeter - Total runtime 29.16 secs, 0.49 min, 0.01 hours
[2015-09-30T15:05Z] INFO  16:05:06,408 MicroScheduler - 122333 reads were filtered out during the traversal out of approximately 1452158 total reads (8.42%)
[2015-09-30T15:05Z] INFO  16:05:06,408 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:05Z] INFO  16:05:06,409 MicroScheduler -   -> 10987 reads (0.76% of total) failing BadMateFilter
[2015-09-30T15:05Z] INFO  16:05:06,409 MicroScheduler -   -> 77923 reads (5.37% of total) failing DuplicateReadFilter
[2015-09-30T15:05Z] INFO  16:05:06,409 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:05Z] INFO  16:05:06,409 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:05Z] INFO  16:05:06,410 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:05Z] INFO  16:05:06,410 MicroScheduler -   -> 33423 reads (2.30% of total) failing MappingQualityZeroFilter
[2015-09-30T15:05Z] INFO  16:05:06,410 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:05Z] INFO  16:05:06,410 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:05Z] INFO  16:05:06,411 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:05Z] INFO  16:05:07,387 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:05Z] GATK: realign ('9', 127737328, 141213431) : syn3-normal
[2015-09-30T15:05Z] INFO  16:05:11,485 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:11,487 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:05Z] INFO  16:05:11,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:05Z] INFO  16:05:11,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:05Z] INFO  16:05:11,491 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign-realign.intervals -L 9:127737329-141213431 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/tx/tmpdRtnW_/1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam
[2015-09-30T15:05Z] INFO  16:05:11,497 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:05Z] INFO  16:05:11,497 HelpFormatter - Date/Time: 2015/09/30 16:05:11
[2015-09-30T15:05Z] INFO  16:05:11,497 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:11,497 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:11,629 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:05Z] INFO  16:05:11,696 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:05Z] INFO  16:05:11,704 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:05Z] INFO  16:05:11,720 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:05Z] INFO  16:05:11,958 IntervalUtils - Processing 13476103 bp from intervals
[2015-09-30T15:05Z] WARN  16:05:11,963 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:05Z] INFO  16:05:12,020 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:05Z] INFO  16:05:12,121 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:05Z] INFO  16:05:12,121 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:05Z] INFO  16:05:12,122 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:05Z] INFO  16:05:12,122 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:05Z] INFO  16:05:12,253 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:05Z] INFO  16:05:12,356 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:05Z] INFO  16:05:20,242 ProgressMeter -     10:52445004    500008.0    60.0 s     120.0 s       68.6%    87.0 s      27.0 s
[2015-09-30T15:05Z] INFO  16:05:27,827 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:05Z] INFO  16:05:27,874 ProgressMeter -            done    637564.0    67.0 s     106.0 s      100.0%    67.0 s       0.0 s
[2015-09-30T15:05Z] INFO  16:05:27,875 ProgressMeter - Total runtime 67.64 secs, 1.13 min, 0.02 hours
[2015-09-30T15:05Z] INFO  16:05:27,875 MicroScheduler - 2488 reads were filtered out during the traversal out of approximately 640052 total reads (0.39%)
[2015-09-30T15:05Z] INFO  16:05:27,875 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:05Z] INFO  16:05:27,876 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:05Z] INFO  16:05:27,876 MicroScheduler -   -> 2488 reads (0.39% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:05Z] INFO  16:05:28,955 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:05Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam
[2015-09-30T15:05Z] INFO  16:05:30,125 ProgressMeter -            done   3.1134673E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T15:05Z] INFO  16:05:30,125 ProgressMeter - Total runtime 28.45 secs, 0.47 min, 0.01 hours
[2015-09-30T15:05Z] INFO  16:05:30,128 MicroScheduler - 68546 reads were filtered out during the traversal out of approximately 766136 total reads (8.95%)
[2015-09-30T15:05Z] INFO  16:05:30,129 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:05Z] INFO  16:05:30,129 MicroScheduler -   -> 10924 reads (1.43% of total) failing BadMateFilter
[2015-09-30T15:05Z] INFO  16:05:30,129 MicroScheduler -   -> 32728 reads (4.27% of total) failing DuplicateReadFilter
[2015-09-30T15:05Z] INFO  16:05:30,129 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:05Z] INFO  16:05:30,130 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:05Z] INFO  16:05:30,130 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:05Z] INFO  16:05:30,130 MicroScheduler -   -> 24894 reads (3.25% of total) failing MappingQualityZeroFilter
[2015-09-30T15:05Z] INFO  16:05:30,130 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:05Z] INFO  16:05:30,130 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:05Z] INFO  16:05:30,131 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:05Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam 10:31137166-62208748
[2015-09-30T15:05Z] GATK: RealignerTargetCreator
[2015-09-30T15:05Z] INFO  16:05:31,072 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:05Z] GATK: realign ('10', 0, 31134673) : syn3-normal
[2015-09-30T15:05Z] INFO  16:05:33,249 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:33,251 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:05Z] INFO  16:05:33,251 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:05Z] INFO  16:05:33,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:05Z] INFO  16:05:33,255 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign-realign.intervals -L 10:1-31134673 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpdlHUfu/1_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam
[2015-09-30T15:05Z] INFO  16:05:33,261 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:05Z] INFO  16:05:33,261 HelpFormatter - Date/Time: 2015/09/30 16:05:33
[2015-09-30T15:05Z] INFO  16:05:33,261 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:33,261 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:33,556 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:05Z] INFO  16:05:33,620 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:05Z] INFO  16:05:33,628 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:05Z] INFO  16:05:33,644 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:05Z] INFO  16:05:33,748 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:33,750 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:05Z] INFO  16:05:33,751 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:05Z] INFO  16:05:33,751 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:05Z] INFO  16:05:33,754 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpY8Q_MD/1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign-realign.intervals -l INFO -L 10:31137166-62208748 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:05Z] INFO  16:05:33,760 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:05Z] INFO  16:05:33,760 HelpFormatter - Date/Time: 2015/09/30 16:05:33
[2015-09-30T15:05Z] INFO  16:05:33,760 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:33,760 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:33,820 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:05Z] INFO  16:05:33,870 IntervalUtils - Processing 31134673 bp from intervals
[2015-09-30T15:05Z] WARN  16:05:33,874 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:05Z] INFO  16:05:33,931 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:05Z] INFO  16:05:33,932 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:05Z] INFO  16:05:33,940 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:05Z] INFO  16:05:33,956 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:05Z] INFO  16:05:34,074 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:05Z] INFO  16:05:34,075 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:05Z] INFO  16:05:34,075 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:05Z] INFO  16:05:34,076 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:05Z] INFO  16:05:34,217 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:05Z] INFO  16:05:34,406 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:05Z] INFO  16:05:34,785 IntervalUtils - Processing 31071583 bp from intervals
[2015-09-30T15:05Z] WARN  16:05:34,789 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:05Z] INFO  16:05:34,844 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:05Z] INFO  16:05:34,968 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:05Z] INFO  16:05:34,969 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:05Z] INFO  16:05:34,969 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:05Z] INFO  16:05:34,970 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:05Z] INFO  16:05:42,125 ProgressMeter -     9:132861823    400006.0    30.0 s      75.0 s       38.0%    78.0 s      48.0 s
[2015-09-30T15:05Z] INFO  16:05:57,384 ProgressMeter -            done   3.1071583E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T15:05Z] INFO  16:05:57,384 ProgressMeter - Total runtime 22.42 secs, 0.37 min, 0.01 hours
[2015-09-30T15:05Z] INFO  16:05:57,387 MicroScheduler - 143000 reads were filtered out during the traversal out of approximately 641688 total reads (22.28%)
[2015-09-30T15:05Z] INFO  16:05:57,388 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:05Z] INFO  16:05:57,388 MicroScheduler -   -> 9316 reads (1.45% of total) failing BadMateFilter
[2015-09-30T15:05Z] INFO  16:05:57,388 MicroScheduler -   -> 24526 reads (3.82% of total) failing DuplicateReadFilter
[2015-09-30T15:05Z] INFO  16:05:57,388 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:05Z] INFO  16:05:57,389 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:05Z] INFO  16:05:57,389 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:05Z] INFO  16:05:57,389 MicroScheduler -   -> 109158 reads (17.01% of total) failing MappingQualityZeroFilter
[2015-09-30T15:05Z] INFO  16:05:57,389 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:05Z] INFO  16:05:57,389 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:05Z] INFO  16:05:57,390 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:05Z] INFO  16:05:58,368 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:05Z] GATK: realign ('10', 31137165, 62208748) : syn3-normal
[2015-09-30T15:05Z] INFO  16:05:59,924 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:59,926 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:05Z] INFO  16:05:59,926 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:05Z] INFO  16:05:59,926 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:05Z] INFO  16:05:59,929 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign-realign.intervals -L 10:31137166-62208748 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmppqUyaH/1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam
[2015-09-30T15:05Z] INFO  16:05:59,935 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:05Z] INFO  16:05:59,935 HelpFormatter - Date/Time: 2015/09/30 16:05:59
[2015-09-30T15:05Z] INFO  16:05:59,935 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:05Z] INFO  16:05:59,935 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:00,064 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:06Z] INFO  16:06:00,126 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:06Z] INFO  16:06:00,134 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:06Z] INFO  16:06:00,150 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:06Z] INFO  16:06:00,973 IntervalUtils - Processing 31071583 bp from intervals
[2015-09-30T15:06Z] WARN  16:06:00,977 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:06Z] INFO  16:06:01,032 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:06Z] INFO  16:06:01,157 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:06Z] INFO  16:06:01,157 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:06Z] INFO  16:06:01,158 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:06Z] INFO  16:06:01,158 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:06Z] INFO  16:06:01,290 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:06Z] INFO  16:06:01,465 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:06Z] INFO  16:06:04,078 ProgressMeter -     10:18790191    400004.0    30.0 s      75.0 s       60.4%    49.0 s      19.0 s
[2015-09-30T15:06Z] INFO  16:06:12,470 ProgressMeter -     9:139747301   1100013.0    60.0 s      54.0 s       89.1%    67.0 s       7.0 s
[2015-09-30T15:06Z] INFO  16:06:14,347 ProgressMeter -            done    760870.0    40.0 s      52.0 s      100.0%    40.0 s       0.0 s
[2015-09-30T15:06Z] INFO  16:06:14,347 ProgressMeter - Total runtime 40.27 secs, 0.67 min, 0.01 hours
[2015-09-30T15:06Z] INFO  16:06:14,350 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 760870 total reads (0.00%)
[2015-09-30T15:06Z] INFO  16:06:14,350 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:06Z] INFO  16:06:14,351 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:06Z] INFO  16:06:14,351 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:06Z] INFO  16:06:15,436 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:06Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam
[2015-09-30T15:06Z] GATK pre-alignment ('10', 62267938, 93388847) : syn3-normal
[2015-09-30T15:06Z] INFO  16:06:20,372 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:20,374 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:06Z] INFO  16:06:20,374 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:06Z] INFO  16:06:20,374 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:06Z] INFO  16:06:20,378 HelpFormatter - Program Args: -T PrintReads -L 10:62267939-93388847 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpkWNz2h/1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam
[2015-09-30T15:06Z] INFO  16:06:20,384 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:06Z] INFO  16:06:20,385 HelpFormatter - Date/Time: 2015/09/30 16:06:20
[2015-09-30T15:06Z] INFO  16:06:20,385 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:20,385 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:20,514 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:06Z] INFO  16:06:22,232 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:06Z] INFO  16:06:22,285 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:06Z] INFO  16:06:22,294 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:06Z] INFO  16:06:22,310 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:06Z] INFO  16:06:22,324 IntervalUtils - Processing 31120909 bp from intervals
[2015-09-30T15:06Z] INFO  16:06:22,386 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:06Z] INFO  16:06:22,611 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:06Z] INFO  16:06:22,612 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:06Z] INFO  16:06:22,612 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:06Z] INFO  16:06:22,612 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:06Z] INFO  16:06:22,624 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:06Z] INFO  16:06:22,835 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:06Z] INFO  16:06:26,900 ProgressMeter -            done   1443569.0    74.0 s      51.0 s       99.5%    74.0 s       0.0 s
[2015-09-30T15:06Z] INFO  16:06:26,900 ProgressMeter - Total runtime 74.78 secs, 1.25 min, 0.02 hours
[2015-09-30T15:06Z] INFO  16:06:26,903 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1443569 total reads (0.00%)
[2015-09-30T15:06Z] INFO  16:06:26,904 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:06Z] INFO  16:06:26,904 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:06Z] INFO  16:06:26,904 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:06Z] INFO  16:06:28,027 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:06Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam
[2015-09-30T15:06Z] GATK pre-alignment ('10', 93389481, 124436664) : syn3-normal
[2015-09-30T15:06Z] INFO  16:06:32,723 ProgressMeter -     10:50964930    400007.0    31.0 s      78.0 s       63.8%    48.0 s      17.0 s
[2015-09-30T15:06Z] INFO  16:06:38,930 ProgressMeter -            done    637564.0    37.0 s      59.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T15:06Z] INFO  16:06:38,931 ProgressMeter - Total runtime 37.77 secs, 0.63 min, 0.01 hours
[2015-09-30T15:06Z] INFO  16:06:38,934 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 637564 total reads (0.00%)
[2015-09-30T15:06Z] INFO  16:06:38,934 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:06Z] INFO  16:06:38,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:06Z] INFO  16:06:38,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:06Z] INFO  16:06:41,201 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:41,203 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:06Z] INFO  16:06:41,203 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:06Z] INFO  16:06:41,203 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:06Z] INFO  16:06:41,206 HelpFormatter - Program Args: -T PrintReads -L 10:93389482-124436664 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpt14N5E/1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam
[2015-09-30T15:06Z] INFO  16:06:41,212 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:06Z] INFO  16:06:41,213 HelpFormatter - Date/Time: 2015/09/30 16:06:41
[2015-09-30T15:06Z] INFO  16:06:41,213 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:41,213 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:41,261 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:06Z] INFO  16:06:41,312 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:06Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam
[2015-09-30T15:06Z] GATK pre-alignment ('10', 124438084, 135534747) : syn3-normal
[2015-09-30T15:06Z] INFO  16:06:45,378 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:06Z] INFO  16:06:45,428 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:06Z] INFO  16:06:45,436 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:06Z] INFO  16:06:45,451 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:06Z] INFO  16:06:45,464 IntervalUtils - Processing 31047183 bp from intervals
[2015-09-30T15:06Z] INFO  16:06:45,521 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:06Z] INFO  16:06:45,723 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:06Z] INFO  16:06:45,723 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:06Z] INFO  16:06:45,724 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:06Z] INFO  16:06:45,724 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:06Z] INFO  16:06:45,735 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:06Z] INFO  16:06:45,922 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:06Z] INFO  16:06:49,074 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:49,076 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:06Z] INFO  16:06:49,076 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:06Z] INFO  16:06:49,076 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:06Z] INFO  16:06:49,079 HelpFormatter - Program Args: -T PrintReads -L 10:124438085-135534747 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpVTyW1_/1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam
[2015-09-30T15:06Z] INFO  16:06:49,085 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:06Z] INFO  16:06:49,085 HelpFormatter - Date/Time: 2015/09/30 16:06:49
[2015-09-30T15:06Z] INFO  16:06:49,086 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:49,086 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:06Z] INFO  16:06:50,655 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:06Z] INFO  16:06:53,655 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:06Z] INFO  16:06:53,705 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:06Z] INFO  16:06:53,713 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:06Z] INFO  16:06:53,727 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:06Z] INFO  16:06:53,741 IntervalUtils - Processing 11096663 bp from intervals
[2015-09-30T15:06Z] INFO  16:06:53,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:06Z] INFO  16:06:53,946 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:06Z] INFO  16:06:53,946 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:06Z] INFO  16:06:53,947 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:06Z] INFO  16:06:53,947 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:06Z] INFO  16:06:53,958 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:06Z] INFO  16:06:54,036 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:06Z] INFO  16:06:55,409 ProgressMeter -     10:72059240    200004.0    32.0 s       2.7 m       31.5%   101.0 s      69.0 s
[2015-09-30T15:07Z] INFO  16:07:15,950 ProgressMeter -     10:99094589    200005.0    30.0 s       2.5 m       18.4%     2.7 m       2.2 m
[2015-09-30T15:07Z] INFO  16:07:24,372 ProgressMeter -    10:133808960    200002.0    30.0 s       2.5 m       84.4%    35.0 s       5.0 s
[2015-09-30T15:07Z] INFO  16:07:25,410 ProgressMeter -     10:79576121    600011.0    62.0 s     104.0 s       55.6%   111.0 s      49.0 s
[2015-09-30T15:07Z] INFO  16:07:38,328 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7857d67
[2015-09-30T15:07Z] INFO  16:07:38,418 ProgressMeter -            done    440994.0    44.0 s     100.0 s       99.8%    44.0 s       0.0 s
[2015-09-30T15:07Z] INFO  16:07:38,418 ProgressMeter - Total runtime 44.47 secs, 0.74 min, 0.01 hours
[2015-09-30T15:07Z] INFO  16:07:38,419 MicroScheduler - 807 reads were filtered out during the traversal out of approximately 441801 total reads (0.18%)
[2015-09-30T15:07Z] INFO  16:07:38,419 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:07Z] INFO  16:07:38,419 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:07Z] INFO  16:07:38,419 MicroScheduler -   -> 807 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:07Z] INFO  16:07:39,378 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:07Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam
[2015-09-30T15:07Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam 10:124438085-135534747
[2015-09-30T15:07Z] GATK: RealignerTargetCreator
[2015-09-30T15:07Z] INFO  16:07:43,061 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:07Z] INFO  16:07:43,063 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:07Z] INFO  16:07:43,063 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:07Z] INFO  16:07:43,064 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:07Z] INFO  16:07:43,067 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpDXKHv0/1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign-realign.intervals -l INFO -L 10:124438085-135534747 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:07Z] INFO  16:07:43,073 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:07Z] INFO  16:07:43,073 HelpFormatter - Date/Time: 2015/09/30 16:07:43
[2015-09-30T15:07Z] INFO  16:07:43,073 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:07Z] INFO  16:07:43,074 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:07Z] INFO  16:07:43,143 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:07Z] INFO  16:07:43,265 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:07Z] INFO  16:07:43,273 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:07Z] INFO  16:07:43,289 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:07Z] INFO  16:07:43,535 IntervalUtils - Processing 11096663 bp from intervals
[2015-09-30T15:07Z] WARN  16:07:43,539 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:07Z] INFO  16:07:43,596 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:07Z] INFO  16:07:43,675 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:07Z] INFO  16:07:43,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:07Z] INFO  16:07:43,676 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:07Z] INFO  16:07:43,676 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:07Z] INFO  16:07:45,951 ProgressMeter -    10:104120890    600009.0    60.0 s     100.0 s       34.6%     2.9 m     113.0 s
[2015-09-30T15:07Z] INFO  16:07:49,930 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:07Z] INFO  16:07:50,084 ProgressMeter -            done    930408.0    87.0 s      94.0 s      100.0%    87.0 s       0.0 s
[2015-09-30T15:07Z] INFO  16:07:50,084 ProgressMeter - Total runtime 87.47 secs, 1.46 min, 0.02 hours
[2015-09-30T15:07Z] INFO  16:07:50,085 MicroScheduler - 1953 reads were filtered out during the traversal out of approximately 932361 total reads (0.21%)
[2015-09-30T15:07Z] INFO  16:07:50,085 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:07Z] INFO  16:07:50,085 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:07Z] INFO  16:07:50,085 MicroScheduler -   -> 1953 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:07Z] INFO  16:07:51,131 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:07Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam
[2015-09-30T15:07Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam 10:62267939-93388847
[2015-09-30T15:07Z] GATK: RealignerTargetCreator
[2015-09-30T15:07Z] INFO  16:07:55,087 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:07Z] INFO  16:07:55,089 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:07Z] INFO  16:07:55,089 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:07Z] INFO  16:07:55,089 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:07Z] INFO  16:07:55,093 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmplMg_4c/1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign-realign.intervals -l INFO -L 10:62267939-93388847 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:07Z] INFO  16:07:55,098 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:07Z] INFO  16:07:55,098 HelpFormatter - Date/Time: 2015/09/30 16:07:55
[2015-09-30T15:07Z] INFO  16:07:55,098 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:07Z] INFO  16:07:55,099 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:07Z] INFO  16:07:55,155 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:07Z] INFO  16:07:55,264 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:07Z] INFO  16:07:55,271 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:07Z] INFO  16:07:55,287 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:07Z] INFO  16:07:57,107 IntervalUtils - Processing 31120909 bp from intervals
[2015-09-30T15:07Z] WARN  16:07:57,111 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:07Z] INFO  16:07:57,166 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:07Z] INFO  16:07:57,309 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:07Z] INFO  16:07:57,310 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:07Z] INFO  16:07:57,310 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:07Z] INFO  16:07:57,311 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:07Z] INFO  16:07:57,419 ProgressMeter -            done   1.1096663E7    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2015-09-30T15:07Z] INFO  16:07:57,419 ProgressMeter - Total runtime 13.74 secs, 0.23 min, 0.00 hours
[2015-09-30T15:07Z] INFO  16:07:57,422 MicroScheduler - 38150 reads were filtered out during the traversal out of approximately 443073 total reads (8.61%)
[2015-09-30T15:07Z] INFO  16:07:57,422 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:07Z] INFO  16:07:57,423 MicroScheduler -   -> 4571 reads (1.03% of total) failing BadMateFilter
[2015-09-30T15:07Z] INFO  16:07:57,423 MicroScheduler -   -> 21993 reads (4.96% of total) failing DuplicateReadFilter
[2015-09-30T15:07Z] INFO  16:07:57,423 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:07Z] INFO  16:07:57,424 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:07Z] INFO  16:07:57,424 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:07Z] INFO  16:07:57,424 MicroScheduler -   -> 11586 reads (2.61% of total) failing MappingQualityZeroFilter
[2015-09-30T15:07Z] INFO  16:07:57,424 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:07Z] INFO  16:07:57,425 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:07Z] INFO  16:07:57,425 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:07Z] INFO  16:07:58,440 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:07Z] GATK: realign ('10', 124438084, 135534747) : syn3-normal
[2015-09-30T15:08Z] INFO  16:08:00,601 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:00,603 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:08Z] INFO  16:08:00,603 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:08Z] INFO  16:08:00,603 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:08Z] INFO  16:08:00,607 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign-realign.intervals -L 10:124438085-135534747 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpRAX74H/1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam
[2015-09-30T15:08Z] INFO  16:08:00,612 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:08Z] INFO  16:08:00,613 HelpFormatter - Date/Time: 2015/09/30 16:08:00
[2015-09-30T15:08Z] INFO  16:08:00,613 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:00,613 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:00,740 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:08Z] INFO  16:08:00,808 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:08Z] INFO  16:08:00,816 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:08Z] INFO  16:08:00,833 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:08Z] INFO  16:08:02,282 IntervalUtils - Processing 11096663 bp from intervals
[2015-09-30T15:08Z] WARN  16:08:02,286 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:08Z] INFO  16:08:02,344 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:08Z] INFO  16:08:02,427 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:08Z] INFO  16:08:02,428 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:08Z] INFO  16:08:02,428 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:08Z] INFO  16:08:02,428 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:08Z] INFO  16:08:02,535 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:08Z] INFO  16:08:02,624 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:08Z] INFO  16:08:17,402 ProgressMeter -    10:115970791   1000013.0    91.0 s      91.0 s       72.7%     2.1 m      34.0 s
[2015-09-30T15:08Z] INFO  16:08:26,873 ProgressMeter -            done   3.1120909E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T15:08Z] INFO  16:08:26,874 ProgressMeter - Total runtime 29.56 secs, 0.49 min, 0.01 hours
[2015-09-30T15:08Z] INFO  16:08:26,877 MicroScheduler - 85388 reads were filtered out during the traversal out of approximately 935892 total reads (9.12%)
[2015-09-30T15:08Z] INFO  16:08:26,877 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:08Z] INFO  16:08:26,877 MicroScheduler -   -> 11079 reads (1.18% of total) failing BadMateFilter
[2015-09-30T15:08Z] INFO  16:08:26,878 MicroScheduler -   -> 42955 reads (4.59% of total) failing DuplicateReadFilter
[2015-09-30T15:08Z] INFO  16:08:26,878 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:08Z] INFO  16:08:26,878 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:08Z] INFO  16:08:26,878 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:08Z] INFO  16:08:26,878 MicroScheduler -   -> 31354 reads (3.35% of total) failing MappingQualityZeroFilter
[2015-09-30T15:08Z] INFO  16:08:26,879 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:08Z] INFO  16:08:26,879 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:08Z] INFO  16:08:26,879 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:08Z] INFO  16:08:28,384 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:08Z] GATK: realign ('10', 62267938, 93388847) : syn3-normal
[2015-09-30T15:08Z] INFO  16:08:29,259 ProgressMeter -            done    440994.0    26.0 s      60.0 s       99.8%    26.0 s       0.0 s
[2015-09-30T15:08Z] INFO  16:08:29,260 ProgressMeter - Total runtime 26.83 secs, 0.45 min, 0.01 hours
[2015-09-30T15:08Z] INFO  16:08:29,263 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 440994 total reads (0.00%)
[2015-09-30T15:08Z] INFO  16:08:29,263 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:08Z] INFO  16:08:29,263 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:08Z] INFO  16:08:29,263 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:08Z] INFO  16:08:30,257 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:08Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam
[2015-09-30T15:08Z] GATK pre-alignment ('11', 0, 31082819) : syn3-normal
[2015-09-30T15:08Z] INFO  16:08:33,458 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:33,460 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:08Z] INFO  16:08:33,461 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:08Z] INFO  16:08:33,461 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:08Z] INFO  16:08:33,464 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign-realign.intervals -L 10:62267939-93388847 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpRyADQv/1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam
[2015-09-30T15:08Z] INFO  16:08:33,470 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:08Z] INFO  16:08:33,470 HelpFormatter - Date/Time: 2015/09/30 16:08:33
[2015-09-30T15:08Z] INFO  16:08:33,470 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:33,471 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:33,606 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:08Z] INFO  16:08:33,675 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:08Z] INFO  16:08:33,683 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:08Z] INFO  16:08:33,699 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:08Z] INFO  16:08:35,222 IntervalUtils - Processing 31120909 bp from intervals
[2015-09-30T15:08Z] WARN  16:08:35,226 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:08Z] INFO  16:08:35,281 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:08Z] INFO  16:08:35,426 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:08Z] INFO  16:08:35,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:08Z] INFO  16:08:35,427 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:08Z] INFO  16:08:35,427 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:08Z] INFO  16:08:35,571 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:08Z] INFO  16:08:35,710 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:35,712 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:08Z] INFO  16:08:35,712 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:08Z] INFO  16:08:35,713 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:08Z] INFO  16:08:35,716 HelpFormatter - Program Args: -T PrintReads -L 11:1-31082819 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmp5tDYdr/1_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam
[2015-09-30T15:08Z] INFO  16:08:35,722 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:08Z] INFO  16:08:35,722 HelpFormatter - Date/Time: 2015/09/30 16:08:35
[2015-09-30T15:08Z] INFO  16:08:35,722 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:35,722 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:35,760 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:08Z] INFO  16:08:35,831 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:08Z] INFO  16:08:36,584 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:08Z] INFO  16:08:36,633 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:08Z] INFO  16:08:36,641 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:08Z] INFO  16:08:36,731 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2015-09-30T15:08Z] INFO  16:08:36,804 IntervalUtils - Processing 31082819 bp from intervals
[2015-09-30T15:08Z] INFO  16:08:36,901 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:08Z] INFO  16:08:37,998 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:08Z] INFO  16:08:37,998 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:08Z] INFO  16:08:37,998 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:08Z] INFO  16:08:37,999 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:08Z] INFO  16:08:38,010 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:08Z] INFO  16:08:38,219 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:08Z] INFO  16:08:39,103 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@74107a99
[2015-09-30T15:08Z] INFO  16:08:39,311 ProgressMeter -            done   1305460.0   113.0 s      87.0 s      100.0%   113.0 s       0.0 s
[2015-09-30T15:08Z] INFO  16:08:39,311 ProgressMeter - Total runtime 113.59 secs, 1.89 min, 0.03 hours
[2015-09-30T15:08Z] INFO  16:08:39,312 MicroScheduler - 2739 reads were filtered out during the traversal out of approximately 1308199 total reads (0.21%)
[2015-09-30T15:08Z] INFO  16:08:39,312 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:08Z] INFO  16:08:39,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:08Z] INFO  16:08:39,312 MicroScheduler -   -> 2739 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:08Z] INFO  16:08:40,423 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:08Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam
[2015-09-30T15:08Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam 10:93389482-124436664
[2015-09-30T15:08Z] GATK: RealignerTargetCreator
[2015-09-30T15:08Z] INFO  16:08:47,270 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:47,272 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:08Z] INFO  16:08:47,272 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:08Z] INFO  16:08:47,272 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:08Z] INFO  16:08:47,276 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmpC4vxSM/1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign-realign.intervals -l INFO -L 10:93389482-124436664 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:08Z] INFO  16:08:47,281 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:08Z] INFO  16:08:47,282 HelpFormatter - Date/Time: 2015/09/30 16:08:47
[2015-09-30T15:08Z] INFO  16:08:47,282 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:47,282 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:08Z] INFO  16:08:47,339 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:08Z] INFO  16:08:47,441 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:08Z] INFO  16:08:47,449 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:08Z] INFO  16:08:47,464 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:08Z] INFO  16:08:47,696 IntervalUtils - Processing 31047183 bp from intervals
[2015-09-30T15:08Z] WARN  16:08:47,700 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:08Z] INFO  16:08:47,754 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:08Z] INFO  16:08:47,906 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:08Z] INFO  16:08:47,906 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:08Z] INFO  16:08:47,906 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:08Z] INFO  16:08:47,907 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:09Z] INFO  16:09:05,949 ProgressMeter -     10:74695571    300005.0    30.0 s     101.0 s       39.9%    75.0 s      45.0 s
[2015-09-30T15:09Z] INFO  16:09:09,009 ProgressMeter -      11:1154543    200003.0    31.0 s       2.6 m        3.7%    13.9 m      13.4 m
[2015-09-30T15:09Z] INFO  16:09:17,909 ProgressMeter -    10:119774841   2.6377559E7    30.0 s       1.0 s       85.0%    35.0 s       5.0 s
[2015-09-30T15:09Z] INFO  16:09:22,714 ProgressMeter -            done   3.1047183E7    34.0 s       1.0 s      100.0%    34.0 s       0.0 s
[2015-09-30T15:09Z] INFO  16:09:22,715 ProgressMeter - Total runtime 34.81 secs, 0.58 min, 0.01 hours
[2015-09-30T15:09Z] INFO  16:09:22,718 MicroScheduler - 105001 reads were filtered out during the traversal out of approximately 1312910 total reads (8.00%)
[2015-09-30T15:09Z] INFO  16:09:22,718 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:09Z] INFO  16:09:22,719 MicroScheduler -   -> 14030 reads (1.07% of total) failing BadMateFilter
[2015-09-30T15:09Z] INFO  16:09:22,719 MicroScheduler -   -> 60208 reads (4.59% of total) failing DuplicateReadFilter
[2015-09-30T15:09Z] INFO  16:09:22,719 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:09Z] INFO  16:09:22,719 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:09Z] INFO  16:09:22,720 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:09Z] INFO  16:09:22,720 MicroScheduler -   -> 30763 reads (2.34% of total) failing MappingQualityZeroFilter
[2015-09-30T15:09Z] INFO  16:09:22,720 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:09Z] INFO  16:09:22,720 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:09Z] INFO  16:09:22,721 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:09Z] INFO  16:09:23,823 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:09Z] GATK: realign ('10', 93389481, 124436664) : syn3-normal
[2015-09-30T15:09Z] INFO  16:09:25,952 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:09Z] INFO  16:09:25,954 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:09Z] INFO  16:09:25,954 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:09Z] INFO  16:09:25,954 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:09Z] INFO  16:09:25,958 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign-realign.intervals -L 10:93389482-124436664 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/tx/tmphqiC6o/1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam
[2015-09-30T15:09Z] INFO  16:09:25,963 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:09Z] INFO  16:09:25,963 HelpFormatter - Date/Time: 2015/09/30 16:09:25
[2015-09-30T15:09Z] INFO  16:09:25,964 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:09Z] INFO  16:09:25,964 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:09Z] INFO  16:09:26,090 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:09Z] INFO  16:09:26,648 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:09Z] INFO  16:09:26,656 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:09Z] INFO  16:09:26,671 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:09Z] INFO  16:09:26,931 IntervalUtils - Processing 31047183 bp from intervals
[2015-09-30T15:09Z] WARN  16:09:26,935 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:09Z] INFO  16:09:27,025 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:09Z] INFO  16:09:27,078 ProgressMeter -            done    930408.0    51.0 s      55.0 s      100.0%    51.0 s       0.0 s
[2015-09-30T15:09Z] INFO  16:09:27,078 ProgressMeter - Total runtime 51.65 secs, 0.86 min, 0.01 hours
[2015-09-30T15:09Z] INFO  16:09:27,081 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 930408 total reads (0.00%)
[2015-09-30T15:09Z] INFO  16:09:27,082 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:09Z] INFO  16:09:27,082 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:09Z] INFO  16:09:27,082 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:09Z] INFO  16:09:27,174 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:09Z] INFO  16:09:27,174 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:09Z] INFO  16:09:27,175 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:09Z] INFO  16:09:27,175 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:09Z] INFO  16:09:27,320 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:09Z] INFO  16:09:27,508 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:09Z] INFO  16:09:28,152 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:09Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam
[2015-09-30T15:09Z] GATK pre-alignment ('11', 31085657, 62105890) : syn3-normal
[2015-09-30T15:09Z] INFO  16:09:33,497 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:09Z] INFO  16:09:33,499 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:09Z] INFO  16:09:33,499 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:09Z] INFO  16:09:33,499 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:09Z] INFO  16:09:33,502 HelpFormatter - Program Args: -T PrintReads -L 11:31085658-62105890 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmpd0s10F/1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam
[2015-09-30T15:09Z] INFO  16:09:33,508 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:09Z] INFO  16:09:33,508 HelpFormatter - Date/Time: 2015/09/30 16:09:33
[2015-09-30T15:09Z] INFO  16:09:33,509 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:09Z] INFO  16:09:33,509 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:09Z] INFO  16:09:33,935 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:09Z] INFO  16:09:34,935 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:09Z] INFO  16:09:34,984 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:09Z] INFO  16:09:34,991 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:09Z] INFO  16:09:35,005 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:09Z] INFO  16:09:35,018 IntervalUtils - Processing 31020233 bp from intervals
[2015-09-30T15:09Z] INFO  16:09:35,074 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:09Z] INFO  16:09:35,273 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:09Z] INFO  16:09:35,273 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:09Z] INFO  16:09:35,274 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:09Z] INFO  16:09:35,274 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:09Z] INFO  16:09:35,285 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:09Z] INFO  16:09:35,495 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:09Z] INFO  16:09:39,010 ProgressMeter -      11:5799753    500007.0    61.0 s       2.0 m       18.7%     5.4 m       4.4 m
[2015-09-30T15:09Z] INFO  16:09:57,177 ProgressMeter -    10:102055080    400007.0    30.0 s      75.0 s       27.9%   107.0 s      77.0 s
[2015-09-30T15:10Z] INFO  16:10:05,276 ProgressMeter -     11:44117588    200004.0    30.0 s       2.5 m       42.0%    71.0 s      41.0 s
[2015-09-30T15:10Z] INFO  16:10:09,041 ProgressMeter -     11:12905041    900014.0    91.0 s     101.0 s       41.5%     3.7 m       2.1 m
[2015-09-30T15:10Z] INFO  16:10:27,178 ProgressMeter -    10:119766856   1100014.0    60.0 s      54.0 s       85.0%    70.0 s      10.0 s
[2015-09-30T15:10Z] INFO  16:10:33,841 ProgressMeter -            done   1305460.0    66.0 s      51.0 s      100.0%    66.0 s       0.0 s
[2015-09-30T15:10Z] INFO  16:10:33,842 ProgressMeter - Total runtime 66.67 secs, 1.11 min, 0.02 hours
[2015-09-30T15:10Z] INFO  16:10:33,845 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1305460 total reads (0.00%)
[2015-09-30T15:10Z] INFO  16:10:33,845 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:10Z] INFO  16:10:33,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:10Z] INFO  16:10:33,846 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:10Z] INFO  16:10:34,920 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:10Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam
[2015-09-30T15:10Z] INFO  16:10:35,277 ProgressMeter -     11:49071070    500008.0    60.0 s     120.0 s       58.0%   103.0 s      43.0 s
[2015-09-30T15:10Z] GATK pre-alignment ('11', 62123540, 93141822) : syn3-normal
[2015-09-30T15:10Z] INFO  16:10:39,080 ProgressMeter -     11:30557712   1300018.0     2.0 m      93.0 s       98.3%     2.1 m       2.0 s
[2015-09-30T15:10Z] INFO  16:10:39,914 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4cebf90c
[2015-09-30T15:10Z] INFO  16:10:40,099 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:10Z] INFO  16:10:40,101 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:10Z] INFO  16:10:40,102 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:10Z] INFO  16:10:40,102 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:10Z] INFO  16:10:40,105 HelpFormatter - Program Args: -T PrintReads -L 11:62123541-93141822 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmpvQXlv2/1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam
[2015-09-30T15:10Z] INFO  16:10:40,111 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:10Z] INFO  16:10:40,112 HelpFormatter - Date/Time: 2015/09/30 16:10:40
[2015-09-30T15:10Z] INFO  16:10:40,112 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:10Z] INFO  16:10:40,112 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:10Z] INFO  16:10:40,112 ProgressMeter -            done   1359395.0     2.0 m      89.0 s      100.0%     2.0 m       0.0 s
[2015-09-30T15:10Z] INFO  16:10:40,113 ProgressMeter - Total runtime 122.12 secs, 2.04 min, 0.03 hours
[2015-09-30T15:10Z] INFO  16:10:40,113 MicroScheduler - 2631 reads were filtered out during the traversal out of approximately 1362026 total reads (0.19%)
[2015-09-30T15:10Z] INFO  16:10:40,114 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:10Z] INFO  16:10:40,114 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:10Z] INFO  16:10:40,114 MicroScheduler -   -> 2631 reads (0.19% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:10Z] INFO  16:10:40,216 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:10Z] INFO  16:10:41,392 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:10Z] INFO  16:10:41,440 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:10Z] INFO  16:10:41,447 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:10Z] INFO  16:10:41,462 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:10Z] INFO  16:10:41,474 IntervalUtils - Processing 31018282 bp from intervals
[2015-09-30T15:10Z] INFO  16:10:41,517 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:10Z] INFO  16:10:41,531 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:10Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam
[2015-09-30T15:10Z] INFO  16:10:42,166 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:10Z] INFO  16:10:42,166 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:10Z] INFO  16:10:42,166 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:10Z] INFO  16:10:42,167 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:10Z] INFO  16:10:42,178 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:10Z] INFO  16:10:42,382 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:10Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam 11:1-31082819
[2015-09-30T15:10Z] GATK: RealignerTargetCreator
[2015-09-30T15:10Z] INFO  16:10:47,483 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:10Z] INFO  16:10:47,485 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:10Z] INFO  16:10:47,485 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:10Z] INFO  16:10:47,485 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:10Z] INFO  16:10:47,489 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmpNx74DG/1_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign-realign.intervals -l INFO -L 11:1-31082819 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:10Z] INFO  16:10:47,494 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:10Z] INFO  16:10:47,495 HelpFormatter - Date/Time: 2015/09/30 16:10:47
[2015-09-30T15:10Z] INFO  16:10:47,495 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:10Z] INFO  16:10:47,495 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:10Z] INFO  16:10:47,556 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:10Z] INFO  16:10:48,515 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:10Z] INFO  16:10:48,524 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:10Z] INFO  16:10:48,541 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:10Z] INFO  16:10:48,787 IntervalUtils - Processing 31082819 bp from intervals
[2015-09-30T15:10Z] WARN  16:10:48,791 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:10Z] INFO  16:10:48,850 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:10Z] INFO  16:10:49,000 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:10Z] INFO  16:10:49,001 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:10Z] INFO  16:10:49,001 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:10Z] INFO  16:10:49,002 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:11Z] INFO  16:11:05,278 ProgressMeter -     11:60538581    800011.0    90.0 s     112.0 s       94.9%    94.0 s       4.0 s
[2015-09-30T15:11Z] INFO  16:11:12,169 ProgressMeter -     11:64074658    200002.0    30.0 s       2.5 m        6.3%     7.9 m       7.4 m
[2015-09-30T15:11Z] INFO  16:11:19,004 ProgressMeter -     11:20057217   2.0054016E7    30.0 s       1.0 s       64.5%    46.0 s      16.0 s
[2015-09-30T15:11Z] INFO  16:11:22,085 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:11Z] INFO  16:11:22,170 ProgressMeter -            done   1019769.0   106.0 s     104.0 s      100.0%   106.0 s       0.0 s
[2015-09-30T15:11Z] INFO  16:11:22,171 ProgressMeter - Total runtime 106.90 secs, 1.78 min, 0.03 hours
[2015-09-30T15:11Z] INFO  16:11:22,171 MicroScheduler - 2413 reads were filtered out during the traversal out of approximately 1022182 total reads (0.24%)
[2015-09-30T15:11Z] INFO  16:11:22,171 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:11Z] INFO  16:11:22,171 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:11Z] INFO  16:11:22,172 MicroScheduler -   -> 2413 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:11Z] INFO  16:11:23,261 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:11Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam
[2015-09-30T15:11Z] INFO  16:11:26,027 ProgressMeter -            done   3.1082819E7    37.0 s       1.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T15:11Z] INFO  16:11:26,027 ProgressMeter - Total runtime 37.03 secs, 0.62 min, 0.01 hours
[2015-09-30T15:11Z] INFO  16:11:26,027 MicroScheduler - 113939 reads were filtered out during the traversal out of approximately 1366943 total reads (8.34%)
[2015-09-30T15:11Z] INFO  16:11:26,028 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:11Z] INFO  16:11:26,028 MicroScheduler -   -> 12966 reads (0.95% of total) failing BadMateFilter
[2015-09-30T15:11Z] INFO  16:11:26,028 MicroScheduler -   -> 67683 reads (4.95% of total) failing DuplicateReadFilter
[2015-09-30T15:11Z] INFO  16:11:26,029 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:11Z] INFO  16:11:26,029 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:11Z] INFO  16:11:26,029 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:11Z] INFO  16:11:26,029 MicroScheduler -   -> 33290 reads (2.44% of total) failing MappingQualityZeroFilter
[2015-09-30T15:11Z] INFO  16:11:26,029 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:11Z] INFO  16:11:26,030 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:11Z] INFO  16:11:26,030 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:11Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam 11:31085658-62105890
[2015-09-30T15:11Z] GATK: RealignerTargetCreator
[2015-09-30T15:11Z] INFO  16:11:27,099 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:11Z] GATK: realign ('11', 0, 31082819) : syn3-normal
[2015-09-30T15:11Z] INFO  16:11:28,723 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:11Z] INFO  16:11:28,725 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:11Z] INFO  16:11:28,725 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:11Z] INFO  16:11:28,726 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:11Z] INFO  16:11:28,729 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmp0n9DsL/1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign-realign.intervals -l INFO -L 11:31085658-62105890 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:11Z] INFO  16:11:28,735 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:11Z] INFO  16:11:28,735 HelpFormatter - Date/Time: 2015/09/30 16:11:28
[2015-09-30T15:11Z] INFO  16:11:28,735 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:11Z] INFO  16:11:28,735 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:11Z] INFO  16:11:28,791 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:11Z] INFO  16:11:28,897 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:11Z] INFO  16:11:28,904 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:11Z] INFO  16:11:28,920 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:11Z] INFO  16:11:29,172 IntervalUtils - Processing 31020233 bp from intervals
[2015-09-30T15:11Z] WARN  16:11:29,176 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:11Z] INFO  16:11:29,233 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:11Z] INFO  16:11:29,347 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:11Z] INFO  16:11:29,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:11Z] INFO  16:11:29,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:11Z] INFO  16:11:29,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:11Z] INFO  16:11:29,352 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign-realign.intervals -L 11:1-31082819 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmprZgfR1/1_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam
[2015-09-30T15:11Z] INFO  16:11:29,358 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:11Z] INFO  16:11:29,358 HelpFormatter - Date/Time: 2015/09/30 16:11:29
[2015-09-30T15:11Z] INFO  16:11:29,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:11Z] INFO  16:11:29,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:11Z] INFO  16:11:29,362 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:11Z] INFO  16:11:29,362 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:11Z] INFO  16:11:29,363 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:11Z] INFO  16:11:29,363 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:11Z] INFO  16:11:29,477 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:11Z] INFO  16:11:29,539 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:11Z] INFO  16:11:29,547 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:11Z] INFO  16:11:29,563 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:11Z] INFO  16:11:30,252 IntervalUtils - Processing 31082819 bp from intervals
[2015-09-30T15:11Z] WARN  16:11:30,256 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:11Z] INFO  16:11:30,311 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:11Z] INFO  16:11:30,459 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:11Z] INFO  16:11:30,459 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:11Z] INFO  16:11:30,460 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:11Z] INFO  16:11:30,460 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:11Z] INFO  16:11:30,610 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:11Z] INFO  16:11:30,799 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:11Z] INFO  16:11:42,496 ProgressMeter -     11:65746947    500007.0    60.0 s     120.0 s       11.7%     8.6 m       7.6 m
[2015-09-30T15:11Z] INFO  16:11:56,959 ProgressMeter -            done   3.1020233E7    27.0 s       0.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T15:11Z] INFO  16:11:56,959 ProgressMeter - Total runtime 27.60 secs, 0.46 min, 0.01 hours
[2015-09-30T15:11Z] INFO  16:11:56,962 MicroScheduler - 85145 reads were filtered out during the traversal out of approximately 1026064 total reads (8.30%)
[2015-09-30T15:11Z] INFO  16:11:56,963 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:11Z] INFO  16:11:56,963 MicroScheduler -   -> 11134 reads (1.09% of total) failing BadMateFilter
[2015-09-30T15:11Z] INFO  16:11:56,963 MicroScheduler -   -> 48238 reads (4.70% of total) failing DuplicateReadFilter
[2015-09-30T15:11Z] INFO  16:11:56,963 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:11Z] INFO  16:11:56,964 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:11Z] INFO  16:11:56,964 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:11Z] INFO  16:11:56,964 MicroScheduler -   -> 25773 reads (2.51% of total) failing MappingQualityZeroFilter
[2015-09-30T15:11Z] INFO  16:11:56,964 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:11Z] INFO  16:11:56,965 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:11Z] INFO  16:11:56,965 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:11Z] INFO  16:11:57,910 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:11Z] GATK: realign ('11', 31085657, 62105890) : syn3-normal
[2015-09-30T15:11Z] INFO  16:11:59,900 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:11Z] INFO  16:11:59,902 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:11Z] INFO  16:11:59,902 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:11Z] INFO  16:11:59,903 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:11Z] INFO  16:11:59,906 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign-realign.intervals -L 11:31085658-62105890 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmp71q6Pn/1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam
[2015-09-30T15:11Z] INFO  16:11:59,911 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:11Z] INFO  16:11:59,912 HelpFormatter - Date/Time: 2015/09/30 16:11:59
[2015-09-30T15:11Z] INFO  16:11:59,912 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:11Z] INFO  16:11:59,912 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:12Z] INFO  16:12:00,035 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:12Z] INFO  16:12:00,097 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:12Z] INFO  16:12:00,105 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:12Z] INFO  16:12:00,119 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:12Z] INFO  16:12:00,344 IntervalUtils - Processing 31020233 bp from intervals
[2015-09-30T15:12Z] WARN  16:12:00,348 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:12Z] INFO  16:12:00,401 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:12Z] INFO  16:12:00,526 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:12Z] INFO  16:12:00,527 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:12Z] INFO  16:12:00,527 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:12Z] INFO  16:12:00,528 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:12Z] INFO  16:12:00,665 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:12Z] INFO  16:12:00,832 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:12Z] INFO  16:12:02,333 ProgressMeter -      11:5618307    500007.0    31.0 s      63.0 s       18.1%     2.9 m       2.3 m
[2015-09-30T15:12Z] INFO  16:12:22,497 ProgressMeter -     11:70182166    900014.0   100.0 s     111.0 s       26.0%     6.4 m       4.7 m
[2015-09-30T15:12Z] INFO  16:12:31,506 ProgressMeter -     11:49884062    500008.0    30.0 s      61.0 s       60.6%    49.0 s      19.0 s
[2015-09-30T15:12Z] INFO  16:12:32,335 ProgressMeter -     11:26353590   1200017.0    61.0 s      51.0 s       84.8%    71.0 s      10.0 s
[2015-09-30T15:12Z] INFO  16:12:34,097 ProgressMeter -            done   1359395.0    63.0 s      46.0 s      100.0%    63.0 s       0.0 s
[2015-09-30T15:12Z] INFO  16:12:34,098 ProgressMeter - Total runtime 63.64 secs, 1.06 min, 0.02 hours
[2015-09-30T15:12Z] INFO  16:12:34,101 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1359395 total reads (0.00%)
[2015-09-30T15:12Z] INFO  16:12:34,101 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:12Z] INFO  16:12:34,101 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:12Z] INFO  16:12:34,101 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:12Z] INFO  16:12:35,152 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:12Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam
[2015-09-30T15:12Z] GATK pre-alignment ('11', 93147865, 124180877) : syn3-normal
[2015-09-30T15:12Z] INFO  16:12:43,035 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:12Z] INFO  16:12:43,037 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:12Z] INFO  16:12:43,037 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:12Z] INFO  16:12:43,037 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:12Z] INFO  16:12:43,040 HelpFormatter - Program Args: -T PrintReads -L 11:93147866-124180877 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmp2HuXtN/1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam
[2015-09-30T15:12Z] INFO  16:12:43,047 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:12Z] INFO  16:12:43,047 HelpFormatter - Date/Time: 2015/09/30 16:12:43
[2015-09-30T15:12Z] INFO  16:12:43,048 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:12Z] INFO  16:12:43,048 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:12Z] INFO  16:12:43,161 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:12Z] INFO  16:12:45,354 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:12Z] INFO  16:12:45,402 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:12Z] INFO  16:12:45,409 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:12Z] INFO  16:12:45,424 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:12Z] INFO  16:12:45,437 IntervalUtils - Processing 31033012 bp from intervals
[2015-09-30T15:12Z] INFO  16:12:45,492 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:12Z] INFO  16:12:45,703 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:12Z] INFO  16:12:45,704 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:12Z] INFO  16:12:45,704 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:12Z] INFO  16:12:45,704 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:12Z] INFO  16:12:45,715 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:12Z] INFO  16:12:45,929 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:12Z] INFO  16:12:49,264 ProgressMeter -            done   1019769.0    48.0 s      47.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T15:12Z] INFO  16:12:49,265 ProgressMeter - Total runtime 48.74 secs, 0.81 min, 0.01 hours
[2015-09-30T15:12Z] INFO  16:12:49,268 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1019769 total reads (0.00%)
[2015-09-30T15:12Z] INFO  16:12:49,268 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:12Z] INFO  16:12:49,269 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:12Z] INFO  16:12:49,269 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:12Z] INFO  16:12:50,383 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:12Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam
[2015-09-30T15:12Z] GATK pre-alignment ('11', 124188917, 135006516) : syn3-normal
[2015-09-30T15:12Z] INFO  16:12:57,904 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:12Z] INFO  16:12:57,906 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:12Z] INFO  16:12:57,906 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:12Z] INFO  16:12:57,906 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:12Z] INFO  16:12:57,910 HelpFormatter - Program Args: -T PrintReads -L 11:124188918-135006516 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmprFN6Xi/1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam
[2015-09-30T15:12Z] INFO  16:12:57,915 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:12Z] INFO  16:12:57,915 HelpFormatter - Date/Time: 2015/09/30 16:12:57
[2015-09-30T15:12Z] INFO  16:12:57,915 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:12Z] INFO  16:12:57,916 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:12Z] INFO  16:12:58,028 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:12Z] INFO  16:12:59,211 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:12Z] INFO  16:12:59,259 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:12Z] INFO  16:12:59,266 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:12Z] INFO  16:12:59,279 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:12Z] INFO  16:12:59,292 IntervalUtils - Processing 10817599 bp from intervals
[2015-09-30T15:12Z] INFO  16:12:59,345 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:12Z] INFO  16:12:59,483 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:12Z] INFO  16:12:59,484 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:12Z] INFO  16:12:59,484 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:12Z] INFO  16:12:59,484 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:12Z] INFO  16:12:59,495 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:12Z] INFO  16:12:59,571 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:13Z] INFO  16:13:02,498 ProgressMeter -     11:76870900   1300021.0     2.3 m     107.0 s       47.5%     4.9 m       2.6 m
[2015-09-30T15:13Z] INFO  16:13:16,216 ProgressMeter -    11:104904835    200003.0    30.0 s       2.5 m       37.9%    79.0 s      49.0 s
[2015-09-30T15:13Z] INFO  16:13:29,487 ProgressMeter -    11:134243607    300003.0    30.0 s     100.0 s       92.9%    32.0 s       2.0 s
[2015-09-30T15:13Z] INFO  16:13:29,981 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@627346b4
[2015-09-30T15:13Z] INFO  16:13:30,184 ProgressMeter -            done    336954.0    30.0 s      91.0 s       97.8%    30.0 s       0.0 s
[2015-09-30T15:13Z] INFO  16:13:30,184 ProgressMeter - Total runtime 30.70 secs, 0.51 min, 0.01 hours
[2015-09-30T15:13Z] INFO  16:13:30,185 MicroScheduler - 571 reads were filtered out during the traversal out of approximately 337525 total reads (0.17%)
[2015-09-30T15:13Z] INFO  16:13:30,185 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:13Z] INFO  16:13:30,185 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:13Z] INFO  16:13:30,185 MicroScheduler -   -> 571 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:13Z] INFO  16:13:30,729 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:13Z] INFO  16:13:30,844 ProgressMeter -            done   1694518.0     2.8 m      99.0 s      100.0%     2.8 m       0.0 s
[2015-09-30T15:13Z] INFO  16:13:30,844 ProgressMeter - Total runtime 168.68 secs, 2.81 min, 0.05 hours
[2015-09-30T15:13Z] INFO  16:13:30,845 MicroScheduler - 2541 reads were filtered out during the traversal out of approximately 1697059 total reads (0.15%)
[2015-09-30T15:13Z] INFO  16:13:30,845 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:13Z] INFO  16:13:30,845 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:13Z] INFO  16:13:30,845 MicroScheduler -   -> 2541 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:13Z] INFO  16:13:31,151 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:13Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam
[2015-09-30T15:13Z] INFO  16:13:31,868 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:13Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam
[2015-09-30T15:13Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam 11:124188918-135006516
[2015-09-30T15:13Z] GATK: RealignerTargetCreator
[2015-09-30T15:13Z] INFO  16:13:33,598 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:13Z] INFO  16:13:33,600 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:13Z] INFO  16:13:33,601 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:13Z] INFO  16:13:33,601 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:13Z] INFO  16:13:33,604 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmp9SHTEW/1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign-realign.intervals -l INFO -L 11:124188918-135006516 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:13Z] INFO  16:13:33,609 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:13Z] INFO  16:13:33,609 HelpFormatter - Date/Time: 2015/09/30 16:13:33
[2015-09-30T15:13Z] INFO  16:13:33,610 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:13Z] INFO  16:13:33,610 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:13Z] INFO  16:13:33,681 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:13Z] INFO  16:13:33,798 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:13Z] INFO  16:13:33,806 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:13Z] INFO  16:13:33,820 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:13Z] INFO  16:13:35,149 IntervalUtils - Processing 10817599 bp from intervals
[2015-09-30T15:13Z] WARN  16:13:35,152 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:13Z] INFO  16:13:35,207 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:13Z] INFO  16:13:35,300 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:13Z] INFO  16:13:35,300 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:13Z] INFO  16:13:35,301 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:13Z] INFO  16:13:35,301 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:13Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam 11:62123541-93141822
[2015-09-30T15:13Z] GATK: RealignerTargetCreator
[2015-09-30T15:13Z] INFO  16:13:37,686 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:13Z] INFO  16:13:37,688 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:13Z] INFO  16:13:37,689 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:13Z] INFO  16:13:37,689 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:13Z] INFO  16:13:37,693 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmp8cB_kg/1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign-realign.intervals -l INFO -L 11:62123541-93141822 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:13Z] INFO  16:13:37,703 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:13Z] INFO  16:13:37,703 HelpFormatter - Date/Time: 2015/09/30 16:13:37
[2015-09-30T15:13Z] INFO  16:13:37,703 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:13Z] INFO  16:13:37,704 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:13Z] INFO  16:13:38,005 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:13Z] INFO  16:13:38,955 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:13Z] INFO  16:13:38,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:13Z] INFO  16:13:39,174 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.20
[2015-09-30T15:13Z] INFO  16:13:40,101 IntervalUtils - Processing 31018282 bp from intervals
[2015-09-30T15:13Z] WARN  16:13:40,105 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:13Z] INFO  16:13:40,165 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:13Z] INFO  16:13:41,451 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:13Z] INFO  16:13:41,452 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:13Z] INFO  16:13:41,452 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:13Z] INFO  16:13:41,452 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:13Z] INFO  16:13:46,458 ProgressMeter -            done   1.0817599E7    11.0 s       1.0 s      100.0%    11.0 s       0.0 s
[2015-09-30T15:13Z] INFO  16:13:46,458 ProgressMeter - Total runtime 11.16 secs, 0.19 min, 0.00 hours
[2015-09-30T15:13Z] INFO  16:13:46,461 MicroScheduler - 25974 reads were filtered out during the traversal out of approximately 338785 total reads (7.67%)
[2015-09-30T15:13Z] INFO  16:13:46,461 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:13Z] INFO  16:13:46,461 MicroScheduler -   -> 3806 reads (1.12% of total) failing BadMateFilter
[2015-09-30T15:13Z] INFO  16:13:46,462 MicroScheduler -   -> 16136 reads (4.76% of total) failing DuplicateReadFilter
[2015-09-30T15:13Z] INFO  16:13:46,462 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:13Z] INFO  16:13:46,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:13Z] INFO  16:13:46,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:13Z] INFO  16:13:46,463 MicroScheduler -   -> 6032 reads (1.78% of total) failing MappingQualityZeroFilter
[2015-09-30T15:13Z] INFO  16:13:46,463 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:13Z] INFO  16:13:46,463 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:13Z] INFO  16:13:46,463 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:13Z] INFO  16:13:47,405 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:13Z] GATK: realign ('11', 124188917, 135006516) : syn3-normal
[2015-09-30T15:13Z] INFO  16:13:47,500 ProgressMeter -    11:115100258    500006.0    61.0 s       2.1 m       70.7%    86.0 s      25.0 s
[2015-09-30T15:13Z] INFO  16:13:49,703 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:13Z] INFO  16:13:49,705 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:13Z] INFO  16:13:49,705 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:13Z] INFO  16:13:49,705 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:13Z] INFO  16:13:49,708 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign-realign.intervals -L 11:124188918-135006516 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmpnFsa5_/1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam
[2015-09-30T15:13Z] INFO  16:13:49,714 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:13Z] INFO  16:13:49,714 HelpFormatter - Date/Time: 2015/09/30 16:13:49
[2015-09-30T15:13Z] INFO  16:13:49,714 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:13Z] INFO  16:13:49,715 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:13Z] INFO  16:13:49,820 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:13Z] INFO  16:13:49,887 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:13Z] INFO  16:13:49,895 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:13Z] INFO  16:13:49,910 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:13Z] INFO  16:13:50,125 IntervalUtils - Processing 10817599 bp from intervals
[2015-09-30T15:13Z] WARN  16:13:50,129 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:13Z] INFO  16:13:50,184 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:13Z] INFO  16:13:50,268 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:13Z] INFO  16:13:50,269 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:13Z] INFO  16:13:50,269 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:13Z] INFO  16:13:50,270 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:13Z] INFO  16:13:50,372 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:13Z] INFO  16:13:50,455 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:14Z] INFO  16:14:10,048 ProgressMeter -            done    336954.0    19.0 s      58.0 s       97.8%    19.0 s       0.0 s
[2015-09-30T15:14Z] INFO  16:14:10,048 ProgressMeter - Total runtime 19.78 secs, 0.33 min, 0.01 hours
[2015-09-30T15:14Z] INFO  16:14:10,051 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 336954 total reads (0.00%)
[2015-09-30T15:14Z] INFO  16:14:10,051 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:14Z] INFO  16:14:10,052 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:14Z] INFO  16:14:10,052 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:14Z] INFO  16:14:11,139 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:14Z] INFO  16:14:11,455 ProgressMeter -     11:78413141   1.62739E7    30.0 s       1.0 s       52.5%    57.0 s      27.0 s
[2015-09-30T15:14Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam
[2015-09-30T15:14Z] GATK pre-alignment ('12', 0, 31107241) : syn3-normal
[2015-09-30T15:14Z] INFO  16:14:14,694 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:14Z] INFO  16:14:14,696 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:14Z] INFO  16:14:14,696 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:14Z] INFO  16:14:14,696 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:14Z] INFO  16:14:14,699 HelpFormatter - Program Args: -T PrintReads -L 12:1-31107241 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpk7L5fZ/1_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam
[2015-09-30T15:14Z] INFO  16:14:14,708 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:14Z] INFO  16:14:14,708 HelpFormatter - Date/Time: 2015/09/30 16:14:14
[2015-09-30T15:14Z] INFO  16:14:14,709 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:14Z] INFO  16:14:14,709 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:14Z] INFO  16:14:14,817 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:14Z] INFO  16:14:16,949 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:14Z] INFO  16:14:16,997 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:14Z] INFO  16:14:17,004 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:14Z] INFO  16:14:18,044 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 1.04
[2015-09-30T15:14Z] INFO  16:14:18,062 IntervalUtils - Processing 31107241 bp from intervals
[2015-09-30T15:14Z] INFO  16:14:18,117 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:14Z] INFO  16:14:18,402 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:14Z] INFO  16:14:18,403 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:14Z] INFO  16:14:18,403 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:14Z] INFO  16:14:18,403 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:14Z] INFO  16:14:18,414 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:14Z] INFO  16:14:18,609 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:14Z] INFO  16:14:21,314 ProgressMeter -            done   3.1018282E7    39.0 s       1.0 s      100.0%    39.0 s       0.0 s
[2015-09-30T15:14Z] INFO  16:14:21,315 ProgressMeter - Total runtime 39.86 secs, 0.66 min, 0.01 hours
[2015-09-30T15:14Z] INFO  16:14:21,318 MicroScheduler - 152407 reads were filtered out during the traversal out of approximately 1704405 total reads (8.94%)
[2015-09-30T15:14Z] INFO  16:14:21,318 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:14Z] INFO  16:14:21,318 MicroScheduler -   -> 15186 reads (0.89% of total) failing BadMateFilter
[2015-09-30T15:14Z] INFO  16:14:21,319 MicroScheduler -   -> 85343 reads (5.01% of total) failing DuplicateReadFilter
[2015-09-30T15:14Z] INFO  16:14:21,319 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:14Z] INFO  16:14:21,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:14Z] INFO  16:14:21,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:14Z] INFO  16:14:21,319 MicroScheduler -   -> 51878 reads (3.04% of total) failing MappingQualityZeroFilter
[2015-09-30T15:14Z] INFO  16:14:21,320 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:14Z] INFO  16:14:21,320 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:14Z] INFO  16:14:21,320 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:14Z] INFO  16:14:22,452 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:14Z] GATK: realign ('11', 62123540, 93141822) : syn3-normal
[2015-09-30T15:14Z] INFO  16:14:25,434 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:14Z] INFO  16:14:25,436 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:14Z] INFO  16:14:25,436 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:14Z] INFO  16:14:25,436 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:14Z] INFO  16:14:25,440 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign-realign.intervals -L 11:62123541-93141822 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmplEP7Qp/1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam
[2015-09-30T15:14Z] INFO  16:14:25,445 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:14Z] INFO  16:14:25,446 HelpFormatter - Date/Time: 2015/09/30 16:14:25
[2015-09-30T15:14Z] INFO  16:14:25,446 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:14Z] INFO  16:14:25,446 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:14Z] INFO  16:14:25,569 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:14Z] INFO  16:14:25,633 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:14Z] INFO  16:14:25,640 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:14Z] INFO  16:14:25,656 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:14Z] INFO  16:14:26,011 IntervalUtils - Processing 31018282 bp from intervals
[2015-09-30T15:14Z] WARN  16:14:26,015 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:14Z] INFO  16:14:26,071 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:14Z] INFO  16:14:26,228 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:14Z] INFO  16:14:26,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:14Z] INFO  16:14:26,229 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:14Z] INFO  16:14:26,229 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:14Z] INFO  16:14:26,369 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:14Z] INFO  16:14:26,560 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:14Z] INFO  16:14:27,501 ProgressMeter -    11:121179499    900011.0   101.0 s     113.0 s       90.3%   111.0 s      10.0 s
[2015-09-30T15:14Z] INFO  16:14:35,499 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:14Z] INFO  16:14:35,628 ProgressMeter -            done   1011349.0   109.0 s     108.0 s      100.0%   109.0 s       0.0 s
[2015-09-30T15:14Z] INFO  16:14:35,628 ProgressMeter - Total runtime 109.92 secs, 1.83 min, 0.03 hours
[2015-09-30T15:14Z] INFO  16:14:35,629 MicroScheduler - 2172 reads were filtered out during the traversal out of approximately 1013521 total reads (0.21%)
[2015-09-30T15:14Z] INFO  16:14:35,629 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:14Z] INFO  16:14:35,629 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:14Z] INFO  16:14:35,629 MicroScheduler -   -> 2172 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:14Z] INFO  16:14:36,718 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:14Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam
[2015-09-30T15:14Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam 11:93147866-124180877
[2015-09-30T15:14Z] GATK: RealignerTargetCreator
[2015-09-30T15:14Z] INFO  16:14:40,984 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:14Z] INFO  16:14:40,986 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:14Z] INFO  16:14:40,986 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:14Z] INFO  16:14:40,986 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:14Z] INFO  16:14:40,990 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmpx29p1s/1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign-realign.intervals -l INFO -L 11:93147866-124180877 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:14Z] INFO  16:14:40,995 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:14Z] INFO  16:14:40,995 HelpFormatter - Date/Time: 2015/09/30 16:14:40
[2015-09-30T15:14Z] INFO  16:14:40,996 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:14Z] INFO  16:14:40,996 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:14Z] INFO  16:14:41,053 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:14Z] INFO  16:14:41,160 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:14Z] INFO  16:14:41,168 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:14Z] INFO  16:14:41,184 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:14Z] INFO  16:14:41,997 IntervalUtils - Processing 31033012 bp from intervals
[2015-09-30T15:14Z] WARN  16:14:42,001 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:14Z] INFO  16:14:42,057 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:14Z] INFO  16:14:43,939 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:14Z] INFO  16:14:43,940 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:14Z] INFO  16:14:43,940 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:14Z] INFO  16:14:43,940 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:14Z] INFO  16:14:48,406 ProgressMeter -      12:4383114    200003.0    30.0 s       2.5 m       14.1%     3.5 m       3.0 m
[2015-09-30T15:14Z] INFO  16:14:57,295 ProgressMeter -     11:66081801    500007.0    31.0 s      62.0 s       12.8%     4.0 m       3.5 m
[2015-09-30T15:15Z] INFO  16:15:13,943 ProgressMeter -    11:122830765   2.9666599E7    30.0 s       1.0 s       95.6%    31.0 s       1.0 s
[2015-09-30T15:15Z] INFO  16:15:15,641 ProgressMeter -            done   3.1033012E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T15:15Z] INFO  16:15:15,642 ProgressMeter - Total runtime 31.70 secs, 0.53 min, 0.01 hours
[2015-09-30T15:15Z] INFO  16:15:15,645 MicroScheduler - 76639 reads were filtered out during the traversal out of approximately 1017813 total reads (7.53%)
[2015-09-30T15:15Z] INFO  16:15:15,645 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:15Z] INFO  16:15:15,646 MicroScheduler -   -> 11805 reads (1.16% of total) failing BadMateFilter
[2015-09-30T15:15Z] INFO  16:15:15,646 MicroScheduler -   -> 45622 reads (4.48% of total) failing DuplicateReadFilter
[2015-09-30T15:15Z] INFO  16:15:15,646 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:15Z] INFO  16:15:15,646 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:15Z] INFO  16:15:15,647 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:15Z] INFO  16:15:15,647 MicroScheduler -   -> 19212 reads (1.89% of total) failing MappingQualityZeroFilter
[2015-09-30T15:15Z] INFO  16:15:15,647 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:15Z] INFO  16:15:15,647 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:15Z] INFO  16:15:15,648 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:15Z] INFO  16:15:16,800 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:15Z] GATK: realign ('11', 93147865, 124180877) : syn3-normal
[2015-09-30T15:15Z] INFO  16:15:18,414 ProgressMeter -      12:7899552    500006.0    60.0 s     120.0 s       25.4%     3.9 m       2.9 m
[2015-09-30T15:15Z] INFO  16:15:18,948 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:15Z] INFO  16:15:18,950 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:15Z] INFO  16:15:18,950 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:15Z] INFO  16:15:18,950 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:15Z] INFO  16:15:18,954 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign-realign.intervals -L 11:93147866-124180877 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/tx/tmpL5m3YA/1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam
[2015-09-30T15:15Z] INFO  16:15:18,960 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:15Z] INFO  16:15:18,960 HelpFormatter - Date/Time: 2015/09/30 16:15:18
[2015-09-30T15:15Z] INFO  16:15:18,960 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:15Z] INFO  16:15:18,961 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:15Z] INFO  16:15:19,069 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:15Z] INFO  16:15:19,138 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:15Z] INFO  16:15:19,145 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:15Z] INFO  16:15:19,162 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:15Z] INFO  16:15:19,394 IntervalUtils - Processing 31033012 bp from intervals
[2015-09-30T15:15Z] WARN  16:15:19,398 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:15Z] INFO  16:15:19,453 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:15Z] INFO  16:15:19,604 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:15Z] INFO  16:15:19,604 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:15Z] INFO  16:15:19,605 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:15Z] INFO  16:15:19,605 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:15Z] INFO  16:15:19,753 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:15Z] INFO  16:15:19,942 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:15Z] INFO  16:15:27,800 ProgressMeter -     11:75111718   1200018.0    61.0 s      51.0 s       41.9%     2.4 m      84.0 s
[2015-09-30T15:15Z] INFO  16:15:43,197 ProgressMeter -            done   1694518.0    76.0 s      45.0 s      100.0%    76.0 s       0.0 s
[2015-09-30T15:15Z] INFO  16:15:43,198 ProgressMeter - Total runtime 76.97 secs, 1.28 min, 0.02 hours
[2015-09-30T15:15Z] INFO  16:15:43,201 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1694518 total reads (0.00%)
[2015-09-30T15:15Z] INFO  16:15:43,201 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:15Z] INFO  16:15:43,201 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:15Z] INFO  16:15:43,202 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:15Z] INFO  16:15:44,319 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:15Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam
[2015-09-30T15:15Z] INFO  16:15:48,415 ProgressMeter -     12:13367246    800009.0    90.0 s     112.0 s       43.0%     3.5 m     119.0 s
[2015-09-30T15:15Z] GATK pre-alignment ('12', 31116488, 62142833) : syn3-normal
[2015-09-30T15:15Z] INFO  16:15:50,079 ProgressMeter -    11:114570068    400005.0    30.0 s      76.0 s       69.0%    43.0 s      13.0 s
[2015-09-30T15:15Z] INFO  16:15:50,322 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:15Z] INFO  16:15:50,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:15Z] INFO  16:15:50,324 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:15Z] INFO  16:15:50,324 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:15Z] INFO  16:15:50,328 HelpFormatter - Program Args: -T PrintReads -L 12:31116489-62142833 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpwdD2U8/1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam
[2015-09-30T15:15Z] INFO  16:15:50,335 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:15Z] INFO  16:15:50,336 HelpFormatter - Date/Time: 2015/09/30 16:15:50
[2015-09-30T15:15Z] INFO  16:15:50,336 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:15Z] INFO  16:15:50,336 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:15Z] INFO  16:15:52,822 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:15Z] INFO  16:15:56,657 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:15Z] INFO  16:15:56,707 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:15Z] INFO  16:15:56,715 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:15Z] INFO  16:15:56,730 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:15Z] INFO  16:15:56,743 IntervalUtils - Processing 31026345 bp from intervals
[2015-09-30T15:15Z] INFO  16:15:56,800 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:15Z] INFO  16:15:57,010 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:15Z] INFO  16:15:57,010 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:15Z] INFO  16:15:57,011 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:15Z] INFO  16:15:57,011 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:15Z] INFO  16:15:57,022 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:15Z] INFO  16:15:57,221 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:16Z] INFO  16:16:10,619 ProgressMeter -            done   1011349.0    51.0 s      50.0 s      100.0%    51.0 s       0.0 s
[2015-09-30T15:16Z] INFO  16:16:10,620 ProgressMeter - Total runtime 51.02 secs, 0.85 min, 0.01 hours
[2015-09-30T15:16Z] INFO  16:16:10,623 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1011349 total reads (0.00%)
[2015-09-30T15:16Z] INFO  16:16:10,623 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:16Z] INFO  16:16:10,624 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:16Z] INFO  16:16:10,624 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:16Z] INFO  16:16:11,661 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:16Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam
[2015-09-30T15:16Z] GATK pre-alignment ('12', 62147092, 93167456) : syn3-normal
[2015-09-30T15:16Z] INFO  16:16:16,703 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:16Z] INFO  16:16:16,705 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:16Z] INFO  16:16:16,705 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:16Z] INFO  16:16:16,706 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:16Z] INFO  16:16:16,709 HelpFormatter - Program Args: -T PrintReads -L 12:62147093-93167456 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpcwISZW/1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam
[2015-09-30T15:16Z] INFO  16:16:16,715 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:16Z] INFO  16:16:16,715 HelpFormatter - Date/Time: 2015/09/30 16:16:16
[2015-09-30T15:16Z] INFO  16:16:16,715 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:16Z] INFO  16:16:16,715 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:16Z] INFO  16:16:16,821 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:16Z] INFO  16:16:17,502 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:16Z] INFO  16:16:17,549 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:16Z] INFO  16:16:17,557 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:16Z] INFO  16:16:17,571 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:16Z] INFO  16:16:17,583 IntervalUtils - Processing 31020364 bp from intervals
[2015-09-30T15:16Z] INFO  16:16:17,639 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:16Z] INFO  16:16:17,835 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:16Z] INFO  16:16:17,836 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:16Z] INFO  16:16:17,836 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:16Z] INFO  16:16:17,836 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:16Z] INFO  16:16:17,847 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:16Z] INFO  16:16:18,038 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:16Z] INFO  16:16:18,499 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:16Z] INFO  16:16:18,643 ProgressMeter -            done   1154770.0   120.0 s     104.0 s      100.0%   120.0 s       0.0 s
[2015-09-30T15:16Z] INFO  16:16:18,643 ProgressMeter - Total runtime 120.24 secs, 2.00 min, 0.03 hours
[2015-09-30T15:16Z] INFO  16:16:18,643 MicroScheduler - 2547 reads were filtered out during the traversal out of approximately 1157317 total reads (0.22%)
[2015-09-30T15:16Z] INFO  16:16:18,643 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:16Z] INFO  16:16:18,644 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:16Z] INFO  16:16:18,644 MicroScheduler -   -> 2547 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:16Z] INFO  16:16:19,761 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:16Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam
[2015-09-30T15:16Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam 12:1-31107241
[2015-09-30T15:16Z] GATK: RealignerTargetCreator
[2015-09-30T15:16Z] INFO  16:16:24,956 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:16Z] INFO  16:16:24,958 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:16Z] INFO  16:16:24,958 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:16Z] INFO  16:16:24,958 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:16Z] INFO  16:16:24,962 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpTFlWAk/1_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign-realign.intervals -l INFO -L 12:1-31107241 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:16Z] INFO  16:16:24,967 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:16Z] INFO  16:16:24,968 HelpFormatter - Date/Time: 2015/09/30 16:16:24
[2015-09-30T15:16Z] INFO  16:16:24,968 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:16Z] INFO  16:16:24,968 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:16Z] INFO  16:16:25,025 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:16Z] INFO  16:16:25,132 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:16Z] INFO  16:16:25,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:16Z] INFO  16:16:25,155 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:16Z] INFO  16:16:25,390 IntervalUtils - Processing 31107241 bp from intervals
[2015-09-30T15:16Z] WARN  16:16:25,394 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:16Z] INFO  16:16:25,451 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:16Z] INFO  16:16:25,591 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:16Z] INFO  16:16:25,591 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:16Z] INFO  16:16:25,592 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:16Z] INFO  16:16:25,592 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:16Z] INFO  16:16:27,511 ProgressMeter -     12:48378867    300004.0    30.0 s     101.0 s       55.6%    53.0 s      23.0 s
[2015-09-30T15:16Z] INFO  16:16:49,198 ProgressMeter -     12:70712617    100003.0    31.0 s       5.2 m       27.6%   112.0 s      81.0 s
[2015-09-30T15:16Z] INFO  16:16:55,594 ProgressMeter -     12:27228525   2.7213824E7    30.0 s       1.0 s       87.5%    34.0 s       4.0 s
[2015-09-30T15:16Z] INFO  16:16:57,511 ProgressMeter -     12:52568063    600008.0    60.0 s     100.0 s       69.1%    86.0 s      26.0 s
[2015-09-30T15:16Z] INFO  16:16:58,662 ProgressMeter -            done   3.1107241E7    33.0 s       1.0 s      100.0%    33.0 s       0.0 s
[2015-09-30T15:16Z] INFO  16:16:58,663 ProgressMeter - Total runtime 33.07 secs, 0.55 min, 0.01 hours
[2015-09-30T15:16Z] INFO  16:16:58,666 MicroScheduler - 99164 reads were filtered out during the traversal out of approximately 1161797 total reads (8.54%)
[2015-09-30T15:16Z] INFO  16:16:58,666 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:16Z] INFO  16:16:58,667 MicroScheduler -   -> 12635 reads (1.09% of total) failing BadMateFilter
[2015-09-30T15:16Z] INFO  16:16:58,667 MicroScheduler -   -> 51154 reads (4.40% of total) failing DuplicateReadFilter
[2015-09-30T15:16Z] INFO  16:16:58,667 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:16Z] INFO  16:16:58,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:16Z] INFO  16:16:58,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:16Z] INFO  16:16:58,668 MicroScheduler -   -> 35375 reads (3.04% of total) failing MappingQualityZeroFilter
[2015-09-30T15:16Z] INFO  16:16:58,668 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:16Z] INFO  16:16:58,668 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:16Z] INFO  16:16:58,669 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:16Z] INFO  16:16:59,683 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:16Z] GATK: realign ('12', 0, 31107241) : syn3-normal
[2015-09-30T15:17Z] INFO  16:17:01,530 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:17Z] INFO  16:17:01,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:17Z] INFO  16:17:01,532 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:17Z] INFO  16:17:01,533 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:17Z] INFO  16:17:01,536 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign-realign.intervals -L 12:1-31107241 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpZj7731/1_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam
[2015-09-30T15:17Z] INFO  16:17:01,541 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:17Z] INFO  16:17:01,542 HelpFormatter - Date/Time: 2015/09/30 16:17:01
[2015-09-30T15:17Z] INFO  16:17:01,542 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:17Z] INFO  16:17:01,542 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:17Z] INFO  16:17:01,673 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:17Z] INFO  16:17:01,738 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:17Z] INFO  16:17:01,745 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:17Z] INFO  16:17:01,761 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:17Z] INFO  16:17:02,002 IntervalUtils - Processing 31107241 bp from intervals
[2015-09-30T15:17Z] WARN  16:17:02,006 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:17Z] INFO  16:17:02,062 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:17Z] INFO  16:17:02,216 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:17Z] INFO  16:17:02,216 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:17Z] INFO  16:17:02,217 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:17Z] INFO  16:17:02,217 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:17Z] INFO  16:17:02,360 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:17Z] INFO  16:17:02,545 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:17Z] INFO  16:17:14,343 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:17Z] INFO  16:17:14,516 ProgressMeter -            done    453456.0    56.0 s       2.1 m      100.0%    56.0 s       0.0 s
[2015-09-30T15:17Z] INFO  16:17:14,516 ProgressMeter - Total runtime 56.68 secs, 0.94 min, 0.02 hours
[2015-09-30T15:17Z] INFO  16:17:14,516 MicroScheduler - 1608 reads were filtered out during the traversal out of approximately 455064 total reads (0.35%)
[2015-09-30T15:17Z] INFO  16:17:14,517 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:17Z] INFO  16:17:14,517 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:17Z] INFO  16:17:14,517 MicroScheduler -   -> 1608 reads (0.35% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:17Z] INFO  16:17:15,534 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:17Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam
[2015-09-30T15:17Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam 12:62147093-93167456
[2015-09-30T15:17Z] GATK: RealignerTargetCreator
[2015-09-30T15:17Z] INFO  16:17:18,576 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:17Z] INFO  16:17:18,578 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:17Z] INFO  16:17:18,578 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:17Z] INFO  16:17:18,578 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:17Z] INFO  16:17:18,582 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpEjdJtC/1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign-realign.intervals -l INFO -L 12:62147093-93167456 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:17Z] INFO  16:17:18,587 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:17Z] INFO  16:17:18,587 HelpFormatter - Date/Time: 2015/09/30 16:17:18
[2015-09-30T15:17Z] INFO  16:17:18,588 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:17Z] INFO  16:17:18,588 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:17Z] INFO  16:17:18,656 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:17Z] INFO  16:17:18,786 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:17Z] INFO  16:17:18,794 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:17Z] INFO  16:17:18,809 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:17Z] INFO  16:17:19,283 IntervalUtils - Processing 31020364 bp from intervals
[2015-09-30T15:17Z] WARN  16:17:19,287 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:17Z] INFO  16:17:19,342 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:17Z] INFO  16:17:19,474 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:17Z] INFO  16:17:19,474 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:17Z] INFO  16:17:19,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:17Z] INFO  16:17:19,475 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:17Z] INFO  16:17:27,749 ProgressMeter -     12:56347813   1000014.0    90.0 s      90.0 s       81.3%   110.0 s      20.0 s
[2015-09-30T15:17Z] INFO  16:17:33,455 ProgressMeter -      12:8430641    500006.0    31.0 s      62.0 s       27.1%   114.0 s      83.0 s
[2015-09-30T15:17Z] INFO  16:17:41,695 ProgressMeter -            done   3.1020364E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T15:17Z] INFO  16:17:41,696 ProgressMeter - Total runtime 22.22 secs, 0.37 min, 0.01 hours
[2015-09-30T15:17Z] INFO  16:17:41,699 MicroScheduler - 33748 reads were filtered out during the traversal out of approximately 455805 total reads (7.40%)
[2015-09-30T15:17Z] INFO  16:17:41,699 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:17Z] INFO  16:17:41,699 MicroScheduler -   -> 7821 reads (1.72% of total) failing BadMateFilter
[2015-09-30T15:17Z] INFO  16:17:41,699 MicroScheduler -   -> 17292 reads (3.79% of total) failing DuplicateReadFilter
[2015-09-30T15:17Z] INFO  16:17:41,700 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:17Z] INFO  16:17:41,700 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:17Z] INFO  16:17:41,700 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:17Z] INFO  16:17:41,700 MicroScheduler -   -> 8635 reads (1.89% of total) failing MappingQualityZeroFilter
[2015-09-30T15:17Z] INFO  16:17:41,701 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:17Z] INFO  16:17:41,701 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:17Z] INFO  16:17:41,701 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:17Z] INFO  16:17:42,690 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:17Z] GATK: realign ('12', 62147092, 93167456) : syn3-normal
[2015-09-30T15:17Z] INFO  16:17:48,417 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:17Z] INFO  16:17:48,419 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:17Z] INFO  16:17:48,420 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:17Z] INFO  16:17:48,420 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:17Z] INFO  16:17:48,423 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign-realign.intervals -L 12:62147093-93167456 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmphcs177/1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam
[2015-09-30T15:17Z] INFO  16:17:48,429 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:17Z] INFO  16:17:48,429 HelpFormatter - Date/Time: 2015/09/30 16:17:48
[2015-09-30T15:17Z] INFO  16:17:48,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:17Z] INFO  16:17:48,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:17Z] INFO  16:17:48,785 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:17Z] INFO  16:17:48,851 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:17Z] INFO  16:17:48,858 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:17Z] INFO  16:17:48,874 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:17Z] INFO  16:17:49,109 IntervalUtils - Processing 31020364 bp from intervals
[2015-09-30T15:17Z] WARN  16:17:49,113 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:17Z] INFO  16:17:49,171 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:17Z] INFO  16:17:49,312 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:17Z] INFO  16:17:49,313 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:17Z] INFO  16:17:49,313 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:17Z] INFO  16:17:49,314 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:17Z] INFO  16:17:49,461 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:17Z] INFO  16:17:49,653 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:17Z] INFO  16:17:54,751 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:17Z] INFO  16:17:54,973 ProgressMeter -            done   1430517.0   117.0 s      82.0 s      100.0%   117.0 s       0.0 s
[2015-09-30T15:17Z] INFO  16:17:54,974 ProgressMeter - Total runtime 117.96 secs, 1.97 min, 0.03 hours
[2015-09-30T15:17Z] INFO  16:17:54,974 MicroScheduler - 2583 reads were filtered out during the traversal out of approximately 1433100 total reads (0.18%)
[2015-09-30T15:17Z] INFO  16:17:54,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:17Z] INFO  16:17:54,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:17Z] INFO  16:17:54,975 MicroScheduler -   -> 2583 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:17Z] INFO  16:17:56,012 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:17Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam
[2015-09-30T15:17Z] INFO  16:17:56,714 ProgressMeter -            done   1154770.0    54.0 s      47.0 s      100.0%    54.0 s       0.0 s
[2015-09-30T15:17Z] INFO  16:17:56,715 ProgressMeter - Total runtime 54.50 secs, 0.91 min, 0.02 hours
[2015-09-30T15:17Z] INFO  16:17:56,718 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1154770 total reads (0.00%)
[2015-09-30T15:17Z] INFO  16:17:56,718 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:17Z] INFO  16:17:56,718 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:17Z] INFO  16:17:56,719 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:17Z] INFO  16:17:57,928 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:17Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam
[2015-09-30T15:17Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam 12:31116489-62142833
[2015-09-30T15:17Z] GATK: RealignerTargetCreator
[2015-09-30T15:18Z] GATK pre-alignment ('12', 93169109, 124189486) : syn3-normal
[2015-09-30T15:18Z] INFO  16:18:01,823 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:01,825 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:18Z] INFO  16:18:01,825 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:18Z] INFO  16:18:01,825 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:18Z] INFO  16:18:01,829 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpIjCcgT/1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign-realign.intervals -l INFO -L 12:31116489-62142833 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:18Z] INFO  16:18:01,834 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:18Z] INFO  16:18:01,835 HelpFormatter - Date/Time: 2015/09/30 16:18:01
[2015-09-30T15:18Z] INFO  16:18:01,835 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:01,835 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:01,896 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:18Z] INFO  16:18:02,006 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:18Z] INFO  16:18:02,365 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:18Z] INFO  16:18:02,382 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:18Z] INFO  16:18:03,488 IntervalUtils - Processing 31026345 bp from intervals
[2015-09-30T15:18Z] WARN  16:18:03,492 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:18Z] INFO  16:18:03,549 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:18Z] INFO  16:18:03,694 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:18Z] INFO  16:18:03,694 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:18Z] INFO  16:18:03,695 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:18Z] INFO  16:18:03,695 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:18Z] INFO  16:18:04,308 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:04,310 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:18Z] INFO  16:18:04,310 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:18Z] INFO  16:18:04,310 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:18Z] INFO  16:18:04,314 HelpFormatter - Program Args: -T PrintReads -L 12:93169110-124189486 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmp_LN8VF/1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam
[2015-09-30T15:18Z] INFO  16:18:04,319 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:18Z] INFO  16:18:04,319 HelpFormatter - Date/Time: 2015/09/30 16:18:04
[2015-09-30T15:18Z] INFO  16:18:04,319 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:04,319 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:04,425 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:18Z] INFO  16:18:05,704 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:18Z] INFO  16:18:05,755 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:18Z] INFO  16:18:05,763 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:18Z] INFO  16:18:05,778 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:18Z] INFO  16:18:05,792 IntervalUtils - Processing 31020377 bp from intervals
[2015-09-30T15:18Z] INFO  16:18:05,850 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:18Z] INFO  16:18:06,062 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:18Z] INFO  16:18:06,062 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:18Z] INFO  16:18:06,062 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:18Z] INFO  16:18:06,063 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:18Z] INFO  16:18:06,074 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:18Z] INFO  16:18:06,277 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:18Z] INFO  16:18:16,115 ProgressMeter -            done    453456.0    26.0 s      59.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T15:18Z] INFO  16:18:16,116 ProgressMeter - Total runtime 26.80 secs, 0.45 min, 0.01 hours
[2015-09-30T15:18Z] INFO  16:18:16,119 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 453456 total reads (0.00%)
[2015-09-30T15:18Z] INFO  16:18:16,119 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:18Z] INFO  16:18:16,119 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:18Z] INFO  16:18:16,120 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:18Z] INFO  16:18:17,234 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:18Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam
[2015-09-30T15:18Z] GATK pre-alignment ('12', 124191013, 133851895) : syn3-normal
[2015-09-30T15:18Z] INFO  16:18:20,261 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:20,263 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:18Z] INFO  16:18:20,263 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:18Z] INFO  16:18:20,264 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:18Z] INFO  16:18:20,267 HelpFormatter - Program Args: -T PrintReads -L 12:124191014-133851895 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpJ6W78Q/1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam
[2015-09-30T15:18Z] INFO  16:18:20,273 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:18Z] INFO  16:18:20,273 HelpFormatter - Date/Time: 2015/09/30 16:18:20
[2015-09-30T15:18Z] INFO  16:18:20,273 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:20,273 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:20,386 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:18Z] INFO  16:18:21,923 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:18Z] INFO  16:18:21,970 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:18Z] INFO  16:18:21,978 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:18Z] INFO  16:18:21,992 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:18Z] INFO  16:18:22,004 IntervalUtils - Processing 9660882 bp from intervals
[2015-09-30T15:18Z] INFO  16:18:22,061 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:18Z] INFO  16:18:22,208 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:18Z] INFO  16:18:22,208 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:18Z] INFO  16:18:22,209 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:18Z] INFO  16:18:22,209 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:18Z] INFO  16:18:22,220 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:18Z] INFO  16:18:22,287 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:18Z] INFO  16:18:33,698 ProgressMeter -     12:56221405   2.5097016E7    30.0 s       1.0 s       80.9%    37.0 s       7.0 s
[2015-09-30T15:18Z] INFO  16:18:36,093 ProgressMeter -    12:104025563    200002.0    30.0 s       2.5 m       35.0%    85.0 s      55.0 s
[2015-09-30T15:18Z] INFO  16:18:41,895 ProgressMeter -            done   3.1026345E7    38.0 s       1.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T15:18Z] INFO  16:18:41,895 ProgressMeter - Total runtime 38.20 secs, 0.64 min, 0.01 hours
[2015-09-30T15:18Z] INFO  16:18:41,899 MicroScheduler - 113419 reads were filtered out during the traversal out of approximately 1438625 total reads (7.88%)
[2015-09-30T15:18Z] INFO  16:18:41,899 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:18Z] INFO  16:18:41,899 MicroScheduler -   -> 14128 reads (0.98% of total) failing BadMateFilter
[2015-09-30T15:18Z] INFO  16:18:41,900 MicroScheduler -   -> 68605 reads (4.77% of total) failing DuplicateReadFilter
[2015-09-30T15:18Z] INFO  16:18:41,900 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:18Z] INFO  16:18:41,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:18Z] INFO  16:18:41,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:18Z] INFO  16:18:41,900 MicroScheduler -   -> 30686 reads (2.13% of total) failing MappingQualityZeroFilter
[2015-09-30T15:18Z] INFO  16:18:41,901 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:18Z] INFO  16:18:41,901 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:18Z] INFO  16:18:41,901 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:18Z] INFO  16:18:42,881 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:18Z] GATK: realign ('12', 31116488, 62142833) : syn3-normal
[2015-09-30T15:18Z] INFO  16:18:46,224 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:46,226 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:18Z] INFO  16:18:46,226 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:18Z] INFO  16:18:46,226 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:18Z] INFO  16:18:46,229 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign-realign.intervals -L 12:31116489-62142833 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpEgz1bX/1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam
[2015-09-30T15:18Z] INFO  16:18:46,235 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:18Z] INFO  16:18:46,235 HelpFormatter - Date/Time: 2015/09/30 16:18:46
[2015-09-30T15:18Z] INFO  16:18:46,235 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:46,235 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:18Z] INFO  16:18:46,361 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:18Z] INFO  16:18:46,421 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:18Z] INFO  16:18:46,428 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:18Z] INFO  16:18:46,443 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:18Z] INFO  16:18:46,672 IntervalUtils - Processing 31026345 bp from intervals
[2015-09-30T15:18Z] WARN  16:18:46,676 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:18Z] INFO  16:18:46,939 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:18Z] INFO  16:18:47,353 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:18Z] INFO  16:18:47,354 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:18Z] INFO  16:18:47,354 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:18Z] INFO  16:18:47,354 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:18Z] INFO  16:18:47,500 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:18Z] INFO  16:18:47,689 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:18Z] INFO  16:18:52,245 ProgressMeter -    12:132405608    200004.0    30.0 s       2.5 m       85.0%    35.0 s       5.0 s
[2015-09-30T15:19Z] INFO  16:19:05,242 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:19Z] INFO  16:19:05,324 ProgressMeter -            done    375771.0    43.0 s     114.0 s       99.6%    43.0 s       0.0 s
[2015-09-30T15:19Z] INFO  16:19:05,324 ProgressMeter - Total runtime 43.12 secs, 0.72 min, 0.01 hours
[2015-09-30T15:19Z] INFO  16:19:05,325 MicroScheduler - 631 reads were filtered out during the traversal out of approximately 376402 total reads (0.17%)
[2015-09-30T15:19Z] INFO  16:19:05,325 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:19Z] INFO  16:19:05,325 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:19Z] INFO  16:19:05,325 MicroScheduler -   -> 631 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:19Z] INFO  16:19:06,334 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:19Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam
[2015-09-30T15:19Z] INFO  16:19:06,548 ProgressMeter -    12:110465080    600007.0    60.0 s     100.0 s       55.8%   107.0 s      47.0 s
[2015-09-30T15:19Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam 12:124191014-133851895
[2015-09-30T15:19Z] GATK: RealignerTargetCreator
[2015-09-30T15:19Z] INFO  16:19:08,939 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:19Z] INFO  16:19:08,941 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:19Z] INFO  16:19:08,941 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:19Z] INFO  16:19:08,941 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:19Z] INFO  16:19:08,944 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpXQFwgG/1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign-realign.intervals -l INFO -L 12:124191014-133851895 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:19Z] INFO  16:19:08,950 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:19Z] INFO  16:19:08,950 HelpFormatter - Date/Time: 2015/09/30 16:19:08
[2015-09-30T15:19Z] INFO  16:19:08,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:19Z] INFO  16:19:08,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:19Z] INFO  16:19:09,020 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:19Z] INFO  16:19:09,347 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:19Z] INFO  16:19:09,355 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:19Z] INFO  16:19:09,581 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.23
[2015-09-30T15:19Z] INFO  16:19:10,089 IntervalUtils - Processing 9660882 bp from intervals
[2015-09-30T15:19Z] WARN  16:19:10,093 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:19Z] INFO  16:19:10,149 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:19Z] INFO  16:19:10,765 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:19Z] INFO  16:19:10,766 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:19Z] INFO  16:19:10,766 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:19Z] INFO  16:19:10,766 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:19Z] INFO  16:19:17,433 ProgressMeter -     12:50483030    500007.0    30.0 s      60.0 s       62.4%    48.0 s      18.0 s
[2015-09-30T15:19Z] INFO  16:19:22,464 ProgressMeter -            done   9660882.0    11.0 s       1.0 s      100.0%    11.0 s       0.0 s
[2015-09-30T15:19Z] INFO  16:19:22,465 ProgressMeter - Total runtime 11.70 secs, 0.19 min, 0.00 hours
[2015-09-30T15:19Z] INFO  16:19:22,468 MicroScheduler - 32981 reads were filtered out during the traversal out of approximately 377898 total reads (8.73%)
[2015-09-30T15:19Z] INFO  16:19:22,468 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:19Z] INFO  16:19:22,468 MicroScheduler -   -> 3827 reads (1.01% of total) failing BadMateFilter
[2015-09-30T15:19Z] INFO  16:19:22,469 MicroScheduler -   -> 19621 reads (5.19% of total) failing DuplicateReadFilter
[2015-09-30T15:19Z] INFO  16:19:22,469 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:19Z] INFO  16:19:22,469 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:19Z] INFO  16:19:22,469 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:19Z] INFO  16:19:22,469 MicroScheduler -   -> 9533 reads (2.52% of total) failing MappingQualityZeroFilter
[2015-09-30T15:19Z] INFO  16:19:22,470 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:19Z] INFO  16:19:22,470 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:19Z] INFO  16:19:22,470 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:19Z] INFO  16:19:23,405 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:19Z] GATK: realign ('12', 124191013, 133851895) : syn3-normal
[2015-09-30T15:19Z] INFO  16:19:25,155 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:19Z] INFO  16:19:25,157 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:19Z] INFO  16:19:25,157 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:19Z] INFO  16:19:25,157 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:19Z] INFO  16:19:25,161 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign-realign.intervals -L 12:124191014-133851895 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpZa9Xw5/1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam
[2015-09-30T15:19Z] INFO  16:19:25,166 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:19Z] INFO  16:19:25,166 HelpFormatter - Date/Time: 2015/09/30 16:19:25
[2015-09-30T15:19Z] INFO  16:19:25,167 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:19Z] INFO  16:19:25,167 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:19Z] INFO  16:19:25,268 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:19Z] INFO  16:19:25,333 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:19Z] INFO  16:19:25,340 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:19Z] INFO  16:19:25,356 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:19Z] INFO  16:19:25,734 IntervalUtils - Processing 9660882 bp from intervals
[2015-09-30T15:19Z] WARN  16:19:25,738 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:19Z] INFO  16:19:25,791 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:19Z] INFO  16:19:25,858 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:19Z] INFO  16:19:25,858 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:19Z] INFO  16:19:25,859 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:19Z] INFO  16:19:25,859 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:19Z] INFO  16:19:25,962 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:19Z] INFO  16:19:26,032 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:19Z] INFO  16:19:36,762 ProgressMeter -    12:118464211   1000011.0    90.0 s      90.0 s       81.5%   110.0 s      20.0 s
[2015-09-30T15:19Z] INFO  16:19:45,568 ProgressMeter -            done    375771.0    19.0 s      52.0 s       99.6%    19.0 s       0.0 s
[2015-09-30T15:19Z] INFO  16:19:45,568 ProgressMeter - Total runtime 19.71 secs, 0.33 min, 0.01 hours
[2015-09-30T15:19Z] INFO  16:19:45,571 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 375771 total reads (0.00%)
[2015-09-30T15:19Z] INFO  16:19:45,571 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:19Z] INFO  16:19:45,572 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:19Z] INFO  16:19:45,572 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:19Z] INFO  16:19:46,650 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:19Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam
[2015-09-30T15:19Z] INFO  16:19:47,629 ProgressMeter -     12:57584456   1200016.0    60.0 s      50.0 s       85.3%    70.0 s      10.0 s
[2015-09-30T15:19Z] GATK pre-alignment ('13', 0, 31036104) : syn3-normal
[2015-09-30T15:19Z] INFO  16:19:49,623 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:19Z] INFO  16:19:49,626 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:19Z] INFO  16:19:49,626 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:19Z] INFO  16:19:49,626 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:19Z] INFO  16:19:49,629 HelpFormatter - Program Args: -T PrintReads -L 13:1-31036104 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmpftbuPp/1_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam
[2015-09-30T15:19Z] INFO  16:19:49,635 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:19Z] INFO  16:19:49,635 HelpFormatter - Date/Time: 2015/09/30 16:19:49
[2015-09-30T15:19Z] INFO  16:19:49,635 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:19Z] INFO  16:19:49,635 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:19Z] INFO  16:19:49,739 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:19Z] INFO  16:19:51,255 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:19Z] INFO  16:19:51,305 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:19Z] INFO  16:19:51,312 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:19Z] INFO  16:19:51,327 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:19Z] INFO  16:19:51,340 IntervalUtils - Processing 31036104 bp from intervals
[2015-09-30T15:19Z] INFO  16:19:51,398 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:19Z] INFO  16:19:51,742 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:19Z] INFO  16:19:51,742 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:19Z] INFO  16:19:51,743 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:19Z] INFO  16:19:51,743 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:19Z] INFO  16:19:51,754 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:19Z] INFO  16:19:51,824 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:19Z] INFO  16:19:52,700 ProgressMeter -            done   1430517.0    65.0 s      45.0 s      100.0%    65.0 s       0.0 s
[2015-09-30T15:19Z] INFO  16:19:52,701 ProgressMeter - Total runtime 65.35 secs, 1.09 min, 0.02 hours
[2015-09-30T15:19Z] INFO  16:19:52,704 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1430517 total reads (0.00%)
[2015-09-30T15:19Z] INFO  16:19:52,704 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:19Z] INFO  16:19:52,704 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:19Z] INFO  16:19:52,704 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:19Z] INFO  16:19:53,859 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:19Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam
[2015-09-30T15:19Z] GATK pre-alignment ('13', 31036377, 62334609) : syn3-normal
[2015-09-30T15:20Z] INFO  16:20:01,754 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:01,757 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:20Z] INFO  16:20:01,757 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:20Z] INFO  16:20:01,757 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:20Z] INFO  16:20:01,761 HelpFormatter - Program Args: -T PrintReads -L 13:31036378-62334609 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmpOHDMUO/1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam
[2015-09-30T15:20Z] INFO  16:20:01,766 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:20Z] INFO  16:20:01,766 HelpFormatter - Date/Time: 2015/09/30 16:20:01
[2015-09-30T15:20Z] INFO  16:20:01,766 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:01,767 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:01,870 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:20Z] INFO  16:20:03,132 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:20Z] INFO  16:20:03,186 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:20Z] INFO  16:20:03,194 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:20Z] INFO  16:20:03,208 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:20Z] INFO  16:20:03,221 IntervalUtils - Processing 31298232 bp from intervals
[2015-09-30T15:20Z] INFO  16:20:03,280 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:20Z] INFO  16:20:03,477 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:20Z] INFO  16:20:03,478 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:20Z] INFO  16:20:03,478 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:20Z] INFO  16:20:03,478 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:20Z] INFO  16:20:03,490 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:20Z] INFO  16:20:03,685 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:20Z] INFO  16:20:06,763 ProgressMeter -    12:123474860   1400015.0   120.0 s      86.0 s       97.7%     2.0 m       2.0 s
[2015-09-30T15:20Z] INFO  16:20:11,378 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:20Z] INFO  16:20:11,558 ProgressMeter -            done   1487915.0     2.1 m      84.0 s      100.0%     2.1 m       0.0 s
[2015-09-30T15:20Z] INFO  16:20:11,558 ProgressMeter - Total runtime 125.50 secs, 2.09 min, 0.03 hours
[2015-09-30T15:20Z] INFO  16:20:11,559 MicroScheduler - 3138 reads were filtered out during the traversal out of approximately 1491053 total reads (0.21%)
[2015-09-30T15:20Z] INFO  16:20:11,559 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:20Z] INFO  16:20:11,559 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:20Z] INFO  16:20:11,559 MicroScheduler -   -> 3138 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:20Z] INFO  16:20:13,267 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:20Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam
[2015-09-30T15:20Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam 12:93169110-124189486
[2015-09-30T15:20Z] GATK: RealignerTargetCreator
[2015-09-30T15:20Z] INFO  16:20:18,678 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:18,680 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:20Z] INFO  16:20:18,680 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:20Z] INFO  16:20:18,681 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:20Z] INFO  16:20:18,684 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpvN_htU/1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign-realign.intervals -l INFO -L 12:93169110-124189486 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:20Z] INFO  16:20:18,690 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:20Z] INFO  16:20:18,691 HelpFormatter - Date/Time: 2015/09/30 16:20:18
[2015-09-30T15:20Z] INFO  16:20:18,691 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:18,691 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:18,753 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:20Z] INFO  16:20:19,214 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:20Z] INFO  16:20:19,222 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:20Z] INFO  16:20:19,238 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:20Z] INFO  16:20:19,482 IntervalUtils - Processing 31020377 bp from intervals
[2015-09-30T15:20Z] WARN  16:20:19,486 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:20Z] INFO  16:20:19,545 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:20Z] INFO  16:20:19,712 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:20Z] INFO  16:20:19,712 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:20Z] INFO  16:20:19,712 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:20Z] INFO  16:20:19,713 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:20Z] INFO  16:20:21,889 ProgressMeter -     13:25743531    100001.0    30.0 s       5.0 m       82.9%    36.0 s       6.0 s
[2015-09-30T15:20Z] INFO  16:20:33,962 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:20Z] INFO  16:20:34,120 ProgressMeter -            done    330227.0    42.0 s       2.1 m      100.0%    42.0 s       0.0 s
[2015-09-30T15:20Z] INFO  16:20:34,120 ProgressMeter - Total runtime 42.38 secs, 0.71 min, 0.01 hours
[2015-09-30T15:20Z] INFO  16:20:34,121 MicroScheduler - 943 reads were filtered out during the traversal out of approximately 331170 total reads (0.28%)
[2015-09-30T15:20Z] INFO  16:20:34,121 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:20Z] INFO  16:20:34,121 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:20Z] INFO  16:20:34,122 MicroScheduler -   -> 943 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:20Z] INFO  16:20:34,153 ProgressMeter -     13:45149045    300003.0    30.0 s     102.0 s       45.1%    66.0 s      36.0 s
[2015-09-30T15:20Z] INFO  16:20:35,206 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:20Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam
[2015-09-30T15:20Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam 13:1-31036104
[2015-09-30T15:20Z] GATK: RealignerTargetCreator
[2015-09-30T15:20Z] INFO  16:20:37,637 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:37,639 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:20Z] INFO  16:20:37,639 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:20Z] INFO  16:20:37,639 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:20Z] INFO  16:20:37,643 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmppxjJvc/1_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign-realign.intervals -l INFO -L 13:1-31036104 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:20Z] INFO  16:20:37,648 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:20Z] INFO  16:20:37,648 HelpFormatter - Date/Time: 2015/09/30 16:20:37
[2015-09-30T15:20Z] INFO  16:20:37,648 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:37,649 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:37,714 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:20Z] INFO  16:20:37,846 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:20Z] INFO  16:20:37,854 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:20Z] INFO  16:20:37,869 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:20Z] INFO  16:20:38,116 IntervalUtils - Processing 31036104 bp from intervals
[2015-09-30T15:20Z] WARN  16:20:38,120 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:20Z] INFO  16:20:38,173 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:20Z] INFO  16:20:38,347 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:20Z] INFO  16:20:38,347 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:20Z] INFO  16:20:38,347 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:20Z] INFO  16:20:38,348 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:20Z] INFO  16:20:49,715 ProgressMeter -    12:119786225   2.6614315E7    30.0 s       1.0 s       85.8%    34.0 s       4.0 s
[2015-09-30T15:20Z] INFO  16:20:56,282 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@627346b4
[2015-09-30T15:20Z] INFO  16:20:56,504 ProgressMeter -            done    593835.0    53.0 s      89.0 s      100.0%    53.0 s       0.0 s
[2015-09-30T15:20Z] INFO  16:20:56,504 ProgressMeter - Total runtime 53.03 secs, 0.88 min, 0.01 hours
[2015-09-30T15:20Z] INFO  16:20:56,505 MicroScheduler - 1762 reads were filtered out during the traversal out of approximately 595597 total reads (0.30%)
[2015-09-30T15:20Z] INFO  16:20:56,505 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:20Z] INFO  16:20:56,505 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:20Z] INFO  16:20:56,505 MicroScheduler -   -> 1762 reads (0.30% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:20Z] INFO  16:20:56,775 ProgressMeter -            done   3.1036104E7    18.0 s       0.0 s      100.0%    18.0 s       0.0 s
[2015-09-30T15:20Z] INFO  16:20:56,776 ProgressMeter - Total runtime 18.43 secs, 0.31 min, 0.01 hours
[2015-09-30T15:20Z] INFO  16:20:56,779 MicroScheduler - 27038 reads were filtered out during the traversal out of approximately 331976 total reads (8.14%)
[2015-09-30T15:20Z] INFO  16:20:56,779 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:20Z] INFO  16:20:56,779 MicroScheduler -   -> 4596 reads (1.38% of total) failing BadMateFilter
[2015-09-30T15:20Z] INFO  16:20:56,780 MicroScheduler -   -> 14111 reads (4.25% of total) failing DuplicateReadFilter
[2015-09-30T15:20Z] INFO  16:20:56,780 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:20Z] INFO  16:20:56,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:20Z] INFO  16:20:56,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:20Z] INFO  16:20:56,781 MicroScheduler -   -> 8331 reads (2.51% of total) failing MappingQualityZeroFilter
[2015-09-30T15:20Z] INFO  16:20:56,781 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:20Z] INFO  16:20:56,781 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:20Z] INFO  16:20:56,781 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:20Z] INFO  16:20:57,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:20Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam
[2015-09-30T15:20Z] INFO  16:20:57,770 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:20Z] GATK: realign ('13', 0, 31036104) : syn3-normal
[2015-09-30T15:20Z] INFO  16:20:58,088 ProgressMeter -            done   3.1020377E7    38.0 s       1.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T15:20Z] INFO  16:20:58,088 ProgressMeter - Total runtime 38.38 secs, 0.64 min, 0.01 hours
[2015-09-30T15:20Z] INFO  16:20:58,091 MicroScheduler - 111663 reads were filtered out during the traversal out of approximately 1496307 total reads (7.46%)
[2015-09-30T15:20Z] INFO  16:20:58,092 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:20Z] INFO  16:20:58,092 MicroScheduler -   -> 16612 reads (1.11% of total) failing BadMateFilter
[2015-09-30T15:20Z] INFO  16:20:58,092 MicroScheduler -   -> 69165 reads (4.62% of total) failing DuplicateReadFilter
[2015-09-30T15:20Z] INFO  16:20:58,093 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:20Z] INFO  16:20:58,093 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:20Z] INFO  16:20:58,093 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:20Z] INFO  16:20:58,093 MicroScheduler -   -> 25886 reads (1.73% of total) failing MappingQualityZeroFilter
[2015-09-30T15:20Z] INFO  16:20:58,093 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:20Z] INFO  16:20:58,094 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:20Z] INFO  16:20:58,094 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:20Z] INFO  16:20:59,047 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:20Z] GATK: realign ('12', 93169109, 124189486) : syn3-normal
[2015-09-30T15:20Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam 13:31036378-62334609
[2015-09-30T15:20Z] GATK: RealignerTargetCreator
[2015-09-30T15:20Z] INFO  16:20:59,381 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:59,383 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:20Z] INFO  16:20:59,384 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:20Z] INFO  16:20:59,384 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:20Z] INFO  16:20:59,387 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign-realign.intervals -L 13:1-31036104 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmpHWl1Lm/1_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam
[2015-09-30T15:20Z] INFO  16:20:59,393 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:20Z] INFO  16:20:59,393 HelpFormatter - Date/Time: 2015/09/30 16:20:59
[2015-09-30T15:20Z] INFO  16:20:59,394 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:59,394 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:20Z] INFO  16:20:59,517 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:21Z] INFO  16:20:59,999 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:21Z] INFO  16:21:00,007 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:21Z] INFO  16:21:00,023 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:21Z] INFO  16:21:01,029 IntervalUtils - Processing 31036104 bp from intervals
[2015-09-30T15:21Z] WARN  16:21:01,033 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:21Z] INFO  16:21:01,088 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:21Z] INFO  16:21:01,273 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:21Z] INFO  16:21:01,274 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:21Z] INFO  16:21:01,274 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:21Z] INFO  16:21:01,275 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:21Z] INFO  16:21:01,385 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:21Z] INFO  16:21:01,456 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:21Z] INFO  16:21:01,516 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:01,518 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:21Z] INFO  16:21:01,518 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:21Z] INFO  16:21:01,518 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:21Z] INFO  16:21:01,522 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmpoalP_1/1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign-realign.intervals -l INFO -L 13:31036378-62334609 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:21Z] INFO  16:21:01,528 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:21Z] INFO  16:21:01,528 HelpFormatter - Date/Time: 2015/09/30 16:21:01
[2015-09-30T15:21Z] INFO  16:21:01,528 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:01,528 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:01,588 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:21Z] INFO  16:21:01,699 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:21Z] INFO  16:21:01,707 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:21Z] INFO  16:21:01,723 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:21Z] INFO  16:21:01,900 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:01,903 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:21Z] INFO  16:21:01,903 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:21Z] INFO  16:21:01,903 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:21Z] INFO  16:21:01,906 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign-realign.intervals -L 12:93169110-124189486 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/tx/tmpO3N0gx/1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam
[2015-09-30T15:21Z] INFO  16:21:01,912 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:21Z] INFO  16:21:01,912 HelpFormatter - Date/Time: 2015/09/30 16:21:01
[2015-09-30T15:21Z] INFO  16:21:01,912 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:01,913 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:02,260 IntervalUtils - Processing 31298232 bp from intervals
[2015-09-30T15:21Z] WARN  16:21:02,264 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:21Z] INFO  16:21:02,324 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:21Z] INFO  16:21:02,424 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:21Z] INFO  16:21:02,475 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:21Z] INFO  16:21:02,476 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:21Z] INFO  16:21:02,476 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:21Z] INFO  16:21:02,476 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:21Z] INFO  16:21:02,487 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:21Z] INFO  16:21:02,494 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:21Z] INFO  16:21:02,510 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:21Z] INFO  16:21:02,732 IntervalUtils - Processing 31020377 bp from intervals
[2015-09-30T15:21Z] WARN  16:21:02,736 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:21Z] INFO  16:21:03,105 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:21Z] INFO  16:21:03,259 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:21Z] INFO  16:21:03,260 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:21Z] INFO  16:21:03,260 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:21Z] INFO  16:21:03,261 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:21Z] INFO  16:21:03,416 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:21Z] INFO  16:21:03,605 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:21Z] INFO  16:21:22,731 ProgressMeter -            done    330227.0    21.0 s      64.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T15:21Z] INFO  16:21:22,732 ProgressMeter - Total runtime 21.46 secs, 0.36 min, 0.01 hours
[2015-09-30T15:21Z] INFO  16:21:22,734 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 330227 total reads (0.00%)
[2015-09-30T15:21Z] INFO  16:21:22,735 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:21Z] INFO  16:21:22,735 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:21Z] INFO  16:21:22,735 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:21Z] INFO  16:21:23,798 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:21Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam
[2015-09-30T15:21Z] GATK pre-alignment ('13', 63745563, 94765401) : syn3-normal
[2015-09-30T15:21Z] INFO  16:21:26,513 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:26,515 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:21Z] INFO  16:21:26,515 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:21Z] INFO  16:21:26,515 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:21Z] INFO  16:21:26,519 HelpFormatter - Program Args: -T PrintReads -L 13:63745564-94765401 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmp3WRQU_/1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam
[2015-09-30T15:21Z] INFO  16:21:26,524 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:21Z] INFO  16:21:26,524 HelpFormatter - Date/Time: 2015/09/30 16:21:26
[2015-09-30T15:21Z] INFO  16:21:26,525 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:26,525 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:26,617 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:21Z] INFO  16:21:27,463 ProgressMeter -            done   3.1298232E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T15:21Z] INFO  16:21:27,463 ProgressMeter - Total runtime 24.99 secs, 0.42 min, 0.01 hours
[2015-09-30T15:21Z] INFO  16:21:27,466 MicroScheduler - 57079 reads were filtered out during the traversal out of approximately 598069 total reads (9.54%)
[2015-09-30T15:21Z] INFO  16:21:27,467 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:21Z] INFO  16:21:27,467 MicroScheduler -   -> 9055 reads (1.51% of total) failing BadMateFilter
[2015-09-30T15:21Z] INFO  16:21:27,467 MicroScheduler -   -> 23667 reads (3.96% of total) failing DuplicateReadFilter
[2015-09-30T15:21Z] INFO  16:21:27,468 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:21Z] INFO  16:21:27,468 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:21Z] INFO  16:21:27,468 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:21Z] INFO  16:21:27,468 MicroScheduler -   -> 24357 reads (4.07% of total) failing MappingQualityZeroFilter
[2015-09-30T15:21Z] INFO  16:21:27,468 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:21Z] INFO  16:21:27,469 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:21Z] INFO  16:21:27,469 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:21Z] INFO  16:21:27,684 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:21Z] INFO  16:21:27,730 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:21Z] INFO  16:21:27,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:21Z] INFO  16:21:27,750 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:21Z] INFO  16:21:27,762 IntervalUtils - Processing 31019838 bp from intervals
[2015-09-30T15:21Z] INFO  16:21:27,815 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:21Z] INFO  16:21:27,997 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:21Z] INFO  16:21:27,998 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:21Z] INFO  16:21:27,998 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:21Z] INFO  16:21:27,998 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:21Z] INFO  16:21:28,009 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:21Z] INFO  16:21:28,192 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:21Z] INFO  16:21:29,356 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:21Z] GATK: realign ('13', 31036377, 62334609) : syn3-normal
[2015-09-30T15:21Z] INFO  16:21:31,829 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:31,831 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:21Z] INFO  16:21:31,831 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:21Z] INFO  16:21:31,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:21Z] INFO  16:21:31,835 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign-realign.intervals -L 13:31036378-62334609 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmptVO5bW/1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam
[2015-09-30T15:21Z] INFO  16:21:31,840 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:21Z] INFO  16:21:31,840 HelpFormatter - Date/Time: 2015/09/30 16:21:31
[2015-09-30T15:21Z] INFO  16:21:31,841 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:31,841 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:31,967 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:21Z] INFO  16:21:32,030 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:21Z] INFO  16:21:32,038 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:21Z] INFO  16:21:32,053 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:21Z] INFO  16:21:32,826 IntervalUtils - Processing 31298232 bp from intervals
[2015-09-30T15:21Z] WARN  16:21:32,830 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:21Z] INFO  16:21:32,887 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:21Z] INFO  16:21:33,034 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:21Z] INFO  16:21:33,035 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:21Z] INFO  16:21:33,035 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:21Z] INFO  16:21:33,036 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:21Z] INFO  16:21:33,178 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:21Z] INFO  16:21:33,366 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:21Z] INFO  16:21:35,274 ProgressMeter -    12:109999656    500006.0    32.0 s      64.0 s       54.3%    58.0 s      26.0 s
[2015-09-30T15:21Z] INFO  16:21:46,114 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:21Z] INFO  16:21:46,224 ProgressMeter -            done    156348.0    18.0 s     116.0 s      100.0%    18.0 s       0.0 s
[2015-09-30T15:21Z] INFO  16:21:46,224 ProgressMeter - Total runtime 18.23 secs, 0.30 min, 0.01 hours
[2015-09-30T15:21Z] INFO  16:21:46,225 MicroScheduler - 765 reads were filtered out during the traversal out of approximately 157113 total reads (0.49%)
[2015-09-30T15:21Z] INFO  16:21:46,225 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:21Z] INFO  16:21:46,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:21Z] INFO  16:21:46,225 MicroScheduler -   -> 765 reads (0.49% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:21Z] INFO  16:21:47,397 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:21Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam
[2015-09-30T15:21Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam 13:63745564-94765401
[2015-09-30T15:21Z] GATK: RealignerTargetCreator
[2015-09-30T15:21Z] INFO  16:21:49,427 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:49,430 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:21Z] INFO  16:21:49,430 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:21Z] INFO  16:21:49,430 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:21Z] INFO  16:21:49,433 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmpwrrKNK/1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign-realign.intervals -l INFO -L 13:63745564-94765401 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:21Z] INFO  16:21:49,439 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:21Z] INFO  16:21:49,440 HelpFormatter - Date/Time: 2015/09/30 16:21:49
[2015-09-30T15:21Z] INFO  16:21:49,440 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:49,440 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:21Z] INFO  16:21:49,498 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:21Z] INFO  16:21:49,607 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:21Z] INFO  16:21:49,615 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:21Z] INFO  16:21:49,632 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:21Z] INFO  16:21:50,339 IntervalUtils - Processing 31019838 bp from intervals
[2015-09-30T15:21Z] WARN  16:21:50,343 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:21Z] INFO  16:21:50,394 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:21Z] INFO  16:21:50,518 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:21Z] INFO  16:21:50,519 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:21Z] INFO  16:21:50,519 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:21Z] INFO  16:21:50,519 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:22Z] INFO  16:22:03,834 ProgressMeter -            done    593835.0    30.0 s      51.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T15:22Z] INFO  16:22:03,835 ProgressMeter - Total runtime 30.80 secs, 0.51 min, 0.01 hours
[2015-09-30T15:22Z] INFO  16:22:03,838 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 593835 total reads (0.00%)
[2015-09-30T15:22Z] INFO  16:22:03,838 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:22Z] INFO  16:22:03,838 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:22Z] INFO  16:22:03,839 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:22Z] INFO  16:22:05,043 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:22Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam
[2015-09-30T15:22Z] INFO  16:22:05,720 ProgressMeter -    12:123023256   1300014.0    62.0 s      48.0 s       96.2%    64.0 s       2.0 s
[2015-09-30T15:22Z] GATK pre-alignment ('13', 94938309, 115169878) : syn3-normal
[2015-09-30T15:22Z] INFO  16:22:07,151 ProgressMeter -            done   3.1019838E7    16.0 s       0.0 s      100.0%    16.0 s       0.0 s
[2015-09-30T15:22Z] INFO  16:22:07,151 ProgressMeter - Total runtime 16.63 secs, 0.28 min, 0.00 hours
[2015-09-30T15:22Z] INFO  16:22:07,154 MicroScheduler - 14583 reads were filtered out during the traversal out of approximately 157263 total reads (9.27%)
[2015-09-30T15:22Z] INFO  16:22:07,155 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:22Z] INFO  16:22:07,155 MicroScheduler -   -> 5384 reads (3.42% of total) failing BadMateFilter
[2015-09-30T15:22Z] INFO  16:22:07,155 MicroScheduler -   -> 5693 reads (3.62% of total) failing DuplicateReadFilter
[2015-09-30T15:22Z] INFO  16:22:07,155 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:22Z] INFO  16:22:07,156 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:22Z] INFO  16:22:07,156 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:22Z] INFO  16:22:07,156 MicroScheduler -   -> 3506 reads (2.23% of total) failing MappingQualityZeroFilter
[2015-09-30T15:22Z] INFO  16:22:07,156 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:22Z] INFO  16:22:07,156 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:22Z] INFO  16:22:07,157 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:22Z] INFO  16:22:08,287 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:22Z] GATK: realign ('13', 63745563, 94765401) : syn3-normal
[2015-09-30T15:22Z] INFO  16:22:08,572 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:08,574 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:22Z] INFO  16:22:08,574 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:22Z] INFO  16:22:08,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:22Z] INFO  16:22:08,577 HelpFormatter - Program Args: -T PrintReads -L 13:94938310-115169878 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmpE6Ujsc/1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam
[2015-09-30T15:22Z] INFO  16:22:08,583 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:22Z] INFO  16:22:08,583 HelpFormatter - Date/Time: 2015/09/30 16:22:08
[2015-09-30T15:22Z] INFO  16:22:08,583 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:08,583 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:08,685 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:22Z] INFO  16:22:09,684 ProgressMeter -            done   1487915.0    66.0 s      44.0 s      100.0%    66.0 s       0.0 s
[2015-09-30T15:22Z] INFO  16:22:09,685 ProgressMeter - Total runtime 66.43 secs, 1.11 min, 0.02 hours
[2015-09-30T15:22Z] INFO  16:22:09,688 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1487915 total reads (0.00%)
[2015-09-30T15:22Z] INFO  16:22:09,688 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:22Z] INFO  16:22:09,688 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:22Z] INFO  16:22:09,688 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:22Z] INFO  16:22:11,291 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:22Z] INFO  16:22:11,341 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:22Z] INFO  16:22:11,349 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:22Z] INFO  16:22:11,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:22Z] INFO  16:22:11,378 IntervalUtils - Processing 20231569 bp from intervals
[2015-09-30T15:22Z] INFO  16:22:11,437 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:22Z] INFO  16:22:11,723 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:22Z] INFO  16:22:12,231 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:22Z] INFO  16:22:12,232 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:22Z] INFO  16:22:12,232 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:22Z] INFO  16:22:12,232 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:22Z] INFO  16:22:12,244 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:22Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam
[2015-09-30T15:22Z] INFO  16:22:12,408 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:22Z] INFO  16:22:12,821 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:12,823 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:22Z] INFO  16:22:12,823 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:22Z] INFO  16:22:12,824 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:22Z] INFO  16:22:12,827 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign-realign.intervals -L 13:63745564-94765401 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmpaJWo0J/1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam
[2015-09-30T15:22Z] INFO  16:22:12,833 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:22Z] INFO  16:22:12,833 HelpFormatter - Date/Time: 2015/09/30 16:22:12
[2015-09-30T15:22Z] INFO  16:22:12,833 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:12,834 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:12,976 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:22Z] INFO  16:22:13,053 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:22Z] INFO  16:22:13,060 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:22Z] INFO  16:22:13,076 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:22Z] INFO  16:22:13,329 IntervalUtils - Processing 31019838 bp from intervals
[2015-09-30T15:22Z] WARN  16:22:13,332 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:22Z] INFO  16:22:13,402 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:22Z] INFO  16:22:13,530 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:22Z] INFO  16:22:13,531 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:22Z] INFO  16:22:13,531 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:22Z] INFO  16:22:13,531 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:22Z] INFO  16:22:13,685 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:22Z] INFO  16:22:13,866 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:22Z] GATK pre-alignment ('14', 0, 31050569) : syn3-normal
[2015-09-30T15:22Z] INFO  16:22:21,001 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:21,003 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:22Z] INFO  16:22:21,004 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:22Z] INFO  16:22:21,004 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:22Z] INFO  16:22:21,007 HelpFormatter - Program Args: -T PrintReads -L 14:1-31050569 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmpM3qBQ3/1_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam
[2015-09-30T15:22Z] INFO  16:22:21,013 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:22Z] INFO  16:22:21,013 HelpFormatter - Date/Time: 2015/09/30 16:22:21
[2015-09-30T15:22Z] INFO  16:22:21,013 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:21,014 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:21,118 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:22Z] INFO  16:22:22,743 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:22Z] INFO  16:22:22,795 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:22Z] INFO  16:22:22,803 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:22Z] INFO  16:22:22,818 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:22Z] INFO  16:22:22,832 IntervalUtils - Processing 31050569 bp from intervals
[2015-09-30T15:22Z] INFO  16:22:22,892 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:22Z] INFO  16:22:23,219 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:22Z] INFO  16:22:23,219 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:22Z] INFO  16:22:23,219 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:22Z] INFO  16:22:23,220 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:22Z] INFO  16:22:23,231 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:22Z] INFO  16:22:23,296 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:22Z] INFO  16:22:28,970 ProgressMeter -            done    156348.0    15.0 s      98.0 s      100.0%    15.0 s       0.0 s
[2015-09-30T15:22Z] INFO  16:22:28,970 ProgressMeter - Total runtime 15.44 secs, 0.26 min, 0.00 hours
[2015-09-30T15:22Z] INFO  16:22:28,973 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 156348 total reads (0.00%)
[2015-09-30T15:22Z] INFO  16:22:28,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:22Z] INFO  16:22:28,974 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:22Z] INFO  16:22:28,974 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:22Z] INFO  16:22:30,004 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:22Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam
[2015-09-30T15:22Z] GATK pre-alignment ('14', 31055710, 62162825) : syn3-normal
[2015-09-30T15:22Z] INFO  16:22:32,058 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:32,061 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:22Z] INFO  16:22:32,061 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:22Z] INFO  16:22:32,061 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:22Z] INFO  16:22:32,064 HelpFormatter - Program Args: -T PrintReads -L 14:31055711-62162825 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmpbH1_m1/1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam
[2015-09-30T15:22Z] INFO  16:22:32,070 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:22Z] INFO  16:22:32,070 HelpFormatter - Date/Time: 2015/09/30 16:22:32
[2015-09-30T15:22Z] INFO  16:22:32,070 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:32,071 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:22Z] INFO  16:22:32,733 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:22Z] INFO  16:22:33,409 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:22Z] INFO  16:22:33,457 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:22Z] INFO  16:22:33,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:22Z] INFO  16:22:33,478 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:22Z] INFO  16:22:33,491 IntervalUtils - Processing 31107115 bp from intervals
[2015-09-30T15:22Z] INFO  16:22:33,546 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:22Z] INFO  16:22:33,747 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:22Z] INFO  16:22:33,747 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:22Z] INFO  16:22:33,748 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:22Z] INFO  16:22:33,748 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:22Z] INFO  16:22:33,758 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:22Z] INFO  16:22:33,942 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:22Z] INFO  16:22:43,300 ProgressMeter -    13:103718663    200002.0    31.0 s       2.6 m       43.4%    71.0 s      40.0 s
[2015-09-30T15:22Z] INFO  16:22:53,451 ProgressMeter -     14:23521420    300003.0    30.0 s     100.0 s       75.8%    39.0 s       9.0 s
[2015-09-30T15:23Z] INFO  16:23:03,766 ProgressMeter -     14:50121341    200004.0    30.0 s       2.5 m       61.3%    48.0 s      18.0 s
[2015-09-30T15:23Z] INFO  16:23:05,950 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:23Z] INFO  16:23:06,083 ProgressMeter -            done    542071.0    53.0 s      99.0 s       99.6%    53.0 s       0.0 s
[2015-09-30T15:23Z] INFO  16:23:06,084 ProgressMeter - Total runtime 53.85 secs, 0.90 min, 0.01 hours
[2015-09-30T15:23Z] INFO  16:23:06,084 MicroScheduler - 1155 reads were filtered out during the traversal out of approximately 543226 total reads (0.21%)
[2015-09-30T15:23Z] INFO  16:23:06,084 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:23Z] INFO  16:23:06,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:23Z] INFO  16:23:06,085 MicroScheduler -   -> 1155 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:23Z] INFO  16:23:07,116 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:23Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam
[2015-09-30T15:23Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam 13:94938310-115169878
[2015-09-30T15:23Z] GATK: RealignerTargetCreator
[2015-09-30T15:23Z] INFO  16:23:10,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:10,363 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:23Z] INFO  16:23:10,363 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:23Z] INFO  16:23:10,363 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:23Z] INFO  16:23:10,367 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmpkQ_iP_/1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign-realign.intervals -l INFO -L 13:94938310-115169878 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:23Z] INFO  16:23:10,375 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:23Z] INFO  16:23:10,375 HelpFormatter - Date/Time: 2015/09/30 16:23:10
[2015-09-30T15:23Z] INFO  16:23:10,375 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:10,376 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:10,442 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:23Z] INFO  16:23:10,549 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:23Z] INFO  16:23:10,556 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:23Z] INFO  16:23:10,572 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:23Z] INFO  16:23:11,635 IntervalUtils - Processing 20231569 bp from intervals
[2015-09-30T15:23Z] WARN  16:23:11,639 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:23Z] INFO  16:23:11,694 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:23Z] INFO  16:23:11,810 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:23Z] INFO  16:23:11,811 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:23Z] INFO  16:23:11,811 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:23Z] INFO  16:23:11,812 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:23Z] INFO  16:23:14,202 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@21424be8
[2015-09-30T15:23Z] INFO  16:23:14,301 ProgressMeter -            done    567222.0    51.0 s      90.0 s      100.0%    51.0 s       0.0 s
[2015-09-30T15:23Z] INFO  16:23:14,302 ProgressMeter - Total runtime 51.08 secs, 0.85 min, 0.01 hours
[2015-09-30T15:23Z] INFO  16:23:14,302 MicroScheduler - 953 reads were filtered out during the traversal out of approximately 568175 total reads (0.17%)
[2015-09-30T15:23Z] INFO  16:23:14,302 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:23Z] INFO  16:23:14,302 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:23Z] INFO  16:23:14,303 MicroScheduler -   -> 953 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:23Z] INFO  16:23:15,327 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:23Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam
[2015-09-30T15:23Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam 14:1-31050569
[2015-09-30T15:23Z] GATK: RealignerTargetCreator
[2015-09-30T15:23Z] INFO  16:23:20,529 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:20,531 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:23Z] INFO  16:23:20,531 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:23Z] INFO  16:23:20,531 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:23Z] INFO  16:23:20,534 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmpqrFlN9/1_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign-realign.intervals -l INFO -L 14:1-31050569 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:23Z] INFO  16:23:20,540 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:23Z] INFO  16:23:20,540 HelpFormatter - Date/Time: 2015/09/30 16:23:20
[2015-09-30T15:23Z] INFO  16:23:20,541 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:20,541 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:20,601 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:23Z] INFO  16:23:20,715 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:23Z] INFO  16:23:20,724 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:23Z] INFO  16:23:20,741 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:23Z] INFO  16:23:20,998 IntervalUtils - Processing 31050569 bp from intervals
[2015-09-30T15:23Z] WARN  16:23:21,002 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:23Z] INFO  16:23:21,060 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:23Z] INFO  16:23:21,332 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:23Z] INFO  16:23:21,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:23Z] INFO  16:23:21,333 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:23Z] INFO  16:23:21,333 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:23Z] INFO  16:23:29,715 ProgressMeter -            done   2.0231569E7    17.0 s       0.0 s      100.0%    17.0 s       0.0 s
[2015-09-30T15:23Z] INFO  16:23:29,716 ProgressMeter - Total runtime 17.90 secs, 0.30 min, 0.00 hours
[2015-09-30T15:23Z] INFO  16:23:29,719 MicroScheduler - 41576 reads were filtered out during the traversal out of approximately 545514 total reads (7.62%)
[2015-09-30T15:23Z] INFO  16:23:29,719 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:23Z] INFO  16:23:29,719 MicroScheduler -   -> 6697 reads (1.23% of total) failing BadMateFilter
[2015-09-30T15:23Z] INFO  16:23:29,720 MicroScheduler -   -> 25312 reads (4.64% of total) failing DuplicateReadFilter
[2015-09-30T15:23Z] INFO  16:23:29,720 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:23Z] INFO  16:23:29,720 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:23Z] INFO  16:23:29,720 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:23Z] INFO  16:23:29,720 MicroScheduler -   -> 9567 reads (1.75% of total) failing MappingQualityZeroFilter
[2015-09-30T15:23Z] INFO  16:23:29,721 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:23Z] INFO  16:23:29,721 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:23Z] INFO  16:23:29,721 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:23Z] INFO  16:23:30,729 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:23Z] GATK: realign ('13', 94938309, 115169878) : syn3-normal
[2015-09-30T15:23Z] INFO  16:23:32,589 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:32,592 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:23Z] INFO  16:23:32,592 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:23Z] INFO  16:23:32,592 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:23Z] INFO  16:23:32,595 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign-realign.intervals -L 13:94938310-115169878 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/tx/tmpmY6ykR/1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam
[2015-09-30T15:23Z] INFO  16:23:32,601 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:23Z] INFO  16:23:32,601 HelpFormatter - Date/Time: 2015/09/30 16:23:32
[2015-09-30T15:23Z] INFO  16:23:32,601 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:32,601 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:32,726 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:23Z] INFO  16:23:32,790 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:23Z] INFO  16:23:32,798 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:23Z] INFO  16:23:32,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:23Z] INFO  16:23:33,202 IntervalUtils - Processing 20231569 bp from intervals
[2015-09-30T15:23Z] WARN  16:23:33,206 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:23Z] INFO  16:23:33,696 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:23Z] INFO  16:23:33,808 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:23Z] INFO  16:23:33,809 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:23Z] INFO  16:23:33,809 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:23Z] INFO  16:23:33,809 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:23Z] INFO  16:23:33,947 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:23Z] INFO  16:23:34,090 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:23Z] INFO  16:23:34,542 ProgressMeter -     14:59660880    500007.0    60.0 s       2.0 m       92.0%    65.0 s       5.0 s
[2015-09-30T15:23Z] INFO  16:23:40,803 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:23Z] INFO  16:23:40,849 ProgressMeter -            done    618589.0    67.0 s     108.0 s      100.0%    67.0 s       0.0 s
[2015-09-30T15:23Z] INFO  16:23:40,849 ProgressMeter - Total runtime 67.10 secs, 1.12 min, 0.02 hours
[2015-09-30T15:23Z] INFO  16:23:40,850 MicroScheduler - 1979 reads were filtered out during the traversal out of approximately 620568 total reads (0.32%)
[2015-09-30T15:23Z] INFO  16:23:40,850 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:23Z] INFO  16:23:40,850 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:23Z] INFO  16:23:40,850 MicroScheduler -   -> 1979 reads (0.32% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:23Z] INFO  16:23:41,867 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:23Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam
[2015-09-30T15:23Z] INFO  16:23:43,744 ProgressMeter -            done   3.1050569E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T15:23Z] INFO  16:23:43,745 ProgressMeter - Total runtime 22.41 secs, 0.37 min, 0.01 hours
[2015-09-30T15:23Z] INFO  16:23:43,748 MicroScheduler - 59606 reads were filtered out during the traversal out of approximately 570442 total reads (10.45%)
[2015-09-30T15:23Z] INFO  16:23:43,748 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:23Z] INFO  16:23:43,748 MicroScheduler -   -> 5413 reads (0.95% of total) failing BadMateFilter
[2015-09-30T15:23Z] INFO  16:23:43,748 MicroScheduler -   -> 26777 reads (4.69% of total) failing DuplicateReadFilter
[2015-09-30T15:23Z] INFO  16:23:43,749 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:23Z] INFO  16:23:43,749 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:23Z] INFO  16:23:43,749 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:23Z] INFO  16:23:43,749 MicroScheduler -   -> 27416 reads (4.81% of total) failing MappingQualityZeroFilter
[2015-09-30T15:23Z] INFO  16:23:43,750 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:23Z] INFO  16:23:43,750 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:23Z] INFO  16:23:43,750 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:23Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam 14:31055711-62162825
[2015-09-30T15:23Z] GATK: RealignerTargetCreator
[2015-09-30T15:23Z] INFO  16:23:44,708 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:23Z] GATK: realign ('14', 0, 31050569) : syn3-normal
[2015-09-30T15:23Z] INFO  16:23:47,464 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:47,466 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:23Z] INFO  16:23:47,467 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:23Z] INFO  16:23:47,467 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:23Z] INFO  16:23:47,470 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign-realign.intervals -L 14:1-31050569 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmpuGMz8X/1_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam
[2015-09-30T15:23Z] INFO  16:23:47,476 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:23Z] INFO  16:23:47,476 HelpFormatter - Date/Time: 2015/09/30 16:23:47
[2015-09-30T15:23Z] INFO  16:23:47,477 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:47,477 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:47,589 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:23Z] INFO  16:23:47,600 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:47,602 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:23Z] INFO  16:23:47,602 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:23Z] INFO  16:23:47,602 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:23Z] INFO  16:23:47,606 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmpwtt_e3/1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign-realign.intervals -l INFO -L 14:31055711-62162825 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:23Z] INFO  16:23:47,611 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:23Z] INFO  16:23:47,612 HelpFormatter - Date/Time: 2015/09/30 16:23:47
[2015-09-30T15:23Z] INFO  16:23:47,612 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:47,612 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:23Z] INFO  16:23:47,660 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:23Z] INFO  16:23:47,668 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:23Z] INFO  16:23:47,671 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:23Z] INFO  16:23:47,684 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:23Z] INFO  16:23:47,775 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:23Z] INFO  16:23:47,782 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:23Z] INFO  16:23:47,797 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:23Z] INFO  16:23:48,030 IntervalUtils - Processing 31107115 bp from intervals
[2015-09-30T15:23Z] WARN  16:23:48,034 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:23Z] INFO  16:23:48,087 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:23Z] INFO  16:23:48,236 IntervalUtils - Processing 31050569 bp from intervals
[2015-09-30T15:23Z] WARN  16:23:48,239 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:23Z] INFO  16:23:48,294 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:23Z] INFO  16:23:48,297 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:23Z] INFO  16:23:48,297 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:23Z] INFO  16:23:48,298 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:23Z] INFO  16:23:48,298 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:23Z] INFO  16:23:48,564 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:23Z] INFO  16:23:48,565 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:23Z] INFO  16:23:48,565 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:23Z] INFO  16:23:48,566 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:23Z] INFO  16:23:48,665 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:23Z] INFO  16:23:48,736 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:24Z] INFO  16:24:03,074 ProgressMeter -            done    542071.0    29.0 s      53.0 s       99.6%    29.0 s       0.0 s
[2015-09-30T15:24Z] INFO  16:24:03,075 ProgressMeter - Total runtime 29.27 secs, 0.49 min, 0.01 hours
[2015-09-30T15:24Z] INFO  16:24:03,077 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 542071 total reads (0.00%)
[2015-09-30T15:24Z] INFO  16:24:03,078 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:24Z] INFO  16:24:03,078 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:24Z] INFO  16:24:03,078 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:24Z] INFO  16:24:04,253 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:24Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam
[2015-09-30T15:24Z] GATK pre-alignment ('14', 62186823, 93262365) : syn3-normal
[2015-09-30T15:24Z] INFO  16:24:07,513 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:07,515 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:24Z] INFO  16:24:07,515 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:24Z] INFO  16:24:07,515 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:24Z] INFO  16:24:07,518 HelpFormatter - Program Args: -T PrintReads -L 14:62186824-93262365 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmpADHLxf/1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam
[2015-09-30T15:24Z] INFO  16:24:07,524 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:24Z] INFO  16:24:07,525 HelpFormatter - Date/Time: 2015/09/30 16:24:07
[2015-09-30T15:24Z] INFO  16:24:07,525 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:07,525 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:07,627 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:24Z] INFO  16:24:08,900 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:24Z] INFO  16:24:08,949 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:24Z] INFO  16:24:08,957 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:24Z] INFO  16:24:08,971 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:24Z] INFO  16:24:08,985 IntervalUtils - Processing 31075542 bp from intervals
[2015-09-30T15:24Z] INFO  16:24:09,042 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:24Z] INFO  16:24:09,246 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:24Z] INFO  16:24:09,247 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:24Z] INFO  16:24:09,247 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:24Z] INFO  16:24:09,247 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:24Z] INFO  16:24:09,258 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:24Z] INFO  16:24:09,451 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:24Z] INFO  16:24:13,041 ProgressMeter -            done   3.1107115E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T15:24Z] INFO  16:24:13,041 ProgressMeter - Total runtime 24.74 secs, 0.41 min, 0.01 hours
[2015-09-30T15:24Z] INFO  16:24:13,044 MicroScheduler - 46056 reads were filtered out during the traversal out of approximately 621813 total reads (7.41%)
[2015-09-30T15:24Z] INFO  16:24:13,044 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:24Z] INFO  16:24:13,045 MicroScheduler -   -> 10008 reads (1.61% of total) failing BadMateFilter
[2015-09-30T15:24Z] INFO  16:24:13,045 MicroScheduler -   -> 24370 reads (3.92% of total) failing DuplicateReadFilter
[2015-09-30T15:24Z] INFO  16:24:13,045 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:24Z] INFO  16:24:13,046 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:24Z] INFO  16:24:13,046 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:24Z] INFO  16:24:13,046 MicroScheduler -   -> 11678 reads (1.88% of total) failing MappingQualityZeroFilter
[2015-09-30T15:24Z] INFO  16:24:13,046 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:24Z] INFO  16:24:13,046 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:24Z] INFO  16:24:13,047 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:24Z] INFO  16:24:14,001 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:24Z] GATK: realign ('14', 31055710, 62162825) : syn3-normal
[2015-09-30T15:24Z] INFO  16:24:16,045 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:16,047 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:24Z] INFO  16:24:16,047 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:24Z] INFO  16:24:16,047 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:24Z] INFO  16:24:16,050 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign-realign.intervals -L 14:31055711-62162825 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmp7JS5g5/1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam
[2015-09-30T15:24Z] INFO  16:24:16,056 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:24Z] INFO  16:24:16,056 HelpFormatter - Date/Time: 2015/09/30 16:24:16
[2015-09-30T15:24Z] INFO  16:24:16,056 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:16,056 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:16,177 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:24Z] INFO  16:24:16,238 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:24Z] INFO  16:24:16,245 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:24Z] INFO  16:24:16,261 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:24Z] INFO  16:24:16,488 IntervalUtils - Processing 31107115 bp from intervals
[2015-09-30T15:24Z] WARN  16:24:16,492 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:24Z] INFO  16:24:16,546 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:24Z] INFO  16:24:16,683 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:24Z] INFO  16:24:16,684 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:24Z] INFO  16:24:16,684 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:24Z] INFO  16:24:16,685 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:24Z] INFO  16:24:16,829 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:24Z] INFO  16:24:17,023 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:24Z] INFO  16:24:17,442 ProgressMeter -            done    567222.0    28.0 s      50.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T15:24Z] INFO  16:24:17,443 ProgressMeter - Total runtime 28.88 secs, 0.48 min, 0.01 hours
[2015-09-30T15:24Z] INFO  16:24:17,446 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 567222 total reads (0.00%)
[2015-09-30T15:24Z] INFO  16:24:17,446 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:24Z] INFO  16:24:17,446 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:24Z] INFO  16:24:17,447 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:24Z] INFO  16:24:18,830 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:24Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam
[2015-09-30T15:24Z] GATK pre-alignment ('14', 93263525, 107349540) : syn3-normal
[2015-09-30T15:24Z] INFO  16:24:22,700 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:22,702 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:24Z] INFO  16:24:22,702 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:24Z] INFO  16:24:22,702 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:24Z] INFO  16:24:22,706 HelpFormatter - Program Args: -T PrintReads -L 14:93263526-107349540 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmp_Y_Yhf/1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam
[2015-09-30T15:24Z] INFO  16:24:22,711 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:24Z] INFO  16:24:22,711 HelpFormatter - Date/Time: 2015/09/30 16:24:22
[2015-09-30T15:24Z] INFO  16:24:22,712 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:22,712 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:22,818 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:24Z] INFO  16:24:24,580 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:24Z] INFO  16:24:24,632 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:24Z] INFO  16:24:24,640 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:24Z] INFO  16:24:24,655 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:24Z] INFO  16:24:24,668 IntervalUtils - Processing 14086015 bp from intervals
[2015-09-30T15:24Z] INFO  16:24:24,725 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:24Z] INFO  16:24:24,886 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:24Z] INFO  16:24:24,886 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:24Z] INFO  16:24:24,886 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:24Z] INFO  16:24:24,887 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:24Z] INFO  16:24:24,898 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:24Z] INFO  16:24:24,994 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:24Z] INFO  16:24:39,249 ProgressMeter -     14:69262607    200003.0    30.0 s       2.5 m       22.8%     2.2 m     101.0 s
[2015-09-30T15:24Z] INFO  16:24:46,687 ProgressMeter -     14:59798024    500007.0    30.0 s      60.0 s       92.4%    32.0 s       2.0 s
[2015-09-30T15:24Z] INFO  16:24:48,844 ProgressMeter -            done    618589.0    32.0 s      51.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T15:24Z] INFO  16:24:48,845 ProgressMeter - Total runtime 32.16 secs, 0.54 min, 0.01 hours
[2015-09-30T15:24Z] INFO  16:24:48,848 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 618589 total reads (0.00%)
[2015-09-30T15:24Z] INFO  16:24:48,848 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:24Z] INFO  16:24:48,848 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:24Z] INFO  16:24:48,849 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:24Z] INFO  16:24:49,946 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:24Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam
[2015-09-30T15:24Z] GATK pre-alignment ('15', 0, 31041107) : syn3-normal
[2015-09-30T15:24Z] INFO  16:24:53,919 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:53,922 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:24Z] INFO  16:24:53,922 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:24Z] INFO  16:24:53,922 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:24Z] INFO  16:24:53,925 HelpFormatter - Program Args: -T PrintReads -L 15:1-31041107 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmpZ6Bmey/1_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam
[2015-09-30T15:24Z] INFO  16:24:53,931 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:24Z] INFO  16:24:53,931 HelpFormatter - Date/Time: 2015/09/30 16:24:53
[2015-09-30T15:24Z] INFO  16:24:53,931 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:53,931 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:24Z] INFO  16:24:54,046 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:24Z] INFO  16:24:54,889 ProgressMeter -    14:100373688    200003.0    30.0 s       2.5 m       50.5%    59.0 s      29.0 s
[2015-09-30T15:24Z] INFO  16:24:55,387 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:24Z] INFO  16:24:55,436 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:24Z] INFO  16:24:55,444 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:24Z] INFO  16:24:55,538 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2015-09-30T15:24Z] INFO  16:24:55,581 IntervalUtils - Processing 31041107 bp from intervals
[2015-09-30T15:24Z] INFO  16:24:55,638 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:24Z] INFO  16:24:56,262 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:24Z] INFO  16:24:56,262 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:24Z] INFO  16:24:56,262 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:24Z] INFO  16:24:56,262 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:24Z] INFO  16:24:56,274 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:24Z] INFO  16:24:56,355 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:25Z] INFO  16:25:09,250 ProgressMeter -     14:75474295    500007.0    60.0 s     120.0 s       42.8%     2.3 m      80.0 s
[2015-09-30T15:25Z] INFO  16:25:24,890 ProgressMeter -    14:105167702    500006.0    60.0 s     120.0 s       84.5%    70.0 s      10.0 s
[2015-09-30T15:25Z] INFO  16:25:26,265 ProgressMeter -     15:25455392    200002.0    30.0 s       2.5 m       82.0%    36.0 s       6.0 s
[2015-09-30T15:25Z] INFO  16:25:39,251 ProgressMeter -     14:91009182    800010.0    90.0 s     112.0 s       92.7%    97.0 s       7.0 s
[2015-09-30T15:25Z] INFO  16:25:42,832 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:25Z] INFO  16:25:42,926 ProgressMeter -            done    739461.0    78.0 s     105.0 s       99.5%    78.0 s       0.0 s
[2015-09-30T15:25Z] INFO  16:25:42,927 ProgressMeter - Total runtime 78.04 secs, 1.30 min, 0.02 hours
[2015-09-30T15:25Z] INFO  16:25:42,927 MicroScheduler - 1816 reads were filtered out during the traversal out of approximately 741277 total reads (0.24%)
[2015-09-30T15:25Z] INFO  16:25:42,927 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:25Z] INFO  16:25:42,927 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:25Z] INFO  16:25:42,928 MicroScheduler -   -> 1816 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:25Z] INFO  16:25:43,953 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:25Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam
[2015-09-30T15:25Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam 14:93263526-107349540
[2015-09-30T15:25Z] GATK: RealignerTargetCreator
[2015-09-30T15:25Z] INFO  16:25:47,114 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:25Z] INFO  16:25:47,216 ProgressMeter -            done    472985.0    50.0 s     107.0 s      100.0%    50.0 s       0.0 s
[2015-09-30T15:25Z] INFO  16:25:47,216 ProgressMeter - Total runtime 50.95 secs, 0.85 min, 0.01 hours
[2015-09-30T15:25Z] INFO  16:25:47,216 MicroScheduler - 817 reads were filtered out during the traversal out of approximately 473802 total reads (0.17%)
[2015-09-30T15:25Z] INFO  16:25:47,217 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:25Z] INFO  16:25:47,217 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:25Z] INFO  16:25:47,217 MicroScheduler -   -> 817 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:25Z] INFO  16:25:48,120 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:25Z] INFO  16:25:48,122 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:25Z] INFO  16:25:48,122 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:25Z] INFO  16:25:48,122 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:25Z] INFO  16:25:48,126 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmpuqxHSh/1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign-realign.intervals -l INFO -L 14:93263526-107349540 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:25Z] INFO  16:25:48,131 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:25Z] INFO  16:25:48,132 HelpFormatter - Date/Time: 2015/09/30 16:25:48
[2015-09-30T15:25Z] INFO  16:25:48,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:25Z] INFO  16:25:48,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:25Z] INFO  16:25:48,197 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:25Z] INFO  16:25:48,273 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:25Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam
[2015-09-30T15:25Z] INFO  16:25:48,989 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:25Z] INFO  16:25:48,997 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:25Z] INFO  16:25:49,013 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:25Z] INFO  16:25:49,243 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:25Z] INFO  16:25:49,288 IntervalUtils - Processing 14086015 bp from intervals
[2015-09-30T15:25Z] WARN  16:25:49,296 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:25Z] INFO  16:25:49,347 ProgressMeter -            done   1008282.0   100.0 s      99.0 s      100.0%   100.0 s       0.0 s
[2015-09-30T15:25Z] INFO  16:25:49,348 ProgressMeter - Total runtime 100.10 secs, 1.67 min, 0.03 hours
[2015-09-30T15:25Z] INFO  16:25:49,348 MicroScheduler - 2506 reads were filtered out during the traversal out of approximately 1010788 total reads (0.25%)
[2015-09-30T15:25Z] INFO  16:25:49,348 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:25Z] INFO  16:25:49,348 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:25Z] INFO  16:25:49,349 MicroScheduler -   -> 2506 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:25Z] INFO  16:25:49,350 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:25Z] INFO  16:25:49,439 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:25Z] INFO  16:25:49,439 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:25Z] INFO  16:25:49,440 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:25Z] INFO  16:25:49,440 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:25Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam 15:1-31041107
[2015-09-30T15:25Z] GATK: RealignerTargetCreator
[2015-09-30T15:25Z] INFO  16:25:50,330 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:25Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam
[2015-09-30T15:25Z] INFO  16:25:51,633 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:25Z] INFO  16:25:51,635 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:25Z] INFO  16:25:51,635 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:25Z] INFO  16:25:51,635 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:25Z] INFO  16:25:51,639 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmp3OMIiB/1_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign-realign.intervals -l INFO -L 15:1-31041107 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:25Z] INFO  16:25:51,645 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:25Z] INFO  16:25:51,645 HelpFormatter - Date/Time: 2015/09/30 16:25:51
[2015-09-30T15:25Z] INFO  16:25:51,645 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:25Z] INFO  16:25:51,645 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:25Z] INFO  16:25:51,713 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:25Z] INFO  16:25:51,822 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:25Z] INFO  16:25:51,851 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:25Z] INFO  16:25:51,877 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T15:25Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam 14:62186824-93262365
[2015-09-30T15:25Z] GATK: RealignerTargetCreator
[2015-09-30T15:25Z] INFO  16:25:53,943 IntervalUtils - Processing 31041107 bp from intervals
[2015-09-30T15:25Z] WARN  16:25:53,947 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:25Z] INFO  16:25:54,002 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:25Z] INFO  16:25:54,180 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:25Z] INFO  16:25:54,180 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:25Z] INFO  16:25:54,181 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:25Z] INFO  16:25:54,181 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:25Z] INFO  16:25:56,109 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:25Z] INFO  16:25:56,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:25Z] INFO  16:25:56,111 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:25Z] INFO  16:25:56,111 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:25Z] INFO  16:25:56,115 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmpEIVq5v/1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign-realign.intervals -l INFO -L 14:62186824-93262365 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:25Z] INFO  16:25:56,120 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:25Z] INFO  16:25:56,121 HelpFormatter - Date/Time: 2015/09/30 16:25:56
[2015-09-30T15:25Z] INFO  16:25:56,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:25Z] INFO  16:25:56,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:25Z] INFO  16:25:56,190 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:25Z] INFO  16:25:56,320 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:25Z] INFO  16:25:56,327 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:25Z] INFO  16:25:56,343 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:25Z] INFO  16:25:57,450 IntervalUtils - Processing 31075542 bp from intervals
[2015-09-30T15:25Z] WARN  16:25:57,454 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:25Z] INFO  16:25:57,512 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:25Z] INFO  16:25:57,664 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:25Z] INFO  16:25:57,665 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:25Z] INFO  16:25:57,665 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:25Z] INFO  16:25:57,666 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:26Z] INFO  16:26:08,523 ProgressMeter -            done   1.4086015E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2015-09-30T15:26Z] INFO  16:26:08,523 ProgressMeter - Total runtime 19.08 secs, 0.32 min, 0.01 hours
[2015-09-30T15:26Z] INFO  16:26:08,526 MicroScheduler - 62043 reads were filtered out during the traversal out of approximately 744457 total reads (8.33%)
[2015-09-30T15:26Z] INFO  16:26:08,527 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:26Z] INFO  16:26:08,527 MicroScheduler -   -> 7465 reads (1.00% of total) failing BadMateFilter
[2015-09-30T15:26Z] INFO  16:26:08,527 MicroScheduler -   -> 37802 reads (5.08% of total) failing DuplicateReadFilter
[2015-09-30T15:26Z] INFO  16:26:08,527 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:26Z] INFO  16:26:08,528 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:26Z] INFO  16:26:08,528 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:26Z] INFO  16:26:08,528 MicroScheduler -   -> 16776 reads (2.25% of total) failing MappingQualityZeroFilter
[2015-09-30T15:26Z] INFO  16:26:08,528 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:26Z] INFO  16:26:08,529 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:26Z] INFO  16:26:08,529 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:26Z] INFO  16:26:12,298 ProgressMeter -            done   3.1041107E7    18.0 s       0.0 s      100.0%    18.0 s       0.0 s
[2015-09-30T15:26Z] INFO  16:26:12,298 ProgressMeter - Total runtime 18.12 secs, 0.30 min, 0.01 hours
[2015-09-30T15:26Z] INFO  16:26:12,301 MicroScheduler - 177874 reads were filtered out during the traversal out of approximately 475976 total reads (37.37%)
[2015-09-30T15:26Z] INFO  16:26:12,301 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:26Z] INFO  16:26:12,302 MicroScheduler -   -> 3458 reads (0.73% of total) failing BadMateFilter
[2015-09-30T15:26Z] INFO  16:26:12,302 MicroScheduler -   -> 15415 reads (3.24% of total) failing DuplicateReadFilter
[2015-09-30T15:26Z] INFO  16:26:12,302 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:26Z] INFO  16:26:12,302 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:26Z] INFO  16:26:12,303 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:26Z] INFO  16:26:12,303 MicroScheduler -   -> 159001 reads (33.41% of total) failing MappingQualityZeroFilter
[2015-09-30T15:26Z] INFO  16:26:12,303 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:26Z] INFO  16:26:12,303 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:26Z] INFO  16:26:12,304 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:26Z] INFO  16:26:13,274 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:26Z] GATK: realign ('15', 0, 31041107) : syn3-normal
[2015-09-30T15:26Z] INFO  16:26:14,801 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:14,803 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:26Z] INFO  16:26:14,803 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:26Z] INFO  16:26:14,803 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:26Z] INFO  16:26:14,807 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign-realign.intervals -L 15:1-31041107 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmpA8VFbB/1_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam
[2015-09-30T15:26Z] INFO  16:26:14,812 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:26Z] INFO  16:26:14,812 HelpFormatter - Date/Time: 2015/09/30 16:26:14
[2015-09-30T15:26Z] INFO  16:26:14,812 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:14,813 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:14,935 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:26Z] INFO  16:26:14,994 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:26Z] INFO  16:26:15,001 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:26Z] INFO  16:26:15,017 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:26Z] INFO  16:26:15,867 IntervalUtils - Processing 31041107 bp from intervals
[2015-09-30T15:26Z] WARN  16:26:15,871 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:26Z] INFO  16:26:15,923 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:26Z] INFO  16:26:16,097 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:26Z] INFO  16:26:16,098 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:26Z] INFO  16:26:16,098 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:26Z] INFO  16:26:16,099 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:26Z] INFO  16:26:16,189 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:26Z] INFO  16:26:16,251 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:26Z] INFO  16:26:22,693 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:26Z] GATK: realign ('14', 93263525, 107349540) : syn3-normal
[2015-09-30T15:26Z] INFO  16:26:25,180 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:25,183 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:26Z] INFO  16:26:25,183 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:26Z] INFO  16:26:25,183 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:26Z] INFO  16:26:25,186 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign-realign.intervals -L 14:93263526-107349540 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmpfyYjES/1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam
[2015-09-30T15:26Z] INFO  16:26:25,192 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:26Z] INFO  16:26:25,193 HelpFormatter - Date/Time: 2015/09/30 16:26:25
[2015-09-30T15:26Z] INFO  16:26:25,193 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:25,193 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:25,320 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:26Z] INFO  16:26:25,383 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:26Z] INFO  16:26:25,390 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:26Z] INFO  16:26:25,406 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:26Z] INFO  16:26:25,633 IntervalUtils - Processing 14086015 bp from intervals
[2015-09-30T15:26Z] WARN  16:26:25,637 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:26Z] INFO  16:26:25,690 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:26Z] INFO  16:26:25,773 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:26Z] INFO  16:26:25,774 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:26Z] INFO  16:26:25,774 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:26Z] INFO  16:26:25,774 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:26Z] INFO  16:26:25,891 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:26Z] INFO  16:26:25,989 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:26Z] INFO  16:26:27,120 ProgressMeter -            done   3.1075542E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T15:26Z] INFO  16:26:27,120 ProgressMeter - Total runtime 29.46 secs, 0.49 min, 0.01 hours
[2015-09-30T15:26Z] INFO  16:26:27,124 MicroScheduler - 76760 reads were filtered out during the traversal out of approximately 1014410 total reads (7.57%)
[2015-09-30T15:26Z] INFO  16:26:27,124 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:26Z] INFO  16:26:27,124 MicroScheduler -   -> 12322 reads (1.21% of total) failing BadMateFilter
[2015-09-30T15:26Z] INFO  16:26:27,124 MicroScheduler -   -> 46417 reads (4.58% of total) failing DuplicateReadFilter
[2015-09-30T15:26Z] INFO  16:26:27,125 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:26Z] INFO  16:26:27,125 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:26Z] INFO  16:26:27,125 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:26Z] INFO  16:26:27,125 MicroScheduler -   -> 18021 reads (1.78% of total) failing MappingQualityZeroFilter
[2015-09-30T15:26Z] INFO  16:26:27,126 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:26Z] INFO  16:26:27,126 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:26Z] INFO  16:26:27,126 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:26Z] INFO  16:26:28,152 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:26Z] GATK: realign ('14', 62186823, 93262365) : syn3-normal
[2015-09-30T15:26Z] INFO  16:26:31,343 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:31,345 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:26Z] INFO  16:26:31,345 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:26Z] INFO  16:26:31,345 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:26Z] INFO  16:26:31,349 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign-realign.intervals -L 14:62186824-93262365 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/tx/tmptIBkOH/1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam
[2015-09-30T15:26Z] INFO  16:26:31,354 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:26Z] INFO  16:26:31,355 HelpFormatter - Date/Time: 2015/09/30 16:26:31
[2015-09-30T15:26Z] INFO  16:26:31,355 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:31,355 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:31,486 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:26Z] INFO  16:26:31,549 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:26Z] INFO  16:26:31,556 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:26Z] INFO  16:26:31,573 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:26Z] INFO  16:26:32,265 IntervalUtils - Processing 31075542 bp from intervals
[2015-09-30T15:26Z] WARN  16:26:32,269 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:26Z] INFO  16:26:32,324 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:26Z] INFO  16:26:32,475 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:26Z] INFO  16:26:32,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:26Z] INFO  16:26:32,476 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:26Z] INFO  16:26:32,476 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:26Z] INFO  16:26:32,630 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:26Z] INFO  16:26:32,826 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:26Z] INFO  16:26:44,665 ProgressMeter -            done    472985.0    28.0 s      60.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T15:26Z] INFO  16:26:44,665 ProgressMeter - Total runtime 28.57 secs, 0.48 min, 0.01 hours
[2015-09-30T15:26Z] INFO  16:26:44,668 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 472985 total reads (0.00%)
[2015-09-30T15:26Z] INFO  16:26:44,668 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:26Z] INFO  16:26:44,669 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:26Z] INFO  16:26:44,669 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:26Z] INFO  16:26:45,834 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:26Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam
[2015-09-30T15:26Z] GATK pre-alignment ('15', 31042312, 62147370) : syn3-normal
[2015-09-30T15:26Z] INFO  16:26:49,551 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:49,553 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:26Z] INFO  16:26:49,553 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:26Z] INFO  16:26:49,553 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:26Z] INFO  16:26:49,557 HelpFormatter - Program Args: -T PrintReads -L 15:31042313-62147370 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmphE528C/1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam
[2015-09-30T15:26Z] INFO  16:26:49,563 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:26Z] INFO  16:26:49,563 HelpFormatter - Date/Time: 2015/09/30 16:26:49
[2015-09-30T15:26Z] INFO  16:26:49,563 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:49,563 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:26Z] INFO  16:26:49,666 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:26Z] INFO  16:26:50,691 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:26Z] INFO  16:26:50,739 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:26Z] INFO  16:26:50,747 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:26Z] INFO  16:26:50,761 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:26Z] INFO  16:26:50,774 IntervalUtils - Processing 31105058 bp from intervals
[2015-09-30T15:26Z] INFO  16:26:50,829 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:26Z] INFO  16:26:51,026 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:26Z] INFO  16:26:51,026 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:26Z] INFO  16:26:51,026 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:26Z] INFO  16:26:51,027 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:26Z] INFO  16:26:51,038 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:26Z] INFO  16:26:51,237 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:26Z] INFO  16:26:58,915 ProgressMeter -    14:104264215    400005.0    33.0 s      82.0 s       78.1%    42.0 s       9.0 s
[2015-09-30T15:27Z] INFO  16:27:04,141 ProgressMeter -     14:74707898    400005.0    31.0 s      79.0 s       40.3%    76.0 s      45.0 s
[2015-09-30T15:27Z] INFO  16:27:08,404 ProgressMeter -            done    739461.0    42.0 s      57.0 s       99.5%    42.0 s       0.0 s
[2015-09-30T15:27Z] INFO  16:27:08,404 ProgressMeter - Total runtime 42.63 secs, 0.71 min, 0.01 hours
[2015-09-30T15:27Z] INFO  16:27:08,407 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 739461 total reads (0.00%)
[2015-09-30T15:27Z] INFO  16:27:08,408 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:27Z] INFO  16:27:08,408 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:27Z] INFO  16:27:08,408 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:27Z] INFO  16:27:09,466 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:27Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam
[2015-09-30T15:27Z] GATK pre-alignment ('15', 62148224, 93170844) : syn3-normal
[2015-09-30T15:27Z] INFO  16:27:14,033 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:27Z] INFO  16:27:14,035 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:27Z] INFO  16:27:14,035 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:27Z] INFO  16:27:14,035 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:27Z] INFO  16:27:14,038 HelpFormatter - Program Args: -T PrintReads -L 15:62148225-93170844 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmpGJZqIu/1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam
[2015-09-30T15:27Z] INFO  16:27:14,044 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:27Z] INFO  16:27:14,044 HelpFormatter - Date/Time: 2015/09/30 16:27:14
[2015-09-30T15:27Z] INFO  16:27:14,044 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:27Z] INFO  16:27:14,045 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:27Z] INFO  16:27:14,147 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:27Z] INFO  16:27:15,952 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:27Z] INFO  16:27:16,000 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:27Z] INFO  16:27:16,008 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:27Z] INFO  16:27:16,023 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:27Z] INFO  16:27:16,036 IntervalUtils - Processing 31022620 bp from intervals
[2015-09-30T15:27Z] INFO  16:27:16,093 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:27Z] INFO  16:27:16,288 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:27Z] INFO  16:27:16,289 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:27Z] INFO  16:27:16,289 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:27Z] INFO  16:27:16,289 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:27Z] INFO  16:27:16,300 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:27Z] INFO  16:27:16,488 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:27Z] INFO  16:27:21,029 ProgressMeter -     15:38616793    200003.0    30.0 s       2.5 m       24.4%     2.1 m      93.0 s
[2015-09-30T15:27Z] INFO  16:27:22,984 ProgressMeter -            done   1008282.0    50.0 s      50.0 s      100.0%    50.0 s       0.0 s
[2015-09-30T15:27Z] INFO  16:27:22,984 ProgressMeter - Total runtime 50.51 secs, 0.84 min, 0.01 hours
[2015-09-30T15:27Z] INFO  16:27:22,987 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1008282 total reads (0.00%)
[2015-09-30T15:27Z] INFO  16:27:22,988 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:27Z] INFO  16:27:22,988 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:27Z] INFO  16:27:22,988 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:27Z] INFO  16:27:24,594 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:27Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam
[2015-09-30T15:27Z] GATK pre-alignment ('15', 93173163, 102531392) : syn3-normal
[2015-09-30T15:27Z] INFO  16:27:29,730 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:27Z] INFO  16:27:29,732 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:27Z] INFO  16:27:29,732 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:27Z] INFO  16:27:29,732 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:27Z] INFO  16:27:29,736 HelpFormatter - Program Args: -T PrintReads -L 15:93173164-102531392 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmpZW02dJ/1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam
[2015-09-30T15:27Z] INFO  16:27:29,741 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:27Z] INFO  16:27:29,741 HelpFormatter - Date/Time: 2015/09/30 16:27:29
[2015-09-30T15:27Z] INFO  16:27:29,742 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:27Z] INFO  16:27:29,742 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:27Z] INFO  16:27:29,853 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:27Z] INFO  16:27:30,534 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:27Z] INFO  16:27:30,582 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:27Z] INFO  16:27:30,589 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:27Z] INFO  16:27:30,605 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:27Z] INFO  16:27:30,618 IntervalUtils - Processing 9358229 bp from intervals
[2015-09-30T15:27Z] INFO  16:27:30,673 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:27Z] INFO  16:27:30,812 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:27Z] INFO  16:27:30,813 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:27Z] INFO  16:27:30,813 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:27Z] INFO  16:27:30,813 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:27Z] INFO  16:27:30,824 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:27Z] INFO  16:27:30,889 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:27Z] INFO  16:27:46,292 ProgressMeter -     15:65666274    200002.0    30.0 s       2.5 m       11.3%     4.4 m       3.9 m
[2015-09-30T15:27Z] INFO  16:27:51,318 ProgressMeter -     15:42294345    500009.0    60.0 s     120.0 s       36.2%     2.8 m     105.0 s
[2015-09-30T15:27Z] INFO  16:27:55,342 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@627346b4
[2015-09-30T15:27Z] INFO  16:27:55,898 ProgressMeter -            done    212365.0    25.0 s     118.0 s       99.8%    25.0 s       0.0 s
[2015-09-30T15:27Z] INFO  16:27:55,899 ProgressMeter - Total runtime 25.09 secs, 0.42 min, 0.01 hours
[2015-09-30T15:27Z] INFO  16:27:55,899 MicroScheduler - 474 reads were filtered out during the traversal out of approximately 212839 total reads (0.22%)
[2015-09-30T15:27Z] INFO  16:27:55,899 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:27Z] INFO  16:27:55,899 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:27Z] INFO  16:27:55,900 MicroScheduler -   -> 474 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:27Z] INFO  16:27:56,956 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:27Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam
[2015-09-30T15:27Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam 15:93173164-102531392
[2015-09-30T15:27Z] GATK: RealignerTargetCreator
[2015-09-30T15:28Z] INFO  16:28:00,257 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:28Z] INFO  16:28:00,259 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:28Z] INFO  16:28:00,259 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:28Z] INFO  16:28:00,259 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:28Z] INFO  16:28:00,263 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmpj2ex6r/1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign-realign.intervals -l INFO -L 15:93173164-102531392 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:28Z] INFO  16:28:00,269 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:28Z] INFO  16:28:00,269 HelpFormatter - Date/Time: 2015/09/30 16:28:00
[2015-09-30T15:28Z] INFO  16:28:00,270 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:28Z] INFO  16:28:00,270 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:28Z] INFO  16:28:00,330 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:28Z] INFO  16:28:00,442 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:28Z] INFO  16:28:00,450 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:28Z] INFO  16:28:00,466 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:28Z] INFO  16:28:00,719 IntervalUtils - Processing 9358229 bp from intervals
[2015-09-30T15:28Z] WARN  16:28:00,723 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:28Z] INFO  16:28:00,783 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:28Z] INFO  16:28:01,316 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:28Z] INFO  16:28:01,316 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:28Z] INFO  16:28:01,317 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:28Z] INFO  16:28:01,317 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:28Z] INFO  16:28:10,746 ProgressMeter -            done   9358229.0     9.0 s       1.0 s      100.0%     9.0 s       0.0 s
[2015-09-30T15:28Z] INFO  16:28:10,747 ProgressMeter - Total runtime 9.43 secs, 0.16 min, 0.00 hours
[2015-09-30T15:28Z] INFO  16:28:10,750 MicroScheduler - 27175 reads were filtered out during the traversal out of approximately 213704 total reads (12.72%)
[2015-09-30T15:28Z] INFO  16:28:10,750 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:28Z] INFO  16:28:10,750 MicroScheduler -   -> 2845 reads (1.33% of total) failing BadMateFilter
[2015-09-30T15:28Z] INFO  16:28:10,750 MicroScheduler -   -> 9757 reads (4.57% of total) failing DuplicateReadFilter
[2015-09-30T15:28Z] INFO  16:28:10,751 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:28Z] INFO  16:28:10,751 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:28Z] INFO  16:28:10,751 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:28Z] INFO  16:28:10,751 MicroScheduler -   -> 14573 reads (6.82% of total) failing MappingQualityZeroFilter
[2015-09-30T15:28Z] INFO  16:28:10,752 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:28Z] INFO  16:28:10,752 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:28Z] INFO  16:28:10,752 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:28Z] INFO  16:28:11,870 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:28Z] GATK: realign ('15', 93173163, 102531392) : syn3-normal
[2015-09-30T15:28Z] INFO  16:28:13,885 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:28Z] INFO  16:28:13,887 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:28Z] INFO  16:28:13,887 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:28Z] INFO  16:28:13,888 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:28Z] INFO  16:28:13,891 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign-realign.intervals -L 15:93173164-102531392 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmpwIiSFF/1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam
[2015-09-30T15:28Z] INFO  16:28:13,898 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:28Z] INFO  16:28:13,898 HelpFormatter - Date/Time: 2015/09/30 16:28:13
[2015-09-30T15:28Z] INFO  16:28:13,898 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:28Z] INFO  16:28:13,899 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:28Z] INFO  16:28:14,055 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:28Z] INFO  16:28:14,121 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:28Z] INFO  16:28:14,128 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:28Z] INFO  16:28:14,144 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:28Z] INFO  16:28:14,368 IntervalUtils - Processing 9358229 bp from intervals
[2015-09-30T15:28Z] WARN  16:28:14,372 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:28Z] INFO  16:28:14,426 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:28Z] INFO  16:28:14,490 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:28Z] INFO  16:28:14,491 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:28Z] INFO  16:28:14,491 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:28Z] INFO  16:28:14,491 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:28Z] INFO  16:28:14,590 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:28Z] INFO  16:28:14,660 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:28Z] INFO  16:28:16,299 ProgressMeter -     15:72577323    500005.0    60.0 s     120.0 s       33.6%     3.0 m     118.0 s
[2015-09-30T15:28Z] INFO  16:28:21,319 ProgressMeter -     15:44968976    800014.0    90.0 s     112.0 s       44.8%     3.4 m     111.0 s
[2015-09-30T15:28Z] INFO  16:28:28,702 ProgressMeter -            done    212365.0    14.0 s      66.0 s       99.8%    14.0 s       0.0 s
[2015-09-30T15:28Z] INFO  16:28:28,702 ProgressMeter - Total runtime 14.21 secs, 0.24 min, 0.00 hours
[2015-09-30T15:28Z] INFO  16:28:28,706 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 212365 total reads (0.00%)
[2015-09-30T15:28Z] INFO  16:28:28,706 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:28Z] INFO  16:28:28,706 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:28Z] INFO  16:28:28,706 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:28Z] INFO  16:28:29,644 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:28Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam
[2015-09-30T15:28Z] GATK pre-alignment ('16', 0, 31021934) : syn3-normal
[2015-09-30T15:28Z] INFO  16:28:31,975 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:28Z] INFO  16:28:31,977 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:28Z] INFO  16:28:31,977 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:28Z] INFO  16:28:31,977 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:28Z] INFO  16:28:31,981 HelpFormatter - Program Args: -T PrintReads -L 16:1-31021934 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/tx/tmpBedgLv/1_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam
[2015-09-30T15:28Z] INFO  16:28:31,986 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:28Z] INFO  16:28:31,987 HelpFormatter - Date/Time: 2015/09/30 16:28:31
[2015-09-30T15:28Z] INFO  16:28:31,987 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:28Z] INFO  16:28:31,987 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:28Z] INFO  16:28:32,096 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:28Z] INFO  16:28:32,814 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:28Z] INFO  16:28:32,865 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:28Z] INFO  16:28:32,873 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:28Z] INFO  16:28:32,888 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:28Z] INFO  16:28:32,902 IntervalUtils - Processing 31021934 bp from intervals
[2015-09-30T15:28Z] INFO  16:28:32,960 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:28Z] INFO  16:28:33,288 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:28Z] INFO  16:28:33,288 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:28Z] INFO  16:28:33,289 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:28Z] INFO  16:28:33,289 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:28Z] INFO  16:28:33,300 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:28Z] INFO  16:28:33,489 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:28Z] INFO  16:28:46,800 ProgressMeter -     15:75966880    800008.0    90.0 s     113.0 s       44.5%     3.4 m     112.0 s
[2015-09-30T15:28Z] INFO  16:28:51,326 ProgressMeter -     15:53049600   1100018.0   120.0 s     109.0 s       70.8%     2.8 m      49.0 s
[2015-09-30T15:29Z] INFO  16:29:03,296 ProgressMeter -      16:1391019    200002.0    30.0 s       2.5 m        4.5%    11.2 m      10.7 m
[2015-09-30T15:29Z] INFO  16:29:08,002 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:29Z] INFO  16:29:08,138 ProgressMeter -            done   1350604.0     2.3 m     101.0 s      100.0%     2.3 m       0.0 s
[2015-09-30T15:29Z] INFO  16:29:08,139 ProgressMeter - Total runtime 137.11 secs, 2.29 min, 0.04 hours
[2015-09-30T15:29Z] INFO  16:29:08,139 MicroScheduler - 2892 reads were filtered out during the traversal out of approximately 1353496 total reads (0.21%)
[2015-09-30T15:29Z] INFO  16:29:08,139 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:29Z] INFO  16:29:08,139 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:29Z] INFO  16:29:08,140 MicroScheduler -   -> 2892 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:29Z] INFO  16:29:09,442 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:29Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam
[2015-09-30T15:29Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam 15:31042313-62147370
[2015-09-30T15:29Z] GATK: RealignerTargetCreator
[2015-09-30T15:29Z] INFO  16:29:14,477 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:29Z] INFO  16:29:14,479 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:29Z] INFO  16:29:14,479 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:29Z] INFO  16:29:14,479 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:29Z] INFO  16:29:14,483 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmps4lBMO/1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign-realign.intervals -l INFO -L 15:31042313-62147370 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:29Z] INFO  16:29:14,488 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:29Z] INFO  16:29:14,488 HelpFormatter - Date/Time: 2015/09/30 16:29:14
[2015-09-30T15:29Z] INFO  16:29:14,489 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:29Z] INFO  16:29:14,489 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:29Z] INFO  16:29:14,546 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:29Z] INFO  16:29:14,654 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:29Z] INFO  16:29:14,662 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:29Z] INFO  16:29:14,678 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:29Z] INFO  16:29:14,929 IntervalUtils - Processing 31105058 bp from intervals
[2015-09-30T15:29Z] WARN  16:29:14,933 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:29Z] INFO  16:29:14,990 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:29Z] INFO  16:29:15,134 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:29Z] INFO  16:29:15,134 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:29Z] INFO  16:29:15,135 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:29Z] INFO  16:29:15,135 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:29Z] INFO  16:29:26,801 ProgressMeter -     15:84488034   1200014.0     2.2 m     108.0 s       72.0%     3.0 m      50.0 s
[2015-09-30T15:29Z] INFO  16:29:33,297 ProgressMeter -      16:2512842    500005.0    60.0 s     120.0 s        8.1%    12.3 m      11.3 m
[2015-09-30T15:29Z] INFO  16:29:45,137 ProgressMeter -     15:53026225   2.1976312E7    30.0 s       1.0 s       70.7%    42.0 s      12.0 s
[2015-09-30T15:29Z] INFO  16:29:52,226 ProgressMeter -            done   3.1105058E7    37.0 s       1.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T15:29Z] INFO  16:29:52,227 ProgressMeter - Total runtime 37.09 secs, 0.62 min, 0.01 hours
[2015-09-30T15:29Z] INFO  16:29:52,230 MicroScheduler - 160349 reads were filtered out during the traversal out of approximately 1358591 total reads (11.80%)
[2015-09-30T15:29Z] INFO  16:29:52,230 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:29Z] INFO  16:29:52,231 MicroScheduler -   -> 14131 reads (1.04% of total) failing BadMateFilter
[2015-09-30T15:29Z] INFO  16:29:52,231 MicroScheduler -   -> 58350 reads (4.29% of total) failing DuplicateReadFilter
[2015-09-30T15:29Z] INFO  16:29:52,231 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:29Z] INFO  16:29:52,231 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:29Z] INFO  16:29:52,232 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:29Z] INFO  16:29:52,232 MicroScheduler -   -> 87868 reads (6.47% of total) failing MappingQualityZeroFilter
[2015-09-30T15:29Z] INFO  16:29:52,232 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:29Z] INFO  16:29:52,232 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:29Z] INFO  16:29:52,232 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:29Z] INFO  16:29:53,295 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:29Z] GATK: realign ('15', 31042312, 62147370) : syn3-normal
[2015-09-30T15:29Z] INFO  16:29:55,367 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:29Z] INFO  16:29:55,369 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:29Z] INFO  16:29:55,369 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:29Z] INFO  16:29:55,369 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:29Z] INFO  16:29:55,373 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign-realign.intervals -L 15:31042313-62147370 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmp2UBIex/1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam
[2015-09-30T15:29Z] INFO  16:29:55,378 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:29Z] INFO  16:29:55,379 HelpFormatter - Date/Time: 2015/09/30 16:29:55
[2015-09-30T15:29Z] INFO  16:29:55,379 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:29Z] INFO  16:29:55,379 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:29Z] INFO  16:29:55,485 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:29Z] INFO  16:29:55,555 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:29Z] INFO  16:29:55,563 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:29Z] INFO  16:29:55,578 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:29Z] INFO  16:29:55,801 IntervalUtils - Processing 31105058 bp from intervals
[2015-09-30T15:29Z] WARN  16:29:55,805 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:29Z] INFO  16:29:55,862 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:29Z] INFO  16:29:56,006 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:29Z] INFO  16:29:56,007 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:29Z] INFO  16:29:56,007 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:29Z] INFO  16:29:56,008 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:29Z] INFO  16:29:56,156 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:29Z] INFO  16:29:56,349 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:29Z] INFO  16:29:56,801 ProgressMeter -     15:91016519   1500018.0     2.7 m     107.0 s       93.1%     2.9 m      11.0 s
[2015-09-30T15:30Z] INFO  16:30:03,298 ProgressMeter -      16:4763845    800009.0    90.0 s     112.0 s       15.4%     9.8 m       8.3 m
[2015-09-30T15:30Z] INFO  16:30:04,682 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:30Z] INFO  16:30:04,830 ProgressMeter -            done   1634695.0     2.8 m     103.0 s      100.0%     2.8 m       0.0 s
[2015-09-30T15:30Z] INFO  16:30:04,831 ProgressMeter - Total runtime 168.54 secs, 2.81 min, 0.05 hours
[2015-09-30T15:30Z] INFO  16:30:04,831 MicroScheduler - 2736 reads were filtered out during the traversal out of approximately 1637431 total reads (0.17%)
[2015-09-30T15:30Z] INFO  16:30:04,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:30Z] INFO  16:30:04,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:30Z] INFO  16:30:04,832 MicroScheduler -   -> 2736 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:30Z] INFO  16:30:05,907 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:30Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam
[2015-09-30T15:30Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam 15:62148225-93170844
[2015-09-30T15:30Z] GATK: RealignerTargetCreator
[2015-09-30T15:30Z] INFO  16:30:12,172 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:30Z] INFO  16:30:12,174 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:30Z] INFO  16:30:12,174 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:30Z] INFO  16:30:12,174 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:30Z] INFO  16:30:12,178 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmp9efvT8/1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign-realign.intervals -l INFO -L 15:62148225-93170844 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:30Z] INFO  16:30:12,184 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:30Z] INFO  16:30:12,184 HelpFormatter - Date/Time: 2015/09/30 16:30:12
[2015-09-30T15:30Z] INFO  16:30:12,184 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:30Z] INFO  16:30:12,185 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:30Z] INFO  16:30:12,253 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:30Z] INFO  16:30:12,644 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:30Z] INFO  16:30:12,652 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:30Z] INFO  16:30:12,668 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:30Z] INFO  16:30:13,426 IntervalUtils - Processing 31022620 bp from intervals
[2015-09-30T15:30Z] WARN  16:30:13,430 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:30Z] INFO  16:30:13,488 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:30Z] INFO  16:30:13,669 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:30Z] INFO  16:30:13,670 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:30Z] INFO  16:30:13,670 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:30Z] INFO  16:30:13,671 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:30Z] INFO  16:30:26,010 ProgressMeter -     15:42117176    400007.0    30.0 s      75.0 s       35.6%    84.0 s      54.0 s
[2015-09-30T15:30Z] INFO  16:30:33,298 ProgressMeter -     16:14970294   1100012.0   120.0 s     109.0 s       48.3%     4.1 m       2.1 m
[2015-09-30T15:30Z] INFO  16:30:43,673 ProgressMeter -     15:85201801   2.3048576E7    30.0 s       1.0 s       74.3%    40.0 s      10.0 s
[2015-09-30T15:30Z] INFO  16:30:52,505 ProgressMeter -            done   3.102262E7    38.0 s       1.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T15:30Z] INFO  16:30:52,505 ProgressMeter - Total runtime 38.84 secs, 0.65 min, 0.01 hours
[2015-09-30T15:30Z] INFO  16:30:52,508 MicroScheduler - 225399 reads were filtered out during the traversal out of approximately 1645442 total reads (13.70%)
[2015-09-30T15:30Z] INFO  16:30:52,508 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:30Z] INFO  16:30:52,509 MicroScheduler -   -> 15237 reads (0.93% of total) failing BadMateFilter
[2015-09-30T15:30Z] INFO  16:30:52,509 MicroScheduler -   -> 74093 reads (4.50% of total) failing DuplicateReadFilter
[2015-09-30T15:30Z] INFO  16:30:52,509 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:30Z] INFO  16:30:52,510 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:30Z] INFO  16:30:52,510 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:30Z] INFO  16:30:52,510 MicroScheduler -   -> 136069 reads (8.27% of total) failing MappingQualityZeroFilter
[2015-09-30T15:30Z] INFO  16:30:52,510 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:30Z] INFO  16:30:52,510 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:30Z] INFO  16:30:52,511 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:30Z] INFO  16:30:53,467 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:30Z] GATK: realign ('15', 62148224, 93170844) : syn3-normal
[2015-09-30T15:30Z] INFO  16:30:56,362 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:30Z] INFO  16:30:56,364 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:30Z] INFO  16:30:56,364 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:30Z] INFO  16:30:56,364 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:30Z] INFO  16:30:56,367 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign-realign.intervals -L 15:62148225-93170844 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/tx/tmpn2oDl9/1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam
[2015-09-30T15:30Z] INFO  16:30:56,373 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:30Z] INFO  16:30:56,374 HelpFormatter - Date/Time: 2015/09/30 16:30:56
[2015-09-30T15:30Z] INFO  16:30:56,374 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:30Z] INFO  16:30:56,374 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:30Z] INFO  16:30:56,670 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:30Z] INFO  16:30:56,740 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:30Z] INFO  16:30:56,748 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:30Z] INFO  16:30:56,985 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.24
[2015-09-30T15:30Z] INFO  16:30:57,215 IntervalUtils - Processing 31022620 bp from intervals
[2015-09-30T15:30Z] WARN  16:30:57,219 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:30Z] INFO  16:30:57,257 ProgressMeter -     15:58254010   1200019.0    61.0 s      51.0 s       87.5%    69.0 s       8.0 s
[2015-09-30T15:30Z] INFO  16:30:57,275 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:30Z] INFO  16:30:57,422 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:30Z] INFO  16:30:57,423 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:30Z] INFO  16:30:57,423 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:30Z] INFO  16:30:57,424 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:30Z] INFO  16:30:57,569 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:30Z] INFO  16:30:57,761 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:30Z] INFO  16:30:59,900 ProgressMeter -            done   1350604.0    63.0 s      47.0 s      100.0%    63.0 s       0.0 s
[2015-09-30T15:30Z] INFO  16:30:59,900 ProgressMeter - Total runtime 63.89 secs, 1.06 min, 0.02 hours
[2015-09-30T15:30Z] INFO  16:30:59,903 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1350604 total reads (0.00%)
[2015-09-30T15:30Z] INFO  16:30:59,904 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:30Z] INFO  16:30:59,904 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:30Z] INFO  16:30:59,904 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:31Z] INFO  16:31:00,968 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:31Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam
[2015-09-30T15:31Z] INFO  16:31:03,299 ProgressMeter -     16:18858576   1400016.0     2.5 m     107.0 s       60.8%     4.1 m      96.0 s
[2015-09-30T15:31Z] GATK pre-alignment ('16', 31044089, 62860191) : syn3-normal
[2015-09-30T15:31Z] INFO  16:31:06,655 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:31Z] INFO  16:31:06,657 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:31Z] INFO  16:31:06,657 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:31Z] INFO  16:31:06,657 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:31Z] INFO  16:31:06,661 HelpFormatter - Program Args: -T PrintReads -L 16:31044090-62860191 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/tx/tmpP4DLML/1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam
[2015-09-30T15:31Z] INFO  16:31:06,667 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:31Z] INFO  16:31:06,668 HelpFormatter - Date/Time: 2015/09/30 16:31:06
[2015-09-30T15:31Z] INFO  16:31:06,668 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:31Z] INFO  16:31:06,668 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:31Z] INFO  16:31:06,791 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:31Z] INFO  16:31:07,523 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:31Z] INFO  16:31:07,573 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:31Z] INFO  16:31:07,581 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:31Z] INFO  16:31:07,595 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:31Z] INFO  16:31:07,609 IntervalUtils - Processing 31816102 bp from intervals
[2015-09-30T15:31Z] INFO  16:31:07,665 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:31Z] INFO  16:31:07,855 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:31Z] INFO  16:31:07,856 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:31Z] INFO  16:31:07,856 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:31Z] INFO  16:31:07,856 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:31Z] INFO  16:31:07,868 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:31Z] INFO  16:31:08,054 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:31Z] INFO  16:31:27,426 ProgressMeter -     15:73621688    500005.0    30.0 s      60.0 s       37.0%    81.0 s      51.0 s
[2015-09-30T15:31Z] INFO  16:31:33,300 ProgressMeter -     16:22826698   1700019.0     3.0 m     105.0 s       73.6%     4.1 m      64.0 s
[2015-09-30T15:31Z] INFO  16:31:37,859 ProgressMeter -     16:46552710    200003.0    30.0 s       2.5 m       48.7%    61.0 s      31.0 s
[2015-09-30T15:31Z] INFO  16:31:57,427 ProgressMeter -     15:85191091   1200014.0    60.0 s      50.0 s       74.3%    80.0 s      20.0 s
[2015-09-30T15:32Z] INFO  16:32:03,301 ProgressMeter -     16:28975532   2000024.0     3.5 m     105.0 s       93.4%     3.7 m      14.0 s
[2015-09-30T15:32Z] INFO  16:32:07,860 ProgressMeter -     16:56602533    500006.0    60.0 s     120.0 s       80.3%    74.0 s      14.0 s
[2015-09-30T15:32Z] INFO  16:32:11,048 ProgressMeter -            done   1634695.0    73.0 s      45.0 s      100.0%    73.0 s       0.0 s
[2015-09-30T15:32Z] INFO  16:32:11,049 ProgressMeter - Total runtime 73.63 secs, 1.23 min, 0.02 hours
[2015-09-30T15:32Z] INFO  16:32:11,052 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1634695 total reads (0.00%)
[2015-09-30T15:32Z] INFO  16:32:11,052 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:32Z] INFO  16:32:11,053 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:32Z] INFO  16:32:11,053 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:32Z] INFO  16:32:12,110 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:32Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam
[2015-09-30T15:32Z] GATK pre-alignment ('16', 64294277, 90354753) : syn3-normal
[2015-09-30T15:32Z] INFO  16:32:19,499 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:32Z] INFO  16:32:19,501 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:32Z] INFO  16:32:19,501 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:32Z] INFO  16:32:19,501 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:32Z] INFO  16:32:19,505 HelpFormatter - Program Args: -T PrintReads -L 16:64294278-90354753 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/tx/tmp0X48FI/1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam
[2015-09-30T15:32Z] INFO  16:32:19,529 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:32Z] INFO  16:32:19,529 HelpFormatter - Date/Time: 2015/09/30 16:32:19
[2015-09-30T15:32Z] INFO  16:32:19,529 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:32Z] INFO  16:32:19,529 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:32Z] INFO  16:32:19,636 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:32Z] INFO  16:32:20,309 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:32Z] INFO  16:32:20,357 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:32Z] INFO  16:32:20,364 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:32Z] INFO  16:32:20,614 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.25
[2015-09-30T15:32Z] INFO  16:32:20,627 IntervalUtils - Processing 26060476 bp from intervals
[2015-09-30T15:32Z] INFO  16:32:20,681 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:32Z] INFO  16:32:20,863 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:32Z] INFO  16:32:20,864 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:32Z] INFO  16:32:20,864 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:32Z] INFO  16:32:20,864 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:32Z] INFO  16:32:20,875 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:32Z] INFO  16:32:21,033 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:32Z] INFO  16:32:31,323 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:32Z] INFO  16:32:31,517 ProgressMeter -            done   2392568.0     4.0 m      99.0 s      100.0%     4.0 m       0.0 s
[2015-09-30T15:32Z] INFO  16:32:31,517 ProgressMeter - Total runtime 238.23 secs, 3.97 min, 0.07 hours
[2015-09-30T15:32Z] INFO  16:32:31,517 MicroScheduler - 3700 reads were filtered out during the traversal out of approximately 2396268 total reads (0.15%)
[2015-09-30T15:32Z] INFO  16:32:31,518 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:32Z] INFO  16:32:31,518 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:32Z] INFO  16:32:31,518 MicroScheduler -   -> 3700 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:32Z] INFO  16:32:32,449 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:32Z] INFO  16:32:32,584 ProgressMeter -            done    806728.0    84.0 s     105.0 s      100.0%    84.0 s       0.0 s
[2015-09-30T15:32Z] INFO  16:32:32,584 ProgressMeter - Total runtime 84.73 secs, 1.41 min, 0.02 hours
[2015-09-30T15:32Z] INFO  16:32:32,585 MicroScheduler - 1605 reads were filtered out during the traversal out of approximately 808333 total reads (0.20%)
[2015-09-30T15:32Z] INFO  16:32:32,585 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:32Z] INFO  16:32:32,585 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:32Z] INFO  16:32:32,585 MicroScheduler -   -> 1605 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:32Z] INFO  16:32:32,616 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:32Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam
[2015-09-30T15:32Z] INFO  16:32:33,710 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:32Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam
[2015-09-30T15:32Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam 16:31044090-62860191
[2015-09-30T15:32Z] GATK: RealignerTargetCreator
[2015-09-30T15:32Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam 16:1-31021934
[2015-09-30T15:32Z] GATK: RealignerTargetCreator
[2015-09-30T15:32Z] INFO  16:32:41,932 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:32Z] INFO  16:32:41,934 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:32Z] INFO  16:32:41,934 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:32Z] INFO  16:32:41,934 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:32Z] INFO  16:32:41,938 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/tx/tmp326_C1/1_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign-realign.intervals -l INFO -L 16:1-31021934 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:32Z] INFO  16:32:41,943 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:32Z] INFO  16:32:41,943 HelpFormatter - Date/Time: 2015/09/30 16:32:41
[2015-09-30T15:32Z] INFO  16:32:41,943 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:32Z] INFO  16:32:41,943 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:32Z] INFO  16:32:41,947 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:32Z] INFO  16:32:41,949 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:32Z] INFO  16:32:41,950 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:32Z] INFO  16:32:41,950 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:32Z] INFO  16:32:41,953 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/tx/tmpbTVkZb/1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign-realign.intervals -l INFO -L 16:31044090-62860191 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:32Z] INFO  16:32:41,959 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:32Z] INFO  16:32:41,959 HelpFormatter - Date/Time: 2015/09/30 16:32:41
[2015-09-30T15:32Z] INFO  16:32:41,960 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:32Z] INFO  16:32:41,960 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:32Z] INFO  16:32:42,002 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:32Z] INFO  16:32:42,017 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:32Z] INFO  16:32:42,115 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:32Z] INFO  16:32:42,122 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:32Z] INFO  16:32:42,128 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:32Z] INFO  16:32:42,136 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:32Z] INFO  16:32:42,139 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:32Z] INFO  16:32:42,152 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:32Z] INFO  16:32:43,240 IntervalUtils - Processing 31021934 bp from intervals
[2015-09-30T15:32Z] INFO  16:32:43,244 IntervalUtils - Processing 31816102 bp from intervals
[2015-09-30T15:32Z] WARN  16:32:43,244 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:32Z] WARN  16:32:43,248 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:32Z] INFO  16:32:43,302 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:32Z] INFO  16:32:43,304 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:32Z] INFO  16:32:43,423 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:32Z] INFO  16:32:43,423 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:32Z] INFO  16:32:43,424 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:32Z] INFO  16:32:43,424 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:32Z] INFO  16:32:43,450 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:32Z] INFO  16:32:43,451 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:32Z] INFO  16:32:43,451 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:32Z] INFO  16:32:43,452 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:32Z] INFO  16:32:50,866 ProgressMeter -     16:67861673    200002.0    30.0 s       2.5 m       13.7%     3.7 m       3.2 m
[2015-09-30T15:33Z] INFO  16:33:08,504 ProgressMeter -            done   3.1816102E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T15:33Z] INFO  16:33:08,505 ProgressMeter - Total runtime 25.08 secs, 0.42 min, 0.01 hours
[2015-09-30T15:33Z] INFO  16:33:08,508 MicroScheduler - 109063 reads were filtered out during the traversal out of approximately 812141 total reads (13.43%)
[2015-09-30T15:33Z] INFO  16:33:08,508 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:33Z] INFO  16:33:08,508 MicroScheduler -   -> 9921 reads (1.22% of total) failing BadMateFilter
[2015-09-30T15:33Z] INFO  16:33:08,508 MicroScheduler -   -> 37171 reads (4.58% of total) failing DuplicateReadFilter
[2015-09-30T15:33Z] INFO  16:33:08,509 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:33Z] INFO  16:33:08,509 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:33Z] INFO  16:33:08,509 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:33Z] INFO  16:33:08,509 MicroScheduler -   -> 61971 reads (7.63% of total) failing MappingQualityZeroFilter
[2015-09-30T15:33Z] INFO  16:33:08,510 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:33Z] INFO  16:33:08,510 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:33Z] INFO  16:33:08,510 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:33Z] INFO  16:33:09,464 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:33Z] GATK: realign ('16', 31044089, 62860191) : syn3-normal
[2015-09-30T15:33Z] INFO  16:33:11,369 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:33Z] INFO  16:33:11,371 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:33Z] INFO  16:33:11,372 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:33Z] INFO  16:33:11,372 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:33Z] INFO  16:33:11,375 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign-realign.intervals -L 16:31044090-62860191 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/tx/tmp1BjWW7/1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam
[2015-09-30T15:33Z] INFO  16:33:11,381 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:33Z] INFO  16:33:11,381 HelpFormatter - Date/Time: 2015/09/30 16:33:11
[2015-09-30T15:33Z] INFO  16:33:11,381 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:33Z] INFO  16:33:11,381 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:33Z] INFO  16:33:11,506 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:33Z] INFO  16:33:11,571 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:33Z] INFO  16:33:11,578 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:33Z] INFO  16:33:11,594 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:33Z] INFO  16:33:12,719 IntervalUtils - Processing 31816102 bp from intervals
[2015-09-30T15:33Z] WARN  16:33:12,723 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:33Z] INFO  16:33:12,777 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:33Z] INFO  16:33:12,897 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:33Z] INFO  16:33:12,897 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:33Z] INFO  16:33:12,897 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:33Z] INFO  16:33:12,898 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:33Z] INFO  16:33:13,016 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:33Z] INFO  16:33:13,194 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:33Z] INFO  16:33:13,454 ProgressMeter -     16:18853601   1.88416E7    30.0 s       1.0 s       60.8%    49.0 s      19.0 s
[2015-09-30T15:33Z] INFO  16:33:20,867 ProgressMeter -     16:70897127    500006.0    60.0 s     120.0 s       25.3%     3.9 m       2.9 m
[2015-09-30T15:33Z] INFO  16:33:31,741 ProgressMeter -            done   3.1021934E7    48.0 s       1.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T15:33Z] INFO  16:33:31,742 ProgressMeter - Total runtime 48.29 secs, 0.80 min, 0.01 hours
[2015-09-30T15:33Z] INFO  16:33:31,745 MicroScheduler - 442036 reads were filtered out during the traversal out of approximately 2406005 total reads (18.37%)
[2015-09-30T15:33Z] INFO  16:33:31,745 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:33Z] INFO  16:33:31,746 MicroScheduler -   -> 19181 reads (0.80% of total) failing BadMateFilter
[2015-09-30T15:33Z] INFO  16:33:31,746 MicroScheduler -   -> 110920 reads (4.61% of total) failing DuplicateReadFilter
[2015-09-30T15:33Z] INFO  16:33:31,746 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:33Z] INFO  16:33:31,746 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:33Z] INFO  16:33:31,746 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:33Z] INFO  16:33:31,747 MicroScheduler -   -> 311935 reads (12.96% of total) failing MappingQualityZeroFilter
[2015-09-30T15:33Z] INFO  16:33:31,747 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:33Z] INFO  16:33:31,747 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:33Z] INFO  16:33:31,747 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:33Z] INFO  16:33:32,719 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:33Z] GATK: realign ('16', 0, 31021934) : syn3-normal
[2015-09-30T15:33Z] INFO  16:33:34,627 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:33Z] INFO  16:33:34,629 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:33Z] INFO  16:33:34,629 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:33Z] INFO  16:33:34,629 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:33Z] INFO  16:33:34,632 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign-realign.intervals -L 16:1-31021934 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/tx/tmpG_uU3A/1_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam
[2015-09-30T15:33Z] INFO  16:33:34,639 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:33Z] INFO  16:33:34,639 HelpFormatter - Date/Time: 2015/09/30 16:33:34
[2015-09-30T15:33Z] INFO  16:33:34,639 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:33Z] INFO  16:33:34,639 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:33Z] INFO  16:33:34,769 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:33Z] INFO  16:33:34,834 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:33Z] INFO  16:33:34,841 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:33Z] INFO  16:33:34,858 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:33Z] INFO  16:33:35,092 IntervalUtils - Processing 31021934 bp from intervals
[2015-09-30T15:33Z] WARN  16:33:35,097 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:33Z] INFO  16:33:35,154 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:33Z] INFO  16:33:35,317 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:33Z] INFO  16:33:35,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:33Z] INFO  16:33:35,317 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:33Z] INFO  16:33:35,318 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:33Z] INFO  16:33:35,466 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:33Z] INFO  16:33:35,664 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:33Z] INFO  16:33:44,416 ProgressMeter -     16:53500946    400005.0    31.0 s      78.0 s       70.6%    43.0 s      12.0 s
[2015-09-30T15:33Z] INFO  16:33:50,868 ProgressMeter -     16:77390518    800011.0    90.0 s     112.0 s       50.3%     3.0 m      89.0 s
[2015-09-30T15:33Z] INFO  16:33:57,852 ProgressMeter -            done    806728.0    44.0 s      55.0 s      100.0%    44.0 s       0.0 s
[2015-09-30T15:33Z] INFO  16:33:57,853 ProgressMeter - Total runtime 44.96 secs, 0.75 min, 0.01 hours
[2015-09-30T15:33Z] INFO  16:33:57,856 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 806728 total reads (0.00%)
[2015-09-30T15:33Z] INFO  16:33:57,856 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:33Z] INFO  16:33:57,856 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:33Z] INFO  16:33:57,856 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:33Z] INFO  16:33:59,006 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:33Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam
[2015-09-30T15:34Z] GATK pre-alignment ('17', 0, 31039439) : syn3-normal
[2015-09-30T15:34Z] INFO  16:34:04,441 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:34Z] INFO  16:34:04,443 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:34Z] INFO  16:34:04,443 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:34Z] INFO  16:34:04,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:34Z] INFO  16:34:04,447 HelpFormatter - Program Args: -T PrintReads -L 17:1-31039439 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/tx/tmp0emMS3/1_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam
[2015-09-30T15:34Z] INFO  16:34:04,453 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:34Z] INFO  16:34:04,453 HelpFormatter - Date/Time: 2015/09/30 16:34:04
[2015-09-30T15:34Z] INFO  16:34:04,453 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:34Z] INFO  16:34:04,453 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:34Z] INFO  16:34:06,521 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:34Z] INFO  16:34:07,682 ProgressMeter -      16:2488646    500005.0    32.0 s      64.0 s        8.0%     6.6 m       6.1 m
[2015-09-30T15:34Z] INFO  16:34:08,065 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:34Z] INFO  16:34:08,115 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:34Z] INFO  16:34:08,122 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:34Z] INFO  16:34:08,137 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:34Z] INFO  16:34:08,150 IntervalUtils - Processing 31039439 bp from intervals
[2015-09-30T15:34Z] INFO  16:34:08,208 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:34Z] INFO  16:34:08,408 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:34Z] INFO  16:34:08,409 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:34Z] INFO  16:34:08,409 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:34Z] INFO  16:34:08,409 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:34Z] INFO  16:34:08,420 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:34Z] INFO  16:34:08,640 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:34Z] INFO  16:34:20,869 ProgressMeter -     16:87873640   1100016.0   120.0 s     109.0 s       90.5%     2.2 m      12.0 s
[2015-09-30T15:34Z] INFO  16:34:38,412 ProgressMeter -      17:3568433    200002.0    30.0 s       2.5 m       11.5%     4.3 m       3.8 m
[2015-09-30T15:34Z] INFO  16:34:39,859 ProgressMeter -     16:16267403   1200013.0    64.0 s      53.0 s       52.4%     2.0 m      58.0 s
[2015-09-30T15:34Z] INFO  16:34:47,020 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:34Z] INFO  16:34:47,343 ProgressMeter -            done   1425211.0     2.4 m     102.0 s       99.6%     2.4 m       0.0 s
[2015-09-30T15:34Z] INFO  16:34:47,344 ProgressMeter - Total runtime 146.48 secs, 2.44 min, 0.04 hours
[2015-09-30T15:34Z] INFO  16:34:47,344 MicroScheduler - 2319 reads were filtered out during the traversal out of approximately 1427530 total reads (0.16%)
[2015-09-30T15:34Z] INFO  16:34:47,344 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:34Z] INFO  16:34:47,344 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:34Z] INFO  16:34:47,345 MicroScheduler -   -> 2319 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:34Z] INFO  16:34:48,467 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:34Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam
[2015-09-30T15:34Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam 16:64294278-90354753
[2015-09-30T15:34Z] GATK: RealignerTargetCreator
[2015-09-30T15:34Z] INFO  16:34:54,060 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:34Z] INFO  16:34:54,062 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:34Z] INFO  16:34:54,062 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:34Z] INFO  16:34:54,062 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:34Z] INFO  16:34:54,066 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/tx/tmp1A_SGU/1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign-realign.intervals -l INFO -L 16:64294278-90354753 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:34Z] INFO  16:34:54,071 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:34Z] INFO  16:34:54,071 HelpFormatter - Date/Time: 2015/09/30 16:34:54
[2015-09-30T15:34Z] INFO  16:34:54,071 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:34Z] INFO  16:34:54,072 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:34Z] INFO  16:34:54,136 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:34Z] INFO  16:34:54,249 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:34Z] INFO  16:34:54,256 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:34Z] INFO  16:34:54,271 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:34Z] INFO  16:34:55,104 IntervalUtils - Processing 26060476 bp from intervals
[2015-09-30T15:34Z] WARN  16:34:55,107 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:34Z] INFO  16:34:55,160 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:34Z] INFO  16:34:55,291 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:34Z] INFO  16:34:55,292 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:34Z] INFO  16:34:55,292 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:34Z] INFO  16:34:55,293 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:35Z] INFO  16:35:08,587 ProgressMeter -      17:6928949    600008.0    60.0 s     100.0 s       22.3%     4.5 m       3.5 m
[2015-09-30T15:35Z] INFO  16:35:09,860 ProgressMeter -     16:28411326   2000024.0    94.0 s      47.0 s       91.6%   102.0 s       8.0 s
[2015-09-30T15:35Z] INFO  16:35:24,976 ProgressMeter -            done   2392568.0   109.0 s      45.0 s      100.0%   109.0 s       0.0 s
[2015-09-30T15:35Z] INFO  16:35:24,976 ProgressMeter - Total runtime 109.66 secs, 1.83 min, 0.03 hours
[2015-09-30T15:35Z] INFO  16:35:24,980 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2392568 total reads (0.00%)
[2015-09-30T15:35Z] INFO  16:35:24,980 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:35Z] INFO  16:35:24,980 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:35Z] INFO  16:35:24,980 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:35Z] INFO  16:35:25,295 ProgressMeter -     16:89711301   2.5408123E7    30.0 s       1.0 s       97.5%    30.0 s       0.0 s
[2015-09-30T15:35Z] INFO  16:35:26,097 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:35Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam
[2015-09-30T15:35Z] INFO  16:35:27,230 ProgressMeter -            done   2.6060476E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T15:35Z] INFO  16:35:27,230 ProgressMeter - Total runtime 31.94 secs, 0.53 min, 0.01 hours
[2015-09-30T15:35Z] INFO  16:35:27,234 MicroScheduler - 137594 reads were filtered out during the traversal out of approximately 1434563 total reads (9.59%)
[2015-09-30T15:35Z] INFO  16:35:27,234 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:35Z] INFO  16:35:27,234 MicroScheduler -   -> 14261 reads (0.99% of total) failing BadMateFilter
[2015-09-30T15:35Z] INFO  16:35:27,235 MicroScheduler -   -> 71313 reads (4.97% of total) failing DuplicateReadFilter
[2015-09-30T15:35Z] INFO  16:35:27,235 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:35Z] INFO  16:35:27,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:35Z] INFO  16:35:27,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:35Z] INFO  16:35:27,235 MicroScheduler -   -> 52020 reads (3.63% of total) failing MappingQualityZeroFilter
[2015-09-30T15:35Z] INFO  16:35:27,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:35Z] INFO  16:35:27,236 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:35Z] INFO  16:35:27,236 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:35Z] INFO  16:35:28,215 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:35Z] GATK: realign ('16', 64294277, 90354753) : syn3-normal
[2015-09-30T15:35Z] INFO  16:35:29,899 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:35Z] INFO  16:35:29,903 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:35Z] INFO  16:35:29,903 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:35Z] INFO  16:35:29,903 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:35Z] INFO  16:35:29,910 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign-realign.intervals -L 16:64294278-90354753 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/tx/tmpBvW4mo/1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam
[2015-09-30T15:35Z] INFO  16:35:29,917 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:35Z] INFO  16:35:29,918 HelpFormatter - Date/Time: 2015/09/30 16:35:29
[2015-09-30T15:35Z] INFO  16:35:29,918 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:35Z] INFO  16:35:29,918 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:35Z] INFO  16:35:30,043 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:35Z] INFO  16:35:30,115 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:35Z] INFO  16:35:30,122 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:35Z] INFO  16:35:30,140 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:35Z] INFO  16:35:30,380 IntervalUtils - Processing 26060476 bp from intervals
[2015-09-30T15:35Z] WARN  16:35:30,384 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:35Z] INFO  16:35:30,438 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:35Z] INFO  16:35:30,582 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:35Z] INFO  16:35:30,582 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:35Z] INFO  16:35:30,583 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:35Z] INFO  16:35:30,583 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:35Z] INFO  16:35:30,740 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:35Z] INFO  16:35:30,896 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:35Z] GATK pre-alignment ('17', 31047756, 62076645) : syn3-normal
[2015-09-30T15:35Z] INFO  16:35:36,407 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:35Z] INFO  16:35:36,409 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:35Z] INFO  16:35:36,409 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:35Z] INFO  16:35:36,409 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:35Z] INFO  16:35:36,413 HelpFormatter - Program Args: -T PrintReads -L 17:31047757-62076645 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/tx/tmpRi4YjR/1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam
[2015-09-30T15:35Z] INFO  16:35:36,418 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:35Z] INFO  16:35:36,418 HelpFormatter - Date/Time: 2015/09/30 16:35:36
[2015-09-30T15:35Z] INFO  16:35:36,419 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:35Z] INFO  16:35:36,419 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:35Z] INFO  16:35:37,338 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:35Z] INFO  16:35:38,713 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:35Z] INFO  16:35:38,764 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:35Z] INFO  16:35:38,771 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:35Z] INFO  16:35:38,786 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:35Z] INFO  16:35:38,799 IntervalUtils - Processing 31028889 bp from intervals
[2015-09-30T15:35Z] INFO  16:35:38,855 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:35Z] INFO  16:35:39,054 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:35Z] INFO  16:35:39,055 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:35Z] INFO  16:35:39,055 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:35Z] INFO  16:35:39,055 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:35Z] INFO  16:35:39,066 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:35Z] INFO  16:35:39,278 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:35Z] INFO  16:35:39,564 ProgressMeter -      17:9531775    900012.0    91.0 s     101.0 s       30.7%     4.9 m       3.4 m
[2015-09-30T15:36Z] INFO  16:36:01,727 ProgressMeter -     16:70588728    400005.0    31.0 s      77.0 s       24.2%     2.1 m      97.0 s
[2015-09-30T15:36Z] INFO  16:36:09,058 ProgressMeter -     17:36486808    300003.0    30.0 s     100.0 s       17.5%     2.9 m       2.4 m
[2015-09-30T15:36Z] INFO  16:36:09,565 ProgressMeter -     17:17962595   1300016.0     2.0 m      93.0 s       57.9%     3.5 m      88.0 s
[2015-09-30T15:36Z] INFO  16:36:32,912 ProgressMeter -     16:89347430   1200018.0    62.0 s      51.0 s       96.1%    64.0 s       2.0 s
[2015-09-30T15:36Z] INFO  16:36:38,662 ProgressMeter -            done   1425211.0    68.0 s      47.0 s       99.6%    68.0 s       0.0 s
[2015-09-30T15:36Z] INFO  16:36:38,662 ProgressMeter - Total runtime 68.08 secs, 1.13 min, 0.02 hours
[2015-09-30T15:36Z] INFO  16:36:38,666 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1425211 total reads (0.00%)
[2015-09-30T15:36Z] INFO  16:36:38,666 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:36Z] INFO  16:36:38,666 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:36Z] INFO  16:36:38,666 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:36Z] INFO  16:36:39,059 ProgressMeter -     17:39633814    600007.0    60.0 s     100.0 s       27.7%     3.6 m       2.6 m
[2015-09-30T15:36Z] INFO  16:36:39,594 ProgressMeter -     17:25753279   1700021.0     2.5 m      88.0 s       83.0%     3.0 m      30.0 s
[2015-09-30T15:36Z] INFO  16:36:39,760 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:36Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam
[2015-09-30T15:36Z] GATK pre-alignment ('17', 62078196, 81195210) : syn3-normal
[2015-09-30T15:36Z] INFO  16:36:45,036 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:36Z] INFO  16:36:45,038 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:36Z] INFO  16:36:45,038 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:36Z] INFO  16:36:45,038 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:36Z] INFO  16:36:45,041 HelpFormatter - Program Args: -T PrintReads -L 17:62078197-81195210 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/tx/tmpUGBDWq/1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam
[2015-09-30T15:36Z] INFO  16:36:45,047 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:36Z] INFO  16:36:45,047 HelpFormatter - Date/Time: 2015/09/30 16:36:45
[2015-09-30T15:36Z] INFO  16:36:45,047 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:36Z] INFO  16:36:45,048 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:36Z] INFO  16:36:45,140 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:36Z] INFO  16:36:46,369 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:36Z] INFO  16:36:46,417 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:36Z] INFO  16:36:46,424 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:36Z] INFO  16:36:46,439 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:36Z] INFO  16:36:46,452 IntervalUtils - Processing 19117014 bp from intervals
[2015-09-30T15:36Z] INFO  16:36:46,507 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:36Z] INFO  16:36:46,678 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:36Z] INFO  16:36:46,679 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:36Z] INFO  16:36:46,679 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:36Z] INFO  16:36:46,679 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:36Z] INFO  16:36:46,690 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:36Z] INFO  16:36:46,817 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:37Z] INFO  16:37:09,093 ProgressMeter -     17:41977776   1000013.0    90.0 s      90.0 s       35.2%     4.3 m       2.8 m
[2015-09-30T15:37Z] INFO  16:37:09,595 ProgressMeter -     17:30327770   2100026.0     3.0 m      86.0 s       97.7%     3.1 m       4.0 s
[2015-09-30T15:37Z] INFO  16:37:12,466 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6dbf2c98
[2015-09-30T15:37Z] INFO  16:37:12,786 ProgressMeter -            done   2172059.0     3.1 m      84.0 s      100.0%     3.1 m       0.0 s
[2015-09-30T15:37Z] INFO  16:37:12,787 ProgressMeter - Total runtime 184.38 secs, 3.07 min, 0.05 hours
[2015-09-30T15:37Z] INFO  16:37:12,787 MicroScheduler - 3546 reads were filtered out during the traversal out of approximately 2175605 total reads (0.16%)
[2015-09-30T15:37Z] INFO  16:37:12,787 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:37Z] INFO  16:37:12,788 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:37Z] INFO  16:37:12,788 MicroScheduler -   -> 3546 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:37Z] INFO  16:37:13,829 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:37Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam
[2015-09-30T15:37Z] INFO  16:37:16,695 ProgressMeter -     17:67290630    200002.0    30.0 s       2.5 m       27.3%   110.0 s      80.0 s
[2015-09-30T15:37Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam 17:1-31039439
[2015-09-30T15:37Z] GATK: RealignerTargetCreator
[2015-09-30T15:37Z] INFO  16:37:21,022 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:37Z] INFO  16:37:21,024 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:37Z] INFO  16:37:21,025 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:37Z] INFO  16:37:21,025 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:37Z] INFO  16:37:21,028 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/tx/tmpPe3PmB/1_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign-realign.intervals -l INFO -L 17:1-31039439 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:37Z] INFO  16:37:21,035 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:37Z] INFO  16:37:21,035 HelpFormatter - Date/Time: 2015/09/30 16:37:21
[2015-09-30T15:37Z] INFO  16:37:21,035 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:37Z] INFO  16:37:21,035 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:37Z] INFO  16:37:21,099 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:37Z] INFO  16:37:21,214 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:37Z] INFO  16:37:21,223 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:37Z] INFO  16:37:21,240 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:37Z] INFO  16:37:22,164 IntervalUtils - Processing 31039439 bp from intervals
[2015-09-30T15:37Z] WARN  16:37:22,168 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:37Z] INFO  16:37:22,228 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:37Z] INFO  16:37:22,373 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:37Z] INFO  16:37:22,373 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:37Z] INFO  16:37:22,374 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:37Z] INFO  16:37:22,374 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:37Z] INFO  16:37:46,695 ProgressMeter -     17:73664886    500006.0    60.0 s     120.0 s       60.6%    98.0 s      38.0 s
[2015-09-30T15:37Z] INFO  16:37:49,094 ProgressMeter -     17:47866454   1500020.0     2.2 m      86.0 s       54.2%     4.0 m     109.0 s
[2015-09-30T15:37Z] INFO  16:37:52,377 ProgressMeter -     17:18405033   1.8399232E7    30.0 s       1.0 s       59.3%    50.0 s      20.0 s
[2015-09-30T15:38Z] INFO  16:38:06,990 ProgressMeter -            done   3.1039439E7    44.0 s       1.0 s      100.0%    44.0 s       0.0 s
[2015-09-30T15:38Z] INFO  16:38:06,991 ProgressMeter - Total runtime 44.62 secs, 0.74 min, 0.01 hours
[2015-09-30T15:38Z] INFO  16:38:06,994 MicroScheduler - 219891 reads were filtered out during the traversal out of approximately 2185502 total reads (10.06%)
[2015-09-30T15:38Z] INFO  16:38:06,995 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:38Z] INFO  16:38:06,995 MicroScheduler -   -> 19408 reads (0.89% of total) failing BadMateFilter
[2015-09-30T15:38Z] INFO  16:38:06,995 MicroScheduler -   -> 106820 reads (4.89% of total) failing DuplicateReadFilter
[2015-09-30T15:38Z] INFO  16:38:06,995 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:38Z] INFO  16:38:06,995 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:38Z] INFO  16:38:06,996 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:38Z] INFO  16:38:06,996 MicroScheduler -   -> 93663 reads (4.29% of total) failing MappingQualityZeroFilter
[2015-09-30T15:38Z] INFO  16:38:06,996 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:38Z] INFO  16:38:06,996 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:38Z] INFO  16:38:06,996 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:38Z] INFO  16:38:07,976 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:38Z] GATK: realign ('17', 0, 31039439) : syn3-normal
[2015-09-30T15:38Z] INFO  16:38:09,663 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:38Z] INFO  16:38:09,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:38Z] INFO  16:38:09,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:38Z] INFO  16:38:09,665 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:38Z] INFO  16:38:09,668 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign-realign.intervals -L 17:1-31039439 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/tx/tmpN8GeEc/1_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam
[2015-09-30T15:38Z] INFO  16:38:09,674 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:38Z] INFO  16:38:09,674 HelpFormatter - Date/Time: 2015/09/30 16:38:09
[2015-09-30T15:38Z] INFO  16:38:09,674 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:38Z] INFO  16:38:09,674 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:38Z] INFO  16:38:09,802 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:38Z] INFO  16:38:09,868 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:38Z] INFO  16:38:09,875 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:38Z] INFO  16:38:09,890 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:38Z] INFO  16:38:10,291 IntervalUtils - Processing 31039439 bp from intervals
[2015-09-30T15:38Z] WARN  16:38:10,295 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:38Z] INFO  16:38:10,347 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:38Z] INFO  16:38:10,482 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:38Z] INFO  16:38:10,483 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:38Z] INFO  16:38:10,483 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:38Z] INFO  16:38:10,484 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:38Z] INFO  16:38:10,636 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:38Z] INFO  16:38:10,814 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:38Z] INFO  16:38:16,696 ProgressMeter -     17:76430324    800010.0    90.0 s     112.0 s       75.1%   119.0 s      29.0 s
[2015-09-30T15:38Z] INFO  16:38:29,095 ProgressMeter -     17:59544865   2000026.0     2.8 m      85.0 s       91.8%     3.1 m      15.0 s
[2015-09-30T15:38Z] INFO  16:38:41,165 ProgressMeter -      17:5384206    500007.0    30.0 s      61.0 s       17.3%     2.9 m       2.4 m
[2015-09-30T15:38Z] INFO  16:38:42,826 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:38Z] INFO  16:38:43,044 ProgressMeter -            done   2230025.0     3.1 m      82.0 s      100.0%     3.1 m       0.0 s
[2015-09-30T15:38Z] INFO  16:38:43,045 ProgressMeter - Total runtime 183.99 secs, 3.07 min, 0.05 hours
[2015-09-30T15:38Z] INFO  16:38:43,045 MicroScheduler - 3356 reads were filtered out during the traversal out of approximately 2233381 total reads (0.15%)
[2015-09-30T15:38Z] INFO  16:38:43,046 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:38Z] INFO  16:38:43,046 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:38Z] INFO  16:38:43,046 MicroScheduler -   -> 3356 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:38Z] INFO  16:38:44,155 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:38Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam
[2015-09-30T15:38Z] INFO  16:38:46,717 ProgressMeter -     17:79497347   1100015.0   120.0 s     109.0 s       91.1%     2.2 m      11.0 s
[2015-09-30T15:38Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam 17:31047757-62076645
[2015-09-30T15:38Z] GATK: RealignerTargetCreator
[2015-09-30T15:38Z] INFO  16:38:51,352 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:38Z] INFO  16:38:51,354 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:38Z] INFO  16:38:51,354 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:38Z] INFO  16:38:51,354 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:38Z] INFO  16:38:51,357 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/tx/tmp_xfL4D/1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign-realign.intervals -l INFO -L 17:31047757-62076645 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:38Z] INFO  16:38:51,363 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:38Z] INFO  16:38:51,363 HelpFormatter - Date/Time: 2015/09/30 16:38:51
[2015-09-30T15:38Z] INFO  16:38:51,364 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:38Z] INFO  16:38:51,364 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:38Z] INFO  16:38:51,419 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:38Z] INFO  16:38:51,529 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:38Z] INFO  16:38:51,536 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:38Z] INFO  16:38:51,551 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:38Z] INFO  16:38:51,798 IntervalUtils - Processing 31028889 bp from intervals
[2015-09-30T15:38Z] WARN  16:38:51,802 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:38Z] INFO  16:38:52,012 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:38Z] INFO  16:38:52,152 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:38Z] INFO  16:38:52,152 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:38Z] INFO  16:38:52,153 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:38Z] INFO  16:38:52,153 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:39Z] INFO  16:39:09,116 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:39Z] INFO  16:39:09,297 ProgressMeter -            done   1415213.0     2.4 m     100.0 s       99.3%     2.4 m       1.0 s
[2015-09-30T15:39Z] INFO  16:39:09,297 ProgressMeter - Total runtime 142.62 secs, 2.38 min, 0.04 hours
[2015-09-30T15:39Z] INFO  16:39:09,298 MicroScheduler - 2149 reads were filtered out during the traversal out of approximately 1417362 total reads (0.15%)
[2015-09-30T15:39Z] INFO  16:39:09,298 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:39Z] INFO  16:39:09,298 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:39Z] INFO  16:39:09,298 MicroScheduler -   -> 2149 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:39Z] INFO  16:39:10,767 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:39Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam
[2015-09-30T15:39Z] INFO  16:39:12,168 ProgressMeter -     17:16893204   1200015.0    61.0 s      51.0 s       54.4%   112.0 s      51.0 s
[2015-09-30T15:39Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam 17:62078197-81195210
[2015-09-30T15:39Z] GATK: RealignerTargetCreator
[2015-09-30T15:39Z] INFO  16:39:16,033 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:16,035 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:39Z] INFO  16:39:16,036 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:39Z] INFO  16:39:16,036 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:39Z] INFO  16:39:16,039 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/tx/tmpqt057c/1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign-realign.intervals -l INFO -L 17:62078197-81195210 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:39Z] INFO  16:39:16,044 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:39Z] INFO  16:39:16,045 HelpFormatter - Date/Time: 2015/09/30 16:39:16
[2015-09-30T15:39Z] INFO  16:39:16,045 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:16,045 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:16,100 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:39Z] INFO  16:39:16,206 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:39Z] INFO  16:39:16,214 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:39Z] INFO  16:39:16,229 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:39Z] INFO  16:39:17,210 IntervalUtils - Processing 19117014 bp from intervals
[2015-09-30T15:39Z] WARN  16:39:17,214 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:39Z] INFO  16:39:17,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:39Z] INFO  16:39:17,859 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:39Z] INFO  16:39:17,859 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:39Z] INFO  16:39:17,859 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:39Z] INFO  16:39:17,860 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:39Z] INFO  16:39:22,155 ProgressMeter -     17:47548069   1.6498612E7    30.0 s       1.0 s       53.2%    56.0 s      26.0 s
[2015-09-30T15:39Z] INFO  16:39:39,014 ProgressMeter -            done   3.1028889E7    46.0 s       1.0 s      100.0%    46.0 s       0.0 s
[2015-09-30T15:39Z] INFO  16:39:39,015 ProgressMeter - Total runtime 46.86 secs, 0.78 min, 0.01 hours
[2015-09-30T15:39Z] INFO  16:39:39,015 MicroScheduler - 246891 reads were filtered out during the traversal out of approximately 2243976 total reads (11.00%)
[2015-09-30T15:39Z] INFO  16:39:39,016 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:39Z] INFO  16:39:39,016 MicroScheduler -   -> 20581 reads (0.92% of total) failing BadMateFilter
[2015-09-30T15:39Z] INFO  16:39:39,016 MicroScheduler -   -> 105861 reads (4.72% of total) failing DuplicateReadFilter
[2015-09-30T15:39Z] INFO  16:39:39,016 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:39Z] INFO  16:39:39,016 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:39Z] INFO  16:39:39,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:39Z] INFO  16:39:39,017 MicroScheduler -   -> 120449 reads (5.37% of total) failing MappingQualityZeroFilter
[2015-09-30T15:39Z] INFO  16:39:39,017 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:39Z] INFO  16:39:39,017 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:39Z] INFO  16:39:39,017 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:39Z] INFO  16:39:40,143 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:39Z] GATK: realign ('17', 31047756, 62076645) : syn3-normal
[2015-09-30T15:39Z] INFO  16:39:42,169 ProgressMeter -     17:27959621   1900024.0    91.0 s      48.0 s       90.1%   101.0 s      10.0 s
[2015-09-30T15:39Z] INFO  16:39:43,175 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:43,177 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:39Z] INFO  16:39:43,177 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:39Z] INFO  16:39:43,177 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:39Z] INFO  16:39:43,180 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign-realign.intervals -L 17:31047757-62076645 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/tx/tmp_iTfER/1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam
[2015-09-30T15:39Z] INFO  16:39:43,185 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:39Z] INFO  16:39:43,186 HelpFormatter - Date/Time: 2015/09/30 16:39:43
[2015-09-30T15:39Z] INFO  16:39:43,186 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:43,186 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:43,302 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:39Z] INFO  16:39:43,363 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:39Z] INFO  16:39:43,369 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:39Z] INFO  16:39:43,385 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:39Z] INFO  16:39:43,607 IntervalUtils - Processing 31028889 bp from intervals
[2015-09-30T15:39Z] WARN  16:39:43,611 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:39Z] INFO  16:39:43,664 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:39Z] INFO  16:39:43,807 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:39Z] INFO  16:39:43,808 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:39Z] INFO  16:39:43,808 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:39Z] INFO  16:39:43,808 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:39Z] INFO  16:39:43,948 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:39Z] INFO  16:39:44,129 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:39Z] INFO  16:39:47,303 ProgressMeter -            done   1.9117014E7    29.0 s       1.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T15:39Z] INFO  16:39:47,304 ProgressMeter - Total runtime 29.44 secs, 0.49 min, 0.01 hours
[2015-09-30T15:39Z] INFO  16:39:47,307 MicroScheduler - 115400 reads were filtered out during the traversal out of approximately 1422937 total reads (8.11%)
[2015-09-30T15:39Z] INFO  16:39:47,307 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:39Z] INFO  16:39:47,307 MicroScheduler -   -> 12785 reads (0.90% of total) failing BadMateFilter
[2015-09-30T15:39Z] INFO  16:39:47,307 MicroScheduler -   -> 73554 reads (5.17% of total) failing DuplicateReadFilter
[2015-09-30T15:39Z] INFO  16:39:47,308 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:39Z] INFO  16:39:47,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:39Z] INFO  16:39:47,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:39Z] INFO  16:39:47,308 MicroScheduler -   -> 29061 reads (2.04% of total) failing MappingQualityZeroFilter
[2015-09-30T15:39Z] INFO  16:39:47,308 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:39Z] INFO  16:39:47,309 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:39Z] INFO  16:39:47,309 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:39Z] INFO  16:39:48,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:39Z] GATK: realign ('17', 62078196, 81195210) : syn3-normal
[2015-09-30T15:39Z] INFO  16:39:48,570 ProgressMeter -            done   2172059.0    98.0 s      45.0 s      100.0%    98.0 s       0.0 s
[2015-09-30T15:39Z] INFO  16:39:48,571 ProgressMeter - Total runtime 98.09 secs, 1.63 min, 0.03 hours
[2015-09-30T15:39Z] INFO  16:39:48,574 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2172059 total reads (0.00%)
[2015-09-30T15:39Z] INFO  16:39:48,574 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:39Z] INFO  16:39:48,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:39Z] INFO  16:39:48,575 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:39Z] INFO  16:39:49,748 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:39Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam
[2015-09-30T15:39Z] INFO  16:39:50,046 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:50,048 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:39Z] INFO  16:39:50,048 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:39Z] INFO  16:39:50,048 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:39Z] INFO  16:39:50,052 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign-realign.intervals -L 17:62078197-81195210 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/tx/tmpo9dxYP/1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam
[2015-09-30T15:39Z] INFO  16:39:50,057 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:39Z] INFO  16:39:50,057 HelpFormatter - Date/Time: 2015/09/30 16:39:50
[2015-09-30T15:39Z] INFO  16:39:50,058 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:50,058 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:50,162 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:39Z] INFO  16:39:50,245 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:39Z] INFO  16:39:50,252 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:39Z] INFO  16:39:50,268 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:39Z] INFO  16:39:51,399 IntervalUtils - Processing 19117014 bp from intervals
[2015-09-30T15:39Z] WARN  16:39:51,403 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:39Z] INFO  16:39:51,456 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:39Z] INFO  16:39:51,584 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:39Z] INFO  16:39:51,585 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:39Z] INFO  16:39:51,585 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:39Z] INFO  16:39:51,586 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:39Z] INFO  16:39:51,741 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:39Z] INFO  16:39:51,872 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:39Z] GATK pre-alignment ('18', 0, 31142016) : syn3-normal
[2015-09-30T15:39Z] INFO  16:39:58,844 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:58,846 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:39Z] INFO  16:39:58,846 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:39Z] INFO  16:39:58,846 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:39Z] INFO  16:39:58,850 HelpFormatter - Program Args: -T PrintReads -L 18:1-31142016 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/tx/tmporbkOR/1_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam
[2015-09-30T15:39Z] INFO  16:39:58,855 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:39Z] INFO  16:39:58,855 HelpFormatter - Date/Time: 2015/09/30 16:39:58
[2015-09-30T15:39Z] INFO  16:39:58,856 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:58,856 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:39Z] INFO  16:39:58,957 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:40Z] INFO  16:40:00,318 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:40Z] INFO  16:40:00,367 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:40Z] INFO  16:40:00,375 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:40Z] INFO  16:40:00,389 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:40Z] INFO  16:40:00,402 IntervalUtils - Processing 31142016 bp from intervals
[2015-09-30T15:40Z] INFO  16:40:00,461 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:40Z] INFO  16:40:00,709 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:40Z] INFO  16:40:00,709 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:40Z] INFO  16:40:00,710 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:40Z] INFO  16:40:00,710 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:40Z] INFO  16:40:00,722 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:40Z] INFO  16:40:00,932 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:40Z] INFO  16:40:13,811 ProgressMeter -     17:38172748    400004.0    30.0 s      75.0 s       23.0%     2.2 m     100.0 s
[2015-09-30T15:40Z] INFO  16:40:21,588 ProgressMeter -     17:73485265    400004.0    30.0 s      75.0 s       59.7%    50.0 s      20.0 s
[2015-09-30T15:40Z] INFO  16:40:30,717 ProgressMeter -     18:12699147    300004.0    30.0 s     100.0 s       40.8%    73.0 s      43.0 s
[2015-09-30T15:40Z] INFO  16:40:45,192 ProgressMeter -     17:42430332   1000013.0    61.0 s      61.0 s       36.7%     2.8 m     105.0 s
[2015-09-30T15:40Z] INFO  16:40:51,589 ProgressMeter -     17:79663553   1200016.0    60.0 s      50.0 s       92.0%    65.0 s       5.0 s
[2015-09-30T15:40Z] INFO  16:40:57,116 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@627346b4
[2015-09-30T15:40Z] INFO  16:40:57,337 ProgressMeter -            done    643735.0    56.0 s      87.0 s      100.0%    56.0 s       0.0 s
[2015-09-30T15:40Z] INFO  16:40:57,337 ProgressMeter - Total runtime 56.63 secs, 0.94 min, 0.02 hours
[2015-09-30T15:40Z] INFO  16:40:57,337 MicroScheduler - 1632 reads were filtered out during the traversal out of approximately 645367 total reads (0.25%)
[2015-09-30T15:40Z] INFO  16:40:57,338 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:40Z] INFO  16:40:57,338 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:40Z] INFO  16:40:57,338 MicroScheduler -   -> 1632 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:40Z] INFO  16:40:58,400 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:40Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam
[2015-09-30T15:41Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam 18:1-31142016
[2015-09-30T15:41Z] GATK: RealignerTargetCreator
[2015-09-30T15:41Z] INFO  16:41:00,953 ProgressMeter -            done   1415213.0    69.0 s      49.0 s       99.3%    69.0 s       0.0 s
[2015-09-30T15:41Z] INFO  16:41:00,954 ProgressMeter - Total runtime 69.37 secs, 1.16 min, 0.02 hours
[2015-09-30T15:41Z] INFO  16:41:00,957 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1415213 total reads (0.00%)
[2015-09-30T15:41Z] INFO  16:41:00,957 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:41Z] INFO  16:41:00,957 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:41Z] INFO  16:41:00,958 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:41Z] INFO  16:41:02,132 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:41Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam
[2015-09-30T15:41Z] INFO  16:41:03,119 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:03,121 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:41Z] INFO  16:41:03,121 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:41Z] INFO  16:41:03,121 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:41Z] INFO  16:41:03,124 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/tx/tmpIRUfZY/1_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign-realign.intervals -l INFO -L 18:1-31142016 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:41Z] INFO  16:41:03,130 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:41Z] INFO  16:41:03,130 HelpFormatter - Date/Time: 2015/09/30 16:41:03
[2015-09-30T15:41Z] INFO  16:41:03,130 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:03,130 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:03,188 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:41Z] INFO  16:41:03,325 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:41Z] INFO  16:41:03,343 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:41Z] INFO  16:41:03,483 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
[2015-09-30T15:41Z] INFO  16:41:03,992 IntervalUtils - Processing 31142016 bp from intervals
[2015-09-30T15:41Z] WARN  16:41:03,996 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:41Z] INFO  16:41:04,090 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:41Z] INFO  16:41:04,548 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:41Z] INFO  16:41:04,548 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:41Z] INFO  16:41:04,549 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:41Z] INFO  16:41:04,551 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:41Z] GATK pre-alignment ('18', 31158315, 63430522) : syn3-normal
[2015-09-30T15:41Z] INFO  16:41:07,564 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:07,566 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:41Z] INFO  16:41:07,567 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:41Z] INFO  16:41:07,567 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:41Z] INFO  16:41:07,570 HelpFormatter - Program Args: -T PrintReads -L 18:31158316-63430522 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/tx/tmpzrZ8VF/1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam
[2015-09-30T15:41Z] INFO  16:41:07,576 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:41Z] INFO  16:41:07,576 HelpFormatter - Date/Time: 2015/09/30 16:41:07
[2015-09-30T15:41Z] INFO  16:41:07,576 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:07,576 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:08,596 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:41Z] INFO  16:41:09,296 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:41Z] INFO  16:41:09,348 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:41Z] INFO  16:41:09,356 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:41Z] INFO  16:41:09,372 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:41Z] INFO  16:41:09,385 IntervalUtils - Processing 32272207 bp from intervals
[2015-09-30T15:41Z] INFO  16:41:09,445 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:41Z] INFO  16:41:09,942 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:41Z] INFO  16:41:09,942 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:41Z] INFO  16:41:09,943 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:41Z] INFO  16:41:09,943 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:41Z] INFO  16:41:09,953 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:41Z] INFO  16:41:10,149 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:41Z] INFO  16:41:16,538 ProgressMeter -     17:56619465   1800023.0    92.0 s      51.0 s       82.4%   111.0 s      19.0 s
[2015-09-30T15:41Z] INFO  16:41:29,872 ProgressMeter -            done   2230025.0   106.0 s      47.0 s      100.0%   106.0 s       0.0 s
[2015-09-30T15:41Z] INFO  16:41:29,873 ProgressMeter - Total runtime 106.07 secs, 1.77 min, 0.03 hours
[2015-09-30T15:41Z] INFO  16:41:29,876 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2230025 total reads (0.00%)
[2015-09-30T15:41Z] INFO  16:41:29,877 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:41Z] INFO  16:41:29,877 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:41Z] INFO  16:41:29,877 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:41Z] INFO  16:41:31,011 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:41Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam
[2015-09-30T15:41Z] INFO  16:41:32,483 ProgressMeter -            done   3.1142016E7    27.0 s       0.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T15:41Z] INFO  16:41:32,483 ProgressMeter - Total runtime 27.94 secs, 0.47 min, 0.01 hours
[2015-09-30T15:41Z] INFO  16:41:32,486 MicroScheduler - 53102 reads were filtered out during the traversal out of approximately 646921 total reads (8.21%)
[2015-09-30T15:41Z] INFO  16:41:32,487 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:41Z] INFO  16:41:32,487 MicroScheduler -   -> 9852 reads (1.52% of total) failing BadMateFilter
[2015-09-30T15:41Z] INFO  16:41:32,487 MicroScheduler -   -> 26976 reads (4.17% of total) failing DuplicateReadFilter
[2015-09-30T15:41Z] INFO  16:41:32,487 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:41Z] INFO  16:41:32,488 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:41Z] INFO  16:41:32,488 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:41Z] INFO  16:41:32,488 MicroScheduler -   -> 16274 reads (2.52% of total) failing MappingQualityZeroFilter
[2015-09-30T15:41Z] INFO  16:41:32,488 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:41Z] INFO  16:41:32,488 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:41Z] INFO  16:41:32,489 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:41Z] INFO  16:41:33,470 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:41Z] GATK: realign ('18', 0, 31142016) : syn3-normal
[2015-09-30T15:41Z] GATK pre-alignment ('18', 63476668, 78077248) : syn3-normal
[2015-09-30T15:41Z] INFO  16:41:37,720 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:37,722 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:41Z] INFO  16:41:37,722 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:41Z] INFO  16:41:37,722 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:41Z] INFO  16:41:37,726 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign-realign.intervals -L 18:1-31142016 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/tx/tmpLju1Jx/1_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam
[2015-09-30T15:41Z] INFO  16:41:37,731 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:41Z] INFO  16:41:37,732 HelpFormatter - Date/Time: 2015/09/30 16:41:37
[2015-09-30T15:41Z] INFO  16:41:37,732 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:37,732 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:38,586 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:41Z] INFO  16:41:38,651 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:41Z] INFO  16:41:38,658 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:41Z] INFO  16:41:38,675 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:41Z] INFO  16:41:39,383 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:39,386 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:41Z] INFO  16:41:39,386 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:41Z] INFO  16:41:39,386 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:41Z] INFO  16:41:39,390 HelpFormatter - Program Args: -T PrintReads -L 18:63476669-78077248 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/tx/tmpzJoO8X/1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam
[2015-09-30T15:41Z] INFO  16:41:39,395 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:41Z] INFO  16:41:39,395 HelpFormatter - Date/Time: 2015/09/30 16:41:39
[2015-09-30T15:41Z] INFO  16:41:39,396 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:39,396 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:41Z] INFO  16:41:39,503 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:41Z] INFO  16:41:39,970 ProgressMeter -     18:44548816    200002.0    30.0 s       2.5 m       41.5%    72.0 s      42.0 s
[2015-09-30T15:41Z] INFO  16:41:40,219 IntervalUtils - Processing 31142016 bp from intervals
[2015-09-30T15:41Z] WARN  16:41:40,223 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:41Z] INFO  16:41:40,282 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:41Z] INFO  16:41:40,282 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:41Z] INFO  16:41:40,333 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:41Z] INFO  16:41:40,341 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:41Z] INFO  16:41:40,356 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:41Z] INFO  16:41:40,370 IntervalUtils - Processing 14600580 bp from intervals
[2015-09-30T15:41Z] INFO  16:41:40,417 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:41Z] INFO  16:41:40,418 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:41Z] INFO  16:41:40,418 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:41Z] INFO  16:41:40,419 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:41Z] INFO  16:41:40,430 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:41Z] INFO  16:41:40,561 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:41Z] INFO  16:41:40,582 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:41Z] INFO  16:41:40,583 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:41Z] INFO  16:41:40,583 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:41Z] INFO  16:41:40,583 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:41Z] INFO  16:41:40,594 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:41Z] INFO  16:41:40,698 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:41Z] INFO  16:41:40,750 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:42Z] INFO  16:42:02,296 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:42Z] INFO  16:42:02,402 ProgressMeter -            done    168759.0    21.0 s       2.2 m       99.5%    21.0 s       0.0 s
[2015-09-30T15:42Z] INFO  16:42:02,402 ProgressMeter - Total runtime 21.82 secs, 0.36 min, 0.01 hours
[2015-09-30T15:42Z] INFO  16:42:02,403 MicroScheduler - 465 reads were filtered out during the traversal out of approximately 169224 total reads (0.27%)
[2015-09-30T15:42Z] INFO  16:42:02,403 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:42Z] INFO  16:42:02,403 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:42Z] INFO  16:42:02,403 MicroScheduler -   -> 465 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:42Z] INFO  16:42:03,481 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:42Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam
[2015-09-30T15:42Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam 18:63476669-78077248
[2015-09-30T15:42Z] GATK: RealignerTargetCreator
[2015-09-30T15:42Z] INFO  16:42:06,182 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:06,184 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:42Z] INFO  16:42:06,184 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:42Z] INFO  16:42:06,184 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:42Z] INFO  16:42:06,188 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/tx/tmpnilJUB/1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign-realign.intervals -l INFO -L 18:63476669-78077248 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:42Z] INFO  16:42:06,193 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:42Z] INFO  16:42:06,193 HelpFormatter - Date/Time: 2015/09/30 16:42:06
[2015-09-30T15:42Z] INFO  16:42:06,194 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:06,194 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:06,248 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:42Z] INFO  16:42:06,350 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:42Z] INFO  16:42:06,358 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:42Z] INFO  16:42:06,373 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:42Z] INFO  16:42:06,611 IntervalUtils - Processing 14600580 bp from intervals
[2015-09-30T15:42Z] WARN  16:42:06,614 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:42Z] INFO  16:42:06,668 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:42Z] INFO  16:42:07,718 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:42Z] INFO  16:42:07,718 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:42Z] INFO  16:42:07,718 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:42Z] INFO  16:42:07,719 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:42Z] INFO  16:42:09,970 ProgressMeter -     18:60806436    500011.0    60.0 s     120.0 s       91.9%    65.0 s       5.0 s
[2015-09-30T15:42Z] INFO  16:42:11,601 ProgressMeter -     18:21501869    400005.0    31.0 s      77.0 s       69.0%    44.0 s      13.0 s
[2015-09-30T15:42Z] INFO  16:42:13,571 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:42Z] INFO  16:42:13,944 ProgressMeter -            done    591700.0    64.0 s     108.0 s       99.9%    64.0 s       0.0 s
[2015-09-30T15:42Z] INFO  16:42:13,944 ProgressMeter - Total runtime 64.00 secs, 1.07 min, 0.02 hours
[2015-09-30T15:42Z] INFO  16:42:13,945 MicroScheduler - 1619 reads were filtered out during the traversal out of approximately 593319 total reads (0.27%)
[2015-09-30T15:42Z] INFO  16:42:13,945 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:42Z] INFO  16:42:13,945 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:42Z] INFO  16:42:13,945 MicroScheduler -   -> 1619 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:42Z] INFO  16:42:14,996 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:42Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam
[2015-09-30T15:42Z] INFO  16:42:16,585 ProgressMeter -            done    643735.0    36.0 s      56.0 s      100.0%    36.0 s       0.0 s
[2015-09-30T15:42Z] INFO  16:42:16,586 ProgressMeter - Total runtime 36.17 secs, 0.60 min, 0.01 hours
[2015-09-30T15:42Z] INFO  16:42:16,589 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 643735 total reads (0.00%)
[2015-09-30T15:42Z] INFO  16:42:16,589 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:42Z] INFO  16:42:16,590 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:42Z] INFO  16:42:16,590 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:42Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam 18:31158316-63430522
[2015-09-30T15:42Z] GATK: RealignerTargetCreator
[2015-09-30T15:42Z] INFO  16:42:17,642 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:42Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam
[2015-09-30T15:42Z] INFO  16:42:18,050 ProgressMeter -            done   1.460058E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2015-09-30T15:42Z] INFO  16:42:18,051 ProgressMeter - Total runtime 10.33 secs, 0.17 min, 0.00 hours
[2015-09-30T15:42Z] INFO  16:42:18,054 MicroScheduler - 14189 reads were filtered out during the traversal out of approximately 169547 total reads (8.37%)
[2015-09-30T15:42Z] INFO  16:42:18,054 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:42Z] INFO  16:42:18,055 MicroScheduler -   -> 3308 reads (1.95% of total) failing BadMateFilter
[2015-09-30T15:42Z] INFO  16:42:18,055 MicroScheduler -   -> 7583 reads (4.47% of total) failing DuplicateReadFilter
[2015-09-30T15:42Z] INFO  16:42:18,055 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:42Z] INFO  16:42:18,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:42Z] INFO  16:42:18,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:42Z] INFO  16:42:18,056 MicroScheduler -   -> 3298 reads (1.95% of total) failing MappingQualityZeroFilter
[2015-09-30T15:42Z] INFO  16:42:18,056 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:42Z] INFO  16:42:18,057 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:42Z] INFO  16:42:18,057 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:42Z] INFO  16:42:18,925 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:18,927 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:42Z] INFO  16:42:18,927 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:42Z] INFO  16:42:18,927 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:42Z] INFO  16:42:18,930 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/tx/tmp7Xfu08/1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign-realign.intervals -l INFO -L 18:31158316-63430522 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:42Z] INFO  16:42:18,936 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:42Z] INFO  16:42:18,936 HelpFormatter - Date/Time: 2015/09/30 16:42:18
[2015-09-30T15:42Z] INFO  16:42:18,936 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:18,936 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:18,992 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:42Z] INFO  16:42:19,002 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:42Z] GATK: realign ('18', 63476668, 78077248) : syn3-normal
[2015-09-30T15:42Z] INFO  16:42:19,103 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:42Z] INFO  16:42:19,112 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:42Z] INFO  16:42:19,155 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T15:42Z] INFO  16:42:19,400 IntervalUtils - Processing 32272207 bp from intervals
[2015-09-30T15:42Z] WARN  16:42:19,404 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:42Z] GATK pre-alignment ('19', 0, 31026185) : syn3-normal
[2015-09-30T15:42Z] INFO  16:42:19,480 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:42Z] INFO  16:42:19,627 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:42Z] INFO  16:42:19,628 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:42Z] INFO  16:42:19,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:42Z] INFO  16:42:19,628 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:42Z] INFO  16:42:23,662 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:23,664 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:42Z] INFO  16:42:23,664 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:42Z] INFO  16:42:23,664 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:42Z] INFO  16:42:23,668 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign-realign.intervals -L 18:63476669-78077248 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/tx/tmpCMqC7c/1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam
[2015-09-30T15:42Z] INFO  16:42:23,673 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:42Z] INFO  16:42:23,673 HelpFormatter - Date/Time: 2015/09/30 16:42:23
[2015-09-30T15:42Z] INFO  16:42:23,673 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:23,673 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:24,600 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:24,602 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:42Z] INFO  16:42:24,602 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:42Z] INFO  16:42:24,602 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:42Z] INFO  16:42:24,606 HelpFormatter - Program Args: -T PrintReads -L 19:1-31026185 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/tx/tmpjt4cVP/1_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam
[2015-09-30T15:42Z] INFO  16:42:24,611 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:42Z] INFO  16:42:24,611 HelpFormatter - Date/Time: 2015/09/30 16:42:24
[2015-09-30T15:42Z] INFO  16:42:24,611 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:24,612 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:24,716 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:42Z] INFO  16:42:24,723 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:42Z] INFO  16:42:24,786 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:42Z] INFO  16:42:24,793 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:42Z] INFO  16:42:24,809 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:42Z] INFO  16:42:25,972 IntervalUtils - Processing 14600580 bp from intervals
[2015-09-30T15:42Z] WARN  16:42:25,976 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:42Z] INFO  16:42:26,031 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:42Z] INFO  16:42:26,106 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:42Z] INFO  16:42:26,107 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:42Z] INFO  16:42:26,107 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:42Z] INFO  16:42:26,107 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:42Z] INFO  16:42:26,221 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:42Z] INFO  16:42:26,310 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:42Z] INFO  16:42:26,322 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:42Z] INFO  16:42:26,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:42Z] INFO  16:42:26,367 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:42Z] INFO  16:42:26,381 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:42Z] INFO  16:42:26,394 IntervalUtils - Processing 31026185 bp from intervals
[2015-09-30T15:42Z] INFO  16:42:26,450 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:42Z] INFO  16:42:26,654 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:42Z] INFO  16:42:26,654 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:42Z] INFO  16:42:26,655 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:42Z] INFO  16:42:26,655 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:42Z] INFO  16:42:26,666 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:42Z] INFO  16:42:26,877 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:42Z] INFO  16:42:37,764 ProgressMeter -            done    168759.0    11.0 s      69.0 s       99.5%    11.0 s       0.0 s
[2015-09-30T15:42Z] INFO  16:42:37,765 ProgressMeter - Total runtime 11.66 secs, 0.19 min, 0.00 hours
[2015-09-30T15:42Z] INFO  16:42:37,768 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 168759 total reads (0.00%)
[2015-09-30T15:42Z] INFO  16:42:37,768 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:42Z] INFO  16:42:37,768 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:42Z] INFO  16:42:37,768 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:42Z] INFO  16:42:38,933 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:42Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam
[2015-09-30T15:42Z] GATK pre-alignment ('19', 31038548, 59128983) : syn3-normal
[2015-09-30T15:42Z] INFO  16:42:41,729 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:41,731 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:42Z] INFO  16:42:41,731 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:42Z] INFO  16:42:41,731 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:42Z] INFO  16:42:41,735 HelpFormatter - Program Args: -T PrintReads -L 19:31038549-59128983 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/tx/tmpvjtY54/1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam
[2015-09-30T15:42Z] INFO  16:42:41,740 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:42Z] INFO  16:42:41,741 HelpFormatter - Date/Time: 2015/09/30 16:42:41
[2015-09-30T15:42Z] INFO  16:42:41,741 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:41,741 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:41,854 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:42Z] INFO  16:42:43,526 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:42Z] INFO  16:42:43,577 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:42Z] INFO  16:42:43,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:42Z] INFO  16:42:43,599 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:42Z] INFO  16:42:43,613 IntervalUtils - Processing 28090435 bp from intervals
[2015-09-30T15:42Z] INFO  16:42:43,671 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:42Z] INFO  16:42:43,901 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:42Z] INFO  16:42:43,901 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:42Z] INFO  16:42:43,902 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:42Z] INFO  16:42:43,902 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:42Z] INFO  16:42:43,914 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:42Z] INFO  16:42:44,104 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:42Z] INFO  16:42:44,919 ProgressMeter -            done   3.2272207E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T15:42Z] INFO  16:42:44,920 ProgressMeter - Total runtime 25.29 secs, 0.42 min, 0.01 hours
[2015-09-30T15:42Z] INFO  16:42:44,922 MicroScheduler - 65741 reads were filtered out during the traversal out of approximately 595518 total reads (11.04%)
[2015-09-30T15:42Z] INFO  16:42:44,923 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:42Z] INFO  16:42:44,923 MicroScheduler -   -> 9087 reads (1.53% of total) failing BadMateFilter
[2015-09-30T15:42Z] INFO  16:42:44,923 MicroScheduler -   -> 24713 reads (4.15% of total) failing DuplicateReadFilter
[2015-09-30T15:42Z] INFO  16:42:44,924 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:42Z] INFO  16:42:44,924 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:42Z] INFO  16:42:44,924 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:42Z] INFO  16:42:44,924 MicroScheduler -   -> 31941 reads (5.36% of total) failing MappingQualityZeroFilter
[2015-09-30T15:42Z] INFO  16:42:44,924 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:42Z] INFO  16:42:44,925 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:42Z] INFO  16:42:44,925 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:42Z] INFO  16:42:45,953 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:42Z] GATK: realign ('18', 31158315, 63430522) : syn3-normal
[2015-09-30T15:42Z] INFO  16:42:48,026 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:48,028 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:42Z] INFO  16:42:48,029 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:42Z] INFO  16:42:48,029 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:42Z] INFO  16:42:48,032 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign-realign.intervals -L 18:31158316-63430522 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/tx/tmpCz0Rsn/1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam
[2015-09-30T15:42Z] INFO  16:42:48,038 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:42Z] INFO  16:42:48,038 HelpFormatter - Date/Time: 2015/09/30 16:42:48
[2015-09-30T15:42Z] INFO  16:42:48,038 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:48,039 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:42Z] INFO  16:42:48,161 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:42Z] INFO  16:42:48,224 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:42Z] INFO  16:42:48,231 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:42Z] INFO  16:42:48,247 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:42Z] INFO  16:42:48,479 IntervalUtils - Processing 32272207 bp from intervals
[2015-09-30T15:42Z] WARN  16:42:48,483 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:42Z] INFO  16:42:48,539 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:42Z] INFO  16:42:49,889 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:42Z] INFO  16:42:49,890 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:42Z] INFO  16:42:49,890 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:42Z] INFO  16:42:49,890 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:42Z] INFO  16:42:50,034 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:42Z] INFO  16:42:50,224 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:42Z] INFO  16:42:56,684 ProgressMeter -      19:1577933    200002.0    30.0 s       2.5 m        5.1%     9.8 m       9.3 m
[2015-09-30T15:43Z] INFO  16:43:14,102 ProgressMeter -     19:36120520    200002.0    30.0 s       2.5 m       18.1%     2.8 m       2.3 m
[2015-09-30T15:43Z] INFO  16:43:20,026 ProgressMeter -            done    591700.0    30.0 s      50.0 s       99.9%    30.0 s       0.0 s
[2015-09-30T15:43Z] INFO  16:43:20,027 ProgressMeter - Total runtime 30.14 secs, 0.50 min, 0.01 hours
[2015-09-30T15:43Z] INFO  16:43:20,030 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 591700 total reads (0.00%)
[2015-09-30T15:43Z] INFO  16:43:20,030 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:43Z] INFO  16:43:20,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:43Z] INFO  16:43:20,030 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:43Z] INFO  16:43:21,212 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:43Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam
[2015-09-30T15:43Z] GATK pre-alignment ('20', 0, 31018105) : syn3-normal
[2015-09-30T15:43Z] INFO  16:43:25,082 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:43Z] INFO  16:43:25,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:43Z] INFO  16:43:25,085 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:43Z] INFO  16:43:25,085 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:43Z] INFO  16:43:25,088 HelpFormatter - Program Args: -T PrintReads -L 20:1-31018105 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/tx/tmpX1vwUk/1_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam
[2015-09-30T15:43Z] INFO  16:43:25,094 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:43Z] INFO  16:43:25,094 HelpFormatter - Date/Time: 2015/09/30 16:43:25
[2015-09-30T15:43Z] INFO  16:43:25,094 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:43Z] INFO  16:43:25,095 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:43Z] INFO  16:43:26,106 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:43Z] INFO  16:43:26,685 ProgressMeter -      19:4304762    600006.0    60.0 s     100.0 s       13.9%     7.2 m       6.2 m
[2015-09-30T15:43Z] INFO  16:43:26,778 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:43Z] INFO  16:43:26,826 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:43Z] INFO  16:43:26,833 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:43Z] INFO  16:43:26,847 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:43Z] INFO  16:43:26,860 IntervalUtils - Processing 31018105 bp from intervals
[2015-09-30T15:43Z] INFO  16:43:26,915 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:43Z] INFO  16:43:27,109 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:43Z] INFO  16:43:27,109 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:43Z] INFO  16:43:27,110 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:43Z] INFO  16:43:27,110 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:43Z] INFO  16:43:27,120 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:43Z] INFO  16:43:27,307 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:43Z] INFO  16:43:44,684 ProgressMeter -     19:39183024    500005.0    60.0 s       2.0 m       29.0%     3.4 m       2.4 m
[2015-09-30T15:43Z] INFO  16:43:56,691 ProgressMeter -      19:7523576   1000052.0    90.0 s      90.0 s       24.2%     6.2 m       4.7 m
[2015-09-30T15:43Z] INFO  16:43:57,141 ProgressMeter -      20:3672144    200005.0    30.0 s       2.5 m       11.8%     4.2 m       3.7 m
[2015-09-30T15:44Z] INFO  16:44:15,800 ProgressMeter -     19:41532524    900010.0    91.0 s     102.0 s       37.4%     4.1 m       2.5 m
[2015-09-30T15:44Z] INFO  16:44:27,045 ProgressMeter -     19:10464148   1300056.0   120.0 s      92.0 s       33.7%     5.9 m       3.9 m
[2015-09-30T15:44Z] INFO  16:44:27,141 ProgressMeter -     20:18436494    500008.0    60.0 s     120.0 s       59.4%   100.0 s      40.0 s
[2015-09-30T15:44Z] INFO  16:44:45,834 ProgressMeter -     19:44660652   1200013.0     2.0 m     101.0 s       48.5%     4.2 m       2.1 m
[2015-09-30T15:44Z] INFO  16:44:57,063 ProgressMeter -     19:13373740   1700060.0     2.5 m      88.0 s       43.1%     5.8 m       3.3 m
[2015-09-30T15:44Z] INFO  16:44:57,142 ProgressMeter -     20:30534701    800011.0    90.0 s     112.0 s       98.4%    91.0 s       1.0 s
[2015-09-30T15:45Z] INFO  16:45:01,016 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:45Z] INFO  16:45:01,158 ProgressMeter -            done    901763.0    94.0 s     104.0 s      100.0%    94.0 s       0.0 s
[2015-09-30T15:45Z] INFO  16:45:01,159 ProgressMeter - Total runtime 94.05 secs, 1.57 min, 0.03 hours
[2015-09-30T15:45Z] INFO  16:45:01,159 MicroScheduler - 1987 reads were filtered out during the traversal out of approximately 903750 total reads (0.22%)
[2015-09-30T15:45Z] INFO  16:45:01,159 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:45Z] INFO  16:45:01,159 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:45Z] INFO  16:45:01,159 MicroScheduler -   -> 1987 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:45Z] INFO  16:45:02,208 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:45Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam
[2015-09-30T15:45Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam 20:1-31018105
[2015-09-30T15:45Z] GATK: RealignerTargetCreator
[2015-09-30T15:45Z] INFO  16:45:06,963 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:45Z] INFO  16:45:06,966 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:45Z] INFO  16:45:06,966 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:45Z] INFO  16:45:06,966 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:45Z] INFO  16:45:06,969 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/tx/tmpxJozMy/1_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign-realign.intervals -l INFO -L 20:1-31018105 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:45Z] INFO  16:45:06,976 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:45Z] INFO  16:45:06,976 HelpFormatter - Date/Time: 2015/09/30 16:45:06
[2015-09-30T15:45Z] INFO  16:45:06,976 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:45Z] INFO  16:45:06,977 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:45Z] INFO  16:45:07,335 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:45Z] INFO  16:45:07,449 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:45Z] INFO  16:45:07,457 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:45Z] INFO  16:45:07,473 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:45Z] INFO  16:45:07,727 IntervalUtils - Processing 31018105 bp from intervals
[2015-09-30T15:45Z] WARN  16:45:07,731 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:45Z] INFO  16:45:07,788 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:45Z] INFO  16:45:07,919 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:45Z] INFO  16:45:07,920 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:45Z] INFO  16:45:07,920 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:45Z] INFO  16:45:07,920 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:45Z] INFO  16:45:15,835 ProgressMeter -     19:47588266   1500016.0     2.5 m     101.0 s       58.9%     4.3 m     105.0 s
[2015-09-30T15:45Z] INFO  16:45:27,064 ProgressMeter -     19:16910347   2100065.0     3.0 m      85.0 s       54.5%     5.5 m       2.5 m
[2015-09-30T15:45Z] INFO  16:45:35,456 ProgressMeter -            done   3.1018105E7    27.0 s       0.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T15:45Z] INFO  16:45:35,457 ProgressMeter - Total runtime 27.54 secs, 0.46 min, 0.01 hours
[2015-09-30T15:45Z] INFO  16:45:35,460 MicroScheduler - 76734 reads were filtered out during the traversal out of approximately 906898 total reads (8.46%)
[2015-09-30T15:45Z] INFO  16:45:35,460 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:45Z] INFO  16:45:35,460 MicroScheduler -   -> 11244 reads (1.24% of total) failing BadMateFilter
[2015-09-30T15:45Z] INFO  16:45:35,460 MicroScheduler -   -> 43046 reads (4.75% of total) failing DuplicateReadFilter
[2015-09-30T15:45Z] INFO  16:45:35,461 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:45Z] INFO  16:45:35,461 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:45Z] INFO  16:45:35,461 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:45Z] INFO  16:45:35,461 MicroScheduler -   -> 22444 reads (2.47% of total) failing MappingQualityZeroFilter
[2015-09-30T15:45Z] INFO  16:45:35,462 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:45Z] INFO  16:45:35,462 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:45Z] INFO  16:45:35,462 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:45Z] INFO  16:45:36,460 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:45Z] GATK: realign ('20', 0, 31018105) : syn3-normal
[2015-09-30T15:45Z] INFO  16:45:39,761 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:45Z] INFO  16:45:39,763 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:45Z] INFO  16:45:39,763 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:45Z] INFO  16:45:39,763 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:45Z] INFO  16:45:39,767 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign-realign.intervals -L 20:1-31018105 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/tx/tmpDaqch3/1_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam
[2015-09-30T15:45Z] INFO  16:45:39,773 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:45Z] INFO  16:45:39,773 HelpFormatter - Date/Time: 2015/09/30 16:45:39
[2015-09-30T15:45Z] INFO  16:45:39,773 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:45Z] INFO  16:45:39,773 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:45Z] INFO  16:45:39,897 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:45Z] INFO  16:45:39,965 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:45Z] INFO  16:45:39,973 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:45Z] INFO  16:45:39,988 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:45Z] INFO  16:45:40,212 IntervalUtils - Processing 31018105 bp from intervals
[2015-09-30T15:45Z] WARN  16:45:40,216 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:45Z] INFO  16:45:40,271 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:45Z] INFO  16:45:40,423 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:45Z] INFO  16:45:40,424 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:45Z] INFO  16:45:40,424 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:45Z] INFO  16:45:40,425 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:45Z] INFO  16:45:40,559 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:45Z] INFO  16:45:40,741 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:45Z] INFO  16:45:46,634 ProgressMeter -     19:49867933   1900021.0     3.0 m      96.0 s       67.0%     4.5 m      89.0 s
[2015-09-30T15:45Z] INFO  16:45:57,065 ProgressMeter -     19:19245552   2500071.0     3.5 m      84.0 s       62.0%     5.6 m       2.1 m
[2015-09-30T15:46Z] INFO  16:46:11,948 ProgressMeter -     20:18576816    500008.0    31.0 s      63.0 s       59.9%    51.0 s      20.0 s
[2015-09-30T15:46Z] INFO  16:46:12,480 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:46Z] INFO  16:46:12,554 ProgressMeter -            done   2750396.0     3.8 m      82.0 s      100.0%     3.8 m       0.0 s
[2015-09-30T15:46Z] INFO  16:46:12,555 ProgressMeter - Total runtime 225.90 secs, 3.77 min, 0.06 hours
[2015-09-30T15:46Z] INFO  16:46:12,555 MicroScheduler - 4239 reads were filtered out during the traversal out of approximately 2754635 total reads (0.15%)
[2015-09-30T15:46Z] INFO  16:46:12,556 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:46Z] INFO  16:46:12,556 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:46Z] INFO  16:46:12,556 MicroScheduler -   -> 4239 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:46Z] INFO  16:46:13,653 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:46Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam
[2015-09-30T15:46Z] INFO  16:46:16,635 ProgressMeter -     19:51841442   2200026.0     3.5 m      96.0 s       74.1%     4.8 m      74.0 s
[2015-09-30T15:46Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam 19:1-31026185
[2015-09-30T15:46Z] GATK: RealignerTargetCreator
[2015-09-30T15:46Z] INFO  16:46:22,383 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:46Z] INFO  16:46:22,385 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:46Z] INFO  16:46:22,385 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:46Z] INFO  16:46:22,385 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:46Z] INFO  16:46:22,389 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/tx/tmpEireWQ/1_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign-realign.intervals -l INFO -L 19:1-31026185 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:46Z] INFO  16:46:22,394 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:46Z] INFO  16:46:22,394 HelpFormatter - Date/Time: 2015/09/30 16:46:22
[2015-09-30T15:46Z] INFO  16:46:22,395 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:46Z] INFO  16:46:22,395 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:46Z] INFO  16:46:22,450 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:46Z] INFO  16:46:22,561 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:46Z] INFO  16:46:22,568 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:46Z] INFO  16:46:22,583 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:46Z] INFO  16:46:22,841 IntervalUtils - Processing 31026185 bp from intervals
[2015-09-30T15:46Z] WARN  16:46:22,844 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:46Z] INFO  16:46:22,899 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:46Z] INFO  16:46:23,043 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:46Z] INFO  16:46:23,043 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:46Z] INFO  16:46:23,044 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:46Z] INFO  16:46:23,044 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:46Z] INFO  16:46:30,707 ProgressMeter -            done    901763.0    50.0 s      55.0 s      100.0%    50.0 s       0.0 s
[2015-09-30T15:46Z] INFO  16:46:30,707 ProgressMeter - Total runtime 50.28 secs, 0.84 min, 0.01 hours
[2015-09-30T15:46Z] INFO  16:46:30,710 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 901763 total reads (0.00%)
[2015-09-30T15:46Z] INFO  16:46:30,711 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:46Z] INFO  16:46:30,711 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:46Z] INFO  16:46:30,711 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:46Z] INFO  16:46:31,845 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:46Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam
[2015-09-30T15:46Z] GATK pre-alignment ('20', 31018873, 62038916) : syn3-normal
[2015-09-30T15:46Z] INFO  16:46:37,877 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:46Z] INFO  16:46:37,879 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:46Z] INFO  16:46:37,879 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:46Z] INFO  16:46:37,880 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:46Z] INFO  16:46:37,883 HelpFormatter - Program Args: -T PrintReads -L 20:31018874-62038916 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/tx/tmpdOkDyq/1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam
[2015-09-30T15:46Z] INFO  16:46:37,888 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:46Z] INFO  16:46:37,889 HelpFormatter - Date/Time: 2015/09/30 16:46:37
[2015-09-30T15:46Z] INFO  16:46:37,889 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:46Z] INFO  16:46:37,889 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:46Z] INFO  16:46:37,994 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:46Z] INFO  16:46:38,685 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:46Z] INFO  16:46:38,735 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:46Z] INFO  16:46:38,742 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:46Z] INFO  16:46:38,757 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:46Z] INFO  16:46:38,770 IntervalUtils - Processing 31020043 bp from intervals
[2015-09-30T15:46Z] INFO  16:46:38,827 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:46Z] INFO  16:46:39,055 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:46Z] INFO  16:46:39,056 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:46Z] INFO  16:46:39,056 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:46Z] INFO  16:46:39,056 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:46Z] INFO  16:46:39,067 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:46Z] INFO  16:46:39,260 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:46Z] INFO  16:46:46,659 ProgressMeter -     19:55247252   2500032.0     4.0 m      97.0 s       86.2%     4.7 m      38.0 s
[2015-09-30T15:46Z] INFO  16:46:53,047 ProgressMeter -     19:12492409   1.2484608E7    30.0 s       2.0 s       40.3%    74.0 s      44.0 s
[2015-09-30T15:47Z] INFO  16:47:09,058 ProgressMeter -     20:33734778    200002.0    30.0 s       2.5 m        8.8%     5.7 m       5.2 m
[2015-09-30T15:47Z] INFO  16:47:16,658 ProgressMeter -            done   3.1026185E7    53.0 s       1.0 s      100.0%    53.0 s       0.0 s
[2015-09-30T15:47Z] INFO  16:47:16,658 ProgressMeter - Total runtime 53.62 secs, 0.89 min, 0.01 hours
[2015-09-30T15:47Z] INFO  16:47:16,659 MicroScheduler - 242251 reads were filtered out during the traversal out of approximately 2766333 total reads (8.76%)
[2015-09-30T15:47Z] INFO  16:47:16,659 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:47Z] INFO  16:47:16,659 MicroScheduler -   -> 25061 reads (0.91% of total) failing BadMateFilter
[2015-09-30T15:47Z] INFO  16:47:16,660 MicroScheduler -   -> 147998 reads (5.35% of total) failing DuplicateReadFilter
[2015-09-30T15:47Z] INFO  16:47:16,660 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:47Z] INFO  16:47:16,660 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:47Z] INFO  16:47:16,660 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:47Z] INFO  16:47:16,660 MicroScheduler -   -> 69192 reads (2.50% of total) failing MappingQualityZeroFilter
[2015-09-30T15:47Z] INFO  16:47:16,661 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:47Z] INFO  16:47:16,661 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:47Z] INFO  16:47:16,661 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:47Z] INFO  16:47:17,004 ProgressMeter -     19:58350328   2900037.0     4.6 m      94.0 s       97.2%     4.7 m       7.0 s
[2015-09-30T15:47Z] INFO  16:47:17,829 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:47Z] GATK: realign ('19', 0, 31026185) : syn3-normal
[2015-09-30T15:47Z] INFO  16:47:19,960 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:47Z] INFO  16:47:19,962 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:47Z] INFO  16:47:19,962 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:47Z] INFO  16:47:19,962 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:47Z] INFO  16:47:19,965 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign-realign.intervals -L 19:1-31026185 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/tx/tmpW2iNS0/1_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam
[2015-09-30T15:47Z] INFO  16:47:19,971 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:47Z] INFO  16:47:19,971 HelpFormatter - Date/Time: 2015/09/30 16:47:19
[2015-09-30T15:47Z] INFO  16:47:19,971 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:47Z] INFO  16:47:19,972 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:47Z] INFO  16:47:20,986 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:47Z] INFO  16:47:21,050 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:47Z] INFO  16:47:21,057 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:47Z] INFO  16:47:21,073 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:47Z] INFO  16:47:21,299 IntervalUtils - Processing 31026185 bp from intervals
[2015-09-30T15:47Z] WARN  16:47:21,303 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:47Z] INFO  16:47:21,358 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:47Z] INFO  16:47:21,501 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:47Z] INFO  16:47:21,502 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:47Z] INFO  16:47:21,502 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:47Z] INFO  16:47:21,502 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:47Z] INFO  16:47:21,653 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:47Z] INFO  16:47:21,833 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:47Z] INFO  16:47:25,188 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:47Z] INFO  16:47:25,291 ProgressMeter -            done   3027078.0     4.7 m      92.0 s       99.9%     4.7 m       0.0 s
[2015-09-30T15:47Z] INFO  16:47:25,292 ProgressMeter - Total runtime 281.39 secs, 4.69 min, 0.08 hours
[2015-09-30T15:47Z] INFO  16:47:25,292 MicroScheduler - 4577 reads were filtered out during the traversal out of approximately 3031655 total reads (0.15%)
[2015-09-30T15:47Z] INFO  16:47:25,293 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:47Z] INFO  16:47:25,293 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:47Z] INFO  16:47:25,293 MicroScheduler -   -> 4577 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:47Z] INFO  16:47:26,409 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:47Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam
[2015-09-30T15:47Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam 19:31038549-59128983
[2015-09-30T15:47Z] GATK: RealignerTargetCreator
[2015-09-30T15:47Z] INFO  16:47:36,869 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:47Z] INFO  16:47:36,871 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:47Z] INFO  16:47:36,871 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:47Z] INFO  16:47:36,871 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:47Z] INFO  16:47:36,875 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/tx/tmpWsjKTa/1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign-realign.intervals -l INFO -L 19:31038549-59128983 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:47Z] INFO  16:47:36,881 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:47Z] INFO  16:47:36,881 HelpFormatter - Date/Time: 2015/09/30 16:47:36
[2015-09-30T15:47Z] INFO  16:47:36,881 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:47Z] INFO  16:47:36,882 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:47Z] INFO  16:47:37,184 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:47Z] INFO  16:47:37,301 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:47Z] INFO  16:47:37,556 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:47Z] INFO  16:47:37,572 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:47Z] INFO  16:47:38,417 IntervalUtils - Processing 28090435 bp from intervals
[2015-09-30T15:47Z] WARN  16:47:38,421 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:47Z] INFO  16:47:38,477 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:47Z] INFO  16:47:38,627 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:47Z] INFO  16:47:38,628 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:47Z] INFO  16:47:38,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:47Z] INFO  16:47:38,629 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:47Z] INFO  16:47:39,259 ProgressMeter -     20:39725804    600009.0    60.0 s     100.0 s       28.1%     3.6 m       2.6 m
[2015-09-30T15:47Z] INFO  16:47:52,228 ProgressMeter -      19:3454260    400004.0    30.0 s      76.0 s       11.1%     4.5 m       4.0 m
[2015-09-30T15:48Z] INFO  16:48:08,631 ProgressMeter -     19:46286601   1.5246252E7    30.0 s       1.0 s       54.3%    55.0 s      25.0 s
[2015-09-30T15:48Z] INFO  16:48:09,962 ProgressMeter -     20:45855477   1000015.0    90.0 s      90.0 s       47.8%     3.1 m      98.0 s
[2015-09-30T15:48Z] INFO  16:48:23,220 ProgressMeter -      19:8183819   1100053.0    61.0 s      56.0 s       26.4%     3.9 m       2.8 m
[2015-09-30T15:48Z] INFO  16:48:36,717 ProgressMeter -            done   2.8090435E7    58.0 s       2.0 s      100.0%    58.0 s       0.0 s
[2015-09-30T15:48Z] INFO  16:48:36,717 ProgressMeter - Total runtime 58.09 secs, 0.97 min, 0.02 hours
[2015-09-30T15:48Z] INFO  16:48:36,720 MicroScheduler - 263179 reads were filtered out during the traversal out of approximately 3043907 total reads (8.65%)
[2015-09-30T15:48Z] INFO  16:48:36,721 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:48Z] INFO  16:48:36,721 MicroScheduler -   -> 26362 reads (0.87% of total) failing BadMateFilter
[2015-09-30T15:48Z] INFO  16:48:36,721 MicroScheduler -   -> 153722 reads (5.05% of total) failing DuplicateReadFilter
[2015-09-30T15:48Z] INFO  16:48:36,722 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:48Z] INFO  16:48:36,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:48Z] INFO  16:48:36,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:48Z] INFO  16:48:36,722 MicroScheduler -   -> 83095 reads (2.73% of total) failing MappingQualityZeroFilter
[2015-09-30T15:48Z] INFO  16:48:36,722 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:48Z] INFO  16:48:36,723 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:48Z] INFO  16:48:36,723 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:48Z] INFO  16:48:37,713 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:48Z] GATK: realign ('19', 31038548, 59128983) : syn3-normal
[2015-09-30T15:48Z] INFO  16:48:39,968 ProgressMeter -     20:58318515   1300018.0   120.0 s      93.0 s       88.0%     2.3 m      16.0 s
[2015-09-30T15:48Z] INFO  16:48:40,087 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:48Z] INFO  16:48:40,089 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:48Z] INFO  16:48:40,089 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:48Z] INFO  16:48:40,090 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:48Z] INFO  16:48:40,093 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign-realign.intervals -L 19:31038549-59128983 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/tx/tmpFsDvkz/1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam
[2015-09-30T15:48Z] INFO  16:48:40,099 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:48Z] INFO  16:48:40,100 HelpFormatter - Date/Time: 2015/09/30 16:48:40
[2015-09-30T15:48Z] INFO  16:48:40,100 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:48Z] INFO  16:48:40,100 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:48Z] INFO  16:48:40,228 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:48Z] INFO  16:48:40,294 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:48Z] INFO  16:48:40,302 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:48Z] INFO  16:48:40,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:48Z] INFO  16:48:40,896 IntervalUtils - Processing 28090435 bp from intervals
[2015-09-30T15:48Z] WARN  16:48:40,900 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:48Z] INFO  16:48:40,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:48Z] INFO  16:48:41,116 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:48Z] INFO  16:48:41,116 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:48Z] INFO  16:48:41,117 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:48Z] INFO  16:48:41,117 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:48Z] INFO  16:48:41,266 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:48Z] INFO  16:48:41,448 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:48Z] INFO  16:48:53,221 ProgressMeter -     19:14037184   1800062.0    91.0 s      50.0 s       45.2%     3.4 m     110.0 s
[2015-09-30T15:48Z] INFO  16:48:58,065 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:48Z] INFO  16:48:58,169 ProgressMeter -            done   1634590.0     2.3 m      85.0 s      100.0%     2.3 m       0.0 s
[2015-09-30T15:48Z] INFO  16:48:58,169 ProgressMeter - Total runtime 139.11 secs, 2.32 min, 0.04 hours
[2015-09-30T15:48Z] INFO  16:48:58,169 MicroScheduler - 2753 reads were filtered out during the traversal out of approximately 1637343 total reads (0.17%)
[2015-09-30T15:48Z] INFO  16:48:58,170 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:48Z] INFO  16:48:58,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:48Z] INFO  16:48:58,170 MicroScheduler -   -> 2753 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:48Z] INFO  16:48:59,219 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:48Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam
[2015-09-30T15:49Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam 20:31018874-62038916
[2015-09-30T15:49Z] GATK: RealignerTargetCreator
[2015-09-30T15:49Z] INFO  16:49:05,136 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:49Z] INFO  16:49:05,138 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:49Z] INFO  16:49:05,138 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:49Z] INFO  16:49:05,138 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:49Z] INFO  16:49:05,141 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/tx/tmpISSmDO/1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign-realign.intervals -l INFO -L 20:31018874-62038916 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:49Z] INFO  16:49:05,147 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:49Z] INFO  16:49:05,147 HelpFormatter - Date/Time: 2015/09/30 16:49:05
[2015-09-30T15:49Z] INFO  16:49:05,147 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:49Z] INFO  16:49:05,147 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:49Z] INFO  16:49:05,202 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:49Z] INFO  16:49:05,800 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:49Z] INFO  16:49:05,808 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:49Z] INFO  16:49:05,823 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:49Z] INFO  16:49:06,070 IntervalUtils - Processing 31020043 bp from intervals
[2015-09-30T15:49Z] WARN  16:49:06,073 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:49Z] INFO  16:49:06,128 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:49Z] INFO  16:49:06,268 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:49Z] INFO  16:49:06,268 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:49Z] INFO  16:49:06,268 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:49Z] INFO  16:49:06,269 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:49Z] INFO  16:49:11,489 ProgressMeter -     19:38847157    500005.0    30.0 s      60.0 s       27.8%   107.0 s      77.0 s
[2015-09-30T15:49Z] INFO  16:49:26,293 ProgressMeter -     19:19737667   2600074.0     2.1 m      47.0 s       63.6%     3.2 m      70.0 s
[2015-09-30T15:49Z] INFO  16:49:30,662 ProgressMeter -            done   2750396.0     2.2 m      46.0 s      100.0%     2.2 m       0.0 s
[2015-09-30T15:49Z] INFO  16:49:30,662 ProgressMeter - Total runtime 129.16 secs, 2.15 min, 0.04 hours
[2015-09-30T15:49Z] INFO  16:49:30,665 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2750396 total reads (0.00%)
[2015-09-30T15:49Z] INFO  16:49:30,666 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:49Z] INFO  16:49:30,666 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:49Z] INFO  16:49:30,666 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:49Z] INFO  16:49:31,885 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:49Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam
[2015-09-30T15:49Z] INFO  16:49:36,272 ProgressMeter -     20:54810981   2.3785607E7    30.0 s       1.0 s       76.7%    39.0 s       9.0 s
[2015-09-30T15:49Z] GATK pre-alignment ('20', 62039427, 63025520) : syn3-normal
[2015-09-30T15:49Z] INFO  16:49:40,588 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:49Z] INFO  16:49:40,590 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:49Z] INFO  16:49:40,591 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:49Z] INFO  16:49:40,591 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:49Z] INFO  16:49:40,594 HelpFormatter - Program Args: -T PrintReads -L 20:62039428-63025520 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/tx/tmpnMs9mI/1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam
[2015-09-30T15:49Z] INFO  16:49:40,599 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:49Z] INFO  16:49:40,600 HelpFormatter - Date/Time: 2015/09/30 16:49:40
[2015-09-30T15:49Z] INFO  16:49:40,600 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:49Z] INFO  16:49:40,600 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:49Z] INFO  16:49:40,711 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:49Z] INFO  16:49:42,173 ProgressMeter -     19:44096452   1100012.0    61.0 s      55.0 s       46.5%     2.2 m      70.0 s
[2015-09-30T15:49Z] INFO  16:49:42,276 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:49Z] INFO  16:49:42,323 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:49Z] INFO  16:49:42,330 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:49Z] INFO  16:49:42,344 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:49Z] INFO  16:49:42,357 IntervalUtils - Processing 986093 bp from intervals
[2015-09-30T15:49Z] INFO  16:49:42,412 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:49Z] INFO  16:49:42,514 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:49Z] INFO  16:49:42,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:49Z] INFO  16:49:42,515 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:49Z] INFO  16:49:42,515 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:49Z] INFO  16:49:42,526 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:49Z] INFO  16:49:42,535 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:49Z] INFO  16:49:45,055 ProgressMeter -            done   3.1020043E7    38.0 s       1.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T15:49Z] INFO  16:49:45,056 ProgressMeter - Total runtime 38.79 secs, 0.65 min, 0.01 hours
[2015-09-30T15:49Z] INFO  16:49:45,059 MicroScheduler - 125331 reads were filtered out during the traversal out of approximately 1644578 total reads (7.62%)
[2015-09-30T15:49Z] INFO  16:49:45,059 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:49Z] INFO  16:49:45,059 MicroScheduler -   -> 16405 reads (1.00% of total) failing BadMateFilter
[2015-09-30T15:49Z] INFO  16:49:45,060 MicroScheduler -   -> 81567 reads (4.96% of total) failing DuplicateReadFilter
[2015-09-30T15:49Z] INFO  16:49:45,060 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:49Z] INFO  16:49:45,060 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:49Z] INFO  16:49:45,060 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:49Z] INFO  16:49:45,060 MicroScheduler -   -> 27359 reads (1.66% of total) failing MappingQualityZeroFilter
[2015-09-30T15:49Z] INFO  16:49:45,061 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:49Z] INFO  16:49:45,061 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:49Z] INFO  16:49:45,061 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:49Z] INFO  16:49:46,025 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:49Z] GATK: realign ('20', 31018873, 62038916) : syn3-normal
[2015-09-30T15:49Z] INFO  16:49:49,785 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:49Z] INFO  16:49:49,787 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:49Z] INFO  16:49:49,787 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:49Z] INFO  16:49:49,787 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:49Z] INFO  16:49:49,791 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign-realign.intervals -L 20:31018874-62038916 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/tx/tmpOryKUo/1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam
[2015-09-30T15:49Z] INFO  16:49:49,797 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:49Z] INFO  16:49:49,797 HelpFormatter - Date/Time: 2015/09/30 16:49:49
[2015-09-30T15:49Z] INFO  16:49:49,797 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:49Z] INFO  16:49:49,798 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:49Z] INFO  16:49:49,908 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:49Z] INFO  16:49:49,976 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:49Z] INFO  16:49:49,984 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:49Z] INFO  16:49:50,000 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:49Z] INFO  16:49:50,209 IntervalUtils - Processing 31020043 bp from intervals
[2015-09-30T15:49Z] WARN  16:49:50,213 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:49Z] INFO  16:49:50,266 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:49Z] INFO  16:49:50,427 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:49Z] INFO  16:49:50,428 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:49Z] INFO  16:49:50,428 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:49Z] INFO  16:49:50,428 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:49Z] INFO  16:49:50,702 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:49Z] INFO  16:49:50,967 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:50Z] INFO  16:50:02,205 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:50Z] INFO  16:50:02,347 ProgressMeter -            done    156231.0    19.0 s       2.1 m       93.3%    20.0 s       1.0 s
[2015-09-30T15:50Z] INFO  16:50:02,347 ProgressMeter - Total runtime 19.83 secs, 0.33 min, 0.01 hours
[2015-09-30T15:50Z] INFO  16:50:02,347 MicroScheduler - 207 reads were filtered out during the traversal out of approximately 156438 total reads (0.13%)
[2015-09-30T15:50Z] INFO  16:50:02,348 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:50Z] INFO  16:50:02,348 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:50Z] INFO  16:50:02,348 MicroScheduler -   -> 207 reads (0.13% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:50Z] INFO  16:50:03,616 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:50Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam
[2015-09-30T15:50Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam 20:62039428-63025520
[2015-09-30T15:50Z] GATK: RealignerTargetCreator
[2015-09-30T15:50Z] INFO  16:50:05,803 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:05,805 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:50Z] INFO  16:50:05,805 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:50Z] INFO  16:50:05,805 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:50Z] INFO  16:50:05,809 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/tx/tmpwb15J4/1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign-realign.intervals -l INFO -L 20:62039428-63025520 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:50Z] INFO  16:50:05,815 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:50Z] INFO  16:50:05,815 HelpFormatter - Date/Time: 2015/09/30 16:50:05
[2015-09-30T15:50Z] INFO  16:50:05,815 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:05,815 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:05,874 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:50Z] INFO  16:50:05,985 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:50Z] INFO  16:50:06,160 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:50Z] INFO  16:50:06,176 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:50Z] INFO  16:50:07,157 IntervalUtils - Processing 986093 bp from intervals
[2015-09-30T15:50Z] WARN  16:50:07,161 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:50Z] INFO  16:50:07,222 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:50Z] INFO  16:50:07,262 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:50Z] INFO  16:50:07,263 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:50Z] INFO  16:50:07,263 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:50Z] INFO  16:50:07,263 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:50Z] INFO  16:50:11,245 ProgressMeter -            done    986093.0     3.0 s       4.0 s      100.0%     3.0 s       0.0 s
[2015-09-30T15:50Z] INFO  16:50:11,245 ProgressMeter - Total runtime 3.98 secs, 0.07 min, 0.00 hours
[2015-09-30T15:50Z] INFO  16:50:11,248 MicroScheduler - 13453 reads were filtered out during the traversal out of approximately 157127 total reads (8.56%)
[2015-09-30T15:50Z] INFO  16:50:11,248 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:50Z] INFO  16:50:11,249 MicroScheduler -   -> 1152 reads (0.73% of total) failing BadMateFilter
[2015-09-30T15:50Z] INFO  16:50:11,249 MicroScheduler -   -> 8691 reads (5.53% of total) failing DuplicateReadFilter
[2015-09-30T15:50Z] INFO  16:50:11,249 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:50Z] INFO  16:50:11,249 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:50Z] INFO  16:50:11,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:50Z] INFO  16:50:11,250 MicroScheduler -   -> 3610 reads (2.30% of total) failing MappingQualityZeroFilter
[2015-09-30T15:50Z] INFO  16:50:11,250 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:50Z] INFO  16:50:11,250 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:50Z] INFO  16:50:11,251 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:50Z] INFO  16:50:12,174 ProgressMeter -     19:49917998   1900021.0    91.0 s      47.0 s       67.2%     2.3 m      44.0 s
[2015-09-30T15:50Z] INFO  16:50:12,186 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:50Z] GATK: realign ('20', 62039427, 63025520) : syn3-normal
[2015-09-30T15:50Z] INFO  16:50:13,741 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:13,743 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:50Z] INFO  16:50:13,744 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:50Z] INFO  16:50:13,744 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:50Z] INFO  16:50:13,747 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign-realign.intervals -L 20:62039428-63025520 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/tx/tmpta13gt/1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam
[2015-09-30T15:50Z] INFO  16:50:13,753 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:50Z] INFO  16:50:13,753 HelpFormatter - Date/Time: 2015/09/30 16:50:13
[2015-09-30T15:50Z] INFO  16:50:13,753 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:13,754 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:13,970 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:50Z] INFO  16:50:14,035 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:50Z] INFO  16:50:14,043 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:50Z] INFO  16:50:14,059 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:50Z] INFO  16:50:14,294 IntervalUtils - Processing 986093 bp from intervals
[2015-09-30T15:50Z] WARN  16:50:14,298 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:50Z] INFO  16:50:14,356 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:50Z] INFO  16:50:14,388 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:50Z] INFO  16:50:14,389 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:50Z] INFO  16:50:14,389 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:50Z] INFO  16:50:14,390 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:50Z] INFO  16:50:14,428 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:50Z] INFO  16:50:14,437 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:50Z] INFO  16:50:20,898 ProgressMeter -     20:36938991    500007.0    30.0 s      60.0 s       19.1%     2.6 m       2.1 m
[2015-09-30T15:50Z] INFO  16:50:24,452 ProgressMeter -            done    156231.0    10.0 s      64.0 s       93.3%    10.0 s       0.0 s
[2015-09-30T15:50Z] INFO  16:50:24,452 ProgressMeter - Total runtime 10.06 secs, 0.17 min, 0.00 hours
[2015-09-30T15:50Z] INFO  16:50:24,455 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 156231 total reads (0.00%)
[2015-09-30T15:50Z] INFO  16:50:24,455 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:50Z] INFO  16:50:24,455 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:50Z] INFO  16:50:24,456 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:50Z] INFO  16:50:25,513 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:50Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam
[2015-09-30T15:50Z] GATK pre-alignment ('21', 0, 31023863) : syn3-normal
[2015-09-30T15:50Z] INFO  16:50:29,042 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:29,044 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:50Z] INFO  16:50:29,044 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:50Z] INFO  16:50:29,044 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:50Z] INFO  16:50:29,047 HelpFormatter - Program Args: -T PrintReads -L 21:1-31023863 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/tx/tmpQBRHwi/1_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam
[2015-09-30T15:50Z] INFO  16:50:29,052 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:50Z] INFO  16:50:29,052 HelpFormatter - Date/Time: 2015/09/30 16:50:29
[2015-09-30T15:50Z] INFO  16:50:29,052 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:29,052 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:29,139 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:50Z] INFO  16:50:29,773 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:50Z] INFO  16:50:29,817 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:50Z] INFO  16:50:29,824 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:50Z] INFO  16:50:29,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:50Z] INFO  16:50:29,849 IntervalUtils - Processing 31023863 bp from intervals
[2015-09-30T15:50Z] INFO  16:50:29,899 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:50Z] INFO  16:50:30,101 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:50Z] INFO  16:50:30,101 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:50Z] INFO  16:50:30,101 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:50Z] INFO  16:50:30,101 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:50Z] INFO  16:50:30,111 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:50Z] INFO  16:50:30,229 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:50Z] INFO  16:50:42,522 ProgressMeter -     19:55672132   2600033.0     2.0 m      46.0 s       87.7%     2.3 m      16.0 s
[2015-09-30T15:50Z] INFO  16:50:51,140 ProgressMeter -     20:54956867   1200017.0    60.0 s      50.0 s       77.2%    77.0 s      17.0 s
[2015-09-30T15:50Z] INFO  16:50:54,624 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:50Z] INFO  16:50:54,746 ProgressMeter -            done    204720.0    24.0 s     120.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T15:50Z] INFO  16:50:54,747 ProgressMeter - Total runtime 24.65 secs, 0.41 min, 0.01 hours
[2015-09-30T15:50Z] INFO  16:50:54,747 MicroScheduler - 1195 reads were filtered out during the traversal out of approximately 205915 total reads (0.58%)
[2015-09-30T15:50Z] INFO  16:50:54,747 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:50Z] INFO  16:50:54,747 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:50Z] INFO  16:50:54,748 MicroScheduler -   -> 1195 reads (0.58% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:50Z] INFO  16:50:55,771 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:50Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam
[2015-09-30T15:50Z] INFO  16:50:57,489 ProgressMeter -            done   3027078.0     2.3 m      45.0 s       99.9%     2.3 m       0.0 s
[2015-09-30T15:50Z] INFO  16:50:57,490 ProgressMeter - Total runtime 136.37 secs, 2.27 min, 0.04 hours
[2015-09-30T15:50Z] INFO  16:50:57,494 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3027078 total reads (0.00%)
[2015-09-30T15:50Z] INFO  16:50:57,494 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:50Z] INFO  16:50:57,495 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:50Z] INFO  16:50:57,495 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:50Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam 21:1-31023863
[2015-09-30T15:50Z] GATK: RealignerTargetCreator
[2015-09-30T15:50Z] INFO  16:50:58,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:50Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam
[2015-09-30T15:50Z] INFO  16:50:59,676 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:59,678 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:50Z] INFO  16:50:59,678 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:50Z] INFO  16:50:59,678 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:50Z] INFO  16:50:59,682 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/tx/tmpvWxsZK/1_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign-realign.intervals -l INFO -L 21:1-31023863 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:50Z] INFO  16:50:59,687 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:50Z] INFO  16:50:59,688 HelpFormatter - Date/Time: 2015/09/30 16:50:59
[2015-09-30T15:50Z] INFO  16:50:59,688 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:59,688 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:50Z] INFO  16:50:59,745 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:50Z] INFO  16:50:59,883 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:50Z] INFO  16:50:59,890 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:50Z] INFO  16:50:59,906 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:51Z] INFO  16:51:00,146 IntervalUtils - Processing 31023863 bp from intervals
[2015-09-30T15:51Z] WARN  16:51:00,150 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:51Z] INFO  16:51:00,232 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:51Z] INFO  16:51:01,258 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:51Z] INFO  16:51:01,259 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:51Z] INFO  16:51:01,259 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:51Z] INFO  16:51:01,259 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:51Z] INFO  16:51:05,762 ProgressMeter -            done   1634590.0    75.0 s      46.0 s      100.0%    75.0 s       0.0 s
[2015-09-30T15:51Z] INFO  16:51:05,763 ProgressMeter - Total runtime 75.34 secs, 1.26 min, 0.02 hours
[2015-09-30T15:51Z] INFO  16:51:05,766 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1634590 total reads (0.00%)
[2015-09-30T15:51Z] INFO  16:51:05,766 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:51Z] INFO  16:51:05,766 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:51Z] INFO  16:51:05,767 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:51Z] INFO  16:51:06,855 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:51Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam
[2015-09-30T15:51Z] GATK pre-alignment ('21', 31026814, 48129895) : syn3-normal
[2015-09-30T15:51Z] INFO  16:51:09,776 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:09,778 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:51Z] INFO  16:51:09,778 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:51Z] INFO  16:51:09,778 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:51Z] INFO  16:51:09,782 HelpFormatter - Program Args: -T PrintReads -L 21:31026815-48129895 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/tx/tmpvXrYON/1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam
[2015-09-30T15:51Z] INFO  16:51:09,787 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:51Z] INFO  16:51:09,787 HelpFormatter - Date/Time: 2015/09/30 16:51:09
[2015-09-30T15:51Z] INFO  16:51:09,788 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:09,788 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:09,893 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:51Z] GATK pre-alignment ('22', 0, 31019358) : syn3-normal
[2015-09-30T15:51Z] INFO  16:51:17,363 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:51Z] INFO  16:51:17,413 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:51Z] INFO  16:51:17,421 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:51Z] INFO  16:51:17,436 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:51Z] INFO  16:51:17,449 IntervalUtils - Processing 17103081 bp from intervals
[2015-09-30T15:51Z] INFO  16:51:17,507 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:51Z] INFO  16:51:17,567 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:17,569 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:51Z] INFO  16:51:17,569 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:51Z] INFO  16:51:17,569 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:51Z] INFO  16:51:17,573 HelpFormatter - Program Args: -T PrintReads -L 22:1-31019358 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/tx/tmptTl9tg/1_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam
[2015-09-30T15:51Z] INFO  16:51:17,578 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:51Z] INFO  16:51:17,578 HelpFormatter - Date/Time: 2015/09/30 16:51:17
[2015-09-30T15:51Z] INFO  16:51:17,578 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:17,579 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:17,660 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:51Z] INFO  16:51:17,661 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:51Z] INFO  16:51:17,661 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:51Z] INFO  16:51:17,661 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:51Z] INFO  16:51:17,673 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:51Z] INFO  16:51:17,794 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:51Z] INFO  16:51:17,992 ProgressMeter -            done   3.1023863E7    16.0 s       0.0 s      100.0%    16.0 s       0.0 s
[2015-09-30T15:51Z] INFO  16:51:17,992 ProgressMeter - Total runtime 16.73 secs, 0.28 min, 0.00 hours
[2015-09-30T15:51Z] INFO  16:51:17,993 MicroScheduler - 28345 reads were filtered out during the traversal out of approximately 205850 total reads (13.77%)
[2015-09-30T15:51Z] INFO  16:51:17,993 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:51Z] INFO  16:51:17,993 MicroScheduler -   -> 5146 reads (2.50% of total) failing BadMateFilter
[2015-09-30T15:51Z] INFO  16:51:17,994 MicroScheduler -   -> 9030 reads (4.39% of total) failing DuplicateReadFilter
[2015-09-30T15:51Z] INFO  16:51:17,994 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:51Z] INFO  16:51:17,994 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:51Z] INFO  16:51:17,994 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:51Z] INFO  16:51:17,995 MicroScheduler -   -> 14169 reads (6.88% of total) failing MappingQualityZeroFilter
[2015-09-30T15:51Z] INFO  16:51:17,995 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:51Z] INFO  16:51:17,995 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:51Z] INFO  16:51:17,995 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:51Z] INFO  16:51:19,277 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:51Z] INFO  16:51:19,994 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:51Z] INFO  16:51:20,044 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:51Z] INFO  16:51:20,052 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:51Z] INFO  16:51:20,066 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:51Z] INFO  16:51:20,079 IntervalUtils - Processing 31019358 bp from intervals
[2015-09-30T15:51Z] INFO  16:51:20,132 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:51Z] INFO  16:51:20,225 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:51Z] GATK: realign ('21', 0, 31023863) : syn3-normal
[2015-09-30T15:51Z] INFO  16:51:20,374 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:51Z] INFO  16:51:20,375 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:51Z] INFO  16:51:20,375 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:51Z] INFO  16:51:20,375 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:51Z] INFO  16:51:20,387 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:51Z] INFO  16:51:20,482 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:51Z] INFO  16:51:22,636 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:22,638 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:51Z] INFO  16:51:22,638 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:51Z] INFO  16:51:22,638 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:51Z] INFO  16:51:22,642 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign-realign.intervals -L 21:1-31023863 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/tx/tmpQNl03W/1_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam
[2015-09-30T15:51Z] INFO  16:51:22,647 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:51Z] INFO  16:51:22,647 HelpFormatter - Date/Time: 2015/09/30 16:51:22
[2015-09-30T15:51Z] INFO  16:51:22,647 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:22,648 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:25,233 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:51Z] INFO  16:51:26,493 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:51Z] INFO  16:51:26,501 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:51Z] INFO  16:51:26,518 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:51Z] INFO  16:51:26,744 IntervalUtils - Processing 31023863 bp from intervals
[2015-09-30T15:51Z] WARN  16:51:26,748 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:51Z] INFO  16:51:26,803 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:51Z] INFO  16:51:26,946 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:51Z] INFO  16:51:26,947 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:51Z] INFO  16:51:26,947 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:51Z] INFO  16:51:26,948 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:51Z] INFO  16:51:27,065 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:51Z] INFO  16:51:27,189 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:51Z] INFO  16:51:41,566 ProgressMeter -            done    204720.0    14.0 s      71.0 s      100.0%    14.0 s       0.0 s
[2015-09-30T15:51Z] INFO  16:51:41,567 ProgressMeter - Total runtime 14.62 secs, 0.24 min, 0.00 hours
[2015-09-30T15:51Z] INFO  16:51:41,570 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 204720 total reads (0.00%)
[2015-09-30T15:51Z] INFO  16:51:41,570 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:51Z] INFO  16:51:41,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:51Z] INFO  16:51:41,571 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:51Z] INFO  16:51:42,634 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:51Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam
[2015-09-30T15:51Z] GATK pre-alignment ('22', 31022170, 51304566) : syn3-normal
[2015-09-30T15:51Z] INFO  16:51:44,812 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:44,814 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:51Z] INFO  16:51:44,814 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:51Z] INFO  16:51:44,814 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:51Z] INFO  16:51:44,818 HelpFormatter - Program Args: -T PrintReads -L 22:31022171-51304566 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/tx/tmpHfA77w/1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam
[2015-09-30T15:51Z] INFO  16:51:44,823 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:51Z] INFO  16:51:44,823 HelpFormatter - Date/Time: 2015/09/30 16:51:44
[2015-09-30T15:51Z] INFO  16:51:44,824 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:44,824 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:51Z] INFO  16:51:44,940 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:51Z] INFO  16:51:46,582 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:51Z] INFO  16:51:46,632 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:51Z] INFO  16:51:46,640 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:51Z] INFO  16:51:46,655 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:51Z] INFO  16:51:46,668 IntervalUtils - Processing 20282396 bp from intervals
[2015-09-30T15:51Z] INFO  16:51:46,727 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:51Z] INFO  16:51:46,928 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:51Z] INFO  16:51:46,928 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:51Z] INFO  16:51:46,929 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:51Z] INFO  16:51:46,929 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:51Z] INFO  16:51:46,940 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:51Z] INFO  16:51:47,078 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:51Z] INFO  16:51:47,664 ProgressMeter -     21:37592239    200002.0    30.0 s       2.5 m       38.4%    78.0 s      48.0 s
[2015-09-30T15:51Z] INFO  16:51:51,111 ProgressMeter -     22:19384482    200004.0    30.0 s       2.6 m       62.5%    48.0 s      18.0 s
[2015-09-30T15:52Z] INFO  16:52:16,936 ProgressMeter -     22:35947654    200002.0    30.0 s       2.5 m       24.3%     2.1 m      93.0 s
[2015-09-30T15:52Z] INFO  16:52:18,066 ProgressMeter -     21:45093960    500005.0    60.0 s     120.0 s       82.2%    72.0 s      12.0 s
[2015-09-30T15:52Z] INFO  16:52:21,131 ProgressMeter -     22:22299842    600008.0    60.0 s     101.0 s       71.9%    83.0 s      23.0 s
[2015-09-30T15:52Z] INFO  16:52:45,336 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:52Z] INFO  16:52:47,489 ProgressMeter -     22:38962184    500005.0    60.0 s       2.0 m       39.1%     2.6 m      93.0 s
[2015-09-30T15:52Z] INFO  16:52:48,896 ProgressMeter -            done    967122.0    91.0 s      94.0 s       99.9%    91.0 s       0.0 s
[2015-09-30T15:52Z] INFO  16:52:48,896 ProgressMeter - Total runtime 91.24 secs, 1.52 min, 0.03 hours
[2015-09-30T15:52Z] INFO  16:52:48,896 MicroScheduler - 1674 reads were filtered out during the traversal out of approximately 968796 total reads (0.17%)
[2015-09-30T15:52Z] INFO  16:52:48,897 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:52Z] INFO  16:52:48,897 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:52Z] INFO  16:52:48,897 MicroScheduler -   -> 1674 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:52Z] INFO  16:52:49,920 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:52Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam
[2015-09-30T15:52Z] INFO  16:52:51,132 ProgressMeter -     22:25627610    900012.0    90.0 s     100.0 s       82.6%   108.0 s      18.0 s
[2015-09-30T15:52Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam 21:31026815-48129895
[2015-09-30T15:52Z] GATK: RealignerTargetCreator
[2015-09-30T15:52Z] INFO  16:52:53,848 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:52Z] INFO  16:52:53,850 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:52Z] INFO  16:52:53,850 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:52Z] INFO  16:52:53,850 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:52Z] INFO  16:52:53,854 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/tx/tmpNyHGb0/1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign-realign.intervals -l INFO -L 21:31026815-48129895 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:52Z] INFO  16:52:53,860 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:52Z] INFO  16:52:53,861 HelpFormatter - Date/Time: 2015/09/30 16:52:53
[2015-09-30T15:52Z] INFO  16:52:53,861 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:52Z] INFO  16:52:53,861 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:52Z] INFO  16:52:53,930 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:52Z] INFO  16:52:54,057 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:52Z] INFO  16:52:54,064 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:52Z] INFO  16:52:54,080 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:52Z] INFO  16:52:54,758 IntervalUtils - Processing 17103081 bp from intervals
[2015-09-30T15:52Z] WARN  16:52:54,762 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:52Z] INFO  16:52:54,816 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:52Z] INFO  16:52:54,906 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:52Z] INFO  16:52:54,907 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:52Z] INFO  16:52:54,907 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:52Z] INFO  16:52:54,907 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:53Z] INFO  16:53:14,619 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@36b93e8f
[2015-09-30T15:53Z] INFO  16:53:14,738 ProgressMeter -            done   1243871.0   114.0 s      91.0 s      100.0%   114.0 s       0.0 s
[2015-09-30T15:53Z] INFO  16:53:14,739 ProgressMeter - Total runtime 114.36 secs, 1.91 min, 0.03 hours
[2015-09-30T15:53Z] INFO  16:53:14,739 MicroScheduler - 1732 reads were filtered out during the traversal out of approximately 1245603 total reads (0.14%)
[2015-09-30T15:53Z] INFO  16:53:14,739 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:53Z] INFO  16:53:14,740 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:53Z] INFO  16:53:14,740 MicroScheduler -   -> 1732 reads (0.14% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:53Z] INFO  16:53:15,878 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:53Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam
[2015-09-30T15:53Z] INFO  16:53:17,490 ProgressMeter -     22:42210147    800009.0    90.0 s     113.0 s       55.2%     2.7 m      73.0 s
[2015-09-30T15:53Z] INFO  16:53:17,581 ProgressMeter -            done   1.7103081E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T15:53Z] INFO  16:53:17,581 ProgressMeter - Total runtime 22.67 secs, 0.38 min, 0.01 hours
[2015-09-30T15:53Z] INFO  16:53:17,584 MicroScheduler - 75058 reads were filtered out during the traversal out of approximately 972969 total reads (7.71%)
[2015-09-30T15:53Z] INFO  16:53:17,585 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:53Z] INFO  16:53:17,585 MicroScheduler -   -> 9504 reads (0.98% of total) failing BadMateFilter
[2015-09-30T15:53Z] INFO  16:53:17,585 MicroScheduler -   -> 48239 reads (4.96% of total) failing DuplicateReadFilter
[2015-09-30T15:53Z] INFO  16:53:17,585 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:53Z] INFO  16:53:17,586 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:53Z] INFO  16:53:17,586 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:53Z] INFO  16:53:17,586 MicroScheduler -   -> 17315 reads (1.78% of total) failing MappingQualityZeroFilter
[2015-09-30T15:53Z] INFO  16:53:17,586 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:53Z] INFO  16:53:17,587 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:53Z] INFO  16:53:17,587 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:53Z] INFO  16:53:18,640 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:53Z] GATK: realign ('21', 31026814, 48129895) : syn3-normal
[2015-09-30T15:53Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam 22:1-31019358
[2015-09-30T15:53Z] GATK: RealignerTargetCreator
[2015-09-30T15:53Z] INFO  16:53:21,643 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:53Z] INFO  16:53:21,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:53Z] INFO  16:53:21,646 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:53Z] INFO  16:53:21,646 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:53Z] INFO  16:53:21,649 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign-realign.intervals -L 21:31026815-48129895 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/tx/tmpOc1lpw/1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam
[2015-09-30T15:53Z] INFO  16:53:21,655 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:53Z] INFO  16:53:21,655 HelpFormatter - Date/Time: 2015/09/30 16:53:21
[2015-09-30T15:53Z] INFO  16:53:21,655 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:53Z] INFO  16:53:21,656 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:53Z] INFO  16:53:21,783 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:53Z] INFO  16:53:21,847 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:53Z] INFO  16:53:21,855 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:53Z] INFO  16:53:21,872 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:53Z] INFO  16:53:21,949 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:53Z] INFO  16:53:21,952 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:53Z] INFO  16:53:21,952 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:53Z] INFO  16:53:21,952 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:53Z] INFO  16:53:21,956 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/tx/tmpDTITsf/1_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign-realign.intervals -l INFO -L 22:1-31019358 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:53Z] INFO  16:53:21,961 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:53Z] INFO  16:53:21,962 HelpFormatter - Date/Time: 2015/09/30 16:53:21
[2015-09-30T15:53Z] INFO  16:53:21,962 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:53Z] INFO  16:53:21,962 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:53Z] INFO  16:53:22,021 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:53Z] INFO  16:53:22,106 IntervalUtils - Processing 17103081 bp from intervals
[2015-09-30T15:53Z] WARN  16:53:22,110 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:53Z] INFO  16:53:22,133 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:53Z] INFO  16:53:22,141 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:53Z] INFO  16:53:22,157 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:53Z] INFO  16:53:22,618 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:53Z] INFO  16:53:22,753 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:53Z] INFO  16:53:22,753 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:53Z] INFO  16:53:22,754 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:53Z] INFO  16:53:22,754 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:53Z] INFO  16:53:22,889 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:53Z] INFO  16:53:23,011 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:53Z] INFO  16:53:23,108 IntervalUtils - Processing 31019358 bp from intervals
[2015-09-30T15:53Z] WARN  16:53:23,112 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:53Z] INFO  16:53:23,168 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:53Z] INFO  16:53:23,336 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:53Z] INFO  16:53:23,337 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:53Z] INFO  16:53:23,337 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:53Z] INFO  16:53:23,338 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:53Z] INFO  16:53:47,491 ProgressMeter -     22:46665145   1100013.0   120.0 s     109.0 s       77.1%     2.6 m      35.0 s
[2015-09-30T15:53Z] INFO  16:53:53,340 ProgressMeter -     22:30762469   3.0752768E7    30.0 s       0.0 s       99.2%    30.0 s       0.0 s
[2015-09-30T15:53Z] INFO  16:53:54,327 ProgressMeter -            done   3.1019358E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T15:53Z] INFO  16:53:54,328 ProgressMeter - Total runtime 30.99 secs, 0.52 min, 0.01 hours
[2015-09-30T15:53Z] INFO  16:53:54,331 MicroScheduler - 213276 reads were filtered out during the traversal out of approximately 1251541 total reads (17.04%)
[2015-09-30T15:53Z] INFO  16:53:54,331 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:53Z] INFO  16:53:54,331 MicroScheduler -   -> 9285 reads (0.74% of total) failing BadMateFilter
[2015-09-30T15:53Z] INFO  16:53:54,332 MicroScheduler -   -> 58928 reads (4.71% of total) failing DuplicateReadFilter
[2015-09-30T15:53Z] INFO  16:53:54,332 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:53Z] INFO  16:53:54,332 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:53Z] INFO  16:53:54,332 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:53Z] INFO  16:53:54,332 MicroScheduler -   -> 145063 reads (11.59% of total) failing MappingQualityZeroFilter
[2015-09-30T15:53Z] INFO  16:53:54,333 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:53Z] INFO  16:53:54,333 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:53Z] INFO  16:53:54,333 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:53Z] INFO  16:53:55,005 ProgressMeter -     21:43808634    400004.0    32.0 s      80.0 s       74.7%    42.0 s      10.0 s
[2015-09-30T15:53Z] INFO  16:53:55,308 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:53Z] GATK: realign ('22', 0, 31019358) : syn3-normal
[2015-09-30T15:53Z] INFO  16:53:57,188 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:53Z] INFO  16:53:57,190 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:53Z] INFO  16:53:57,190 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:53Z] INFO  16:53:57,190 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:53Z] INFO  16:53:57,194 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign-realign.intervals -L 22:1-31019358 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/tx/tmpRNffrA/1_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam
[2015-09-30T15:53Z] INFO  16:53:57,199 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:53Z] INFO  16:53:57,199 HelpFormatter - Date/Time: 2015/09/30 16:53:57
[2015-09-30T15:53Z] INFO  16:53:57,200 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:53Z] INFO  16:53:57,200 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:53Z] INFO  16:53:57,325 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:53Z] INFO  16:53:57,388 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:53Z] INFO  16:53:57,396 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:53Z] INFO  16:53:57,412 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:53Z] INFO  16:53:57,641 IntervalUtils - Processing 31019358 bp from intervals
[2015-09-30T15:53Z] WARN  16:53:57,645 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:53Z] INFO  16:53:57,701 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:53Z] INFO  16:53:57,872 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:53Z] INFO  16:53:57,872 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:53Z] INFO  16:53:57,872 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:53Z] INFO  16:53:57,873 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:53Z] INFO  16:53:57,985 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:53Z] INFO  16:53:58,076 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:54Z] INFO  16:54:14,442 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:54Z] INFO  16:54:14,541 ProgressMeter -            done    967122.0    51.0 s      53.0 s       99.9%    51.0 s       0.0 s
[2015-09-30T15:54Z] INFO  16:54:14,541 ProgressMeter - Total runtime 51.79 secs, 0.86 min, 0.01 hours
[2015-09-30T15:54Z] INFO  16:54:14,545 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 967122 total reads (0.00%)
[2015-09-30T15:54Z] INFO  16:54:14,545 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:54Z] INFO  16:54:14,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:54Z] INFO  16:54:14,545 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:54Z] INFO  16:54:14,581 ProgressMeter -            done   1460498.0     2.5 m     101.0 s       99.7%     2.5 m       0.0 s
[2015-09-30T15:54Z] INFO  16:54:14,581 ProgressMeter - Total runtime 147.65 secs, 2.46 min, 0.04 hours
[2015-09-30T15:54Z] INFO  16:54:14,582 MicroScheduler - 2121 reads were filtered out during the traversal out of approximately 1462619 total reads (0.15%)
[2015-09-30T15:54Z] INFO  16:54:14,582 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:54Z] INFO  16:54:14,582 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:54Z] INFO  16:54:14,582 MicroScheduler -   -> 2121 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:54Z] INFO  16:54:15,736 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:54Z] INFO  16:54:15,759 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:54Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam
[2015-09-30T15:54Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam
[2015-09-30T15:54Z] GATK pre-alignment ('X', 0, 31090302) : syn3-normal
[2015-09-30T15:54Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam 22:31022171-51304566
[2015-09-30T15:54Z] GATK: RealignerTargetCreator
[2015-09-30T15:54Z] INFO  16:54:23,299 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:54Z] INFO  16:54:23,301 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:54Z] INFO  16:54:23,301 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:54Z] INFO  16:54:23,302 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:54Z] INFO  16:54:23,305 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/tx/tmpjZv832/1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign-realign.intervals -l INFO -L 22:31022171-51304566 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:54Z] INFO  16:54:23,311 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:54Z] INFO  16:54:23,311 HelpFormatter - Date/Time: 2015/09/30 16:54:23
[2015-09-30T15:54Z] INFO  16:54:23,311 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:54Z] INFO  16:54:23,311 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:54Z] INFO  16:54:23,368 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:54Z] INFO  16:54:23,425 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:54Z] INFO  16:54:23,428 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:54Z] INFO  16:54:23,428 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:54Z] INFO  16:54:23,428 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:54Z] INFO  16:54:23,431 HelpFormatter - Program Args: -T PrintReads -L X:1-31090302 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmp3yPx0t/1_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam
[2015-09-30T15:54Z] INFO  16:54:23,436 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:54Z] INFO  16:54:23,436 HelpFormatter - Date/Time: 2015/09/30 16:54:23
[2015-09-30T15:54Z] INFO  16:54:23,437 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:54Z] INFO  16:54:23,437 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:54Z] INFO  16:54:25,638 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:54Z] INFO  16:54:25,649 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:54Z] INFO  16:54:26,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:54Z] INFO  16:54:26,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:54Z] INFO  16:54:26,567 IntervalUtils - Processing 20282396 bp from intervals
[2015-09-30T15:54Z] WARN  16:54:26,571 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:54Z] INFO  16:54:26,625 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:54Z] INFO  16:54:26,731 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:54Z] INFO  16:54:26,731 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:54Z] INFO  16:54:26,732 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:54Z] INFO  16:54:26,732 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:54Z] INFO  16:54:27,829 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:54Z] INFO  16:54:27,879 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:54Z] INFO  16:54:27,887 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:54Z] INFO  16:54:27,902 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:54Z] INFO  16:54:27,915 IntervalUtils - Processing 31090302 bp from intervals
[2015-09-30T15:54Z] INFO  16:54:27,971 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:54Z] INFO  16:54:28,160 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:54Z] INFO  16:54:28,160 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:54Z] INFO  16:54:28,160 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:54Z] INFO  16:54:28,161 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:54Z] INFO  16:54:28,172 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:54Z] INFO  16:54:28,280 ProgressMeter -     22:21411890    400006.0    30.0 s      76.0 s       69.0%    43.0 s      13.0 s
[2015-09-30T15:54Z] INFO  16:54:28,356 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:54Z] INFO  16:54:56,735 ProgressMeter -     22:51137265   2.0112294E7    30.0 s       1.0 s       99.2%    30.0 s       0.0 s
[2015-09-30T15:54Z] INFO  16:54:57,274 ProgressMeter -            done   2.0282396E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T15:54Z] INFO  16:54:57,274 ProgressMeter - Total runtime 30.54 secs, 0.51 min, 0.01 hours
[2015-09-30T15:54Z] INFO  16:54:57,277 MicroScheduler - 123199 reads were filtered out during the traversal out of approximately 1468841 total reads (8.39%)
[2015-09-30T15:54Z] INFO  16:54:57,278 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:54Z] INFO  16:54:57,278 MicroScheduler -   -> 13542 reads (0.92% of total) failing BadMateFilter
[2015-09-30T15:54Z] INFO  16:54:57,278 MicroScheduler -   -> 76095 reads (5.18% of total) failing DuplicateReadFilter
[2015-09-30T15:54Z] INFO  16:54:57,278 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:54Z] INFO  16:54:57,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:54Z] INFO  16:54:57,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:54Z] INFO  16:54:57,279 MicroScheduler -   -> 33562 reads (2.28% of total) failing MappingQualityZeroFilter
[2015-09-30T15:54Z] INFO  16:54:57,279 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:54Z] INFO  16:54:57,280 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:54Z] INFO  16:54:57,280 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:54Z] INFO  16:54:58,022 ProgressMeter -            done   1243871.0    60.0 s      48.0 s      100.0%    60.0 s       0.0 s
[2015-09-30T15:54Z] INFO  16:54:58,023 ProgressMeter - Total runtime 60.15 secs, 1.00 min, 0.02 hours
[2015-09-30T15:54Z] INFO  16:54:58,026 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1243871 total reads (0.00%)
[2015-09-30T15:54Z] INFO  16:54:58,026 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:54Z] INFO  16:54:58,027 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:54Z] INFO  16:54:58,027 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:54Z] INFO  16:54:58,163 ProgressMeter -      X:15554431    200004.0    30.0 s       2.5 m       50.0%    59.0 s      29.0 s
[2015-09-30T15:54Z] INFO  16:54:58,244 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:54Z] GATK: realign ('22', 31022170, 51304566) : syn3-normal
[2015-09-30T15:54Z] INFO  16:54:59,223 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:54Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam
[2015-09-30T15:54Z] INFO  16:54:59,876 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:54Z] INFO  16:54:59,878 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:54Z] INFO  16:54:59,879 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:54Z] INFO  16:54:59,879 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:54Z] INFO  16:54:59,882 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign-realign.intervals -L 22:31022171-51304566 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/tx/tmpz_y1eD/1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam
[2015-09-30T15:54Z] INFO  16:54:59,888 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:54Z] INFO  16:54:59,888 HelpFormatter - Date/Time: 2015/09/30 16:54:59
[2015-09-30T15:54Z] INFO  16:54:59,888 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:54Z] INFO  16:54:59,889 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:00,027 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:55Z] INFO  16:55:00,091 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:55Z] INFO  16:55:00,099 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:55Z] INFO  16:55:00,114 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:55Z] INFO  16:55:01,115 IntervalUtils - Processing 20282396 bp from intervals
[2015-09-30T15:55Z] WARN  16:55:01,119 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:55Z] INFO  16:55:01,173 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:55Z] INFO  16:55:01,307 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:55Z] INFO  16:55:01,308 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:55Z] INFO  16:55:01,308 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:55Z] INFO  16:55:01,308 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:55Z] INFO  16:55:01,462 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:55Z] INFO  16:55:01,619 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:55Z] GATK pre-alignment ('X', 31132529, 62519711) : syn3-normal
[2015-09-30T15:55Z] INFO  16:55:05,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:05,135 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:55Z] INFO  16:55:05,135 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:55Z] INFO  16:55:05,135 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:55Z] INFO  16:55:05,138 HelpFormatter - Program Args: -T PrintReads -L X:31132530-62519711 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmptldGs_/1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam
[2015-09-30T15:55Z] INFO  16:55:05,144 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:55Z] INFO  16:55:05,144 HelpFormatter - Date/Time: 2015/09/30 16:55:05
[2015-09-30T15:55Z] INFO  16:55:05,145 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:05,145 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:05,673 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:55Z] INFO  16:55:06,765 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:55Z] INFO  16:55:06,815 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:55Z] INFO  16:55:06,823 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:55Z] INFO  16:55:06,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:55Z] INFO  16:55:06,850 IntervalUtils - Processing 31387182 bp from intervals
[2015-09-30T15:55Z] INFO  16:55:06,907 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:55Z] INFO  16:55:07,104 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:55Z] INFO  16:55:07,105 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:55Z] INFO  16:55:07,105 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:55Z] INFO  16:55:07,105 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:55Z] INFO  16:55:07,116 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:55Z] INFO  16:55:07,313 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:55Z] INFO  16:55:22,799 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:55Z] INFO  16:55:23,152 ProgressMeter -            done    614276.0    54.0 s      89.0 s      100.0%    54.0 s       0.0 s
[2015-09-30T15:55Z] INFO  16:55:23,152 ProgressMeter - Total runtime 54.99 secs, 0.92 min, 0.02 hours
[2015-09-30T15:55Z] INFO  16:55:23,152 MicroScheduler - 2078 reads were filtered out during the traversal out of approximately 616354 total reads (0.34%)
[2015-09-30T15:55Z] INFO  16:55:23,152 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:55Z] INFO  16:55:23,153 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:55Z] INFO  16:55:23,153 MicroScheduler -   -> 2078 reads (0.34% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:55Z] INFO  16:55:24,207 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:55Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam
[2015-09-30T15:55Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam X:1-31090302
[2015-09-30T15:55Z] GATK: RealignerTargetCreator
[2015-09-30T15:55Z] INFO  16:55:27,405 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:27,407 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:55Z] INFO  16:55:27,407 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:55Z] INFO  16:55:27,408 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:55Z] INFO  16:55:27,411 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpDI2lL3/1_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign-realign.intervals -l INFO -L X:1-31090302 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:55Z] INFO  16:55:27,417 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:55Z] INFO  16:55:27,417 HelpFormatter - Date/Time: 2015/09/30 16:55:27
[2015-09-30T15:55Z] INFO  16:55:27,418 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:27,418 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:27,665 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:55Z] INFO  16:55:27,928 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:55Z] INFO  16:55:28,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:55Z] INFO  16:55:28,392 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:55Z] INFO  16:55:29,506 IntervalUtils - Processing 31090302 bp from intervals
[2015-09-30T15:55Z] WARN  16:55:29,510 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:55Z] INFO  16:55:29,567 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:55Z] INFO  16:55:29,726 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:55Z] INFO  16:55:29,726 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:55Z] INFO  16:55:29,727 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:55Z] INFO  16:55:29,727 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:55Z] INFO  16:55:32,163 ProgressMeter -     22:39266938    500005.0    30.0 s      61.0 s       40.6%    73.0 s      43.0 s
[2015-09-30T15:55Z] INFO  16:55:37,107 ProgressMeter -      X:47007147    200004.0    30.0 s       2.5 m       50.6%    59.0 s      29.0 s
[2015-09-30T15:55Z] INFO  16:55:52,796 ProgressMeter -            done   3.1090302E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T15:55Z] INFO  16:55:52,797 ProgressMeter - Total runtime 23.07 secs, 0.38 min, 0.01 hours
[2015-09-30T15:55Z] INFO  16:55:52,800 MicroScheduler - 53057 reads were filtered out during the traversal out of approximately 618486 total reads (8.58%)
[2015-09-30T15:55Z] INFO  16:55:52,800 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:55Z] INFO  16:55:52,800 MicroScheduler -   -> 9762 reads (1.58% of total) failing BadMateFilter
[2015-09-30T15:55Z] INFO  16:55:52,801 MicroScheduler -   -> 26847 reads (4.34% of total) failing DuplicateReadFilter
[2015-09-30T15:55Z] INFO  16:55:52,801 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:55Z] INFO  16:55:52,801 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:55Z] INFO  16:55:52,801 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:55Z] INFO  16:55:52,802 MicroScheduler -   -> 16448 reads (2.66% of total) failing MappingQualityZeroFilter
[2015-09-30T15:55Z] INFO  16:55:52,802 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:55Z] INFO  16:55:52,802 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:55Z] INFO  16:55:52,802 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:55Z] INFO  16:55:53,749 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:55Z] GATK: realign ('X', 0, 31090302) : syn3-normal
[2015-09-30T15:55Z] INFO  16:55:55,332 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:55,334 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:55Z] INFO  16:55:55,334 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:55Z] INFO  16:55:55,334 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:55Z] INFO  16:55:55,338 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign-realign.intervals -L X:1-31090302 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpOAdL0k/1_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam
[2015-09-30T15:55Z] INFO  16:55:55,343 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:55Z] INFO  16:55:55,343 HelpFormatter - Date/Time: 2015/09/30 16:55:55
[2015-09-30T15:55Z] INFO  16:55:55,343 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:55,343 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:55Z] INFO  16:55:55,466 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:55Z] INFO  16:55:56,175 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:55Z] INFO  16:55:56,182 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:55Z] INFO  16:55:56,198 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:55Z] INFO  16:55:57,071 IntervalUtils - Processing 31090302 bp from intervals
[2015-09-30T15:55Z] WARN  16:55:57,077 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:55Z] INFO  16:55:57,437 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:55Z] INFO  16:55:57,868 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:55Z] INFO  16:55:57,868 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:55Z] INFO  16:55:57,869 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:55Z] INFO  16:55:57,869 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:55Z] INFO  16:55:58,283 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:55Z] INFO  16:55:58,474 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:56Z] INFO  16:56:02,726 ProgressMeter -     22:50495530   1200015.0    61.0 s      51.0 s       96.0%    63.0 s       2.0 s
[2015-09-30T15:56Z] INFO  16:56:07,108 ProgressMeter -      X:50114176    500007.0    60.0 s     120.0 s       60.5%    99.0 s      39.0 s
[2015-09-30T15:56Z] INFO  16:56:08,781 ProgressMeter -            done   1460498.0    67.0 s      46.0 s       99.7%    67.0 s       0.0 s
[2015-09-30T15:56Z] INFO  16:56:08,782 ProgressMeter - Total runtime 67.47 secs, 1.12 min, 0.02 hours
[2015-09-30T15:56Z] INFO  16:56:08,785 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1460498 total reads (0.00%)
[2015-09-30T15:56Z] INFO  16:56:08,785 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:56Z] INFO  16:56:08,785 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:56Z] INFO  16:56:08,786 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:56Z] INFO  16:56:09,841 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:56Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam
[2015-09-30T15:56Z] GATK pre-alignment ('X', 62568928, 94148729) : syn3-normal
[2015-09-30T15:56Z] INFO  16:56:15,807 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:56Z] INFO  16:56:15,809 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:56Z] INFO  16:56:15,810 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:56Z] INFO  16:56:15,810 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:56Z] INFO  16:56:15,813 HelpFormatter - Program Args: -T PrintReads -L X:62568929-94148729 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpnh4S9t/1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam
[2015-09-30T15:56Z] INFO  16:56:15,819 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:56Z] INFO  16:56:15,819 HelpFormatter - Date/Time: 2015/09/30 16:56:15
[2015-09-30T15:56Z] INFO  16:56:15,819 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:56Z] INFO  16:56:15,819 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:56Z] INFO  16:56:15,924 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:56Z] INFO  16:56:17,456 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:56Z] INFO  16:56:17,505 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:56Z] INFO  16:56:17,512 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:56Z] INFO  16:56:17,527 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:56Z] INFO  16:56:17,540 IntervalUtils - Processing 31579801 bp from intervals
[2015-09-30T15:56Z] INFO  16:56:17,595 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:56Z] INFO  16:56:17,806 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:56Z] INFO  16:56:17,806 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:56Z] INFO  16:56:17,806 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:56Z] INFO  16:56:17,807 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:56Z] INFO  16:56:17,818 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:56Z] INFO  16:56:18,033 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:56Z] INFO  16:56:27,872 ProgressMeter -      X:18938484    400006.0    30.0 s      75.0 s       60.9%    49.0 s      19.0 s
[2015-09-30T15:56Z] INFO  16:56:31,620 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:56Z] INFO  16:56:32,187 ProgressMeter -            done    811652.0    85.0 s     104.0 s      100.0%    85.0 s       0.0 s
[2015-09-30T15:56Z] INFO  16:56:32,188 ProgressMeter - Total runtime 85.08 secs, 1.42 min, 0.02 hours
[2015-09-30T15:56Z] INFO  16:56:32,188 MicroScheduler - 1796 reads were filtered out during the traversal out of approximately 813448 total reads (0.22%)
[2015-09-30T15:56Z] INFO  16:56:32,188 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:56Z] INFO  16:56:32,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:56Z] INFO  16:56:32,189 MicroScheduler -   -> 1796 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:56Z] INFO  16:56:33,193 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:56Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam
[2015-09-30T15:56Z] INFO  16:56:35,373 ProgressMeter -            done    614276.0    37.0 s      61.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T15:56Z] INFO  16:56:35,373 ProgressMeter - Total runtime 37.51 secs, 0.63 min, 0.01 hours
[2015-09-30T15:56Z] INFO  16:56:35,377 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 614276 total reads (0.00%)
[2015-09-30T15:56Z] INFO  16:56:35,377 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:56Z] INFO  16:56:35,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:56Z] INFO  16:56:35,378 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:56Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam X:31132530-62519711
[2015-09-30T15:56Z] GATK: RealignerTargetCreator
[2015-09-30T15:56Z] INFO  16:56:36,428 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:56Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam
[2015-09-30T15:56Z] INFO  16:56:37,576 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:56Z] INFO  16:56:37,578 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:56Z] INFO  16:56:37,578 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:56Z] INFO  16:56:37,578 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:56Z] INFO  16:56:37,581 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpqz1VFc/1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign-realign.intervals -l INFO -L X:31132530-62519711 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:56Z] INFO  16:56:37,587 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:56Z] INFO  16:56:37,587 HelpFormatter - Date/Time: 2015/09/30 16:56:37
[2015-09-30T15:56Z] INFO  16:56:37,587 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:56Z] INFO  16:56:37,587 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:56Z] INFO  16:56:37,643 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:56Z] INFO  16:56:37,768 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:56Z] INFO  16:56:37,777 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:56Z] INFO  16:56:37,793 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:56Z] INFO  16:56:38,056 IntervalUtils - Processing 31387182 bp from intervals
[2015-09-30T15:56Z] WARN  16:56:38,060 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:56Z] INFO  16:56:38,115 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:56Z] GATK pre-alignment ('X', 94317773, 125687021) : syn3-normal
[2015-09-30T15:56Z] INFO  16:56:38,243 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:56Z] INFO  16:56:38,243 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:56Z] INFO  16:56:38,244 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:56Z] INFO  16:56:38,244 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:56Z] INFO  16:56:41,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:56Z] INFO  16:56:41,952 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:56Z] INFO  16:56:41,953 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:56Z] INFO  16:56:41,953 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:56Z] INFO  16:56:41,956 HelpFormatter - Program Args: -T PrintReads -L X:94317774-125687021 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpRbGbdo/1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam
[2015-09-30T15:56Z] INFO  16:56:41,962 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:56Z] INFO  16:56:41,962 HelpFormatter - Date/Time: 2015/09/30 16:56:41
[2015-09-30T15:56Z] INFO  16:56:41,962 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:56Z] INFO  16:56:41,962 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:56Z] INFO  16:56:42,069 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:56Z] INFO  16:56:43,872 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:56Z] INFO  16:56:43,923 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:56Z] INFO  16:56:43,931 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:56Z] INFO  16:56:43,946 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:56Z] INFO  16:56:43,960 IntervalUtils - Processing 31369248 bp from intervals
[2015-09-30T15:56Z] INFO  16:56:44,019 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:56Z] INFO  16:56:44,225 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:56Z] INFO  16:56:44,225 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:56Z] INFO  16:56:44,226 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:56Z] INFO  16:56:44,226 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:56Z] INFO  16:56:44,237 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:56Z] INFO  16:56:44,430 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:56Z] INFO  16:56:47,809 ProgressMeter -      X:70825677    200002.0    30.0 s       2.5 m       26.1%   114.0 s      84.0 s
[2015-09-30T15:57Z] INFO  16:57:03,505 ProgressMeter -            done   3.1387182E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T15:57Z] INFO  16:57:03,505 ProgressMeter - Total runtime 25.26 secs, 0.42 min, 0.01 hours
[2015-09-30T15:57Z] INFO  16:57:03,508 MicroScheduler - 138978 reads were filtered out during the traversal out of approximately 816674 total reads (17.02%)
[2015-09-30T15:57Z] INFO  16:57:03,508 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:57Z] INFO  16:57:03,509 MicroScheduler -   -> 9466 reads (1.16% of total) failing BadMateFilter
[2015-09-30T15:57Z] INFO  16:57:03,509 MicroScheduler -   -> 33949 reads (4.16% of total) failing DuplicateReadFilter
[2015-09-30T15:57Z] INFO  16:57:03,509 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:57Z] INFO  16:57:03,509 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:57Z] INFO  16:57:03,510 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:57Z] INFO  16:57:03,510 MicroScheduler -   -> 95563 reads (11.70% of total) failing MappingQualityZeroFilter
[2015-09-30T15:57Z] INFO  16:57:03,510 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:57Z] INFO  16:57:03,510 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:57Z] INFO  16:57:03,511 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:57Z] INFO  16:57:04,554 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:57Z] GATK: realign ('X', 31132529, 62519711) : syn3-normal
[2015-09-30T15:57Z] INFO  16:57:06,556 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:06,559 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:57Z] INFO  16:57:06,559 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:57Z] INFO  16:57:06,559 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:57Z] INFO  16:57:06,562 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign-realign.intervals -L X:31132530-62519711 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpHC48dc/1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam
[2015-09-30T15:57Z] INFO  16:57:06,569 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:57Z] INFO  16:57:06,569 HelpFormatter - Date/Time: 2015/09/30 16:57:06
[2015-09-30T15:57Z] INFO  16:57:06,569 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:06,570 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:06,693 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:57Z] INFO  16:57:06,833 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:57Z] INFO  16:57:06,841 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:57Z] INFO  16:57:07,015 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17
[2015-09-30T15:57Z] INFO  16:57:07,397 IntervalUtils - Processing 31387182 bp from intervals
[2015-09-30T15:57Z] WARN  16:57:07,401 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:57Z] INFO  16:57:07,507 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:57Z] INFO  16:57:07,929 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:57Z] INFO  16:57:07,930 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:57Z] INFO  16:57:07,930 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:57Z] INFO  16:57:07,931 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:57Z] INFO  16:57:08,153 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:57Z] INFO  16:57:08,344 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:57Z] INFO  16:57:08,410 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T15:57Z] INFO  16:57:08,525 ProgressMeter -            done    465059.0    50.0 s     109.0 s      100.0%    50.0 s       0.0 s
[2015-09-30T15:57Z] INFO  16:57:08,525 ProgressMeter - Total runtime 50.72 secs, 0.85 min, 0.01 hours
[2015-09-30T15:57Z] INFO  16:57:08,526 MicroScheduler - 1325 reads were filtered out during the traversal out of approximately 466384 total reads (0.28%)
[2015-09-30T15:57Z] INFO  16:57:08,526 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:57Z] INFO  16:57:08,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:57Z] INFO  16:57:08,526 MicroScheduler -   -> 1325 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:57Z] INFO  16:57:09,533 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:57Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam
[2015-09-30T15:57Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam X:62568929-94148729
[2015-09-30T15:57Z] GATK: RealignerTargetCreator
[2015-09-30T15:57Z] INFO  16:57:13,349 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:13,351 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:57Z] INFO  16:57:13,351 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:57Z] INFO  16:57:13,351 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:57Z] INFO  16:57:13,355 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpUUSgqE/1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign-realign.intervals -l INFO -L X:62568929-94148729 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:57Z] INFO  16:57:13,361 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:57Z] INFO  16:57:13,361 HelpFormatter - Date/Time: 2015/09/30 16:57:13
[2015-09-30T15:57Z] INFO  16:57:13,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:13,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:13,430 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:57Z] INFO  16:57:14,229 ProgressMeter -     X:106144011    200002.0    30.0 s       2.5 m       37.7%    79.0 s      49.0 s
[2015-09-30T15:57Z] INFO  16:57:14,250 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:57Z] INFO  16:57:14,258 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:57Z] INFO  16:57:14,273 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:57Z] INFO  16:57:14,511 IntervalUtils - Processing 31579801 bp from intervals
[2015-09-30T15:57Z] WARN  16:57:14,515 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:57Z] INFO  16:57:14,572 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:57Z] INFO  16:57:14,719 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:57Z] INFO  16:57:14,719 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:57Z] INFO  16:57:14,719 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:57Z] INFO  16:57:14,720 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:57Z] INFO  16:57:37,523 ProgressMeter -            done   3.1579801E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T15:57Z] INFO  16:57:37,523 ProgressMeter - Total runtime 22.80 secs, 0.38 min, 0.01 hours
[2015-09-30T15:57Z] INFO  16:57:37,528 MicroScheduler - 51824 reads were filtered out during the traversal out of approximately 467668 total reads (11.08%)
[2015-09-30T15:57Z] INFO  16:57:37,528 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:57Z] INFO  16:57:37,529 MicroScheduler -   -> 7492 reads (1.60% of total) failing BadMateFilter
[2015-09-30T15:57Z] INFO  16:57:37,529 MicroScheduler -   -> 19380 reads (4.14% of total) failing DuplicateReadFilter
[2015-09-30T15:57Z] INFO  16:57:37,529 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:57Z] INFO  16:57:37,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:57Z] INFO  16:57:37,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:57Z] INFO  16:57:37,530 MicroScheduler -   -> 24952 reads (5.34% of total) failing MappingQualityZeroFilter
[2015-09-30T15:57Z] INFO  16:57:37,530 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:57Z] INFO  16:57:37,531 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:57Z] INFO  16:57:37,532 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:57Z] INFO  16:57:38,121 ProgressMeter -      X:49298697    400006.0    30.0 s      75.0 s       57.9%    51.0 s      21.0 s
[2015-09-30T15:57Z] INFO  16:57:38,536 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:57Z] GATK: realign ('X', 62568928, 94148729) : syn3-normal
[2015-09-30T15:57Z] INFO  16:57:40,817 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:40,819 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:57Z] INFO  16:57:40,819 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:57Z] INFO  16:57:40,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:57Z] INFO  16:57:40,822 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign-realign.intervals -L X:62568929-94148729 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpqSKb46/1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam
[2015-09-30T15:57Z] INFO  16:57:40,828 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:57Z] INFO  16:57:40,828 HelpFormatter - Date/Time: 2015/09/30 16:57:40
[2015-09-30T15:57Z] INFO  16:57:40,828 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:40,828 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:40,945 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:57Z] INFO  16:57:41,008 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:57Z] INFO  16:57:41,015 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:57Z] INFO  16:57:41,030 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:57Z] INFO  16:57:41,656 IntervalUtils - Processing 31579801 bp from intervals
[2015-09-30T15:57Z] WARN  16:57:41,660 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:57Z] INFO  16:57:41,711 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:57Z] INFO  16:57:43,015 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:57Z] INFO  16:57:43,016 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:57Z] INFO  16:57:43,016 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:57Z] INFO  16:57:43,016 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:57Z] INFO  16:57:43,109 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:57Z] INFO  16:57:43,310 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:57Z] INFO  16:57:44,229 ProgressMeter -     X:123175937    600007.0    60.0 s     100.0 s       92.0%    65.0 s       5.0 s
[2015-09-30T15:57Z] INFO  16:57:46,295 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@2c97c9cf
[2015-09-30T15:57Z] INFO  16:57:46,457 ProgressMeter -            done    639841.0    62.0 s      97.0 s      100.0%    62.0 s       0.0 s
[2015-09-30T15:57Z] INFO  16:57:46,457 ProgressMeter - Total runtime 62.23 secs, 1.04 min, 0.02 hours
[2015-09-30T15:57Z] INFO  16:57:46,458 MicroScheduler - 1696 reads were filtered out during the traversal out of approximately 641537 total reads (0.26%)
[2015-09-30T15:57Z] INFO  16:57:46,458 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:57Z] INFO  16:57:46,458 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:57Z] INFO  16:57:46,458 MicroScheduler -   -> 1696 reads (0.26% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:57Z] INFO  16:57:47,900 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:57Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam
[2015-09-30T15:57Z] INFO  16:57:48,436 ProgressMeter -            done    811652.0    40.0 s      49.0 s      100.0%    40.0 s       0.0 s
[2015-09-30T15:57Z] INFO  16:57:48,437 ProgressMeter - Total runtime 40.51 secs, 0.68 min, 0.01 hours
[2015-09-30T15:57Z] INFO  16:57:48,440 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 811652 total reads (0.00%)
[2015-09-30T15:57Z] INFO  16:57:48,440 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:57Z] INFO  16:57:48,440 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:57Z] INFO  16:57:48,440 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:57Z] INFO  16:57:49,554 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:57Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam X:94317774-125687021
[2015-09-30T15:57Z] GATK: RealignerTargetCreator
[2015-09-30T15:57Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam
[2015-09-30T15:57Z] INFO  16:57:51,289 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:51,291 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:57Z] INFO  16:57:51,291 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:57Z] INFO  16:57:51,291 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:57Z] INFO  16:57:51,295 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpqSahqT/1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign-realign.intervals -l INFO -L X:94317774-125687021 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:57Z] INFO  16:57:51,300 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:57Z] INFO  16:57:51,301 HelpFormatter - Date/Time: 2015/09/30 16:57:51
[2015-09-30T15:57Z] INFO  16:57:51,301 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:51,301 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:51,358 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:57Z] INFO  16:57:51,474 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:57Z] INFO  16:57:51,481 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:57Z] INFO  16:57:51,497 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:57Z] GATK pre-alignment ('X', 125953527, 155270560) : syn3-normal
[2015-09-30T15:57Z] INFO  16:57:51,755 IntervalUtils - Processing 31369248 bp from intervals
[2015-09-30T15:57Z] WARN  16:57:51,759 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:57Z] INFO  16:57:51,817 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:57Z] INFO  16:57:51,957 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:57Z] INFO  16:57:51,958 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:57Z] INFO  16:57:51,958 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:57Z] INFO  16:57:51,958 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:57Z] INFO  16:57:53,295 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:53,297 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:57Z] INFO  16:57:53,297 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:57Z] INFO  16:57:53,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:57Z] INFO  16:57:53,301 HelpFormatter - Program Args: -T PrintReads -L X:125953528-155270560 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpkf1aZj/1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam
[2015-09-30T15:57Z] INFO  16:57:53,307 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:57Z] INFO  16:57:53,307 HelpFormatter - Date/Time: 2015/09/30 16:57:53
[2015-09-30T15:57Z] INFO  16:57:53,307 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:53,307 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:57Z] INFO  16:57:57,569 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:57Z] INFO  16:57:59,174 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:57Z] INFO  16:57:59,226 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:57Z] INFO  16:57:59,234 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:57Z] INFO  16:57:59,250 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:57Z] INFO  16:57:59,264 IntervalUtils - Processing 29317033 bp from intervals
[2015-09-30T15:57Z] INFO  16:57:59,324 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:57Z] INFO  16:57:59,529 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:57Z] INFO  16:57:59,529 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:57Z] INFO  16:57:59,530 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:57Z] INFO  16:57:59,530 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:57Z] INFO  16:57:59,542 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:57Z] INFO  16:57:59,733 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:58Z] INFO  16:58:07,814 ProgressMeter -            done    465059.0    24.0 s      53.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T15:58Z] INFO  16:58:07,815 ProgressMeter - Total runtime 24.80 secs, 0.41 min, 0.01 hours
[2015-09-30T15:58Z] INFO  16:58:07,818 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 465059 total reads (0.00%)
[2015-09-30T15:58Z] INFO  16:58:07,818 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:58Z] INFO  16:58:07,818 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:58Z] INFO  16:58:07,819 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:58Z] INFO  16:58:08,892 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:58Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam
[2015-09-30T15:58Z] GATK pre-alignment ('Y', 0, 28716339) : syn3-normal
[2015-09-30T15:58Z] INFO  16:58:13,314 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:13,316 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:58Z] INFO  16:58:13,316 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:58Z] INFO  16:58:13,316 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:58Z] INFO  16:58:13,320 HelpFormatter - Program Args: -T PrintReads -L Y:1-28716339 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-normal/1_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/Y/tx/tmpisUknK/1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam
[2015-09-30T15:58Z] INFO  16:58:13,326 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:58Z] INFO  16:58:13,326 HelpFormatter - Date/Time: 2015/09/30 16:58:13
[2015-09-30T15:58Z] INFO  16:58:13,326 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:13,326 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:13,435 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:58Z] INFO  16:58:14,905 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:58Z] INFO  16:58:14,955 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:58Z] INFO  16:58:14,963 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:58Z] INFO  16:58:14,978 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:58Z] INFO  16:58:14,992 IntervalUtils - Processing 28716339 bp from intervals
[2015-09-30T15:58Z] INFO  16:58:15,740 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:58Z] INFO  16:58:15,917 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:58Z] INFO  16:58:15,917 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:58Z] INFO  16:58:15,918 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:58Z] INFO  16:58:15,918 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:58Z] INFO  16:58:15,934 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:58Z] INFO  16:58:16,073 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:58Z] INFO  16:58:16,885 ProgressMeter -            done   3.1369248E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T15:58Z] INFO  16:58:16,885 ProgressMeter - Total runtime 24.93 secs, 0.42 min, 0.01 hours
[2015-09-30T15:58Z] INFO  16:58:16,888 MicroScheduler - 76019 reads were filtered out during the traversal out of approximately 643926 total reads (11.81%)
[2015-09-30T15:58Z] INFO  16:58:16,888 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:58Z] INFO  16:58:16,889 MicroScheduler -   -> 8940 reads (1.39% of total) failing BadMateFilter
[2015-09-30T15:58Z] INFO  16:58:16,889 MicroScheduler -   -> 25582 reads (3.97% of total) failing DuplicateReadFilter
[2015-09-30T15:58Z] INFO  16:58:16,889 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:58Z] INFO  16:58:16,889 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:58Z] INFO  16:58:16,889 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:58Z] INFO  16:58:16,890 MicroScheduler -   -> 41497 reads (6.44% of total) failing MappingQualityZeroFilter
[2015-09-30T15:58Z] INFO  16:58:16,890 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:58Z] INFO  16:58:16,890 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:58Z] INFO  16:58:16,890 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:58Z] INFO  16:58:17,857 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:58Z] GATK: realign ('X', 94317773, 125687021) : syn3-normal
[2015-09-30T15:58Z] INFO  16:58:19,155 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T15:58Z] INFO  16:58:19,187 ProgressMeter -            done     16739.0     3.0 s       3.3 m       99.8%     3.0 s       0.0 s
[2015-09-30T15:58Z] INFO  16:58:19,187 ProgressMeter - Total runtime 3.27 secs, 0.05 min, 0.00 hours
[2015-09-30T15:58Z] INFO  16:58:19,188 MicroScheduler - 781 reads were filtered out during the traversal out of approximately 17520 total reads (4.46%)
[2015-09-30T15:58Z] INFO  16:58:19,188 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:58Z] INFO  16:58:19,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:58Z] INFO  16:58:19,188 MicroScheduler -   -> 781 reads (4.46% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:58Z] INFO  16:58:19,436 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:19,438 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:58Z] INFO  16:58:19,438 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:58Z] INFO  16:58:19,438 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:58Z] INFO  16:58:19,441 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign-realign.intervals -L X:94317774-125687021 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmpfxIC0S/1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam
[2015-09-30T15:58Z] INFO  16:58:19,447 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:58Z] INFO  16:58:19,447 HelpFormatter - Date/Time: 2015/09/30 16:58:19
[2015-09-30T15:58Z] INFO  16:58:19,447 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:19,447 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:19,572 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:58Z] INFO  16:58:19,633 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:58Z] INFO  16:58:19,641 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:58Z] INFO  16:58:19,656 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:58Z] INFO  16:58:19,886 IntervalUtils - Processing 31369248 bp from intervals
[2015-09-30T15:58Z] WARN  16:58:19,890 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:58Z] INFO  16:58:19,943 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:58Z] INFO  16:58:20,136 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:58Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam
[2015-09-30T15:58Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam Y:1-28716339
[2015-09-30T15:58Z] GATK: RealignerTargetCreator
[2015-09-30T15:58Z] INFO  16:58:20,440 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:58Z] INFO  16:58:20,440 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:58Z] INFO  16:58:20,441 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:58Z] INFO  16:58:20,441 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:58Z] INFO  16:58:20,535 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:58Z] INFO  16:58:20,727 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:58Z] INFO  16:58:22,053 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:22,055 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:58Z] INFO  16:58:22,055 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:58Z] INFO  16:58:22,055 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:58Z] INFO  16:58:22,059 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/Y/1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/Y/tx/tmpUvdorK/1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign-realign.intervals -l INFO -L Y:1-28716339 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:58Z] INFO  16:58:22,064 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:58Z] INFO  16:58:22,064 HelpFormatter - Date/Time: 2015/09/30 16:58:22
[2015-09-30T15:58Z] INFO  16:58:22,064 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:22,064 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:22,122 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:58Z] INFO  16:58:23,007 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:58Z] INFO  16:58:23,015 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:58Z] INFO  16:58:23,030 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:58Z] INFO  16:58:23,283 IntervalUtils - Processing 28716339 bp from intervals
[2015-09-30T15:58Z] WARN  16:58:23,287 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:58Z] INFO  16:58:23,343 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:58Z] INFO  16:58:23,428 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:58Z] INFO  16:58:23,429 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:58Z] INFO  16:58:23,429 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:58Z] INFO  16:58:23,430 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:58Z] INFO  16:58:29,556 ProgressMeter -     X:138869578    200002.0    30.0 s       2.5 m       44.1%    68.0 s      38.0 s
[2015-09-30T15:58Z] INFO  16:58:34,540 ProgressMeter -            done   2.8716339E7    11.0 s       0.0 s      100.0%    11.0 s       0.0 s
[2015-09-30T15:58Z] INFO  16:58:34,540 ProgressMeter - Total runtime 11.11 secs, 0.19 min, 0.00 hours
[2015-09-30T15:58Z] INFO  16:58:34,543 MicroScheduler - 8581 reads were filtered out during the traversal out of approximately 16770 total reads (51.17%)
[2015-09-30T15:58Z] INFO  16:58:34,543 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:58Z] INFO  16:58:34,543 MicroScheduler -   -> 2292 reads (13.67% of total) failing BadMateFilter
[2015-09-30T15:58Z] INFO  16:58:34,544 MicroScheduler -   -> 647 reads (3.86% of total) failing DuplicateReadFilter
[2015-09-30T15:58Z] INFO  16:58:34,544 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:58Z] INFO  16:58:34,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:58Z] INFO  16:58:34,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:58Z] INFO  16:58:34,545 MicroScheduler -   -> 5642 reads (33.64% of total) failing MappingQualityZeroFilter
[2015-09-30T15:58Z] INFO  16:58:34,545 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:58Z] INFO  16:58:34,545 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:58Z] INFO  16:58:34,545 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:58Z] INFO  16:58:35,512 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:58Z] GATK: realign ('Y', 0, 28716339) : syn3-normal
[2015-09-30T15:58Z] INFO  16:58:37,457 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:37,459 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:58Z] INFO  16:58:37,460 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:58Z] INFO  16:58:37,460 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:58Z] INFO  16:58:37,463 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/Y/1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/Y/1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign-realign.intervals -L Y:1-28716339 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/Y/tx/tmpmM67N8/1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam
[2015-09-30T15:58Z] INFO  16:58:37,468 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:58Z] INFO  16:58:37,468 HelpFormatter - Date/Time: 2015/09/30 16:58:37
[2015-09-30T15:58Z] INFO  16:58:37,469 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:37,469 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:58Z] INFO  16:58:37,592 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:58Z] INFO  16:58:37,655 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:58Z] INFO  16:58:37,663 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:58Z] INFO  16:58:37,679 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:58Z] INFO  16:58:38,301 IntervalUtils - Processing 28716339 bp from intervals
[2015-09-30T15:58Z] WARN  16:58:38,305 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:58Z] INFO  16:58:38,360 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:58Z] INFO  16:58:38,457 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:58Z] INFO  16:58:38,457 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:58Z] INFO  16:58:38,458 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:58Z] INFO  16:58:38,458 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:58Z] INFO  16:58:38,491 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:58Z] INFO  16:58:38,632 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:58Z] INFO  16:58:41,284 ProgressMeter -            done     16739.0     2.0 s       2.8 m       99.8%     2.0 s       0.0 s
[2015-09-30T15:58Z] INFO  16:58:41,285 ProgressMeter - Total runtime 2.83 secs, 0.05 min, 0.00 hours
[2015-09-30T15:58Z] INFO  16:58:41,288 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 16739 total reads (0.00%)
[2015-09-30T15:58Z] INFO  16:58:41,288 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:58Z] INFO  16:58:41,289 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:58Z] INFO  16:58:41,289 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:58Z] INFO  16:58:42,284 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:58Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam
[2015-09-30T15:58Z] Select unmapped reads
[2015-09-30T15:58Z] INFO  16:58:52,911 ProgressMeter -     X:119692041    500006.0    32.0 s      64.0 s       80.9%    39.0 s       7.0 s
[2015-09-30T15:58Z] INFO  16:58:55,308 ProgressMeter -            done    639841.0    34.0 s      54.0 s      100.0%    34.0 s       0.0 s
[2015-09-30T15:58Z] INFO  16:58:55,309 ProgressMeter - Total runtime 34.87 secs, 0.58 min, 0.01 hours
[2015-09-30T15:58Z] INFO  16:58:55,312 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 639841 total reads (0.00%)
[2015-09-30T15:58Z] INFO  16:58:55,312 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:58Z] INFO  16:58:55,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:58Z] INFO  16:58:55,313 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:58Z] INFO  16:58:56,335 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:58Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam
[2015-09-30T15:58Z] Select unanalyzed reads
[2015-09-30T15:58Z] INFO  16:58:59,824 ProgressMeter -     X:153524341    600008.0    60.0 s     100.0 s       94.0%    63.0 s       3.0 s
[2015-09-30T15:59Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-noanalysis-prep.bam
[2015-09-30T15:59Z] GATK pre-alignment ('1', 0, 31187470) : syn3-tumor
[2015-09-30T15:59Z] INFO  16:59:06,784 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:59Z] INFO  16:59:06,786 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:59Z] INFO  16:59:06,786 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:59Z] INFO  16:59:06,786 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:59Z] INFO  16:59:06,790 HelpFormatter - Program Args: -T PrintReads -L 1:1-31187470 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpHNQFnC/2_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam
[2015-09-30T15:59Z] INFO  16:59:06,795 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:59Z] INFO  16:59:06,795 HelpFormatter - Date/Time: 2015/09/30 16:59:06
[2015-09-30T15:59Z] INFO  16:59:06,795 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:59Z] INFO  16:59:06,796 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:59Z] INFO  16:59:07,199 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:59Z] INFO  16:59:09,238 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T15:59Z] INFO  16:59:09,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T15:59Z] INFO  16:59:09,294 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:59Z] INFO  16:59:09,309 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:59Z] INFO  16:59:09,333 IntervalUtils - Processing 31187470 bp from intervals
[2015-09-30T15:59Z] INFO  16:59:09,390 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:59Z] INFO  16:59:09,573 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:59Z] INFO  16:59:09,573 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:59Z] INFO  16:59:09,573 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:59Z] INFO  16:59:09,574 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:59Z] INFO  16:59:09,585 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:59Z] INFO  16:59:09,807 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T15:59Z] INFO  16:59:10,111 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T15:59Z] INFO  16:59:10,183 ProgressMeter -            done    811360.0    70.0 s      87.0 s      100.0%    70.0 s       0.0 s
[2015-09-30T15:59Z] INFO  16:59:10,183 ProgressMeter - Total runtime 70.65 secs, 1.18 min, 0.02 hours
[2015-09-30T15:59Z] INFO  16:59:10,184 MicroScheduler - 1791 reads were filtered out during the traversal out of approximately 813151 total reads (0.22%)
[2015-09-30T15:59Z] INFO  16:59:10,184 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:59Z] INFO  16:59:10,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:59Z] INFO  16:59:10,185 MicroScheduler -   -> 1791 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:59Z] INFO  16:59:11,193 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:59Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam
[2015-09-30T15:59Z] GATK RealignerTargetCreator: 1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam X:125953528-155270560
[2015-09-30T15:59Z] GATK: RealignerTargetCreator
[2015-09-30T15:59Z] INFO  16:59:15,302 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:59Z] INFO  16:59:15,304 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:59Z] INFO  16:59:15,304 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:59Z] INFO  16:59:15,305 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:59Z] INFO  16:59:15,308 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmphI_bLn/1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign-realign.intervals -l INFO -L X:125953528-155270560 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T15:59Z] INFO  16:59:15,314 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:59Z] INFO  16:59:15,314 HelpFormatter - Date/Time: 2015/09/30 16:59:15
[2015-09-30T15:59Z] INFO  16:59:15,315 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:59Z] INFO  16:59:15,315 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:59Z] INFO  16:59:15,385 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:59Z] INFO  16:59:15,668 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T15:59Z] INFO  16:59:15,677 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:59Z] INFO  16:59:15,693 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T15:59Z] INFO  16:59:15,935 IntervalUtils - Processing 29317033 bp from intervals
[2015-09-30T15:59Z] WARN  16:59:15,939 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:59Z] INFO  16:59:15,996 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:59Z] INFO  16:59:16,161 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:59Z] INFO  16:59:16,162 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:59Z] INFO  16:59:16,162 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:59Z] INFO  16:59:16,163 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T15:59Z] INFO  16:59:39,576 ProgressMeter -       1:2126674    300006.0    30.0 s     100.0 s        6.8%     7.3 m       6.8 m
[2015-09-30T15:59Z] INFO  16:59:41,848 ProgressMeter -            done   2.9317033E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T15:59Z] INFO  16:59:41,849 ProgressMeter - Total runtime 25.69 secs, 0.43 min, 0.01 hours
[2015-09-30T15:59Z] INFO  16:59:41,852 MicroScheduler - 138452 reads were filtered out during the traversal out of approximately 816317 total reads (16.96%)
[2015-09-30T15:59Z] INFO  16:59:41,852 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T15:59Z] INFO  16:59:41,852 MicroScheduler -   -> 8685 reads (1.06% of total) failing BadMateFilter
[2015-09-30T15:59Z] INFO  16:59:41,852 MicroScheduler -   -> 35390 reads (4.34% of total) failing DuplicateReadFilter
[2015-09-30T15:59Z] INFO  16:59:41,853 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T15:59Z] INFO  16:59:41,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T15:59Z] INFO  16:59:41,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T15:59Z] INFO  16:59:41,853 MicroScheduler -   -> 94377 reads (11.56% of total) failing MappingQualityZeroFilter
[2015-09-30T15:59Z] INFO  16:59:41,854 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T15:59Z] INFO  16:59:41,854 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T15:59Z] INFO  16:59:41,854 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T15:59Z] INFO  16:59:42,845 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T15:59Z] GATK: realign ('X', 125953527, 155270560) : syn3-normal
[2015-09-30T15:59Z] INFO  16:59:44,715 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:59Z] INFO  16:59:44,717 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T15:59Z] INFO  16:59:44,717 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T15:59Z] INFO  16:59:44,718 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T15:59Z] INFO  16:59:44,721 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign-realign.intervals -L X:125953528-155270560 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/tx/tmp8HbakW/1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam
[2015-09-30T15:59Z] INFO  16:59:44,727 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T15:59Z] INFO  16:59:44,727 HelpFormatter - Date/Time: 2015/09/30 16:59:44
[2015-09-30T15:59Z] INFO  16:59:44,727 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:59Z] INFO  16:59:44,727 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T15:59Z] INFO  16:59:44,850 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T15:59Z] INFO  16:59:44,922 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T15:59Z] INFO  16:59:44,929 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T15:59Z] INFO  16:59:44,945 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T15:59Z] INFO  16:59:45,217 IntervalUtils - Processing 29317033 bp from intervals
[2015-09-30T15:59Z] WARN  16:59:45,221 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T15:59Z] INFO  16:59:45,272 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T15:59Z] INFO  16:59:45,426 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T15:59Z] INFO  16:59:45,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T15:59Z] INFO  16:59:45,427 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T15:59Z] INFO  16:59:45,427 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T15:59Z] INFO  16:59:45,523 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T15:59Z] INFO  16:59:45,707 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:00Z] INFO  17:00:09,577 ProgressMeter -       1:8921263    600009.0    60.0 s     100.0 s       28.6%     3.5 m       2.5 m
[2015-09-30T16:00Z] INFO  17:00:15,804 ProgressMeter -     X:153170164    500006.0    30.0 s      60.0 s       92.8%    32.0 s       2.0 s
[2015-09-30T16:00Z] INFO  17:00:23,160 ProgressMeter -            done    811360.0    37.0 s      46.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T16:00Z] INFO  17:00:23,160 ProgressMeter - Total runtime 37.73 secs, 0.63 min, 0.01 hours
[2015-09-30T16:00Z] INFO  17:00:23,163 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 811360 total reads (0.00%)
[2015-09-30T16:00Z] INFO  17:00:23,163 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:00Z] INFO  17:00:23,164 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:00Z] INFO  17:00:23,164 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:00Z] INFO  17:00:24,235 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:00Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam
[2015-09-30T16:00Z] GATK pre-alignment ('1', 31187762, 62229084) : syn3-tumor
[2015-09-30T16:00Z] INFO  17:00:28,107 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:00Z] INFO  17:00:28,109 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:00Z] INFO  17:00:28,109 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:00Z] INFO  17:00:28,109 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:00Z] INFO  17:00:28,113 HelpFormatter - Program Args: -T PrintReads -L 1:31187763-62229084 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpjnbheG/2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam
[2015-09-30T16:00Z] INFO  17:00:28,521 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:00Z] INFO  17:00:28,521 HelpFormatter - Date/Time: 2015/09/30 17:00:28
[2015-09-30T16:00Z] INFO  17:00:28,521 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:00Z] INFO  17:00:28,521 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:00Z] INFO  17:00:28,629 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:00Z] INFO  17:00:31,869 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:00Z] INFO  17:00:31,919 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:00Z] INFO  17:00:31,926 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:00Z] INFO  17:00:31,941 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:00Z] INFO  17:00:31,954 IntervalUtils - Processing 31041322 bp from intervals
[2015-09-30T16:00Z] INFO  17:00:32,010 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:00Z] INFO  17:00:32,194 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:00Z] INFO  17:00:32,194 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:00Z] INFO  17:00:32,195 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:00Z] INFO  17:00:32,195 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:00Z] INFO  17:00:32,206 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:00Z] INFO  17:00:32,420 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:00Z] INFO  17:00:39,620 ProgressMeter -      1:13202839   1000015.0    90.0 s      90.0 s       42.3%     3.5 m       2.0 m
[2015-09-30T16:01Z] INFO  17:01:02,222 ProgressMeter -      1:35260711    300005.0    30.0 s     100.0 s       13.1%     3.8 m       3.3 m
[2015-09-30T16:01Z] INFO  17:01:09,621 ProgressMeter -      1:17550083   1400020.0   120.0 s      85.0 s       56.3%     3.6 m      93.0 s
[2015-09-30T16:01Z] Index BAM file: 1_2014-08-13_dream-syn3-sort-nochrom-prep.bam
[2015-09-30T16:01Z] GATK pre-alignment ('1', 62231753, 93258244) : syn3-tumor
[2015-09-30T16:01Z] INFO  17:01:25,628 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:01Z] INFO  17:01:25,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:01Z] INFO  17:01:25,631 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:01Z] INFO  17:01:25,631 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:01Z] INFO  17:01:25,635 HelpFormatter - Program Args: -T PrintReads -L 1:62231754-93258244 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpNPLWey/2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam
[2015-09-30T16:01Z] INFO  17:01:25,794 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:01Z] INFO  17:01:25,794 HelpFormatter - Date/Time: 2015/09/30 17:01:25
[2015-09-30T16:01Z] INFO  17:01:25,794 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:01Z] INFO  17:01:25,794 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:01Z] INFO  17:01:25,909 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:01Z] INFO  17:01:26,695 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:01Z] INFO  17:01:26,744 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:01Z] INFO  17:01:26,752 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:01Z] INFO  17:01:26,766 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:01Z] INFO  17:01:26,779 IntervalUtils - Processing 31026491 bp from intervals
[2015-09-30T16:01Z] INFO  17:01:26,835 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:01Z] INFO  17:01:27,008 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:01Z] INFO  17:01:27,009 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:01Z] INFO  17:01:27,009 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:01Z] INFO  17:01:27,009 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:01Z] INFO  17:01:27,020 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:01Z] INFO  17:01:27,208 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:01Z] INFO  17:01:32,222 ProgressMeter -      1:41174626    600009.0    60.0 s     100.0 s       32.2%     3.1 m       2.1 m
[2015-09-30T16:01Z] INFO  17:01:39,622 ProgressMeter -      1:22262448   1800026.0     2.5 m      83.0 s       71.4%     3.5 m      60.0 s
[2015-09-30T16:01Z] INFO  17:01:57,012 ProgressMeter -      1:75680398    200002.0    30.0 s       2.5 m       43.3%    69.0 s      39.0 s
[2015-09-30T16:02Z] INFO  17:02:02,223 ProgressMeter -      1:46511965   1000014.0    90.0 s      90.0 s       49.4%     3.0 m      92.0 s
[2015-09-30T16:02Z] INFO  17:02:09,623 ProgressMeter -      1:27276517   2200033.0     3.0 m      81.0 s       87.5%     3.4 m      25.0 s
[2015-09-30T16:02Z] INFO  17:02:23,878 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:02Z] INFO  17:02:24,105 ProgressMeter -            done   2397226.0     3.2 m      81.0 s      100.0%     3.2 m       0.0 s
[2015-09-30T16:02Z] INFO  17:02:24,105 ProgressMeter - Total runtime 194.53 secs, 3.24 min, 0.05 hours
[2015-09-30T16:02Z] INFO  17:02:24,105 MicroScheduler - 3599 reads were filtered out during the traversal out of approximately 2400825 total reads (0.15%)
[2015-09-30T16:02Z] INFO  17:02:24,106 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:02Z] INFO  17:02:24,106 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:02Z] INFO  17:02:24,106 MicroScheduler -   -> 3599 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:02Z] INFO  17:02:25,109 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:02Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam
[2015-09-30T16:02Z] INFO  17:02:27,013 ProgressMeter -      1:92446038    500005.0    60.0 s     120.0 s       97.4%    61.0 s       1.0 s
[2015-09-30T16:02Z] INFO  17:02:29,725 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:02Z] INFO  17:02:29,941 ProgressMeter -            done    599838.0    62.0 s     104.0 s      100.0%    62.0 s       0.0 s
[2015-09-30T16:02Z] INFO  17:02:29,942 ProgressMeter - Total runtime 62.93 secs, 1.05 min, 0.02 hours
[2015-09-30T16:02Z] INFO  17:02:29,942 MicroScheduler - 1963 reads were filtered out during the traversal out of approximately 601801 total reads (0.33%)
[2015-09-30T16:02Z] INFO  17:02:29,942 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:02Z] INFO  17:02:29,942 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:02Z] INFO  17:02:29,943 MicroScheduler -   -> 1963 reads (0.33% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:02Z] INFO  17:02:30,977 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:02Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam 1:1-31187470
[2015-09-30T16:02Z] GATK: RealignerTargetCreator
[2015-09-30T16:02Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam
[2015-09-30T16:02Z] INFO  17:02:32,224 ProgressMeter -      1:55081194   1400020.0   120.0 s      85.0 s       77.0%     2.6 m      35.0 s
[2015-09-30T16:02Z] INFO  17:02:32,557 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:02Z] INFO  17:02:32,559 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:02Z] INFO  17:02:32,559 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:02Z] INFO  17:02:32,559 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:02Z] INFO  17:02:32,563 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmphBUyci/2_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign-realign.intervals -l INFO -L 1:1-31187470 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:02Z] INFO  17:02:32,568 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:02Z] INFO  17:02:32,569 HelpFormatter - Date/Time: 2015/09/30 17:02:32
[2015-09-30T16:02Z] INFO  17:02:32,569 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:02Z] INFO  17:02:32,569 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:02Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam 1:62231754-93258244
[2015-09-30T16:02Z] GATK: RealignerTargetCreator
[2015-09-30T16:02Z] INFO  17:02:32,626 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:02Z] INFO  17:02:32,733 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:02Z] INFO  17:02:32,741 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:02Z] INFO  17:02:32,757 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:02Z] INFO  17:02:33,535 IntervalUtils - Processing 31187470 bp from intervals
[2015-09-30T16:02Z] WARN  17:02:33,539 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:02Z] INFO  17:02:33,631 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:02Z] INFO  17:02:34,023 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:02Z] INFO  17:02:34,023 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:02Z] INFO  17:02:34,023 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:02Z] INFO  17:02:34,024 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:02Z] INFO  17:02:34,476 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:02Z] INFO  17:02:34,478 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:02Z] INFO  17:02:34,478 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:02Z] INFO  17:02:34,479 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:02Z] INFO  17:02:34,482 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpxFAsVF/2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign-realign.intervals -l INFO -L 1:62231754-93258244 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:02Z] INFO  17:02:34,487 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:02Z] INFO  17:02:34,487 HelpFormatter - Date/Time: 2015/09/30 17:02:34
[2015-09-30T16:02Z] INFO  17:02:34,488 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:02Z] INFO  17:02:34,488 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:02Z] INFO  17:02:34,542 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:02Z] INFO  17:02:34,649 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:02Z] INFO  17:02:34,657 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:02Z] INFO  17:02:34,672 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:02Z] INFO  17:02:34,923 IntervalUtils - Processing 31026491 bp from intervals
[2015-09-30T16:02Z] WARN  17:02:34,927 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:02Z] INFO  17:02:34,982 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:02Z] INFO  17:02:37,900 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:02Z] INFO  17:02:37,900 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:02Z] INFO  17:02:37,901 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:02Z] INFO  17:02:37,901 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:02Z] INFO  17:02:42,931 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:02Z] INFO  17:02:43,013 ProgressMeter -            done   1605431.0     2.2 m      81.0 s      100.0%     2.2 m       0.0 s
[2015-09-30T16:02Z] INFO  17:02:43,014 ProgressMeter - Total runtime 130.82 secs, 2.18 min, 0.04 hours
[2015-09-30T16:02Z] INFO  17:02:43,014 MicroScheduler - 2929 reads were filtered out during the traversal out of approximately 1608360 total reads (0.18%)
[2015-09-30T16:02Z] INFO  17:02:43,015 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:02Z] INFO  17:02:43,015 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:02Z] INFO  17:02:43,015 MicroScheduler -   -> 2929 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:02Z] INFO  17:02:44,412 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:02Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam
[2015-09-30T16:02Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam 1:31187763-62229084
[2015-09-30T16:02Z] GATK: RealignerTargetCreator
[2015-09-30T16:02Z] INFO  17:02:49,934 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:02Z] INFO  17:02:49,936 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:02Z] INFO  17:02:49,936 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:02Z] INFO  17:02:49,936 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:02Z] INFO  17:02:49,940 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpHdX_66/2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign-realign.intervals -l INFO -L 1:31187763-62229084 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:02Z] INFO  17:02:49,945 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:02Z] INFO  17:02:49,945 HelpFormatter - Date/Time: 2015/09/30 17:02:49
[2015-09-30T16:02Z] INFO  17:02:49,945 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:02Z] INFO  17:02:49,945 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:02Z] INFO  17:02:50,002 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:02Z] INFO  17:02:50,111 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:02Z] INFO  17:02:50,119 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:02Z] INFO  17:02:50,134 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:02Z] INFO  17:02:50,383 IntervalUtils - Processing 31041322 bp from intervals
[2015-09-30T16:02Z] WARN  17:02:50,387 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:02Z] INFO  17:02:50,442 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:02Z] INFO  17:02:50,584 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:02Z] INFO  17:02:50,585 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:02Z] INFO  17:02:50,585 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:02Z] INFO  17:02:50,585 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:03Z] INFO  17:03:01,990 ProgressMeter -            done   3.1026491E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T16:03Z] INFO  17:03:01,991 ProgressMeter - Total runtime 24.09 secs, 0.40 min, 0.01 hours
[2015-09-30T16:03Z] INFO  17:03:01,994 MicroScheduler - 43275 reads were filtered out during the traversal out of approximately 603511 total reads (7.17%)
[2015-09-30T16:03Z] INFO  17:03:01,994 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:03Z] INFO  17:03:01,994 MicroScheduler -   -> 8668 reads (1.44% of total) failing BadMateFilter
[2015-09-30T16:03Z] INFO  17:03:01,995 MicroScheduler -   -> 23511 reads (3.90% of total) failing DuplicateReadFilter
[2015-09-30T16:03Z] INFO  17:03:01,995 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:03Z] INFO  17:03:01,995 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:03Z] INFO  17:03:01,995 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:03Z] INFO  17:03:01,996 MicroScheduler -   -> 11096 reads (1.84% of total) failing MappingQualityZeroFilter
[2015-09-30T16:03Z] INFO  17:03:01,996 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:03Z] INFO  17:03:01,996 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:03Z] INFO  17:03:01,996 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:03Z] INFO  17:03:02,972 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:03Z] GATK: realign ('1', 62231753, 93258244) : syn3-tumor
[2015-09-30T16:03Z] INFO  17:03:04,026 ProgressMeter -      1:18823133   1.8808832E7    30.0 s       1.0 s       60.4%    49.0 s      19.0 s
[2015-09-30T16:03Z] INFO  17:03:05,774 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:05,776 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:03Z] INFO  17:03:05,776 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:03Z] INFO  17:03:05,776 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:03Z] INFO  17:03:05,779 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep-prealign-realign.intervals -L 1:62231754-93258244 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpKdwmwX/2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam
[2015-09-30T16:03Z] INFO  17:03:05,785 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:03Z] INFO  17:03:05,785 HelpFormatter - Date/Time: 2015/09/30 17:03:05
[2015-09-30T16:03Z] INFO  17:03:05,785 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:05,785 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:05,916 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:03Z] INFO  17:03:06,128 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:03Z] INFO  17:03:06,135 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:03Z] INFO  17:03:06,152 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:03Z] INFO  17:03:06,384 IntervalUtils - Processing 31026491 bp from intervals
[2015-09-30T16:03Z] WARN  17:03:06,387 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:03Z] INFO  17:03:06,443 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:03Z] INFO  17:03:06,588 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:03Z] INFO  17:03:06,588 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:03Z] INFO  17:03:06,589 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:03Z] INFO  17:03:06,589 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:03Z] INFO  17:03:06,731 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:03Z] INFO  17:03:06,908 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:03Z] INFO  17:03:20,588 ProgressMeter -      1:53927445   2.2731982E7    30.0 s       1.0 s       73.3%    40.0 s      10.0 s
[2015-09-30T16:03Z] INFO  17:03:22,395 ProgressMeter -            done   3.118747E7    48.0 s       1.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T16:03Z] INFO  17:03:22,395 ProgressMeter - Total runtime 48.37 secs, 0.81 min, 0.01 hours
[2015-09-30T16:03Z] INFO  17:03:22,395 MicroScheduler - 274959 reads were filtered out during the traversal out of approximately 2411404 total reads (11.40%)
[2015-09-30T16:03Z] INFO  17:03:22,396 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:03Z] INFO  17:03:22,396 MicroScheduler -   -> 19514 reads (0.81% of total) failing BadMateFilter
[2015-09-30T16:03Z] INFO  17:03:22,396 MicroScheduler -   -> 121150 reads (5.02% of total) failing DuplicateReadFilter
[2015-09-30T16:03Z] INFO  17:03:22,396 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:03Z] INFO  17:03:22,397 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:03Z] INFO  17:03:22,397 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:03Z] INFO  17:03:22,397 MicroScheduler -   -> 134295 reads (5.57% of total) failing MappingQualityZeroFilter
[2015-09-30T16:03Z] INFO  17:03:22,397 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:03Z] INFO  17:03:22,397 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:03Z] INFO  17:03:22,397 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:03Z] INFO  17:03:23,433 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:03Z] GATK: realign ('1', 0, 31187470) : syn3-tumor
[2015-09-30T16:03Z] INFO  17:03:24,969 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:24,971 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:03Z] INFO  17:03:24,971 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:03Z] INFO  17:03:24,971 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:03Z] INFO  17:03:24,975 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_0_31187470-prep-prealign-realign.intervals -L 1:1-31187470 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpu16XQS/2_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam
[2015-09-30T16:03Z] INFO  17:03:24,980 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:03Z] INFO  17:03:24,980 HelpFormatter - Date/Time: 2015/09/30 17:03:24
[2015-09-30T16:03Z] INFO  17:03:24,980 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:24,981 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:25,113 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:03Z] INFO  17:03:25,175 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:03Z] INFO  17:03:25,182 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:03Z] INFO  17:03:25,198 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:03Z] INFO  17:03:25,715 IntervalUtils - Processing 31187470 bp from intervals
[2015-09-30T16:03Z] WARN  17:03:25,719 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:03Z] INFO  17:03:25,773 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:03Z] INFO  17:03:25,920 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:03Z] INFO  17:03:25,920 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:03Z] INFO  17:03:25,920 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:03Z] INFO  17:03:25,921 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:03Z] INFO  17:03:26,063 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:03Z] INFO  17:03:26,251 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:03Z] INFO  17:03:27,382 ProgressMeter -            done   3.1041322E7    36.0 s       1.0 s      100.0%    36.0 s       0.0 s
[2015-09-30T16:03Z] INFO  17:03:27,383 ProgressMeter - Total runtime 36.80 secs, 0.61 min, 0.01 hours
[2015-09-30T16:03Z] INFO  17:03:27,386 MicroScheduler - 126140 reads were filtered out during the traversal out of approximately 1615203 total reads (7.81%)
[2015-09-30T16:03Z] INFO  17:03:27,386 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:03Z] INFO  17:03:27,386 MicroScheduler -   -> 15413 reads (0.95% of total) failing BadMateFilter
[2015-09-30T16:03Z] INFO  17:03:27,387 MicroScheduler -   -> 77966 reads (4.83% of total) failing DuplicateReadFilter
[2015-09-30T16:03Z] INFO  17:03:27,387 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:03Z] INFO  17:03:27,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:03Z] INFO  17:03:27,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:03Z] INFO  17:03:27,387 MicroScheduler -   -> 32761 reads (2.03% of total) failing MappingQualityZeroFilter
[2015-09-30T16:03Z] INFO  17:03:27,388 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:03Z] INFO  17:03:27,388 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:03Z] INFO  17:03:27,388 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:03Z] INFO  17:03:28,343 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:03Z] GATK: realign ('1', 31187762, 62229084) : syn3-tumor
[2015-09-30T16:03Z] INFO  17:03:30,043 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:30,045 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:03Z] INFO  17:03:30,045 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:03Z] INFO  17:03:30,045 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:03Z] INFO  17:03:30,049 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep-prealign-realign.intervals -L 1:31187763-62229084 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpPCmvMX/2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam
[2015-09-30T16:03Z] INFO  17:03:30,055 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:03Z] INFO  17:03:30,055 HelpFormatter - Date/Time: 2015/09/30 17:03:30
[2015-09-30T16:03Z] INFO  17:03:30,055 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:30,055 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:30,190 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:03Z] INFO  17:03:30,257 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:03Z] INFO  17:03:30,265 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:03Z] INFO  17:03:30,281 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:03Z] INFO  17:03:30,784 IntervalUtils - Processing 31041322 bp from intervals
[2015-09-30T16:03Z] WARN  17:03:30,787 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:03Z] INFO  17:03:30,842 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:03Z] INFO  17:03:30,990 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:03Z] INFO  17:03:30,991 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:03Z] INFO  17:03:30,991 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:03Z] INFO  17:03:30,992 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:03Z] INFO  17:03:31,134 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:03Z] INFO  17:03:31,322 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:03Z] INFO  17:03:36,021 ProgressMeter -            done    599838.0    29.0 s      49.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T16:03Z] INFO  17:03:36,021 ProgressMeter - Total runtime 29.43 secs, 0.49 min, 0.01 hours
[2015-09-30T16:03Z] INFO  17:03:36,024 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 599838 total reads (0.00%)
[2015-09-30T16:03Z] INFO  17:03:36,024 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:03Z] INFO  17:03:36,025 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:03Z] INFO  17:03:36,025 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:03Z] INFO  17:03:37,175 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:03Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam
[2015-09-30T16:03Z] GATK pre-alignment ('1', 93297335, 142653959) : syn3-tumor
[2015-09-30T16:03Z] INFO  17:03:41,577 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:41,579 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:03Z] INFO  17:03:41,580 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:03Z] INFO  17:03:41,580 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:03Z] INFO  17:03:41,583 HelpFormatter - Program Args: -T PrintReads -L 1:93297336-142653959 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpF3L9Mi/2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam
[2015-09-30T16:03Z] INFO  17:03:41,589 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:03Z] INFO  17:03:41,589 HelpFormatter - Date/Time: 2015/09/30 17:03:41
[2015-09-30T16:03Z] INFO  17:03:41,589 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:41,590 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:03Z] INFO  17:03:42,008 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:03Z] INFO  17:03:42,689 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:03Z] INFO  17:03:42,737 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:03Z] INFO  17:03:42,744 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:03Z] INFO  17:03:42,758 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:03Z] INFO  17:03:42,770 IntervalUtils - Processing 49356624 bp from intervals
[2015-09-30T16:03Z] INFO  17:03:42,825 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:03Z] INFO  17:03:43,002 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:03Z] INFO  17:03:43,002 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:03Z] INFO  17:03:43,002 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:03Z] INFO  17:03:43,003 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:03Z] INFO  17:03:43,013 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:03Z] INFO  17:03:43,267 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:03Z] INFO  17:03:56,842 ProgressMeter -       1:3418768    400007.0    30.0 s      77.0 s       11.0%     4.6 m       4.1 m
[2015-09-30T16:04Z] INFO  17:04:02,024 ProgressMeter -      1:39986656    500008.0    31.0 s      62.0 s       28.3%   109.0 s      78.0 s
[2015-09-30T16:04Z] INFO  17:04:13,010 ProgressMeter -     1:108963632    200002.0    30.0 s       2.5 m       31.7%    94.0 s      64.0 s
[2015-09-30T16:04Z] INFO  17:04:27,235 ProgressMeter -      1:15707098   1100016.0    61.0 s      55.0 s       50.4%     2.0 m      60.0 s
[2015-09-30T16:04Z] INFO  17:04:32,669 ProgressMeter -      1:54301080   1300019.0    61.0 s      47.0 s       74.5%    81.0 s      20.0 s
[2015-09-30T16:04Z] INFO  17:04:39,979 ProgressMeter -            done   1605431.0    68.0 s      42.0 s      100.0%    68.0 s       0.0 s
[2015-09-30T16:04Z] INFO  17:04:39,980 ProgressMeter - Total runtime 68.99 secs, 1.15 min, 0.02 hours
[2015-09-30T16:04Z] INFO  17:04:39,983 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1605431 total reads (0.00%)
[2015-09-30T16:04Z] INFO  17:04:39,983 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:04Z] INFO  17:04:39,984 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:04Z] INFO  17:04:39,984 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:04Z] INFO  17:04:41,150 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:04Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam
[2015-09-30T16:04Z] INFO  17:04:43,054 ProgressMeter -     1:113242380    500006.0    60.0 s     120.0 s       40.4%     2.5 m      88.0 s
[2015-09-30T16:04Z] GATK pre-alignment ('1', 142666976, 173685474) : syn3-tumor
[2015-09-30T16:04Z] INFO  17:04:47,104 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:04Z] INFO  17:04:47,106 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:04Z] INFO  17:04:47,106 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:04Z] INFO  17:04:47,106 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:04Z] INFO  17:04:47,110 HelpFormatter - Program Args: -T PrintReads -L 1:142666977-173685474 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpVYZE72/2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam
[2015-09-30T16:04Z] INFO  17:04:47,115 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:04Z] INFO  17:04:47,116 HelpFormatter - Date/Time: 2015/09/30 17:04:47
[2015-09-30T16:04Z] INFO  17:04:47,116 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:04Z] INFO  17:04:47,116 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:04Z] INFO  17:04:47,832 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:04Z] INFO  17:04:48,532 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:04Z] INFO  17:04:48,583 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:04Z] INFO  17:04:48,592 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:04Z] INFO  17:04:48,607 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:04Z] INFO  17:04:48,619 IntervalUtils - Processing 31018498 bp from intervals
[2015-09-30T16:04Z] INFO  17:04:48,671 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:04Z] INFO  17:04:48,851 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:04Z] INFO  17:04:48,851 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:04Z] INFO  17:04:48,852 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:04Z] INFO  17:04:48,852 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:04Z] INFO  17:04:48,862 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:04Z] INFO  17:04:49,044 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:04Z] INFO  17:04:57,235 ProgressMeter -      1:22446840   1800026.0    91.0 s      50.0 s       72.0%     2.1 m      35.0 s
[2015-09-30T16:05Z] INFO  17:05:12,539 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:05Z] INFO  17:05:12,736 ProgressMeter -            done    880552.0    89.0 s     101.0 s      100.0%    89.0 s       0.0 s
[2015-09-30T16:05Z] INFO  17:05:12,736 ProgressMeter - Total runtime 89.73 secs, 1.50 min, 0.02 hours
[2015-09-30T16:05Z] INFO  17:05:12,736 MicroScheduler - 2104 reads were filtered out during the traversal out of approximately 882656 total reads (0.24%)
[2015-09-30T16:05Z] INFO  17:05:12,737 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:05Z] INFO  17:05:12,737 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:05Z] INFO  17:05:12,737 MicroScheduler -   -> 2104 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:05Z] INFO  17:05:13,744 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:05Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam
[2015-09-30T16:05Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam 1:93297336-142653959
[2015-09-30T16:05Z] GATK: RealignerTargetCreator
[2015-09-30T16:05Z] INFO  17:05:17,917 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:05Z] INFO  17:05:17,919 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:05Z] INFO  17:05:17,919 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:05Z] INFO  17:05:17,919 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:05Z] INFO  17:05:17,923 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmplrZRlK/2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign-realign.intervals -l INFO -L 1:93297336-142653959 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:05Z] INFO  17:05:17,929 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:05Z] INFO  17:05:17,929 HelpFormatter - Date/Time: 2015/09/30 17:05:17
[2015-09-30T16:05Z] INFO  17:05:17,929 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:05Z] INFO  17:05:17,929 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:05Z] INFO  17:05:17,984 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:05Z] INFO  17:05:18,092 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:05Z] INFO  17:05:18,100 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:05Z] INFO  17:05:18,115 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:05Z] INFO  17:05:18,360 IntervalUtils - Processing 49356624 bp from intervals
[2015-09-30T16:05Z] WARN  17:05:18,364 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:05Z] INFO  17:05:18,430 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:05Z] INFO  17:05:18,854 ProgressMeter -     1:146633904    200002.0    30.0 s       2.5 m       12.8%     3.9 m       3.4 m
[2015-09-30T16:05Z] INFO  17:05:18,885 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:05Z] INFO  17:05:18,885 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:05Z] INFO  17:05:18,886 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:05Z] INFO  17:05:18,886 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:05Z] INFO  17:05:20,508 ProgressMeter -            done   2397226.0   114.0 s      47.0 s      100.0%   114.0 s       0.0 s
[2015-09-30T16:05Z] INFO  17:05:20,508 ProgressMeter - Total runtime 114.59 secs, 1.91 min, 0.03 hours
[2015-09-30T16:05Z] INFO  17:05:20,511 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2397226 total reads (0.00%)
[2015-09-30T16:05Z] INFO  17:05:20,511 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:05Z] INFO  17:05:20,512 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:05Z] INFO  17:05:20,512 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:05Z] INFO  17:05:21,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:05Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam
[2015-09-30T16:05Z] GATK pre-alignment ('1', 173702591, 204798081) : syn3-tumor
[2015-09-30T16:05Z] INFO  17:05:28,918 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:05Z] INFO  17:05:28,920 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:05Z] INFO  17:05:28,920 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:05Z] INFO  17:05:28,920 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:05Z] INFO  17:05:28,923 HelpFormatter - Program Args: -T PrintReads -L 1:173702592-204798081 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpBocQ2A/2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam
[2015-09-30T16:05Z] INFO  17:05:28,929 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:05Z] INFO  17:05:28,929 HelpFormatter - Date/Time: 2015/09/30 17:05:28
[2015-09-30T16:05Z] INFO  17:05:28,929 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:05Z] INFO  17:05:28,929 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:05Z] INFO  17:05:29,034 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:05Z] INFO  17:05:31,421 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:05Z] INFO  17:05:31,468 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:05Z] INFO  17:05:31,475 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:05Z] INFO  17:05:31,488 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:05Z] INFO  17:05:31,500 IntervalUtils - Processing 31095490 bp from intervals
[2015-09-30T16:05Z] INFO  17:05:31,924 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:05Z] INFO  17:05:32,095 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:05Z] INFO  17:05:32,096 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:05Z] INFO  17:05:32,096 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:05Z] INFO  17:05:32,096 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:05Z] INFO  17:05:32,107 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:05Z] INFO  17:05:32,282 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:05Z] INFO  17:05:48,855 ProgressMeter -     1:151252290    500007.0    60.0 s     120.0 s       27.7%     3.6 m       2.6 m
[2015-09-30T16:05Z] INFO  17:05:48,889 ProgressMeter -     1:128103161   2.8190025E7    30.0 s       1.0 s       70.5%    42.0 s      12.0 s
[2015-09-30T16:05Z] INFO  17:05:54,783 ProgressMeter -            done   4.9356624E7    35.0 s       0.0 s      100.0%    35.0 s       0.0 s
[2015-09-30T16:05Z] INFO  17:05:54,783 ProgressMeter - Total runtime 35.90 secs, 0.60 min, 0.01 hours
[2015-09-30T16:05Z] INFO  17:05:54,787 MicroScheduler - 98838 reads were filtered out during the traversal out of approximately 885254 total reads (11.16%)
[2015-09-30T16:05Z] INFO  17:05:54,787 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:05Z] INFO  17:05:54,787 MicroScheduler -   -> 10537 reads (1.19% of total) failing BadMateFilter
[2015-09-30T16:05Z] INFO  17:05:54,787 MicroScheduler -   -> 37197 reads (4.20% of total) failing DuplicateReadFilter
[2015-09-30T16:05Z] INFO  17:05:54,788 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:05Z] INFO  17:05:54,788 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:05Z] INFO  17:05:54,788 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:05Z] INFO  17:05:54,788 MicroScheduler -   -> 51104 reads (5.77% of total) failing MappingQualityZeroFilter
[2015-09-30T16:05Z] INFO  17:05:54,789 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:05Z] INFO  17:05:54,789 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:05Z] INFO  17:05:54,789 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:05Z] INFO  17:05:55,756 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:05Z] GATK: realign ('1', 93297335, 142653959) : syn3-tumor
[2015-09-30T16:05Z] INFO  17:05:58,137 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:05Z] INFO  17:05:58,139 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:05Z] INFO  17:05:58,139 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:05Z] INFO  17:05:58,139 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:05Z] INFO  17:05:58,142 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep-prealign-realign.intervals -L 1:93297336-142653959 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpstLTI3/2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam
[2015-09-30T16:05Z] INFO  17:05:58,148 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:05Z] INFO  17:05:58,148 HelpFormatter - Date/Time: 2015/09/30 17:05:58
[2015-09-30T16:05Z] INFO  17:05:58,148 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:05Z] INFO  17:05:58,149 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:05Z] INFO  17:05:58,276 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:05Z] INFO  17:05:58,341 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:05Z] INFO  17:05:58,348 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:05Z] INFO  17:05:58,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:05Z] INFO  17:05:58,592 IntervalUtils - Processing 49356624 bp from intervals
[2015-09-30T16:05Z] WARN  17:05:58,596 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:05Z] INFO  17:05:58,650 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:05Z] INFO  17:05:58,875 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:05Z] INFO  17:05:58,875 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:05Z] INFO  17:05:58,876 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:05Z] INFO  17:05:58,876 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:05Z] INFO  17:05:59,015 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:05Z] INFO  17:05:59,244 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:06Z] INFO  17:06:02,121 ProgressMeter -     1:180885271    200003.0    30.0 s       2.5 m       23.1%     2.2 m      99.0 s
[2015-09-30T16:06Z] INFO  17:06:18,856 ProgressMeter -     1:154456670    800010.0    90.0 s     112.0 s       38.0%     3.9 m       2.4 m
[2015-09-30T16:06Z] INFO  17:06:29,494 ProgressMeter -     1:112270422    500006.0    30.0 s      61.0 s       38.4%    78.0 s      48.0 s
[2015-09-30T16:06Z] INFO  17:06:32,125 ProgressMeter -     1:197019706    500006.0    60.0 s     120.0 s       75.0%    80.0 s      20.0 s
[2015-09-30T16:06Z] INFO  17:06:42,436 ProgressMeter -            done    880552.0    43.0 s      49.0 s      100.0%    43.0 s       0.0 s
[2015-09-30T16:06Z] INFO  17:06:42,436 ProgressMeter - Total runtime 43.56 secs, 0.73 min, 0.01 hours
[2015-09-30T16:06Z] INFO  17:06:42,439 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 880552 total reads (0.00%)
[2015-09-30T16:06Z] INFO  17:06:42,440 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:06Z] INFO  17:06:42,440 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:06Z] INFO  17:06:42,440 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:06Z] INFO  17:06:43,583 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:06Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam
[2015-09-30T16:06Z] GATK pre-alignment ('1', 204839842, 235860787) : syn3-tumor
[2015-09-30T16:06Z] INFO  17:06:47,878 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:06Z] INFO  17:06:47,880 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:06Z] INFO  17:06:47,880 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:06Z] INFO  17:06:47,880 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:06Z] INFO  17:06:47,884 HelpFormatter - Program Args: -T PrintReads -L 1:204839843-235860787 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpbfqXzK/2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam
[2015-09-30T16:06Z] INFO  17:06:47,890 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:06Z] INFO  17:06:47,890 HelpFormatter - Date/Time: 2015/09/30 17:06:47
[2015-09-30T16:06Z] INFO  17:06:47,890 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:06Z] INFO  17:06:47,890 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:06Z] INFO  17:06:48,877 ProgressMeter -     1:156500771   1100013.0   120.0 s     109.0 s       44.6%     4.5 m       2.5 m
[2015-09-30T16:06Z] INFO  17:06:48,998 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:06Z] INFO  17:06:49,724 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:06Z] INFO  17:06:49,777 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:06Z] INFO  17:06:49,785 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:06Z] INFO  17:06:49,800 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:06Z] INFO  17:06:49,813 IntervalUtils - Processing 31020945 bp from intervals
[2015-09-30T16:06Z] INFO  17:06:49,870 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:06Z] INFO  17:06:50,766 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:06Z] INFO  17:06:50,767 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:06Z] INFO  17:06:50,767 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:06Z] INFO  17:06:50,767 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:06Z] INFO  17:06:50,778 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:06Z] INFO  17:06:50,978 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:07Z] INFO  17:07:02,152 ProgressMeter -     1:202912889    800009.0    90.0 s     112.0 s       93.9%    95.0 s       5.0 s
[2015-09-30T16:07Z] INFO  17:07:15,942 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:07Z] INFO  17:07:16,082 ProgressMeter -            done   1003109.0   103.0 s     103.0 s      100.0%   103.0 s       0.0 s
[2015-09-30T16:07Z] INFO  17:07:16,083 ProgressMeter - Total runtime 103.99 secs, 1.73 min, 0.03 hours
[2015-09-30T16:07Z] INFO  17:07:16,083 MicroScheduler - 2274 reads were filtered out during the traversal out of approximately 1005383 total reads (0.23%)
[2015-09-30T16:07Z] INFO  17:07:16,083 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:07Z] INFO  17:07:16,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:07Z] INFO  17:07:16,084 MicroScheduler -   -> 2274 reads (0.23% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:07Z] INFO  17:07:17,085 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:07Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam
[2015-09-30T16:07Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam 1:173702592-204798081
[2015-09-30T16:07Z] GATK: RealignerTargetCreator
[2015-09-30T16:07Z] INFO  17:07:19,791 ProgressMeter -     1:160304756   1400019.0     2.5 m     107.0 s       56.9%     4.4 m     113.0 s
[2015-09-30T16:07Z] INFO  17:07:20,769 ProgressMeter -     1:207897058    200002.0    30.0 s       2.5 m        9.9%     5.1 m       4.6 m
[2015-09-30T16:07Z] INFO  17:07:21,252 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:07Z] INFO  17:07:21,254 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:07Z] INFO  17:07:21,254 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:07Z] INFO  17:07:21,255 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:07Z] INFO  17:07:21,258 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpvcTO8x/2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign-realign.intervals -l INFO -L 1:173702592-204798081 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:07Z] INFO  17:07:21,263 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:07Z] INFO  17:07:21,264 HelpFormatter - Date/Time: 2015/09/30 17:07:21
[2015-09-30T16:07Z] INFO  17:07:21,264 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:07Z] INFO  17:07:21,264 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:07Z] INFO  17:07:21,320 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:07Z] INFO  17:07:21,425 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:07Z] INFO  17:07:21,432 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:07Z] INFO  17:07:21,448 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:07Z] INFO  17:07:21,685 IntervalUtils - Processing 31095490 bp from intervals
[2015-09-30T16:07Z] WARN  17:07:21,689 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:07Z] INFO  17:07:21,745 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:07Z] INFO  17:07:21,891 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:07Z] INFO  17:07:21,891 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:07Z] INFO  17:07:21,891 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:07Z] INFO  17:07:21,892 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:07Z] INFO  17:07:50,033 ProgressMeter -     1:168025520   1800023.0     3.0 m     100.0 s       81.8%     3.7 m      40.0 s
[2015-09-30T16:07Z] INFO  17:07:50,812 ProgressMeter -     1:222806360    500005.0    60.0 s     120.0 s       57.9%   103.0 s      43.0 s
[2015-09-30T16:07Z] INFO  17:07:51,544 ProgressMeter -            done   3.109549E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T16:07Z] INFO  17:07:51,544 ProgressMeter - Total runtime 29.65 secs, 0.49 min, 0.01 hours
[2015-09-30T16:07Z] INFO  17:07:51,548 MicroScheduler - 73012 reads were filtered out during the traversal out of approximately 1009632 total reads (7.23%)
[2015-09-30T16:07Z] INFO  17:07:51,548 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:07Z] INFO  17:07:51,548 MicroScheduler -   -> 10901 reads (1.08% of total) failing BadMateFilter
[2015-09-30T16:07Z] INFO  17:07:51,548 MicroScheduler -   -> 44311 reads (4.39% of total) failing DuplicateReadFilter
[2015-09-30T16:07Z] INFO  17:07:51,549 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:07Z] INFO  17:07:51,549 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:07Z] INFO  17:07:51,549 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:07Z] INFO  17:07:51,549 MicroScheduler -   -> 17800 reads (1.76% of total) failing MappingQualityZeroFilter
[2015-09-30T16:07Z] INFO  17:07:51,550 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:07Z] INFO  17:07:51,550 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:07Z] INFO  17:07:51,550 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:07Z] INFO  17:07:52,511 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:07Z] GATK: realign ('1', 173702591, 204798081) : syn3-tumor
[2015-09-30T16:07Z] INFO  17:07:54,714 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:07Z] INFO  17:07:54,716 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:07Z] INFO  17:07:54,716 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:07Z] INFO  17:07:54,716 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:07Z] INFO  17:07:54,719 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep-prealign-realign.intervals -L 1:173702592-204798081 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpsWZ6Je/2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam
[2015-09-30T16:07Z] INFO  17:07:54,724 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:07Z] INFO  17:07:54,725 HelpFormatter - Date/Time: 2015/09/30 17:07:54
[2015-09-30T16:07Z] INFO  17:07:54,725 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:07Z] INFO  17:07:54,725 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:07Z] INFO  17:07:54,865 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:07Z] INFO  17:07:54,928 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:07Z] INFO  17:07:54,936 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:07Z] INFO  17:07:54,952 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:07Z] INFO  17:07:55,608 IntervalUtils - Processing 31095490 bp from intervals
[2015-09-30T16:07Z] WARN  17:07:55,612 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:07Z] INFO  17:07:55,667 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:07Z] INFO  17:07:55,814 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:07Z] INFO  17:07:55,815 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:07Z] INFO  17:07:55,815 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:07Z] INFO  17:07:55,815 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:07Z] INFO  17:07:55,959 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:07Z] INFO  17:07:56,134 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:08Z] INFO  17:08:06,022 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:08Z] INFO  17:08:06,210 ProgressMeter -            done   1988457.0     3.3 m      99.0 s      100.0%     3.3 m       0.0 s
[2015-09-30T16:08Z] INFO  17:08:06,211 ProgressMeter - Total runtime 197.36 secs, 3.29 min, 0.05 hours
[2015-09-30T16:08Z] INFO  17:08:06,211 MicroScheduler - 3483 reads were filtered out during the traversal out of approximately 1991940 total reads (0.17%)
[2015-09-30T16:08Z] INFO  17:08:06,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:08Z] INFO  17:08:06,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:08Z] INFO  17:08:06,212 MicroScheduler -   -> 3483 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:08Z] INFO  17:08:07,194 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:08Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam
[2015-09-30T16:08Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam 1:142666977-173685474
[2015-09-30T16:08Z] GATK: RealignerTargetCreator
[2015-09-30T16:08Z] INFO  17:08:15,135 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:08Z] INFO  17:08:15,137 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:08Z] INFO  17:08:15,137 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:08Z] INFO  17:08:15,137 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:08Z] INFO  17:08:15,141 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmp6wZfYg/2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign-realign.intervals -l INFO -L 1:142666977-173685474 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:08Z] INFO  17:08:15,146 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:08Z] INFO  17:08:15,146 HelpFormatter - Date/Time: 2015/09/30 17:08:15
[2015-09-30T16:08Z] INFO  17:08:15,147 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:08Z] INFO  17:08:15,147 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:08Z] INFO  17:08:15,204 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:08Z] INFO  17:08:15,313 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:08Z] INFO  17:08:15,321 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:08Z] INFO  17:08:15,337 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:08Z] INFO  17:08:16,413 IntervalUtils - Processing 31018498 bp from intervals
[2015-09-30T16:08Z] WARN  17:08:16,417 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:08Z] INFO  17:08:16,473 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:08Z] INFO  17:08:16,626 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:08Z] INFO  17:08:16,626 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:08Z] INFO  17:08:16,627 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:08Z] INFO  17:08:16,627 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:08Z] INFO  17:08:20,812 ProgressMeter -     1:228565587    800008.0    90.0 s     112.0 s       76.5%   117.0 s      27.0 s
[2015-09-30T16:08Z] INFO  17:08:29,049 ProgressMeter -     1:200529609    500006.0    33.0 s      66.0 s       86.3%    38.0 s       5.0 s
[2015-09-30T16:08Z] INFO  17:08:40,913 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:08Z] INFO  17:08:41,030 ProgressMeter -            done   1111078.0   110.0 s      99.0 s      100.0%   110.0 s       0.0 s
[2015-09-30T16:08Z] INFO  17:08:41,030 ProgressMeter - Total runtime 110.26 secs, 1.84 min, 0.03 hours
[2015-09-30T16:08Z] INFO  17:08:41,030 MicroScheduler - 2507 reads were filtered out during the traversal out of approximately 1113585 total reads (0.23%)
[2015-09-30T16:08Z] INFO  17:08:41,031 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:08Z] INFO  17:08:41,031 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:08Z] INFO  17:08:41,031 MicroScheduler -   -> 2507 reads (0.23% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:08Z] INFO  17:08:42,026 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:08Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam
[2015-09-30T16:08Z] INFO  17:08:44,013 ProgressMeter -            done   1003109.0    48.0 s      48.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T16:08Z] INFO  17:08:44,013 ProgressMeter - Total runtime 48.20 secs, 0.80 min, 0.01 hours
[2015-09-30T16:08Z] INFO  17:08:44,016 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1003109 total reads (0.00%)
[2015-09-30T16:08Z] INFO  17:08:44,017 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:08Z] INFO  17:08:44,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:08Z] INFO  17:08:44,017 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:08Z] INFO  17:08:45,098 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:08Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam 1:204839843-235860787
[2015-09-30T16:08Z] GATK: RealignerTargetCreator
[2015-09-30T16:08Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam
[2015-09-30T16:08Z] INFO  17:08:46,629 ProgressMeter -     1:160110949   1.7437472E7    30.0 s       1.0 s       56.2%    53.0 s      23.0 s
[2015-09-30T16:08Z] INFO  17:08:46,788 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:08Z] INFO  17:08:46,790 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:08Z] INFO  17:08:46,790 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:08Z] INFO  17:08:46,790 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:08Z] INFO  17:08:46,794 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmppziU61/2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign-realign.intervals -l INFO -L 1:204839843-235860787 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:08Z] INFO  17:08:46,799 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:08Z] INFO  17:08:46,800 HelpFormatter - Date/Time: 2015/09/30 17:08:46
[2015-09-30T16:08Z] INFO  17:08:46,800 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:08Z] INFO  17:08:46,800 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:08Z] INFO  17:08:46,856 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:08Z] INFO  17:08:46,973 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:08Z] INFO  17:08:46,982 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:08Z] INFO  17:08:46,998 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:08Z] INFO  17:08:47,271 IntervalUtils - Processing 31020945 bp from intervals
[2015-09-30T16:08Z] WARN  17:08:47,275 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:08Z] INFO  17:08:47,330 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:08Z] INFO  17:08:47,492 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:08Z] INFO  17:08:47,493 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:08Z] INFO  17:08:47,493 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:08Z] INFO  17:08:47,493 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:08Z] GATK pre-alignment ('1', 235865791, 249250621) : syn3-tumor
[2015-09-30T16:08Z] INFO  17:08:49,280 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:08Z] INFO  17:08:49,282 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:08Z] INFO  17:08:49,282 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:08Z] INFO  17:08:49,282 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:08Z] INFO  17:08:49,286 HelpFormatter - Program Args: -T PrintReads -L 1:235865792-249250621 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmp4SvuUP/2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam
[2015-09-30T16:08Z] INFO  17:08:49,291 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:08Z] INFO  17:08:49,291 HelpFormatter - Date/Time: 2015/09/30 17:08:49
[2015-09-30T16:08Z] INFO  17:08:49,292 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:08Z] INFO  17:08:49,292 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:08Z] INFO  17:08:50,390 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:08Z] INFO  17:08:51,339 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:08Z] INFO  17:08:51,389 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:08Z] INFO  17:08:51,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:08Z] INFO  17:08:51,412 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:08Z] INFO  17:08:51,425 IntervalUtils - Processing 13384830 bp from intervals
[2015-09-30T16:08Z] INFO  17:08:51,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:08Z] INFO  17:08:51,658 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:08Z] INFO  17:08:51,658 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:08Z] INFO  17:08:51,658 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:08Z] INFO  17:08:51,659 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:08Z] INFO  17:08:51,670 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:08Z] INFO  17:08:51,760 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:09Z] INFO  17:09:01,356 ProgressMeter -            done   3.1018498E7    44.0 s       1.0 s      100.0%    44.0 s       0.0 s
[2015-09-30T16:09Z] INFO  17:09:01,357 ProgressMeter - Total runtime 44.73 secs, 0.75 min, 0.01 hours
[2015-09-30T16:09Z] INFO  17:09:01,360 MicroScheduler - 275334 reads were filtered out during the traversal out of approximately 1999390 total reads (13.77%)
[2015-09-30T16:09Z] INFO  17:09:01,360 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:09Z] INFO  17:09:01,360 MicroScheduler -   -> 16061 reads (0.80% of total) failing BadMateFilter
[2015-09-30T16:09Z] INFO  17:09:01,361 MicroScheduler -   -> 87445 reads (4.37% of total) failing DuplicateReadFilter
[2015-09-30T16:09Z] INFO  17:09:01,361 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:09Z] INFO  17:09:01,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:09Z] INFO  17:09:01,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:09Z] INFO  17:09:01,361 MicroScheduler -   -> 171828 reads (8.59% of total) failing MappingQualityZeroFilter
[2015-09-30T16:09Z] INFO  17:09:01,362 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:09Z] INFO  17:09:01,362 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:09Z] INFO  17:09:01,362 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:09Z] INFO  17:09:02,343 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:09Z] GATK: realign ('1', 142666976, 173685474) : syn3-tumor
[2015-09-30T16:09Z] INFO  17:09:04,613 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:04,615 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:09Z] INFO  17:09:04,615 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:09Z] INFO  17:09:04,615 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:09Z] INFO  17:09:04,619 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep-prealign-realign.intervals -L 1:142666977-173685474 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpzXuvuI/2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam
[2015-09-30T16:09Z] INFO  17:09:04,624 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:09Z] INFO  17:09:04,625 HelpFormatter - Date/Time: 2015/09/30 17:09:04
[2015-09-30T16:09Z] INFO  17:09:04,625 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:04,625 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:05,046 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:09Z] INFO  17:09:05,181 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:09Z] INFO  17:09:05,189 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:09Z] INFO  17:09:05,360 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17
[2015-09-30T16:09Z] INFO  17:09:06,270 IntervalUtils - Processing 31018498 bp from intervals
[2015-09-30T16:09Z] WARN  17:09:06,274 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:09Z] INFO  17:09:06,331 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:09Z] INFO  17:09:06,956 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:09Z] INFO  17:09:06,957 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:09Z] INFO  17:09:06,957 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:09Z] INFO  17:09:06,957 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:09Z] INFO  17:09:07,099 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:09Z] INFO  17:09:07,298 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:09Z] INFO  17:09:17,496 ProgressMeter -     1:235498733   3.064739E7    30.0 s       0.0 s       98.8%    30.0 s       0.0 s
[2015-09-30T16:09Z] INFO  17:09:18,144 ProgressMeter -            done   3.1020945E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T16:09Z] INFO  17:09:18,144 ProgressMeter - Total runtime 30.65 secs, 0.51 min, 0.01 hours
[2015-09-30T16:09Z] INFO  17:09:18,148 MicroScheduler - 93756 reads were filtered out during the traversal out of approximately 1117183 total reads (8.39%)
[2015-09-30T16:09Z] INFO  17:09:18,148 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:09Z] INFO  17:09:18,148 MicroScheduler -   -> 11784 reads (1.05% of total) failing BadMateFilter
[2015-09-30T16:09Z] INFO  17:09:18,149 MicroScheduler -   -> 51074 reads (4.57% of total) failing DuplicateReadFilter
[2015-09-30T16:09Z] INFO  17:09:18,149 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:09Z] INFO  17:09:18,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:09Z] INFO  17:09:18,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:09Z] INFO  17:09:18,149 MicroScheduler -   -> 30898 reads (2.77% of total) failing MappingQualityZeroFilter
[2015-09-30T16:09Z] INFO  17:09:18,150 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:09Z] INFO  17:09:18,150 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:09Z] INFO  17:09:18,150 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:09Z] INFO  17:09:19,154 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:09Z] GATK: realign ('1', 204839842, 235860787) : syn3-tumor
[2015-09-30T16:09Z] INFO  17:09:21,162 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:21,164 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:09Z] INFO  17:09:21,164 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:09Z] INFO  17:09:21,164 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:09Z] INFO  17:09:21,168 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep-prealign-realign.intervals -L 1:204839843-235860787 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpvl1Q35/2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam
[2015-09-30T16:09Z] INFO  17:09:21,173 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:09Z] INFO  17:09:21,173 HelpFormatter - Date/Time: 2015/09/30 17:09:21
[2015-09-30T16:09Z] INFO  17:09:21,173 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:21,173 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:21,300 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:09Z] INFO  17:09:21,363 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:09Z] INFO  17:09:21,370 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:09Z] INFO  17:09:21,386 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:09Z] INFO  17:09:21,661 ProgressMeter -     1:245027055    200002.0    30.0 s       2.5 m       68.4%    43.0 s      13.0 s
[2015-09-30T16:09Z] INFO  17:09:22,098 IntervalUtils - Processing 31020945 bp from intervals
[2015-09-30T16:09Z] WARN  17:09:22,101 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:09Z] INFO  17:09:22,157 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:09Z] INFO  17:09:22,303 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:09Z] INFO  17:09:22,304 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:09Z] INFO  17:09:22,304 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:09Z] INFO  17:09:22,304 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:09Z] INFO  17:09:22,444 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:09Z] INFO  17:09:22,630 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:09Z] INFO  17:09:34,129 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:09Z] INFO  17:09:34,210 ProgressMeter -            done    370892.0    42.0 s     114.0 s       99.9%    42.0 s       0.0 s
[2015-09-30T16:09Z] INFO  17:09:34,210 ProgressMeter - Total runtime 42.55 secs, 0.71 min, 0.01 hours
[2015-09-30T16:09Z] INFO  17:09:34,210 MicroScheduler - 1074 reads were filtered out during the traversal out of approximately 371966 total reads (0.29%)
[2015-09-30T16:09Z] INFO  17:09:34,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:09Z] INFO  17:09:34,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:09Z] INFO  17:09:34,211 MicroScheduler -   -> 1074 reads (0.29% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:09Z] INFO  17:09:35,208 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:09Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam
[2015-09-30T16:09Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam 1:235865792-249250621
[2015-09-30T16:09Z] GATK: RealignerTargetCreator
[2015-09-30T16:09Z] INFO  17:09:37,699 ProgressMeter -     1:150902222    400005.0    30.0 s      76.0 s       26.5%   112.0 s      82.0 s
[2015-09-30T16:09Z] INFO  17:09:38,487 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:38,489 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:09Z] INFO  17:09:38,489 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:09Z] INFO  17:09:38,489 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:09Z] INFO  17:09:38,492 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpY1unGe/2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign-realign.intervals -l INFO -L 1:235865792-249250621 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:09Z] INFO  17:09:38,498 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:09Z] INFO  17:09:38,498 HelpFormatter - Date/Time: 2015/09/30 17:09:38
[2015-09-30T16:09Z] INFO  17:09:38,499 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:38,499 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:38,554 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:09Z] INFO  17:09:38,660 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:09Z] INFO  17:09:38,667 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:09Z] INFO  17:09:38,683 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:09Z] INFO  17:09:38,921 IntervalUtils - Processing 13384830 bp from intervals
[2015-09-30T16:09Z] WARN  17:09:38,925 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:09Z] INFO  17:09:38,979 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:09Z] INFO  17:09:39,070 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:09Z] INFO  17:09:39,071 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:09Z] INFO  17:09:39,071 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:09Z] INFO  17:09:39,071 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:09Z] INFO  17:09:51,896 ProgressMeter -            done   1.338483E7    12.0 s       0.0 s      100.0%    12.0 s       0.0 s
[2015-09-30T16:09Z] INFO  17:09:51,897 ProgressMeter - Total runtime 12.83 secs, 0.21 min, 0.00 hours
[2015-09-30T16:09Z] INFO  17:09:51,900 MicroScheduler - 33616 reads were filtered out during the traversal out of approximately 373546 total reads (9.00%)
[2015-09-30T16:09Z] INFO  17:09:51,900 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:09Z] INFO  17:09:51,901 MicroScheduler -   -> 4622 reads (1.24% of total) failing BadMateFilter
[2015-09-30T16:09Z] INFO  17:09:51,901 MicroScheduler -   -> 16347 reads (4.38% of total) failing DuplicateReadFilter
[2015-09-30T16:09Z] INFO  17:09:51,901 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:09Z] INFO  17:09:51,901 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:09Z] INFO  17:09:51,902 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:09Z] INFO  17:09:51,902 MicroScheduler -   -> 12647 reads (3.39% of total) failing MappingQualityZeroFilter
[2015-09-30T16:09Z] INFO  17:09:51,902 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:09Z] INFO  17:09:51,902 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:09Z] INFO  17:09:51,903 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:09Z] INFO  17:09:52,413 ProgressMeter -     1:218942077    400004.0    30.0 s      75.0 s       45.5%    65.0 s      35.0 s
[2015-09-30T16:09Z] INFO  17:09:52,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:09Z] GATK: realign ('1', 235865791, 249250621) : syn3-tumor
[2015-09-30T16:09Z] INFO  17:09:54,455 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:54,457 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:09Z] INFO  17:09:54,457 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:09Z] INFO  17:09:54,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:09Z] INFO  17:09:54,460 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep-prealign-realign.intervals -L 1:235865792-249250621 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/tx/tmpZ9yyJu/2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam
[2015-09-30T16:09Z] INFO  17:09:54,467 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:09Z] INFO  17:09:54,467 HelpFormatter - Date/Time: 2015/09/30 17:09:54
[2015-09-30T16:09Z] INFO  17:09:54,467 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:54,467 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:09Z] INFO  17:09:54,594 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:09Z] INFO  17:09:54,664 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:09Z] INFO  17:09:54,672 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:09Z] INFO  17:09:54,689 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:09Z] INFO  17:09:55,487 IntervalUtils - Processing 13384830 bp from intervals
[2015-09-30T16:09Z] WARN  17:09:55,491 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:09Z] INFO  17:09:55,679 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:09Z] INFO  17:09:55,770 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:09Z] INFO  17:09:55,771 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:09Z] INFO  17:09:55,771 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:09Z] INFO  17:09:55,772 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:09Z] INFO  17:09:55,891 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:09Z] INFO  17:09:55,990 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:10Z] INFO  17:10:07,878 ProgressMeter -     1:156553664   1100013.0    60.0 s      55.0 s       44.8%     2.2 m      74.0 s
[2015-09-30T16:10Z] INFO  17:10:15,384 ProgressMeter -            done    370892.0    19.0 s      52.0 s       99.9%    19.0 s       0.0 s
[2015-09-30T16:10Z] INFO  17:10:15,384 ProgressMeter - Total runtime 19.61 secs, 0.33 min, 0.01 hours
[2015-09-30T16:10Z] INFO  17:10:15,387 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 370892 total reads (0.00%)
[2015-09-30T16:10Z] INFO  17:10:15,388 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:10Z] INFO  17:10:15,388 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:10Z] INFO  17:10:15,388 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:10Z] INFO  17:10:15,601 ProgressMeter -            done   1111078.0    53.0 s      47.0 s      100.0%    53.0 s       0.0 s
[2015-09-30T16:10Z] INFO  17:10:15,602 ProgressMeter - Total runtime 53.30 secs, 0.89 min, 0.01 hours
[2015-09-30T16:10Z] INFO  17:10:15,605 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1111078 total reads (0.00%)
[2015-09-30T16:10Z] INFO  17:10:15,605 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:10Z] INFO  17:10:15,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:10Z] INFO  17:10:15,606 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:10Z] INFO  17:10:16,468 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:10Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam
[2015-09-30T16:10Z] INFO  17:10:16,661 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:10Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam
[2015-09-30T16:10Z] GATK pre-alignment ('2', 0, 31134137) : syn3-tumor
[2015-09-30T16:10Z] INFO  17:10:19,310 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:10Z] INFO  17:10:19,311 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:10Z] INFO  17:10:19,312 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:10Z] INFO  17:10:19,312 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:10Z] INFO  17:10:19,315 HelpFormatter - Program Args: -T PrintReads -L 2:1-31134137 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpPtUoF6/2_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam
[2015-09-30T16:10Z] INFO  17:10:19,360 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:10Z] INFO  17:10:19,360 HelpFormatter - Date/Time: 2015/09/30 17:10:19
[2015-09-30T16:10Z] INFO  17:10:19,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:10Z] INFO  17:10:19,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:10Z] INFO  17:10:19,456 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:10Z] GATK pre-alignment ('2', 31134801, 62196287) : syn3-tumor
[2015-09-30T16:10Z] INFO  17:10:20,849 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:10Z] INFO  17:10:20,897 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:10Z] INFO  17:10:20,905 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:10Z] INFO  17:10:20,919 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:10Z] INFO  17:10:20,931 IntervalUtils - Processing 31134137 bp from intervals
[2015-09-30T16:10Z] INFO  17:10:20,988 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:10Z] INFO  17:10:21,170 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:10Z] INFO  17:10:21,170 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:10Z] INFO  17:10:21,171 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:10Z] INFO  17:10:21,171 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:10Z] INFO  17:10:21,181 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:10Z] INFO  17:10:21,364 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:10Z] INFO  17:10:22,102 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:10Z] INFO  17:10:22,104 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:10Z] INFO  17:10:22,104 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:10Z] INFO  17:10:22,104 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:10Z] INFO  17:10:22,107 HelpFormatter - Program Args: -T PrintReads -L 2:31134802-62196287 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmp1ForbH/2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam
[2015-09-30T16:10Z] INFO  17:10:22,113 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:10Z] INFO  17:10:22,113 HelpFormatter - Date/Time: 2015/09/30 17:10:22
[2015-09-30T16:10Z] INFO  17:10:22,113 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:10Z] INFO  17:10:22,114 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:10Z] INFO  17:10:22,225 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:10Z] INFO  17:10:24,046 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:10Z] INFO  17:10:24,098 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:10Z] INFO  17:10:24,106 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:10Z] INFO  17:10:24,121 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:10Z] INFO  17:10:24,135 IntervalUtils - Processing 31061486 bp from intervals
[2015-09-30T16:10Z] INFO  17:10:24,192 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:10Z] INFO  17:10:24,386 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:10Z] INFO  17:10:24,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:10Z] INFO  17:10:24,386 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:10Z] INFO  17:10:24,386 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:10Z] INFO  17:10:24,398 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:10Z] INFO  17:10:24,597 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:10Z] INFO  17:10:37,879 ProgressMeter -     1:173685248   1900024.0    90.0 s      47.0 s      100.0%    90.0 s       0.0 s
[2015-09-30T16:10Z] INFO  17:10:38,162 ProgressMeter -            done   1988457.0    91.0 s      45.0 s      100.0%    91.0 s       0.0 s
[2015-09-30T16:10Z] INFO  17:10:38,163 ProgressMeter - Total runtime 91.21 secs, 1.52 min, 0.03 hours
[2015-09-30T16:10Z] INFO  17:10:38,166 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1988457 total reads (0.00%)
[2015-09-30T16:10Z] INFO  17:10:38,166 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:10Z] INFO  17:10:38,167 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:10Z] INFO  17:10:38,167 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:10Z] INFO  17:10:39,286 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:10Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam
[2015-09-30T16:10Z] GATK pre-alignment ('2', 62227535, 95457199) : syn3-tumor
[2015-09-30T16:10Z] INFO  17:10:49,621 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:10Z] INFO  17:10:49,623 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:10Z] INFO  17:10:49,623 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:10Z] INFO  17:10:49,624 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:10Z] INFO  17:10:49,627 HelpFormatter - Program Args: -T PrintReads -L 2:62227536-95457199 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpaBlHaj/2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam
[2015-09-30T16:10Z] INFO  17:10:49,633 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:10Z] INFO  17:10:49,633 HelpFormatter - Date/Time: 2015/09/30 17:10:49
[2015-09-30T16:10Z] INFO  17:10:49,633 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:10Z] INFO  17:10:49,633 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:10Z] INFO  17:10:49,736 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:10Z] INFO  17:10:50,900 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:10Z] INFO  17:10:50,950 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:10Z] INFO  17:10:50,957 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:10Z] INFO  17:10:50,972 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:10Z] INFO  17:10:50,984 IntervalUtils - Processing 33229664 bp from intervals
[2015-09-30T16:10Z] INFO  17:10:51,039 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:10Z] INFO  17:10:51,173 ProgressMeter -      2:11054345    200004.0    30.0 s       2.5 m       35.5%    84.0 s      54.0 s
[2015-09-30T16:10Z] INFO  17:10:51,236 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:10Z] INFO  17:10:51,237 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:10Z] INFO  17:10:51,237 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:10Z] INFO  17:10:51,237 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:10Z] INFO  17:10:51,248 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:10Z] INFO  17:10:51,459 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:10Z] INFO  17:10:54,389 ProgressMeter -      2:38961627    200138.0    30.0 s       2.5 m       25.2%   119.0 s      89.0 s
[2015-09-30T16:11Z] INFO  17:11:21,174 ProgressMeter -      2:25851226    500009.0    60.0 s     120.0 s       83.0%    72.0 s      12.0 s
[2015-09-30T16:11Z] INFO  17:11:21,239 ProgressMeter -      2:71621333    200002.0    30.0 s       2.5 m       28.3%   106.0 s      76.0 s
[2015-09-30T16:11Z] INFO  17:11:24,389 ProgressMeter -      2:54013846    500141.0    60.0 s     119.0 s       73.7%    81.0 s      21.0 s
[2015-09-30T16:11Z] INFO  17:11:42,296 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:11Z] INFO  17:11:42,469 ProgressMeter -            done    740617.0    78.0 s     105.0 s      100.0%    78.0 s       0.0 s
[2015-09-30T16:11Z] INFO  17:11:42,469 ProgressMeter - Total runtime 78.08 secs, 1.30 min, 0.02 hours
[2015-09-30T16:11Z] INFO  17:11:42,470 MicroScheduler - 8195 reads were filtered out during the traversal out of approximately 748812 total reads (1.09%)
[2015-09-30T16:11Z] INFO  17:11:42,470 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:11Z] INFO  17:11:42,470 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:11Z] INFO  17:11:42,470 MicroScheduler -   -> 8195 reads (1.09% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:11Z] INFO  17:11:43,475 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:11Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam
[2015-09-30T16:11Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam 2:31134802-62196287
[2015-09-30T16:11Z] GATK: RealignerTargetCreator
[2015-09-30T16:11Z] INFO  17:11:47,706 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:11Z] INFO  17:11:47,708 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:11Z] INFO  17:11:47,708 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:11Z] INFO  17:11:47,708 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:11Z] INFO  17:11:47,712 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpJSdfaQ/2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign-realign.intervals -l INFO -L 2:31134802-62196287 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:11Z] INFO  17:11:47,717 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:11Z] INFO  17:11:47,717 HelpFormatter - Date/Time: 2015/09/30 17:11:47
[2015-09-30T16:11Z] INFO  17:11:47,718 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:11Z] INFO  17:11:47,718 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:11Z] INFO  17:11:47,771 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:11Z] INFO  17:11:47,867 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:11Z] INFO  17:11:47,874 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:11Z] INFO  17:11:47,889 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:11Z] INFO  17:11:48,122 IntervalUtils - Processing 31061486 bp from intervals
[2015-09-30T16:11Z] WARN  17:11:48,126 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:11Z] INFO  17:11:48,180 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:11Z] INFO  17:11:48,319 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:11Z] INFO  17:11:48,319 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:11Z] INFO  17:11:48,320 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:11Z] INFO  17:11:48,320 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:11Z] INFO  17:11:51,188 ProgressMeter -      2:29256133    800012.0    90.0 s     112.0 s       94.0%    95.0 s       5.0 s
[2015-09-30T16:11Z] INFO  17:11:51,240 ProgressMeter -      2:80472328    500006.0    60.0 s     120.0 s       54.9%   109.0 s      49.0 s
[2015-09-30T16:11Z] INFO  17:11:55,419 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:11Z] INFO  17:11:55,606 ProgressMeter -            done    935310.0    94.0 s     100.0 s      100.0%    94.0 s       0.0 s
[2015-09-30T16:11Z] INFO  17:11:55,607 ProgressMeter - Total runtime 94.44 secs, 1.57 min, 0.03 hours
[2015-09-30T16:11Z] INFO  17:11:55,607 MicroScheduler - 1884 reads were filtered out during the traversal out of approximately 937194 total reads (0.20%)
[2015-09-30T16:11Z] INFO  17:11:55,607 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:11Z] INFO  17:11:55,607 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:11Z] INFO  17:11:55,607 MicroScheduler -   -> 1884 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:11Z] INFO  17:11:56,667 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:11Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam
[2015-09-30T16:11Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam 2:1-31134137
[2015-09-30T16:11Z] GATK: RealignerTargetCreator
[2015-09-30T16:12Z] INFO  17:12:00,676 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:00,678 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:12Z] INFO  17:12:00,678 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:12Z] INFO  17:12:00,678 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:12Z] INFO  17:12:00,681 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpujK998/2_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign-realign.intervals -l INFO -L 2:1-31134137 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:12Z] INFO  17:12:00,686 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:12Z] INFO  17:12:00,687 HelpFormatter - Date/Time: 2015/09/30 17:12:00
[2015-09-30T16:12Z] INFO  17:12:00,687 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:00,687 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:00,747 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:12Z] INFO  17:12:00,849 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:12Z] INFO  17:12:00,856 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:12Z] INFO  17:12:00,871 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:12Z] INFO  17:12:01,429 IntervalUtils - Processing 31134137 bp from intervals
[2015-09-30T16:12Z] WARN  17:12:01,433 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:12Z] INFO  17:12:01,488 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:12Z] INFO  17:12:01,625 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:12Z] INFO  17:12:01,625 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:12Z] INFO  17:12:01,626 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:12Z] INFO  17:12:01,626 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:12Z] INFO  17:12:13,307 ProgressMeter -            done   3.1061486E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T16:12Z] INFO  17:12:13,307 ProgressMeter - Total runtime 24.99 secs, 0.42 min, 0.01 hours
[2015-09-30T16:12Z] INFO  17:12:13,310 MicroScheduler - 77059 reads were filtered out during the traversal out of approximately 744971 total reads (10.34%)
[2015-09-30T16:12Z] INFO  17:12:13,311 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:12Z] INFO  17:12:13,311 MicroScheduler -   -> 17529 reads (2.35% of total) failing BadMateFilter
[2015-09-30T16:12Z] INFO  17:12:13,311 MicroScheduler -   -> 29592 reads (3.97% of total) failing DuplicateReadFilter
[2015-09-30T16:12Z] INFO  17:12:13,311 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:12Z] INFO  17:12:13,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:12Z] INFO  17:12:13,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:12Z] INFO  17:12:13,312 MicroScheduler -   -> 29938 reads (4.02% of total) failing MappingQualityZeroFilter
[2015-09-30T16:12Z] INFO  17:12:13,312 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:12Z] INFO  17:12:13,313 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:12Z] INFO  17:12:13,313 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:12Z] INFO  17:12:14,253 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:12Z] GATK: realign ('2', 31134801, 62196287) : syn3-tumor
[2015-09-30T16:12Z] INFO  17:12:15,817 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:15,819 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:12Z] INFO  17:12:15,819 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:12Z] INFO  17:12:15,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:12Z] INFO  17:12:15,822 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep-prealign-realign.intervals -L 2:31134802-62196287 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpcBqyFj/2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam
[2015-09-30T16:12Z] INFO  17:12:15,828 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:12Z] INFO  17:12:15,828 HelpFormatter - Date/Time: 2015/09/30 17:12:15
[2015-09-30T16:12Z] INFO  17:12:15,828 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:15,829 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:15,957 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:12Z] INFO  17:12:16,016 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:12Z] INFO  17:12:16,024 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:12Z] INFO  17:12:16,038 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:12Z] INFO  17:12:16,922 IntervalUtils - Processing 31061486 bp from intervals
[2015-09-30T16:12Z] WARN  17:12:16,926 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:12Z] INFO  17:12:16,981 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:12Z] INFO  17:12:17,120 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:12Z] INFO  17:12:17,121 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:12Z] INFO  17:12:17,121 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:12Z] INFO  17:12:17,121 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:12Z] INFO  17:12:17,263 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:12Z] INFO  17:12:17,442 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:12Z] INFO  17:12:21,241 ProgressMeter -      2:90024782    800011.0    90.0 s     112.0 s       83.7%   107.0 s      17.0 s
[2015-09-30T16:12Z] INFO  17:12:26,546 IndelRealigner - Not attempting realignment in interval 2:33141296-33141667 because there are too many reads.
[2015-09-30T16:12Z] INFO  17:12:28,821 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:12Z] INFO  17:12:29,270 ProgressMeter -            done    943960.0    98.0 s     103.0 s      100.0%    98.0 s       0.0 s
[2015-09-30T16:12Z] INFO  17:12:29,270 ProgressMeter - Total runtime 98.03 secs, 1.63 min, 0.03 hours
[2015-09-30T16:12Z] INFO  17:12:29,271 MicroScheduler - 2376 reads were filtered out during the traversal out of approximately 946336 total reads (0.25%)
[2015-09-30T16:12Z] INFO  17:12:29,271 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:12Z] INFO  17:12:29,271 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:12Z] INFO  17:12:29,271 MicroScheduler -   -> 2376 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:12Z] INFO  17:12:30,040 ProgressMeter -            done   3.1134137E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T16:12Z] INFO  17:12:30,041 ProgressMeter - Total runtime 28.42 secs, 0.47 min, 0.01 hours
[2015-09-30T16:12Z] INFO  17:12:30,043 MicroScheduler - 71324 reads were filtered out during the traversal out of approximately 940735 total reads (7.58%)
[2015-09-30T16:12Z] INFO  17:12:30,044 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:12Z] INFO  17:12:30,044 MicroScheduler -   -> 10666 reads (1.13% of total) failing BadMateFilter
[2015-09-30T16:12Z] INFO  17:12:30,044 MicroScheduler -   -> 44495 reads (4.73% of total) failing DuplicateReadFilter
[2015-09-30T16:12Z] INFO  17:12:30,044 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:12Z] INFO  17:12:30,045 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:12Z] INFO  17:12:30,045 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:12Z] INFO  17:12:30,045 MicroScheduler -   -> 16163 reads (1.72% of total) failing MappingQualityZeroFilter
[2015-09-30T16:12Z] INFO  17:12:30,045 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:12Z] INFO  17:12:30,045 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:12Z] INFO  17:12:30,046 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:12Z] INFO  17:12:30,261 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:12Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam
[2015-09-30T16:12Z] INFO  17:12:31,033 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:12Z] GATK: realign ('2', 0, 31134137) : syn3-tumor
[2015-09-30T16:12Z] INFO  17:12:32,640 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:32,642 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:12Z] INFO  17:12:32,642 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:12Z] INFO  17:12:32,642 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:12Z] INFO  17:12:32,646 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_0_31134137-prep-prealign-realign.intervals -L 2:1-31134137 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpciNwx4/2_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam
[2015-09-30T16:12Z] INFO  17:12:32,652 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:12Z] INFO  17:12:32,652 HelpFormatter - Date/Time: 2015/09/30 17:12:32
[2015-09-30T16:12Z] INFO  17:12:32,653 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:32,653 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:32,838 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:12Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam 2:62227536-95457199
[2015-09-30T16:12Z] GATK: RealignerTargetCreator
[2015-09-30T16:12Z] INFO  17:12:32,908 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:12Z] INFO  17:12:32,915 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:12Z] INFO  17:12:32,931 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:12Z] INFO  17:12:33,408 IntervalUtils - Processing 31134137 bp from intervals
[2015-09-30T16:12Z] WARN  17:12:33,412 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:12Z] INFO  17:12:33,468 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:12Z] INFO  17:12:33,666 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:12Z] INFO  17:12:33,667 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:12Z] INFO  17:12:33,667 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:12Z] INFO  17:12:33,667 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:12Z] INFO  17:12:33,811 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:12Z] INFO  17:12:33,996 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:12Z] INFO  17:12:35,552 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:35,554 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:12Z] INFO  17:12:35,554 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:12Z] INFO  17:12:35,554 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:12Z] INFO  17:12:35,558 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpckXIFi/2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign-realign.intervals -l INFO -L 2:62227536-95457199 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:12Z] INFO  17:12:35,564 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:12Z] INFO  17:12:35,564 HelpFormatter - Date/Time: 2015/09/30 17:12:35
[2015-09-30T16:12Z] INFO  17:12:35,564 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:35,564 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:35,624 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:12Z] INFO  17:12:35,735 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:12Z] INFO  17:12:35,743 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:12Z] INFO  17:12:35,759 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:12Z] INFO  17:12:36,025 IntervalUtils - Processing 33229664 bp from intervals
[2015-09-30T16:12Z] WARN  17:12:36,029 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:12Z] INFO  17:12:36,152 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:12Z] INFO  17:12:36,294 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:12Z] INFO  17:12:36,294 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:12Z] INFO  17:12:36,295 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:12Z] INFO  17:12:36,295 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:12Z] INFO  17:12:47,410 ProgressMeter -      2:55122136    500141.0    30.0 s      60.0 s       77.2%    38.0 s       8.0 s
[2015-09-30T16:12Z] INFO  17:12:51,477 ProgressMeter -            done    740617.0    34.0 s      46.0 s      100.0%    34.0 s       0.0 s
[2015-09-30T16:12Z] INFO  17:12:51,477 ProgressMeter - Total runtime 34.36 secs, 0.57 min, 0.01 hours
[2015-09-30T16:12Z] INFO  17:12:51,481 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 740617 total reads (0.00%)
[2015-09-30T16:12Z] INFO  17:12:51,481 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:12Z] INFO  17:12:51,481 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:12Z] INFO  17:12:51,481 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:12Z] INFO  17:12:52,606 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:12Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam
[2015-09-30T16:12Z] GATK pre-alignment ('2', 95457728, 127315933) : syn3-tumor
[2015-09-30T16:12Z] INFO  17:12:56,362 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:56,364 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:12Z] INFO  17:12:56,364 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:12Z] INFO  17:12:56,364 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:12Z] INFO  17:12:56,367 HelpFormatter - Program Args: -T PrintReads -L 2:95457729-127315933 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpd6_M1b/2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam
[2015-09-30T16:12Z] INFO  17:12:56,372 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:12Z] INFO  17:12:56,373 HelpFormatter - Date/Time: 2015/09/30 17:12:56
[2015-09-30T16:12Z] INFO  17:12:56,373 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:56,373 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:12Z] INFO  17:12:56,465 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:12Z] INFO  17:12:57,677 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:12Z] INFO  17:12:57,727 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:12Z] INFO  17:12:57,734 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:12Z] INFO  17:12:57,749 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:12Z] INFO  17:12:57,762 IntervalUtils - Processing 31858205 bp from intervals
[2015-09-30T16:12Z] INFO  17:12:57,818 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:12Z] INFO  17:12:58,029 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:12Z] INFO  17:12:58,029 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:12Z] INFO  17:12:58,029 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:12Z] INFO  17:12:58,029 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:12Z] INFO  17:12:58,040 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:12Z] INFO  17:12:58,236 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:13Z] INFO  17:13:04,794 ProgressMeter -      2:26539232    500009.0    31.0 s      62.0 s       85.2%    36.0 s       5.0 s
[2015-09-30T16:13Z] INFO  17:13:05,323 ProgressMeter -            done   3.3229664E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T16:13Z] INFO  17:13:05,323 ProgressMeter - Total runtime 29.03 secs, 0.48 min, 0.01 hours
[2015-09-30T16:13Z] INFO  17:13:05,326 MicroScheduler - 129979 reads were filtered out during the traversal out of approximately 949692 total reads (13.69%)
[2015-09-30T16:13Z] INFO  17:13:05,326 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:13Z] INFO  17:13:05,327 MicroScheduler -   -> 10345 reads (1.09% of total) failing BadMateFilter
[2015-09-30T16:13Z] INFO  17:13:05,327 MicroScheduler -   -> 41066 reads (4.32% of total) failing DuplicateReadFilter
[2015-09-30T16:13Z] INFO  17:13:05,327 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:13Z] INFO  17:13:05,327 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:13Z] INFO  17:13:05,328 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:13Z] INFO  17:13:05,328 MicroScheduler -   -> 78568 reads (8.27% of total) failing MappingQualityZeroFilter
[2015-09-30T16:13Z] INFO  17:13:05,328 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:13Z] INFO  17:13:05,328 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:13Z] INFO  17:13:05,329 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:13Z] INFO  17:13:06,323 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:13Z] GATK: realign ('2', 62227535, 95457199) : syn3-tumor
[2015-09-30T16:13Z] INFO  17:13:08,455 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:13Z] INFO  17:13:08,458 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:13Z] INFO  17:13:08,458 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:13Z] INFO  17:13:08,458 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:13Z] INFO  17:13:08,462 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep-prealign-realign.intervals -L 2:62227536-95457199 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmp3_vbsU/2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam
[2015-09-30T16:13Z] INFO  17:13:08,467 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:13Z] INFO  17:13:08,467 HelpFormatter - Date/Time: 2015/09/30 17:13:08
[2015-09-30T16:13Z] INFO  17:13:08,468 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:13Z] INFO  17:13:08,468 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:13Z] INFO  17:13:08,595 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:13Z] INFO  17:13:08,661 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:13Z] INFO  17:13:08,669 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:13Z] INFO  17:13:08,685 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:13Z] INFO  17:13:08,916 IntervalUtils - Processing 33229664 bp from intervals
[2015-09-30T16:13Z] WARN  17:13:08,920 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:13Z] INFO  17:13:08,978 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:13Z] INFO  17:13:09,144 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:13Z] INFO  17:13:09,144 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:13Z] INFO  17:13:09,144 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:13Z] INFO  17:13:09,145 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:13Z] INFO  17:13:09,283 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:13Z] INFO  17:13:09,477 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:13Z] INFO  17:13:16,414 ProgressMeter -            done    935310.0    42.0 s      45.0 s      100.0%    42.0 s       0.0 s
[2015-09-30T16:13Z] INFO  17:13:16,414 ProgressMeter - Total runtime 42.75 secs, 0.71 min, 0.01 hours
[2015-09-30T16:13Z] INFO  17:13:16,418 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 935310 total reads (0.00%)
[2015-09-30T16:13Z] INFO  17:13:16,418 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:13Z] INFO  17:13:16,418 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:13Z] INFO  17:13:16,418 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:13Z] INFO  17:13:17,582 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:13Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam
[2015-09-30T16:13Z] GATK pre-alignment ('2', 127413596, 158444156) : syn3-tumor
[2015-09-30T16:13Z] INFO  17:13:23,546 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:13Z] INFO  17:13:23,548 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:13Z] INFO  17:13:23,549 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:13Z] INFO  17:13:23,549 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:13Z] INFO  17:13:23,552 HelpFormatter - Program Args: -T PrintReads -L 2:127413597-158444156 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpIYpWyg/2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam
[2015-09-30T16:13Z] INFO  17:13:23,558 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:13Z] INFO  17:13:23,558 HelpFormatter - Date/Time: 2015/09/30 17:13:23
[2015-09-30T16:13Z] INFO  17:13:23,558 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:13Z] INFO  17:13:23,559 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:13Z] INFO  17:13:23,667 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:13Z] INFO  17:13:24,940 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:13Z] INFO  17:13:24,991 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:13Z] INFO  17:13:24,999 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:13Z] INFO  17:13:25,014 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:13Z] INFO  17:13:25,027 IntervalUtils - Processing 31030560 bp from intervals
[2015-09-30T16:13Z] INFO  17:13:25,084 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:13Z] INFO  17:13:25,277 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:13Z] INFO  17:13:25,277 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:13Z] INFO  17:13:25,277 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:13Z] INFO  17:13:25,278 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:13Z] INFO  17:13:25,288 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:13Z] INFO  17:13:25,485 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:13Z] INFO  17:13:28,032 ProgressMeter -      2:97911229    200004.0    30.0 s       2.5 m        7.7%     6.5 m       6.0 m
[2015-09-30T16:13Z] INFO  17:13:39,717 ProgressMeter -      2:74776316    400004.0    30.0 s      76.0 s       37.8%    79.0 s      49.0 s
[2015-09-30T16:13Z] INFO  17:13:55,280 ProgressMeter -     2:132263991    200002.0    30.0 s       2.5 m       15.6%     3.2 m       2.7 m
[2015-09-30T16:13Z] INFO  17:13:57,504 ProgressMeter -            done    943960.0    48.0 s      51.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T16:13Z] INFO  17:13:57,504 ProgressMeter - Total runtime 48.36 secs, 0.81 min, 0.01 hours
[2015-09-30T16:13Z] INFO  17:13:57,507 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 943960 total reads (0.00%)
[2015-09-30T16:13Z] INFO  17:13:57,508 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:13Z] INFO  17:13:57,508 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:13Z] INFO  17:13:57,508 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:13Z] INFO  17:13:58,062 ProgressMeter -     2:108489271    500007.0    60.0 s     120.0 s       40.9%     2.4 m      86.0 s
[2015-09-30T16:13Z] INFO  17:13:58,610 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:13Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam
[2015-09-30T16:14Z] GATK pre-alignment ('2', 158484801, 189599894) : syn3-tumor
[2015-09-30T16:14Z] INFO  17:14:06,033 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:14Z] INFO  17:14:06,035 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:14Z] INFO  17:14:06,035 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:14Z] INFO  17:14:06,036 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:14Z] INFO  17:14:06,039 HelpFormatter - Program Args: -T PrintReads -L 2:158484802-189599894 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpJ_24JR/2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam
[2015-09-30T16:14Z] INFO  17:14:06,045 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:14Z] INFO  17:14:06,045 HelpFormatter - Date/Time: 2015/09/30 17:14:06
[2015-09-30T16:14Z] INFO  17:14:06,046 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:14Z] INFO  17:14:06,046 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:14Z] INFO  17:14:06,151 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:14Z] INFO  17:14:07,284 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:14Z] INFO  17:14:07,332 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:14Z] INFO  17:14:07,339 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:14Z] INFO  17:14:07,354 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:14Z] INFO  17:14:07,366 IntervalUtils - Processing 31115093 bp from intervals
[2015-09-30T16:14Z] INFO  17:14:07,421 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:14Z] INFO  17:14:07,830 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:14Z] INFO  17:14:07,831 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:14Z] INFO  17:14:07,831 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:14Z] INFO  17:14:07,831 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:14Z] INFO  17:14:07,842 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:14Z] INFO  17:14:08,030 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:14Z] INFO  17:14:25,281 ProgressMeter -     2:152539838    500005.0    60.0 s     120.0 s       81.0%    74.0 s      14.0 s
[2015-09-30T16:14Z] INFO  17:14:28,063 ProgressMeter -     2:114016923    800010.0    90.0 s     112.0 s       58.3%     2.6 m      64.0 s
[2015-09-30T16:14Z] INFO  17:14:31,740 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:14Z] INFO  17:14:31,811 ProgressMeter -            done    659690.0    66.0 s     100.0 s      100.0%    66.0 s       0.0 s
[2015-09-30T16:14Z] INFO  17:14:31,812 ProgressMeter - Total runtime 66.53 secs, 1.11 min, 0.02 hours
[2015-09-30T16:14Z] INFO  17:14:31,812 MicroScheduler - 1723 reads were filtered out during the traversal out of approximately 661413 total reads (0.26%)
[2015-09-30T16:14Z] INFO  17:14:31,812 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:14Z] INFO  17:14:31,813 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:14Z] INFO  17:14:31,813 MicroScheduler -   -> 1723 reads (0.26% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:14Z] INFO  17:14:32,879 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:14Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam
[2015-09-30T16:14Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam 2:127413597-158444156
[2015-09-30T16:14Z] GATK: RealignerTargetCreator
[2015-09-30T16:14Z] INFO  17:14:36,599 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:14Z] INFO  17:14:36,601 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:14Z] INFO  17:14:36,602 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:14Z] INFO  17:14:36,602 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:14Z] INFO  17:14:36,605 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpwrvEu0/2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign-realign.intervals -l INFO -L 2:127413597-158444156 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:14Z] INFO  17:14:36,612 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:14Z] INFO  17:14:36,612 HelpFormatter - Date/Time: 2015/09/30 17:14:36
[2015-09-30T16:14Z] INFO  17:14:36,612 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:14Z] INFO  17:14:36,612 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:14Z] INFO  17:14:36,673 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:14Z] INFO  17:14:36,781 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:14Z] INFO  17:14:36,789 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:14Z] INFO  17:14:36,807 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:14Z] INFO  17:14:37,419 IntervalUtils - Processing 31030560 bp from intervals
[2015-09-30T16:14Z] WARN  17:14:37,423 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:14Z] INFO  17:14:37,477 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:14Z] INFO  17:14:37,712 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:14Z] INFO  17:14:37,712 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:14Z] INFO  17:14:37,712 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:14Z] INFO  17:14:37,713 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:14Z] INFO  17:14:37,833 ProgressMeter -     2:169948169    200002.0    30.0 s       2.5 m       36.8%    81.0 s      51.0 s
[2015-09-30T16:14Z] INFO  17:14:45,454 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:14Z] INFO  17:14:45,580 ProgressMeter -            done   1038287.0   107.0 s     103.0 s      100.0%   107.0 s       0.0 s
[2015-09-30T16:14Z] INFO  17:14:45,581 ProgressMeter - Total runtime 107.55 secs, 1.79 min, 0.03 hours
[2015-09-30T16:14Z] INFO  17:14:45,581 MicroScheduler - 2473 reads were filtered out during the traversal out of approximately 1040760 total reads (0.24%)
[2015-09-30T16:14Z] INFO  17:14:45,581 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:14Z] INFO  17:14:45,582 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:14Z] INFO  17:14:45,582 MicroScheduler -   -> 2473 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:14Z] INFO  17:14:46,640 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:14Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam
[2015-09-30T16:14Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam 2:95457729-127315933
[2015-09-30T16:14Z] GATK: RealignerTargetCreator
[2015-09-30T16:14Z] INFO  17:14:50,816 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:14Z] INFO  17:14:50,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:14Z] INFO  17:14:50,818 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:14Z] INFO  17:14:50,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:14Z] INFO  17:14:50,822 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpgZr5My/2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign-realign.intervals -l INFO -L 2:95457729-127315933 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:14Z] INFO  17:14:50,827 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:14Z] INFO  17:14:50,828 HelpFormatter - Date/Time: 2015/09/30 17:14:50
[2015-09-30T16:14Z] INFO  17:14:50,828 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:14Z] INFO  17:14:50,828 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:14Z] INFO  17:14:50,882 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:14Z] INFO  17:14:50,980 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:14Z] INFO  17:14:50,988 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:14Z] INFO  17:14:51,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:14Z] INFO  17:14:51,242 IntervalUtils - Processing 31858205 bp from intervals
[2015-09-30T16:14Z] WARN  17:14:51,246 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:14Z] INFO  17:14:51,301 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:14Z] INFO  17:14:51,459 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:14Z] INFO  17:14:51,459 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:14Z] INFO  17:14:51,460 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:14Z] INFO  17:14:51,460 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:15Z] INFO  17:15:01,519 ProgressMeter -            done   3.103056E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T16:15Z] INFO  17:15:01,519 ProgressMeter - Total runtime 23.81 secs, 0.40 min, 0.01 hours
[2015-09-30T16:15Z] INFO  17:15:01,522 MicroScheduler - 85579 reads were filtered out during the traversal out of approximately 663469 total reads (12.90%)
[2015-09-30T16:15Z] INFO  17:15:01,523 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:15Z] INFO  17:15:01,523 MicroScheduler -   -> 8720 reads (1.31% of total) failing BadMateFilter
[2015-09-30T16:15Z] INFO  17:15:01,523 MicroScheduler -   -> 28310 reads (4.27% of total) failing DuplicateReadFilter
[2015-09-30T16:15Z] INFO  17:15:01,523 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:15Z] INFO  17:15:01,524 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:15Z] INFO  17:15:01,524 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:15Z] INFO  17:15:01,524 MicroScheduler -   -> 48549 reads (7.32% of total) failing MappingQualityZeroFilter
[2015-09-30T16:15Z] INFO  17:15:01,524 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:15Z] INFO  17:15:01,524 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:15Z] INFO  17:15:01,525 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:15Z] INFO  17:15:02,488 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:15Z] GATK: realign ('2', 127413596, 158444156) : syn3-tumor
[2015-09-30T16:15Z] INFO  17:15:04,555 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:04,557 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:15Z] INFO  17:15:04,557 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:15Z] INFO  17:15:04,557 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:15Z] INFO  17:15:04,561 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep-prealign-realign.intervals -L 2:127413597-158444156 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpJiBRwn/2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam
[2015-09-30T16:15Z] INFO  17:15:04,566 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:15Z] INFO  17:15:04,567 HelpFormatter - Date/Time: 2015/09/30 17:15:04
[2015-09-30T16:15Z] INFO  17:15:04,567 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:04,567 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:05,011 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:15Z] INFO  17:15:05,072 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:15Z] INFO  17:15:05,079 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:15Z] INFO  17:15:05,094 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:15Z] INFO  17:15:05,343 IntervalUtils - Processing 31030560 bp from intervals
[2015-09-30T16:15Z] WARN  17:15:05,347 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:15Z] INFO  17:15:05,606 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:15Z] INFO  17:15:06,219 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:15Z] INFO  17:15:06,219 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:15Z] INFO  17:15:06,220 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:15Z] INFO  17:15:06,220 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:15Z] INFO  17:15:06,670 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:15Z] INFO  17:15:06,853 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:15Z] INFO  17:15:07,840 ProgressMeter -     2:179310333    500005.0    60.0 s     120.0 s       66.9%    89.0 s      29.0 s
[2015-09-30T16:15Z] INFO  17:15:20,894 ProgressMeter -            done   3.1858205E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T16:15Z] INFO  17:15:20,895 ProgressMeter - Total runtime 29.44 secs, 0.49 min, 0.01 hours
[2015-09-30T16:15Z] INFO  17:15:20,898 MicroScheduler - 173341 reads were filtered out during the traversal out of approximately 1045191 total reads (16.58%)
[2015-09-30T16:15Z] INFO  17:15:20,898 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:15Z] INFO  17:15:20,898 MicroScheduler -   -> 10485 reads (1.00% of total) failing BadMateFilter
[2015-09-30T16:15Z] INFO  17:15:20,898 MicroScheduler -   -> 42570 reads (4.07% of total) failing DuplicateReadFilter
[2015-09-30T16:15Z] INFO  17:15:20,899 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:15Z] INFO  17:15:20,899 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:15Z] INFO  17:15:20,899 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:15Z] INFO  17:15:20,899 MicroScheduler -   -> 120286 reads (11.51% of total) failing MappingQualityZeroFilter
[2015-09-30T16:15Z] INFO  17:15:20,900 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:15Z] INFO  17:15:20,900 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:15Z] INFO  17:15:20,900 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:15Z] INFO  17:15:21,928 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:15Z] GATK: realign ('2', 95457728, 127315933) : syn3-tumor
[2015-09-30T16:15Z] INFO  17:15:23,482 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:23,484 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:15Z] INFO  17:15:23,484 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:15Z] INFO  17:15:23,485 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:15Z] INFO  17:15:23,488 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep-prealign-realign.intervals -L 2:95457729-127315933 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpDNgflo/2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam
[2015-09-30T16:15Z] INFO  17:15:23,493 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:15Z] INFO  17:15:23,493 HelpFormatter - Date/Time: 2015/09/30 17:15:23
[2015-09-30T16:15Z] INFO  17:15:23,494 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:23,494 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:23,598 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:15Z] INFO  17:15:23,665 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:15Z] INFO  17:15:23,673 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:15Z] INFO  17:15:23,689 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:15Z] INFO  17:15:24,102 IntervalUtils - Processing 31858205 bp from intervals
[2015-09-30T16:15Z] WARN  17:15:24,106 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:15Z] INFO  17:15:24,162 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:15Z] INFO  17:15:24,374 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:15Z] INFO  17:15:24,374 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:15Z] INFO  17:15:24,375 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:15Z] INFO  17:15:24,375 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:15Z] INFO  17:15:24,519 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:15Z] INFO  17:15:24,711 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:15Z] INFO  17:15:28,155 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:15Z] INFO  17:15:28,293 ProgressMeter -            done    789010.0    80.0 s     101.0 s      100.0%    80.0 s       0.0 s
[2015-09-30T16:15Z] INFO  17:15:28,293 ProgressMeter - Total runtime 80.46 secs, 1.34 min, 0.02 hours
[2015-09-30T16:15Z] INFO  17:15:28,294 MicroScheduler - 2350 reads were filtered out during the traversal out of approximately 791360 total reads (0.30%)
[2015-09-30T16:15Z] INFO  17:15:28,294 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:15Z] INFO  17:15:28,294 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:15Z] INFO  17:15:28,294 MicroScheduler -   -> 2350 reads (0.30% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:15Z] INFO  17:15:29,264 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:15Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam
[2015-09-30T16:15Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam 2:158484802-189599894
[2015-09-30T16:15Z] GATK: RealignerTargetCreator
[2015-09-30T16:15Z] INFO  17:15:33,751 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:33,753 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:15Z] INFO  17:15:33,753 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:15Z] INFO  17:15:33,753 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:15Z] INFO  17:15:33,757 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmppUOmVe/2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign-realign.intervals -l INFO -L 2:158484802-189599894 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:15Z] INFO  17:15:33,762 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:15Z] INFO  17:15:33,762 HelpFormatter - Date/Time: 2015/09/30 17:15:33
[2015-09-30T16:15Z] INFO  17:15:33,762 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:33,763 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:33,817 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:15Z] INFO  17:15:34,306 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:15Z] INFO  17:15:34,409 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:15Z] INFO  17:15:34,425 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:15Z] INFO  17:15:34,676 IntervalUtils - Processing 31115093 bp from intervals
[2015-09-30T16:15Z] WARN  17:15:34,680 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:15Z] INFO  17:15:34,737 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:15Z] INFO  17:15:34,886 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:15Z] INFO  17:15:34,887 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:15Z] INFO  17:15:34,887 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:15Z] INFO  17:15:34,888 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:15Z] INFO  17:15:36,222 ProgressMeter -     2:137990897    400004.0    30.0 s      75.0 s       34.1%    88.0 s      58.0 s
[2015-09-30T16:15Z] INFO  17:15:43,931 ProgressMeter -            done    659690.0    37.0 s      57.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T16:15Z] INFO  17:15:43,931 ProgressMeter - Total runtime 37.71 secs, 0.63 min, 0.01 hours
[2015-09-30T16:15Z] INFO  17:15:43,935 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 659690 total reads (0.00%)
[2015-09-30T16:15Z] INFO  17:15:43,935 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:15Z] INFO  17:15:43,935 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:15Z] INFO  17:15:43,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:15Z] INFO  17:15:45,137 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:15Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam
[2015-09-30T16:15Z] GATK pre-alignment ('2', 189838937, 221056966) : syn3-tumor
[2015-09-30T16:15Z] INFO  17:15:52,349 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:52,351 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:15Z] INFO  17:15:52,351 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:15Z] INFO  17:15:52,351 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:15Z] INFO  17:15:52,355 HelpFormatter - Program Args: -T PrintReads -L 2:189838938-221056966 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpcH0Qk0/2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam
[2015-09-30T16:15Z] INFO  17:15:52,360 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:15Z] INFO  17:15:52,360 HelpFormatter - Date/Time: 2015/09/30 17:15:52
[2015-09-30T16:15Z] INFO  17:15:52,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:52,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:15Z] INFO  17:15:52,474 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:15Z] INFO  17:15:53,905 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:15Z] INFO  17:15:53,954 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:15Z] INFO  17:15:53,962 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:15Z] INFO  17:15:53,976 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:15Z] INFO  17:15:53,989 IntervalUtils - Processing 31218029 bp from intervals
[2015-09-30T16:15Z] INFO  17:15:54,046 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:15Z] INFO  17:15:54,237 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:15Z] INFO  17:15:54,237 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:15Z] INFO  17:15:54,237 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:15Z] INFO  17:15:54,238 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:15Z] INFO  17:15:54,248 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:15Z] INFO  17:15:54,377 ProgressMeter -     2:109123896    500007.0    30.0 s      60.0 s       42.9%    69.0 s      39.0 s
[2015-09-30T16:15Z] INFO  17:15:54,440 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:16Z] INFO  17:16:01,222 ProgressMeter -            done   3.1115093E7    26.0 s       0.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T16:16Z] INFO  17:16:01,223 ProgressMeter - Total runtime 26.34 secs, 0.44 min, 0.01 hours
[2015-09-30T16:16Z] INFO  17:16:01,226 MicroScheduler - 55420 reads were filtered out during the traversal out of approximately 793849 total reads (6.98%)
[2015-09-30T16:16Z] INFO  17:16:01,226 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:16Z] INFO  17:16:01,226 MicroScheduler -   -> 9601 reads (1.21% of total) failing BadMateFilter
[2015-09-30T16:16Z] INFO  17:16:01,227 MicroScheduler -   -> 30751 reads (3.87% of total) failing DuplicateReadFilter
[2015-09-30T16:16Z] INFO  17:16:01,227 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:16Z] INFO  17:16:01,227 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:16Z] INFO  17:16:01,227 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:16Z] INFO  17:16:01,228 MicroScheduler -   -> 15068 reads (1.90% of total) failing MappingQualityZeroFilter
[2015-09-30T16:16Z] INFO  17:16:01,228 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:16Z] INFO  17:16:01,228 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:16Z] INFO  17:16:01,228 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:16Z] INFO  17:16:02,159 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:16Z] GATK: realign ('2', 158484801, 189599894) : syn3-tumor
[2015-09-30T16:16Z] INFO  17:16:04,045 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:16Z] INFO  17:16:04,047 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:16Z] INFO  17:16:04,047 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:16Z] INFO  17:16:04,047 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:16Z] INFO  17:16:04,051 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep-prealign-realign.intervals -L 2:158484802-189599894 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpAEui9U/2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam
[2015-09-30T16:16Z] INFO  17:16:04,057 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:16Z] INFO  17:16:04,057 HelpFormatter - Date/Time: 2015/09/30 17:16:04
[2015-09-30T16:16Z] INFO  17:16:04,057 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:16Z] INFO  17:16:04,057 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:16Z] INFO  17:16:04,190 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:16Z] INFO  17:16:04,260 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:16Z] INFO  17:16:04,268 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:16Z] INFO  17:16:04,284 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:16Z] INFO  17:16:04,517 IntervalUtils - Processing 31115093 bp from intervals
[2015-09-30T16:16Z] WARN  17:16:04,521 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:16Z] INFO  17:16:04,608 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:16Z] INFO  17:16:05,028 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:16Z] INFO  17:16:05,029 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:16Z] INFO  17:16:05,029 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:16Z] INFO  17:16:05,030 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:16Z] INFO  17:16:05,364 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:16Z] INFO  17:16:05,563 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:16Z] INFO  17:16:11,764 ProgressMeter -            done   1038287.0    47.0 s      45.0 s      100.0%    47.0 s       0.0 s
[2015-09-30T16:16Z] INFO  17:16:11,765 ProgressMeter - Total runtime 47.39 secs, 0.79 min, 0.01 hours
[2015-09-30T16:16Z] INFO  17:16:11,768 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1038287 total reads (0.00%)
[2015-09-30T16:16Z] INFO  17:16:11,768 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:16Z] INFO  17:16:11,768 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:16Z] INFO  17:16:11,768 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:16Z] INFO  17:16:12,897 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:16Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam
[2015-09-30T16:16Z] GATK pre-alignment ('2', 221341378, 243199373) : syn3-tumor
[2015-09-30T16:16Z] INFO  17:16:17,491 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:16Z] INFO  17:16:17,493 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:16Z] INFO  17:16:17,493 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:16Z] INFO  17:16:17,493 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:16Z] INFO  17:16:17,497 HelpFormatter - Program Args: -T PrintReads -L 2:221341379-243199373 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmp5fAxfC/2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam
[2015-09-30T16:16Z] INFO  17:16:17,502 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:16Z] INFO  17:16:17,502 HelpFormatter - Date/Time: 2015/09/30 17:16:17
[2015-09-30T16:16Z] INFO  17:16:17,503 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:16Z] INFO  17:16:17,503 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:16Z] INFO  17:16:17,606 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:16Z] INFO  17:16:19,076 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:16Z] INFO  17:16:19,126 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:16Z] INFO  17:16:19,133 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:16Z] INFO  17:16:19,147 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:16Z] INFO  17:16:19,160 IntervalUtils - Processing 21857995 bp from intervals
[2015-09-30T16:16Z] INFO  17:16:19,216 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:16Z] INFO  17:16:19,394 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:16Z] INFO  17:16:19,394 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:16Z] INFO  17:16:19,394 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:16Z] INFO  17:16:19,395 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:16Z] INFO  17:16:19,405 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:16Z] INFO  17:16:19,547 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:16Z] INFO  17:16:24,240 ProgressMeter -     2:201407177    200002.0    30.0 s       2.5 m       37.1%    80.0 s      50.0 s
[2015-09-30T16:16Z] INFO  17:16:35,633 ProgressMeter -     2:179367192    500005.0    30.0 s      61.0 s       67.1%    44.0 s      14.0 s
[2015-09-30T16:16Z] INFO  17:16:43,430 ProgressMeter -            done    789010.0    38.0 s      48.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T16:16Z] INFO  17:16:43,430 ProgressMeter - Total runtime 38.40 secs, 0.64 min, 0.01 hours
[2015-09-30T16:16Z] INFO  17:16:43,434 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 789010 total reads (0.00%)
[2015-09-30T16:16Z] INFO  17:16:43,434 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:16Z] INFO  17:16:43,434 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:16Z] INFO  17:16:43,434 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:16Z] INFO  17:16:44,516 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:16Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam
[2015-09-30T16:16Z] GATK pre-alignment ('3', 0, 31203562) : syn3-tumor
[2015-09-30T16:16Z] INFO  17:16:49,125 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:16Z] INFO  17:16:49,127 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:16Z] INFO  17:16:49,127 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:16Z] INFO  17:16:49,127 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:16Z] INFO  17:16:49,130 HelpFormatter - Program Args: -T PrintReads -L 3:1-31203562 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpfOxf4W/2_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam
[2015-09-30T16:16Z] INFO  17:16:49,136 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:16Z] INFO  17:16:49,136 HelpFormatter - Date/Time: 2015/09/30 17:16:49
[2015-09-30T16:16Z] INFO  17:16:49,136 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:16Z] INFO  17:16:49,136 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:16Z] INFO  17:16:49,242 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:16Z] INFO  17:16:49,425 ProgressMeter -     2:231911567    200002.0    30.0 s       2.5 m       48.4%    62.0 s      32.0 s
[2015-09-30T16:16Z] INFO  17:16:50,486 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:16Z] INFO  17:16:50,533 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:16Z] INFO  17:16:50,541 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:16Z] INFO  17:16:50,555 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:16Z] INFO  17:16:50,567 IntervalUtils - Processing 31203562 bp from intervals
[2015-09-30T16:16Z] INFO  17:16:50,622 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:16Z] INFO  17:16:50,817 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:16Z] INFO  17:16:50,818 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:16Z] INFO  17:16:50,818 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:16Z] INFO  17:16:50,818 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:16Z] INFO  17:16:50,829 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:16Z] INFO  17:16:51,034 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:16Z] INFO  17:16:54,241 ProgressMeter -     2:208134140    500006.0    60.0 s     120.0 s       58.6%   102.0 s      42.0 s
[2015-09-30T16:17Z] INFO  17:17:19,426 ProgressMeter -     2:238289694    500006.0    60.0 s     120.0 s       77.5%    77.0 s      17.0 s
[2015-09-30T16:17Z] INFO  17:17:20,848 ProgressMeter -      3:10074486    200002.0    30.0 s       2.5 m       32.3%    92.0 s      62.0 s
[2015-09-30T16:17Z] INFO  17:17:34,242 ProgressMeter -     2:219827174    900011.0   100.0 s     111.0 s       96.1%   104.0 s       4.0 s
[2015-09-30T16:17Z] INFO  17:17:48,435 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:17Z] INFO  17:17:48,636 ProgressMeter -            done   1087358.0   114.0 s     105.0 s      100.0%   114.0 s       0.0 s
[2015-09-30T16:17Z] INFO  17:17:48,636 ProgressMeter - Total runtime 114.40 secs, 1.91 min, 0.03 hours
[2015-09-30T16:17Z] INFO  17:17:48,637 MicroScheduler - 2535 reads were filtered out during the traversal out of approximately 1089893 total reads (0.23%)
[2015-09-30T16:17Z] INFO  17:17:48,637 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:17Z] INFO  17:17:48,637 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:17Z] INFO  17:17:48,637 MicroScheduler -   -> 2535 reads (0.23% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:17Z] INFO  17:17:49,427 ProgressMeter -     2:242263554    800010.0    90.0 s     112.0 s       95.7%    94.0 s       4.0 s
[2015-09-30T16:17Z] INFO  17:17:49,695 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:17Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam
[2015-09-30T16:17Z] INFO  17:17:50,848 ProgressMeter -      3:15282284    500008.0    60.0 s     120.0 s       49.0%     2.0 m      62.0 s
[2015-09-30T16:17Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam 2:189838938-221056966
[2015-09-30T16:17Z] GATK: RealignerTargetCreator
[2015-09-30T16:17Z] INFO  17:17:54,544 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:17Z] INFO  17:17:54,546 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:17Z] INFO  17:17:54,546 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:17Z] INFO  17:17:54,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:17Z] INFO  17:17:54,550 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpEdYU1m/2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign-realign.intervals -l INFO -L 2:189838938-221056966 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:17Z] INFO  17:17:54,555 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:17Z] INFO  17:17:54,556 HelpFormatter - Date/Time: 2015/09/30 17:17:54
[2015-09-30T16:17Z] INFO  17:17:54,556 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:17Z] INFO  17:17:54,556 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:17Z] INFO  17:17:54,612 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:17Z] INFO  17:17:54,722 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:17Z] INFO  17:17:54,729 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:17Z] INFO  17:17:54,745 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:17Z] INFO  17:17:55,526 IntervalUtils - Processing 31218029 bp from intervals
[2015-09-30T16:17Z] WARN  17:17:55,530 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:17Z] INFO  17:17:55,585 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:17Z] INFO  17:17:55,729 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:17Z] INFO  17:17:55,729 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:17Z] INFO  17:17:55,730 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:17Z] INFO  17:17:55,730 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:17Z] INFO  17:17:56,648 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:17Z] INFO  17:17:56,731 ProgressMeter -            done    966930.0    97.0 s     100.0 s       99.8%    97.0 s       0.0 s
[2015-09-30T16:17Z] INFO  17:17:56,731 ProgressMeter - Total runtime 97.34 secs, 1.62 min, 0.03 hours
[2015-09-30T16:17Z] INFO  17:17:56,731 MicroScheduler - 1925 reads were filtered out during the traversal out of approximately 968855 total reads (0.20%)
[2015-09-30T16:17Z] INFO  17:17:56,731 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:17Z] INFO  17:17:56,732 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:17Z] INFO  17:17:56,732 MicroScheduler -   -> 1925 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:17Z] INFO  17:17:57,742 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:17Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam
[2015-09-30T16:18Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam 2:221341379-243199373
[2015-09-30T16:18Z] GATK: RealignerTargetCreator
[2015-09-30T16:18Z] INFO  17:18:01,798 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:01,800 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:18Z] INFO  17:18:01,800 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:18Z] INFO  17:18:01,801 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:18Z] INFO  17:18:01,804 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpR5Rsgm/2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign-realign.intervals -l INFO -L 2:221341379-243199373 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:18Z] INFO  17:18:01,810 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:18Z] INFO  17:18:01,810 HelpFormatter - Date/Time: 2015/09/30 17:18:01
[2015-09-30T16:18Z] INFO  17:18:01,810 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:01,810 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:01,869 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:18Z] INFO  17:18:01,978 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:18Z] INFO  17:18:01,986 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:18Z] INFO  17:18:02,002 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:18Z] INFO  17:18:02,256 IntervalUtils - Processing 21857995 bp from intervals
[2015-09-30T16:18Z] WARN  17:18:02,260 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:18Z] INFO  17:18:02,319 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:18Z] INFO  17:18:02,463 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:18Z] INFO  17:18:02,464 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:18Z] INFO  17:18:02,464 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:18Z] INFO  17:18:02,465 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:18Z] INFO  17:18:10,089 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:18Z] INFO  17:18:10,198 ProgressMeter -            done    769735.0    79.0 s     103.0 s      100.0%    79.0 s       0.0 s
[2015-09-30T16:18Z] INFO  17:18:10,199 ProgressMeter - Total runtime 79.38 secs, 1.32 min, 0.02 hours
[2015-09-30T16:18Z] INFO  17:18:10,199 MicroScheduler - 1877 reads were filtered out during the traversal out of approximately 771612 total reads (0.24%)
[2015-09-30T16:18Z] INFO  17:18:10,199 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:18Z] INFO  17:18:10,199 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:18Z] INFO  17:18:10,200 MicroScheduler -   -> 1877 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:18Z] INFO  17:18:11,227 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:18Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam
[2015-09-30T16:18Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam 3:1-31203562
[2015-09-30T16:18Z] GATK: RealignerTargetCreator
[2015-09-30T16:18Z] INFO  17:18:14,807 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:14,809 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:18Z] INFO  17:18:14,810 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:18Z] INFO  17:18:14,810 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:18Z] INFO  17:18:14,813 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmp1y3jdh/2_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign-realign.intervals -l INFO -L 3:1-31203562 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:18Z] INFO  17:18:14,819 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:18Z] INFO  17:18:14,819 HelpFormatter - Date/Time: 2015/09/30 17:18:14
[2015-09-30T16:18Z] INFO  17:18:14,819 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:14,819 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:14,956 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:18Z] INFO  17:18:15,060 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:18Z] INFO  17:18:15,067 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:18Z] INFO  17:18:15,082 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:18Z] INFO  17:18:15,792 IntervalUtils - Processing 31203562 bp from intervals
[2015-09-30T16:18Z] WARN  17:18:15,796 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:18Z] INFO  17:18:15,851 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:18Z] INFO  17:18:16,206 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:18Z] INFO  17:18:16,206 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:18Z] INFO  17:18:16,207 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:18Z] INFO  17:18:16,207 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:18Z] INFO  17:18:25,732 ProgressMeter -     2:220344733   3.0493095E7    30.0 s       0.0 s       97.7%    30.0 s       0.0 s
[2015-09-30T16:18Z] INFO  17:18:26,987 ProgressMeter -            done   3.1218029E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T16:18Z] INFO  17:18:26,988 ProgressMeter - Total runtime 31.26 secs, 0.52 min, 0.01 hours
[2015-09-30T16:18Z] INFO  17:18:26,991 MicroScheduler - 77815 reads were filtered out during the traversal out of approximately 1094316 total reads (7.11%)
[2015-09-30T16:18Z] INFO  17:18:26,991 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:18Z] INFO  17:18:26,992 MicroScheduler -   -> 11834 reads (1.08% of total) failing BadMateFilter
[2015-09-30T16:18Z] INFO  17:18:26,992 MicroScheduler -   -> 47165 reads (4.31% of total) failing DuplicateReadFilter
[2015-09-30T16:18Z] INFO  17:18:26,992 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:18Z] INFO  17:18:26,992 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:18Z] INFO  17:18:26,993 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:18Z] INFO  17:18:26,993 MicroScheduler -   -> 18816 reads (1.72% of total) failing MappingQualityZeroFilter
[2015-09-30T16:18Z] INFO  17:18:26,993 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:18Z] INFO  17:18:26,993 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:18Z] INFO  17:18:26,993 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:18Z] INFO  17:18:27,872 ProgressMeter -            done   2.1857995E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T16:18Z] INFO  17:18:27,873 ProgressMeter - Total runtime 25.41 secs, 0.42 min, 0.01 hours
[2015-09-30T16:18Z] INFO  17:18:27,876 MicroScheduler - 78492 reads were filtered out during the traversal out of approximately 972632 total reads (8.07%)
[2015-09-30T16:18Z] INFO  17:18:27,876 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:18Z] INFO  17:18:27,876 MicroScheduler -   -> 8750 reads (0.90% of total) failing BadMateFilter
[2015-09-30T16:18Z] INFO  17:18:27,877 MicroScheduler -   -> 46719 reads (4.80% of total) failing DuplicateReadFilter
[2015-09-30T16:18Z] INFO  17:18:27,877 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:18Z] INFO  17:18:27,877 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:18Z] INFO  17:18:27,877 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:18Z] INFO  17:18:27,878 MicroScheduler -   -> 23023 reads (2.37% of total) failing MappingQualityZeroFilter
[2015-09-30T16:18Z] INFO  17:18:27,878 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:18Z] INFO  17:18:27,878 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:18Z] INFO  17:18:27,878 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:18Z] INFO  17:18:27,951 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:18Z] GATK: realign ('2', 189838937, 221056966) : syn3-tumor
[2015-09-30T16:18Z] INFO  17:18:28,886 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:18Z] GATK: realign ('2', 221341378, 243199373) : syn3-tumor
[2015-09-30T16:18Z] INFO  17:18:30,010 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:30,012 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:18Z] INFO  17:18:30,012 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:18Z] INFO  17:18:30,013 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:18Z] INFO  17:18:30,016 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep-prealign-realign.intervals -L 2:189838938-221056966 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmpqKAIBV/2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam
[2015-09-30T16:18Z] INFO  17:18:30,022 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:18Z] INFO  17:18:30,022 HelpFormatter - Date/Time: 2015/09/30 17:18:30
[2015-09-30T16:18Z] INFO  17:18:30,022 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:30,022 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:30,149 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:18Z] INFO  17:18:30,316 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:18Z] INFO  17:18:30,323 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:18Z] INFO  17:18:30,339 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:18Z] INFO  17:18:30,568 IntervalUtils - Processing 31218029 bp from intervals
[2015-09-30T16:18Z] WARN  17:18:30,572 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:18Z] INFO  17:18:30,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:18Z] INFO  17:18:31,162 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:18Z] INFO  17:18:31,162 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:18Z] INFO  17:18:31,163 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:18Z] INFO  17:18:31,163 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:18Z] INFO  17:18:31,303 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:18Z] INFO  17:18:31,487 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:18Z] INFO  17:18:33,744 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:33,746 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:18Z] INFO  17:18:33,746 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:18Z] INFO  17:18:33,746 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:18Z] INFO  17:18:33,750 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep-prealign-realign.intervals -L 2:221341379-243199373 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/tx/tmp6Ah_Fh/2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam
[2015-09-30T16:18Z] INFO  17:18:33,756 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:18Z] INFO  17:18:33,756 HelpFormatter - Date/Time: 2015/09/30 17:18:33
[2015-09-30T16:18Z] INFO  17:18:33,757 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:33,757 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:33,894 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:18Z] INFO  17:18:33,960 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:18Z] INFO  17:18:33,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:18Z] INFO  17:18:33,983 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:18Z] INFO  17:18:34,213 IntervalUtils - Processing 21857995 bp from intervals
[2015-09-30T16:18Z] WARN  17:18:34,217 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:18Z] INFO  17:18:34,271 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:18Z] INFO  17:18:34,382 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:18Z] INFO  17:18:34,383 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:18Z] INFO  17:18:34,383 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:18Z] INFO  17:18:34,384 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:18Z] INFO  17:18:34,525 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:18Z] INFO  17:18:34,669 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:18Z] INFO  17:18:42,920 ProgressMeter -            done   3.1203562E7    26.0 s       0.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T16:18Z] INFO  17:18:42,920 ProgressMeter - Total runtime 26.71 secs, 0.45 min, 0.01 hours
[2015-09-30T16:18Z] INFO  17:18:42,923 MicroScheduler - 58607 reads were filtered out during the traversal out of approximately 774608 total reads (7.57%)
[2015-09-30T16:18Z] INFO  17:18:42,924 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:18Z] INFO  17:18:42,924 MicroScheduler -   -> 9990 reads (1.29% of total) failing BadMateFilter
[2015-09-30T16:18Z] INFO  17:18:42,924 MicroScheduler -   -> 35302 reads (4.56% of total) failing DuplicateReadFilter
[2015-09-30T16:18Z] INFO  17:18:42,925 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:18Z] INFO  17:18:42,925 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:18Z] INFO  17:18:42,925 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:18Z] INFO  17:18:42,925 MicroScheduler -   -> 13315 reads (1.72% of total) failing MappingQualityZeroFilter
[2015-09-30T16:18Z] INFO  17:18:42,925 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:18Z] INFO  17:18:42,926 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:18Z] INFO  17:18:42,926 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:18Z] INFO  17:18:43,860 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:18Z] GATK: realign ('3', 0, 31203562) : syn3-tumor
[2015-09-30T16:18Z] INFO  17:18:45,735 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:45,737 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:18Z] INFO  17:18:45,737 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:18Z] INFO  17:18:45,738 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:18Z] INFO  17:18:45,741 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_0_31203562-prep-prealign-realign.intervals -L 3:1-31203562 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmppYw6f2/2_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam
[2015-09-30T16:18Z] INFO  17:18:45,747 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:18Z] INFO  17:18:45,747 HelpFormatter - Date/Time: 2015/09/30 17:18:45
[2015-09-30T16:18Z] INFO  17:18:45,747 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:45,747 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:18Z] INFO  17:18:45,848 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:18Z] INFO  17:18:45,911 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:18Z] INFO  17:18:45,918 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:18Z] INFO  17:18:45,934 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:18Z] INFO  17:18:46,155 IntervalUtils - Processing 31203562 bp from intervals
[2015-09-30T16:18Z] WARN  17:18:46,159 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:18Z] INFO  17:18:46,215 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:18Z] INFO  17:18:46,365 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:18Z] INFO  17:18:46,366 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:18Z] INFO  17:18:46,366 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:18Z] INFO  17:18:46,366 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:18Z] INFO  17:18:46,507 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:18Z] INFO  17:18:46,687 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:19Z] INFO  17:19:01,165 ProgressMeter -     2:205968890    400005.0    30.0 s      75.0 s       51.7%    58.0 s      28.0 s
[2015-09-30T16:19Z] INFO  17:19:05,969 ProgressMeter -     2:236432652    400005.0    31.0 s      78.0 s       69.0%    44.0 s      13.0 s
[2015-09-30T16:19Z] INFO  17:19:17,199 ProgressMeter -      3:15004560    500008.0    30.0 s      61.0 s       48.1%    62.0 s      32.0 s
[2015-09-30T16:19Z] INFO  17:19:23,794 ProgressMeter -            done    966930.0    49.0 s      51.0 s       99.8%    49.0 s       0.0 s
[2015-09-30T16:19Z] INFO  17:19:23,794 ProgressMeter - Total runtime 49.41 secs, 0.82 min, 0.01 hours
[2015-09-30T16:19Z] INFO  17:19:23,797 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 966930 total reads (0.00%)
[2015-09-30T16:19Z] INFO  17:19:23,797 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:19Z] INFO  17:19:23,798 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:19Z] INFO  17:19:23,798 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:19Z] INFO  17:19:24,745 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:19Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam
[2015-09-30T16:19Z] INFO  17:19:25,297 ProgressMeter -            done    769735.0    38.0 s      50.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T16:19Z] INFO  17:19:25,297 ProgressMeter - Total runtime 38.93 secs, 0.65 min, 0.01 hours
[2015-09-30T16:19Z] INFO  17:19:25,300 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 769735 total reads (0.00%)
[2015-09-30T16:19Z] INFO  17:19:25,301 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:19Z] INFO  17:19:25,301 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:19Z] INFO  17:19:25,301 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:19Z] INFO  17:19:26,435 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:19Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam
[2015-09-30T16:19Z] INFO  17:19:26,818 ProgressMeter -            done   1087358.0    55.0 s      51.0 s      100.0%    55.0 s       0.0 s
[2015-09-30T16:19Z] INFO  17:19:26,818 ProgressMeter - Total runtime 55.66 secs, 0.93 min, 0.02 hours
[2015-09-30T16:19Z] INFO  17:19:26,822 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1087358 total reads (0.00%)
[2015-09-30T16:19Z] INFO  17:19:26,822 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:19Z] INFO  17:19:26,822 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:19Z] INFO  17:19:26,822 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:19Z] GATK pre-alignment ('3', 31494593, 62516713) : syn3-tumor
[2015-09-30T16:19Z] INFO  17:19:27,938 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:19Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam
[2015-09-30T16:19Z] GATK pre-alignment ('3', 62518267, 93593495) : syn3-tumor
[2015-09-30T16:19Z] INFO  17:19:29,322 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:19Z] INFO  17:19:29,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:19Z] INFO  17:19:29,325 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:19Z] INFO  17:19:29,325 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:19Z] INFO  17:19:29,328 HelpFormatter - Program Args: -T PrintReads -L 3:31494594-62516713 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpqYeB6u/2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam
[2015-09-30T16:19Z] INFO  17:19:29,334 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:19Z] INFO  17:19:29,335 HelpFormatter - Date/Time: 2015/09/30 17:19:29
[2015-09-30T16:19Z] INFO  17:19:29,335 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:19Z] INFO  17:19:29,335 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:19Z] INFO  17:19:29,437 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:19Z] GATK pre-alignment ('3', 93595554, 124625281) : syn3-tumor
[2015-09-30T16:19Z] INFO  17:19:31,523 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:19Z] INFO  17:19:31,558 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:19Z] INFO  17:19:31,559 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:19Z] INFO  17:19:31,560 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:19Z] INFO  17:19:31,560 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:19Z] INFO  17:19:31,563 HelpFormatter - Program Args: -T PrintReads -L 3:62518268-93593495 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpUMBQCO/2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam
[2015-09-30T16:19Z] INFO  17:19:31,569 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:19Z] INFO  17:19:31,569 HelpFormatter - Date/Time: 2015/09/30 17:19:31
[2015-09-30T16:19Z] INFO  17:19:31,569 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:19Z] INFO  17:19:31,569 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:19Z] INFO  17:19:31,573 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:19Z] INFO  17:19:31,581 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:19Z] INFO  17:19:31,596 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:19Z] INFO  17:19:31,609 IntervalUtils - Processing 31022120 bp from intervals
[2015-09-30T16:19Z] INFO  17:19:31,668 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:19Z] INFO  17:19:31,675 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:19Z] INFO  17:19:31,865 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:19Z] INFO  17:19:31,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:19Z] INFO  17:19:31,866 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:19Z] INFO  17:19:31,866 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:19Z] INFO  17:19:31,877 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:19Z] INFO  17:19:32,077 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:19Z] INFO  17:19:33,943 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:19Z] INFO  17:19:33,945 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:19Z] INFO  17:19:33,945 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:19Z] INFO  17:19:33,946 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:19Z] INFO  17:19:33,949 HelpFormatter - Program Args: -T PrintReads -L 3:93595555-124625281 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpMnn2Qs/2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam
[2015-09-30T16:19Z] INFO  17:19:33,954 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:19Z] INFO  17:19:33,955 HelpFormatter - Date/Time: 2015/09/30 17:19:33
[2015-09-30T16:19Z] INFO  17:19:33,955 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:19Z] INFO  17:19:33,955 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:19Z] INFO  17:19:35,152 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:19Z] INFO  17:19:36,440 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:19Z] INFO  17:19:36,490 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:19Z] INFO  17:19:36,498 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:19Z] INFO  17:19:36,513 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:19Z] INFO  17:19:36,526 IntervalUtils - Processing 31075228 bp from intervals
[2015-09-30T16:19Z] INFO  17:19:36,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:19Z] INFO  17:19:37,814 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:19Z] INFO  17:19:37,865 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:19Z] INFO  17:19:37,872 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:19Z] INFO  17:19:37,887 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:19Z] INFO  17:19:37,895 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:19Z] INFO  17:19:37,895 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:19Z] INFO  17:19:37,896 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:19Z] INFO  17:19:37,896 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:19Z] INFO  17:19:37,901 IntervalUtils - Processing 31029727 bp from intervals
[2015-09-30T16:19Z] INFO  17:19:37,907 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:19Z] INFO  17:19:37,961 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:19Z] INFO  17:19:38,105 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:19Z] INFO  17:19:38,164 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:19Z] INFO  17:19:38,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:19Z] INFO  17:19:38,165 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:19Z] INFO  17:19:38,165 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:19Z] INFO  17:19:38,176 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:19Z] INFO  17:19:38,383 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:20Z] INFO  17:20:02,289 ProgressMeter -      3:38161860    200002.0    30.0 s       2.5 m       21.5%     2.3 m     109.0 s
[2015-09-30T16:20Z] INFO  17:20:06,962 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:20Z] INFO  17:20:07,140 ProgressMeter -            done    286344.0    29.0 s     102.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T16:20Z] INFO  17:20:07,141 ProgressMeter - Total runtime 29.25 secs, 0.49 min, 0.01 hours
[2015-09-30T16:20Z] INFO  17:20:07,141 MicroScheduler - 1141 reads were filtered out during the traversal out of approximately 287485 total reads (0.40%)
[2015-09-30T16:20Z] INFO  17:20:07,141 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:20Z] INFO  17:20:07,142 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:20Z] INFO  17:20:07,142 MicroScheduler -   -> 1141 reads (0.40% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:20Z] INFO  17:20:08,167 ProgressMeter -     3:108354309    200002.0    30.0 s       2.5 m       47.6%    63.0 s      33.0 s
[2015-09-30T16:20Z] INFO  17:20:08,634 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:20Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam
[2015-09-30T16:20Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam 3:62518268-93593495
[2015-09-30T16:20Z] GATK: RealignerTargetCreator
[2015-09-30T16:20Z] INFO  17:20:11,248 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:11,250 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:20Z] INFO  17:20:11,251 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:20Z] INFO  17:20:11,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:20Z] INFO  17:20:11,254 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpJwEpeL/2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign-realign.intervals -l INFO -L 3:62518268-93593495 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:20Z] INFO  17:20:11,259 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:20Z] INFO  17:20:11,260 HelpFormatter - Date/Time: 2015/09/30 17:20:11
[2015-09-30T16:20Z] INFO  17:20:11,260 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:11,260 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:11,315 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:20Z] INFO  17:20:11,448 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:20Z] INFO  17:20:11,460 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:20Z] INFO  17:20:11,537 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2015-09-30T16:20Z] INFO  17:20:12,767 IntervalUtils - Processing 31075228 bp from intervals
[2015-09-30T16:20Z] WARN  17:20:12,771 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:20Z] INFO  17:20:12,824 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:20Z] INFO  17:20:12,952 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:20Z] INFO  17:20:12,952 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:20Z] INFO  17:20:12,952 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:20Z] INFO  17:20:12,953 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:20Z] INFO  17:20:31,349 ProgressMeter -            done   3.1075228E7    18.0 s       0.0 s      100.0%    18.0 s       0.0 s
[2015-09-30T16:20Z] INFO  17:20:31,350 ProgressMeter - Total runtime 18.40 secs, 0.31 min, 0.01 hours
[2015-09-30T16:20Z] INFO  17:20:31,353 MicroScheduler - 41468 reads were filtered out during the traversal out of approximately 288002 total reads (14.40%)
[2015-09-30T16:20Z] INFO  17:20:31,353 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:20Z] INFO  17:20:31,353 MicroScheduler -   -> 6110 reads (2.12% of total) failing BadMateFilter
[2015-09-30T16:20Z] INFO  17:20:31,354 MicroScheduler -   -> 10927 reads (3.79% of total) failing DuplicateReadFilter
[2015-09-30T16:20Z] INFO  17:20:31,354 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:20Z] INFO  17:20:31,354 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:20Z] INFO  17:20:31,354 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:20Z] INFO  17:20:31,355 MicroScheduler -   -> 24431 reads (8.48% of total) failing MappingQualityZeroFilter
[2015-09-30T16:20Z] INFO  17:20:31,355 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:20Z] INFO  17:20:31,355 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:20Z] INFO  17:20:31,355 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:20Z] INFO  17:20:32,322 ProgressMeter -      3:44685163    500005.0    60.0 s     120.0 s       42.5%     2.4 m      81.0 s
[2015-09-30T16:20Z] INFO  17:20:32,388 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:20Z] GATK: realign ('3', 62518267, 93593495) : syn3-tumor
[2015-09-30T16:20Z] INFO  17:20:35,507 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:35,509 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:20Z] INFO  17:20:35,509 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:20Z] INFO  17:20:35,510 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:20Z] INFO  17:20:35,513 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep-prealign-realign.intervals -L 3:62518268-93593495 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpifaDDP/2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam
[2015-09-30T16:20Z] INFO  17:20:35,519 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:20Z] INFO  17:20:35,519 HelpFormatter - Date/Time: 2015/09/30 17:20:35
[2015-09-30T16:20Z] INFO  17:20:35,519 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:35,520 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:35,649 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:20Z] INFO  17:20:35,712 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:20Z] INFO  17:20:35,720 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:20Z] INFO  17:20:35,735 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:20Z] INFO  17:20:35,960 IntervalUtils - Processing 31075228 bp from intervals
[2015-09-30T16:20Z] WARN  17:20:35,964 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:20Z] INFO  17:20:36,018 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:20Z] INFO  17:20:36,503 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:20Z] INFO  17:20:36,504 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:20Z] INFO  17:20:36,504 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:20Z] INFO  17:20:36,505 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:20Z] INFO  17:20:36,644 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:20Z] INFO  17:20:36,819 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:20Z] INFO  17:20:38,168 ProgressMeter -     3:122176686    500006.0    60.0 s     120.0 s       92.1%    65.0 s       5.0 s
[2015-09-30T16:20Z] INFO  17:20:49,152 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:20Z] INFO  17:20:49,227 ProgressMeter -            done    747697.0    71.0 s      95.0 s      100.0%    71.0 s       0.0 s
[2015-09-30T16:20Z] INFO  17:20:49,227 ProgressMeter - Total runtime 71.06 secs, 1.18 min, 0.02 hours
[2015-09-30T16:20Z] INFO  17:20:49,228 MicroScheduler - 2097 reads were filtered out during the traversal out of approximately 749794 total reads (0.28%)
[2015-09-30T16:20Z] INFO  17:20:49,228 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:20Z] INFO  17:20:49,228 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:20Z] INFO  17:20:49,229 MicroScheduler -   -> 2097 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:20Z] INFO  17:20:50,311 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:20Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam
[2015-09-30T16:20Z] INFO  17:20:52,207 ProgressMeter -            done    286344.0    15.0 s      54.0 s      100.0%    15.0 s       0.0 s
[2015-09-30T16:20Z] INFO  17:20:52,208 ProgressMeter - Total runtime 15.70 secs, 0.26 min, 0.00 hours
[2015-09-30T16:20Z] INFO  17:20:52,211 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 286344 total reads (0.00%)
[2015-09-30T16:20Z] INFO  17:20:52,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:20Z] INFO  17:20:52,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:20Z] INFO  17:20:52,211 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:20Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam 3:93595555-124625281
[2015-09-30T16:20Z] GATK: RealignerTargetCreator
[2015-09-30T16:20Z] INFO  17:20:53,340 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:20Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam
[2015-09-30T16:20Z] GATK pre-alignment ('3', 124626733, 155649953) : syn3-tumor
[2015-09-30T16:20Z] INFO  17:20:54,328 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:54,330 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:20Z] INFO  17:20:54,331 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:20Z] INFO  17:20:54,331 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:20Z] INFO  17:20:54,334 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpgjgiqg/2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign-realign.intervals -l INFO -L 3:93595555-124625281 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:20Z] INFO  17:20:54,340 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:20Z] INFO  17:20:54,340 HelpFormatter - Date/Time: 2015/09/30 17:20:54
[2015-09-30T16:20Z] INFO  17:20:54,340 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:54,340 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:54,396 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:20Z] INFO  17:20:54,494 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:20Z] INFO  17:20:54,502 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:20Z] INFO  17:20:54,518 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:20Z] INFO  17:20:55,466 IntervalUtils - Processing 31029727 bp from intervals
[2015-09-30T16:20Z] WARN  17:20:55,470 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:20Z] INFO  17:20:55,526 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:20Z] INFO  17:20:55,677 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:20Z] INFO  17:20:55,677 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:20Z] INFO  17:20:55,678 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:20Z] INFO  17:20:55,678 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:20Z] INFO  17:20:56,851 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:56,853 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:20Z] INFO  17:20:56,853 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:20Z] INFO  17:20:56,853 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:20Z] INFO  17:20:56,857 HelpFormatter - Program Args: -T PrintReads -L 3:124626734-155649953 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpPaBkoz/2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam
[2015-09-30T16:20Z] INFO  17:20:56,862 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:20Z] INFO  17:20:56,863 HelpFormatter - Date/Time: 2015/09/30 17:20:56
[2015-09-30T16:20Z] INFO  17:20:56,863 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:56,863 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:20Z] INFO  17:20:56,976 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:20Z] INFO  17:20:58,320 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:20Z] INFO  17:20:58,369 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:20Z] INFO  17:20:58,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:20Z] INFO  17:20:58,391 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:20Z] INFO  17:20:58,404 IntervalUtils - Processing 31023220 bp from intervals
[2015-09-30T16:20Z] INFO  17:20:58,461 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:20Z] INFO  17:20:58,827 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:20Z] INFO  17:20:58,828 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:20Z] INFO  17:20:58,828 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:20Z] INFO  17:20:58,828 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:20Z] INFO  17:20:58,839 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:20Z] INFO  17:20:59,062 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:21Z] INFO  17:21:02,325 ProgressMeter -      3:48222469    800009.0    90.0 s     113.0 s       53.9%     2.8 m      76.0 s
[2015-09-30T16:21Z] INFO  17:21:22,913 ProgressMeter -            done   3.1029727E7    27.0 s       0.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T16:21Z] INFO  17:21:22,914 ProgressMeter - Total runtime 27.24 secs, 0.45 min, 0.01 hours
[2015-09-30T16:21Z] INFO  17:21:22,916 MicroScheduler - 54241 reads were filtered out during the traversal out of approximately 752616 total reads (7.21%)
[2015-09-30T16:21Z] INFO  17:21:22,917 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:21Z] INFO  17:21:22,917 MicroScheduler -   -> 9082 reads (1.21% of total) failing BadMateFilter
[2015-09-30T16:21Z] INFO  17:21:22,917 MicroScheduler -   -> 31318 reads (4.16% of total) failing DuplicateReadFilter
[2015-09-30T16:21Z] INFO  17:21:22,918 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:21Z] INFO  17:21:22,918 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:21Z] INFO  17:21:22,918 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:21Z] INFO  17:21:22,918 MicroScheduler -   -> 13841 reads (1.84% of total) failing MappingQualityZeroFilter
[2015-09-30T16:21Z] INFO  17:21:22,918 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:21Z] INFO  17:21:22,919 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:21Z] INFO  17:21:22,919 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:21Z] INFO  17:21:23,854 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:21Z] GATK: realign ('3', 93595554, 124625281) : syn3-tumor
[2015-09-30T16:21Z] INFO  17:21:25,874 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:21Z] INFO  17:21:25,877 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:21Z] INFO  17:21:25,877 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:21Z] INFO  17:21:25,877 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:21Z] INFO  17:21:25,881 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep-prealign-realign.intervals -L 3:93595555-124625281 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpgcSwyL/2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam
[2015-09-30T16:21Z] INFO  17:21:25,886 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:21Z] INFO  17:21:25,887 HelpFormatter - Date/Time: 2015/09/30 17:21:25
[2015-09-30T16:21Z] INFO  17:21:25,887 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:21Z] INFO  17:21:25,887 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:21Z] INFO  17:21:26,042 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:21Z] INFO  17:21:26,110 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:21Z] INFO  17:21:26,117 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:21Z] INFO  17:21:26,134 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:21Z] INFO  17:21:27,172 IntervalUtils - Processing 31029727 bp from intervals
[2015-09-30T16:21Z] WARN  17:21:27,176 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:21Z] INFO  17:21:27,230 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:21Z] INFO  17:21:27,377 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:21Z] INFO  17:21:27,378 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:21Z] INFO  17:21:27,378 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:21Z] INFO  17:21:27,379 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:21Z] INFO  17:21:27,522 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:21Z] INFO  17:21:27,711 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:21Z] INFO  17:21:28,831 ProgressMeter -     3:129168435    200002.0    30.0 s       2.5 m       14.6%     3.4 m       2.9 m
[2015-09-30T16:21Z] INFO  17:21:32,326 ProgressMeter -      3:49947221   1100013.0   120.0 s     109.0 s       59.5%     3.4 m      81.0 s
[2015-09-30T16:21Z] INFO  17:21:58,584 ProgressMeter -     3:119914035    400005.0    31.0 s      78.0 s       84.8%    36.0 s       5.0 s
[2015-09-30T16:21Z] INFO  17:21:58,832 ProgressMeter -     3:138176174    600009.0    60.0 s     100.0 s       43.7%     2.3 m      77.0 s
[2015-09-30T16:22Z] INFO  17:22:08,403 ProgressMeter -            done    747697.0    41.0 s      54.0 s      100.0%    41.0 s       0.0 s
[2015-09-30T16:22Z] INFO  17:22:08,403 ProgressMeter - Total runtime 41.03 secs, 0.68 min, 0.01 hours
[2015-09-30T16:22Z] INFO  17:22:08,407 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 747697 total reads (0.00%)
[2015-09-30T16:22Z] INFO  17:22:08,407 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:22Z] INFO  17:22:08,407 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:22Z] INFO  17:22:08,407 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:22Z] INFO  17:22:09,541 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:22Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam
[2015-09-30T16:22Z] INFO  17:22:12,327 ProgressMeter -      3:53212885   1500021.0     2.7 m     106.0 s       70.0%     3.8 m      68.0 s
[2015-09-30T16:22Z] GATK pre-alignment ('3', 155652401, 186761310) : syn3-tumor
[2015-09-30T16:22Z] INFO  17:22:15,062 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:22Z] INFO  17:22:15,064 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:22Z] INFO  17:22:15,064 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:22Z] INFO  17:22:15,064 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:22Z] INFO  17:22:15,067 HelpFormatter - Program Args: -T PrintReads -L 3:155652402-186761310 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpmewDC5/2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam
[2015-09-30T16:22Z] INFO  17:22:15,073 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:22Z] INFO  17:22:15,073 HelpFormatter - Date/Time: 2015/09/30 17:22:15
[2015-09-30T16:22Z] INFO  17:22:15,073 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:22Z] INFO  17:22:15,074 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:22Z] INFO  17:22:15,179 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:22Z] INFO  17:22:17,128 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:22Z] INFO  17:22:17,177 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:22Z] INFO  17:22:17,184 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:22Z] INFO  17:22:17,198 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:22Z] INFO  17:22:17,211 IntervalUtils - Processing 31108909 bp from intervals
[2015-09-30T16:22Z] INFO  17:22:17,266 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:22Z] INFO  17:22:17,709 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:22Z] INFO  17:22:17,709 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:22Z] INFO  17:22:17,710 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:22Z] INFO  17:22:17,710 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:22Z] INFO  17:22:17,721 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:22Z] INFO  17:22:17,902 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:22Z] INFO  17:22:25,701 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:22Z] INFO  17:22:25,886 ProgressMeter -            done    986520.0    87.0 s      88.0 s      100.0%    87.0 s       0.0 s
[2015-09-30T16:22Z] INFO  17:22:25,886 ProgressMeter - Total runtime 87.06 secs, 1.45 min, 0.02 hours
[2015-09-30T16:22Z] INFO  17:22:25,887 MicroScheduler - 2588 reads were filtered out during the traversal out of approximately 989108 total reads (0.26%)
[2015-09-30T16:22Z] INFO  17:22:25,887 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:22Z] INFO  17:22:25,887 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:22Z] INFO  17:22:25,888 MicroScheduler -   -> 2588 reads (0.26% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:22Z] INFO  17:22:26,976 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:22Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam
[2015-09-30T16:22Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam 3:124626734-155649953
[2015-09-30T16:22Z] GATK: RealignerTargetCreator
[2015-09-30T16:22Z] INFO  17:22:31,106 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:22Z] INFO  17:22:31,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:22Z] INFO  17:22:31,108 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:22Z] INFO  17:22:31,108 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:22Z] INFO  17:22:31,112 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmp9o0PDo/2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign-realign.intervals -l INFO -L 3:124626734-155649953 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:22Z] INFO  17:22:31,117 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:22Z] INFO  17:22:31,117 HelpFormatter - Date/Time: 2015/09/30 17:22:31
[2015-09-30T16:22Z] INFO  17:22:31,117 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:22Z] INFO  17:22:31,118 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:22Z] INFO  17:22:31,177 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:22Z] INFO  17:22:32,018 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:22Z] INFO  17:22:32,026 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:22Z] INFO  17:22:32,043 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:22Z] INFO  17:22:32,679 IntervalUtils - Processing 31023220 bp from intervals
[2015-09-30T16:22Z] WARN  17:22:32,683 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:22Z] INFO  17:22:32,744 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:22Z] INFO  17:22:32,901 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:22Z] INFO  17:22:32,901 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:22Z] INFO  17:22:32,902 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:22Z] INFO  17:22:32,902 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:22Z] INFO  17:22:38,321 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:22Z] INFO  17:22:38,503 ProgressMeter -            done   1815567.0     3.1 m     102.0 s      100.0%     3.1 m       0.0 s
[2015-09-30T16:22Z] INFO  17:22:38,503 ProgressMeter - Total runtime 186.64 secs, 3.11 min, 0.05 hours
[2015-09-30T16:22Z] INFO  17:22:38,503 MicroScheduler - 3051 reads were filtered out during the traversal out of approximately 1818618 total reads (0.17%)
[2015-09-30T16:22Z] INFO  17:22:38,504 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:22Z] INFO  17:22:38,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:22Z] INFO  17:22:38,504 MicroScheduler -   -> 3051 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:22Z] INFO  17:22:39,611 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:22Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam
[2015-09-30T16:22Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam 3:31494594-62516713
[2015-09-30T16:22Z] GATK: RealignerTargetCreator
[2015-09-30T16:22Z] INFO  17:22:45,578 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:22Z] INFO  17:22:45,580 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:22Z] INFO  17:22:45,581 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:22Z] INFO  17:22:45,581 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:22Z] INFO  17:22:45,584 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpUVhrDe/2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign-realign.intervals -l INFO -L 3:31494594-62516713 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:22Z] INFO  17:22:45,590 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:22Z] INFO  17:22:45,590 HelpFormatter - Date/Time: 2015/09/30 17:22:45
[2015-09-30T16:22Z] INFO  17:22:45,591 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:22Z] INFO  17:22:45,591 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:22Z] INFO  17:22:45,762 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:22Z] INFO  17:22:45,877 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:22Z] INFO  17:22:45,885 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:22Z] INFO  17:22:45,901 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:22Z] INFO  17:22:46,162 IntervalUtils - Processing 31022120 bp from intervals
[2015-09-30T16:22Z] WARN  17:22:46,166 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:22Z] INFO  17:22:46,224 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:22Z] INFO  17:22:46,373 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:22Z] INFO  17:22:46,373 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:22Z] INFO  17:22:46,374 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:22Z] INFO  17:22:46,374 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:22Z] INFO  17:22:47,712 ProgressMeter -     3:175293901    200002.0    30.0 s       2.5 m       63.1%    47.0 s      17.0 s
[2015-09-30T16:23Z] INFO  17:23:02,905 ProgressMeter -     3:154139389   2.9497555E7    30.0 s       1.0 s       95.1%    31.0 s       1.0 s
[2015-09-30T16:23Z] INFO  17:23:04,196 ProgressMeter -            done   3.102322E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T16:23Z] INFO  17:23:04,197 ProgressMeter - Total runtime 31.30 secs, 0.52 min, 0.01 hours
[2015-09-30T16:23Z] INFO  17:23:04,200 MicroScheduler - 73876 reads were filtered out during the traversal out of approximately 992944 total reads (7.44%)
[2015-09-30T16:23Z] INFO  17:23:04,201 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:23Z] INFO  17:23:04,201 MicroScheduler -   -> 11238 reads (1.13% of total) failing BadMateFilter
[2015-09-30T16:23Z] INFO  17:23:04,201 MicroScheduler -   -> 44295 reads (4.46% of total) failing DuplicateReadFilter
[2015-09-30T16:23Z] INFO  17:23:04,201 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:23Z] INFO  17:23:04,202 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:23Z] INFO  17:23:04,202 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:23Z] INFO  17:23:04,202 MicroScheduler -   -> 18343 reads (1.85% of total) failing MappingQualityZeroFilter
[2015-09-30T16:23Z] INFO  17:23:04,202 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:23Z] INFO  17:23:04,203 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:23Z] INFO  17:23:04,203 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:23Z] INFO  17:23:05,198 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:23Z] GATK: realign ('3', 124626733, 155649953) : syn3-tumor
[2015-09-30T16:23Z] INFO  17:23:07,193 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:07,195 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:23Z] INFO  17:23:07,195 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:23Z] INFO  17:23:07,195 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:23Z] INFO  17:23:07,199 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep-prealign-realign.intervals -L 3:124626734-155649953 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpsXmQCe/2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam
[2015-09-30T16:23Z] INFO  17:23:07,204 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:23Z] INFO  17:23:07,204 HelpFormatter - Date/Time: 2015/09/30 17:23:07
[2015-09-30T16:23Z] INFO  17:23:07,204 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:07,205 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:07,331 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:23Z] INFO  17:23:07,393 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:23Z] INFO  17:23:07,401 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:23Z] INFO  17:23:07,416 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:23Z] INFO  17:23:07,651 IntervalUtils - Processing 31023220 bp from intervals
[2015-09-30T16:23Z] WARN  17:23:07,655 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:23Z] INFO  17:23:07,708 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:23Z] INFO  17:23:07,855 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:23Z] INFO  17:23:07,855 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:23Z] INFO  17:23:07,856 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:23Z] INFO  17:23:07,856 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:23Z] INFO  17:23:08,024 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:23Z] INFO  17:23:08,208 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:23Z] INFO  17:23:16,376 ProgressMeter -      3:52385749   2.0885055E7    30.0 s       1.0 s       67.3%    44.0 s      14.0 s
[2015-09-30T16:23Z] INFO  17:23:16,450 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:23Z] INFO  17:23:16,803 ProgressMeter -            done    648178.0    59.0 s      91.0 s      100.0%    59.0 s       0.0 s
[2015-09-30T16:23Z] INFO  17:23:16,803 ProgressMeter - Total runtime 59.09 secs, 0.98 min, 0.02 hours
[2015-09-30T16:23Z] INFO  17:23:16,804 MicroScheduler - 1769 reads were filtered out during the traversal out of approximately 649947 total reads (0.27%)
[2015-09-30T16:23Z] INFO  17:23:16,804 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:23Z] INFO  17:23:16,804 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:23Z] INFO  17:23:16,804 MicroScheduler -   -> 1769 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:23Z] INFO  17:23:17,869 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:23Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam
[2015-09-30T16:23Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam 3:155652402-186761310
[2015-09-30T16:23Z] GATK: RealignerTargetCreator
[2015-09-30T16:23Z] INFO  17:23:22,434 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:22,436 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:23Z] INFO  17:23:22,436 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:23Z] INFO  17:23:22,436 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:23Z] INFO  17:23:22,440 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpPunHYa/2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign-realign.intervals -l INFO -L 3:155652402-186761310 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:23Z] INFO  17:23:22,445 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:23Z] INFO  17:23:22,445 HelpFormatter - Date/Time: 2015/09/30 17:23:22
[2015-09-30T16:23Z] INFO  17:23:22,446 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:22,446 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:22,500 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:23Z] INFO  17:23:22,609 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:23Z] INFO  17:23:22,617 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:23Z] INFO  17:23:22,632 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:23Z] INFO  17:23:22,892 IntervalUtils - Processing 31108909 bp from intervals
[2015-09-30T16:23Z] WARN  17:23:22,896 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:23Z] INFO  17:23:22,952 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:23Z] INFO  17:23:23,091 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:23Z] INFO  17:23:23,091 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:23Z] INFO  17:23:23,091 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:23Z] INFO  17:23:23,092 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:23Z] INFO  17:23:27,157 ProgressMeter -            done   3.102212E7    40.0 s       1.0 s      100.0%    40.0 s       0.0 s
[2015-09-30T16:23Z] INFO  17:23:27,157 ProgressMeter - Total runtime 40.78 secs, 0.68 min, 0.01 hours
[2015-09-30T16:23Z] INFO  17:23:27,160 MicroScheduler - 137732 reads were filtered out during the traversal out of approximately 1826984 total reads (7.54%)
[2015-09-30T16:23Z] INFO  17:23:27,161 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:23Z] INFO  17:23:27,161 MicroScheduler -   -> 16735 reads (0.92% of total) failing BadMateFilter
[2015-09-30T16:23Z] INFO  17:23:27,161 MicroScheduler -   -> 89573 reads (4.90% of total) failing DuplicateReadFilter
[2015-09-30T16:23Z] INFO  17:23:27,161 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:23Z] INFO  17:23:27,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:23Z] INFO  17:23:27,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:23Z] INFO  17:23:27,162 MicroScheduler -   -> 31424 reads (1.72% of total) failing MappingQualityZeroFilter
[2015-09-30T16:23Z] INFO  17:23:27,162 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:23Z] INFO  17:23:27,162 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:23Z] INFO  17:23:27,163 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:23Z] INFO  17:23:28,137 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:23Z] GATK: realign ('3', 31494593, 62516713) : syn3-tumor
[2015-09-30T16:23Z] INFO  17:23:29,856 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:29,858 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:23Z] INFO  17:23:29,858 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:23Z] INFO  17:23:29,858 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:23Z] INFO  17:23:29,862 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep-prealign-realign.intervals -L 3:31494594-62516713 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpzR5SC4/2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam
[2015-09-30T16:23Z] INFO  17:23:29,867 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:23Z] INFO  17:23:29,868 HelpFormatter - Date/Time: 2015/09/30 17:23:29
[2015-09-30T16:23Z] INFO  17:23:29,868 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:29,868 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:29,988 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:23Z] INFO  17:23:30,052 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:23Z] INFO  17:23:30,059 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:23Z] INFO  17:23:30,074 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:23Z] INFO  17:23:30,296 IntervalUtils - Processing 31022120 bp from intervals
[2015-09-30T16:23Z] WARN  17:23:30,300 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:23Z] INFO  17:23:30,356 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:23Z] INFO  17:23:30,506 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:23Z] INFO  17:23:30,506 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:23Z] INFO  17:23:30,507 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:23Z] INFO  17:23:30,507 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:23Z] INFO  17:23:30,654 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:23Z] INFO  17:23:30,842 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:23Z] INFO  17:23:39,519 ProgressMeter -     3:134960472    500007.0    31.0 s      63.0 s       33.3%    93.0 s      62.0 s
[2015-09-30T16:23Z] INFO  17:23:46,538 ProgressMeter -            done   3.1108909E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T16:23Z] INFO  17:23:46,538 ProgressMeter - Total runtime 23.45 secs, 0.39 min, 0.01 hours
[2015-09-30T16:23Z] INFO  17:23:46,541 MicroScheduler - 48198 reads were filtered out during the traversal out of approximately 652532 total reads (7.39%)
[2015-09-30T16:23Z] INFO  17:23:46,541 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:23Z] INFO  17:23:46,542 MicroScheduler -   -> 9101 reads (1.39% of total) failing BadMateFilter
[2015-09-30T16:23Z] INFO  17:23:46,542 MicroScheduler -   -> 27368 reads (4.19% of total) failing DuplicateReadFilter
[2015-09-30T16:23Z] INFO  17:23:46,542 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:23Z] INFO  17:23:46,542 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:23Z] INFO  17:23:46,542 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:23Z] INFO  17:23:46,543 MicroScheduler -   -> 11729 reads (1.80% of total) failing MappingQualityZeroFilter
[2015-09-30T16:23Z] INFO  17:23:46,543 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:23Z] INFO  17:23:46,543 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:23Z] INFO  17:23:46,543 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:23Z] INFO  17:23:47,511 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:23Z] GATK: realign ('3', 155652401, 186761310) : syn3-tumor
[2015-09-30T16:23Z] INFO  17:23:51,322 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:51,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:23Z] INFO  17:23:51,324 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:23Z] INFO  17:23:51,324 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:23Z] INFO  17:23:51,328 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep-prealign-realign.intervals -L 3:155652402-186761310 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpzn56Tu/2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam
[2015-09-30T16:23Z] INFO  17:23:51,333 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:23Z] INFO  17:23:51,333 HelpFormatter - Date/Time: 2015/09/30 17:23:51
[2015-09-30T16:23Z] INFO  17:23:51,334 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:51,334 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:23Z] INFO  17:23:51,435 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:23Z] INFO  17:23:51,498 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:23Z] INFO  17:23:51,505 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:23Z] INFO  17:23:51,521 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:23Z] INFO  17:23:51,748 IntervalUtils - Processing 31108909 bp from intervals
[2015-09-30T16:23Z] WARN  17:23:51,752 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:23Z] INFO  17:23:51,804 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:23Z] INFO  17:23:51,940 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:23Z] INFO  17:23:51,940 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:23Z] INFO  17:23:51,941 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:23Z] INFO  17:23:51,941 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:23Z] INFO  17:23:52,084 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:23Z] INFO  17:23:52,262 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:23Z] INFO  17:23:57,373 ProgressMeter -            done    986520.0    49.0 s      50.0 s      100.0%    49.0 s       0.0 s
[2015-09-30T16:23Z] INFO  17:23:57,373 ProgressMeter - Total runtime 49.52 secs, 0.83 min, 0.01 hours
[2015-09-30T16:23Z] INFO  17:23:57,376 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 986520 total reads (0.00%)
[2015-09-30T16:23Z] INFO  17:23:57,377 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:23Z] INFO  17:23:57,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:23Z] INFO  17:23:57,377 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:23Z] INFO  17:23:58,811 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:23Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam
[2015-09-30T16:24Z] INFO  17:24:00,509 ProgressMeter -      3:41504867    300003.0    30.0 s     100.0 s       32.3%    92.0 s      62.0 s
[2015-09-30T16:24Z] GATK pre-alignment ('3', 186768753, 198022430) : syn3-tumor
[2015-09-30T16:24Z] INFO  17:24:03,109 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:24Z] INFO  17:24:03,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:24Z] INFO  17:24:03,111 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:24Z] INFO  17:24:03,112 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:24Z] INFO  17:24:03,115 HelpFormatter - Program Args: -T PrintReads -L 3:186768754-198022430 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmp1jPXQU/2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam
[2015-09-30T16:24Z] INFO  17:24:03,121 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:24Z] INFO  17:24:03,121 HelpFormatter - Date/Time: 2015/09/30 17:24:03
[2015-09-30T16:24Z] INFO  17:24:03,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:24Z] INFO  17:24:03,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:24Z] INFO  17:24:03,228 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:24Z] INFO  17:24:04,429 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:24Z] INFO  17:24:04,480 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:24Z] INFO  17:24:04,488 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:24Z] INFO  17:24:04,502 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:24Z] INFO  17:24:04,516 IntervalUtils - Processing 11253677 bp from intervals
[2015-09-30T16:24Z] INFO  17:24:04,573 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:24Z] INFO  17:24:04,820 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:24Z] INFO  17:24:04,820 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:24Z] INFO  17:24:04,821 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:24Z] INFO  17:24:04,821 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:24Z] INFO  17:24:04,832 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:24Z] INFO  17:24:04,913 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:24Z] INFO  17:24:22,134 ProgressMeter -     3:183961873    400004.0    30.0 s      75.0 s       91.0%    32.0 s       2.0 s
[2015-09-30T16:24Z] INFO  17:24:27,618 ProgressMeter -            done    648178.0    35.0 s      55.0 s      100.0%    35.0 s       0.0 s
[2015-09-30T16:24Z] INFO  17:24:27,619 ProgressMeter - Total runtime 35.68 secs, 0.59 min, 0.01 hours
[2015-09-30T16:24Z] INFO  17:24:27,622 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 648178 total reads (0.00%)
[2015-09-30T16:24Z] INFO  17:24:27,622 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:24Z] INFO  17:24:27,623 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:24Z] INFO  17:24:27,623 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:24Z] INFO  17:24:28,895 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:24Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam
[2015-09-30T16:24Z] GATK pre-alignment ('4', 0, 31018607) : syn3-tumor
[2015-09-30T16:24Z] INFO  17:24:30,902 ProgressMeter -      3:50130684   1100013.0    60.0 s      54.0 s       60.1%    99.0 s      39.0 s
[2015-09-30T16:24Z] INFO  17:24:33,030 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:24Z] INFO  17:24:33,032 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:24Z] INFO  17:24:33,032 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:24Z] INFO  17:24:33,032 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:24Z] INFO  17:24:33,036 HelpFormatter - Program Args: -T PrintReads -L 4:1-31018607 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpMddIGc/2_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam
[2015-09-30T16:24Z] INFO  17:24:33,041 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:24Z] INFO  17:24:33,041 HelpFormatter - Date/Time: 2015/09/30 17:24:33
[2015-09-30T16:24Z] INFO  17:24:33,042 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:24Z] INFO  17:24:33,042 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:24Z] INFO  17:24:33,149 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:24Z] INFO  17:24:33,842 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:24Z] INFO  17:24:33,892 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:24Z] INFO  17:24:33,900 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:24Z] INFO  17:24:33,922 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:24Z] INFO  17:24:33,935 IntervalUtils - Processing 31018607 bp from intervals
[2015-09-30T16:24Z] INFO  17:24:33,991 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:24Z] INFO  17:24:34,180 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:24Z] INFO  17:24:34,180 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:24Z] INFO  17:24:34,181 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:24Z] INFO  17:24:34,181 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:24Z] INFO  17:24:34,191 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:24Z] INFO  17:24:34,381 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:24Z] INFO  17:24:34,823 ProgressMeter -     3:195597568    200003.0    30.0 s       2.5 m       78.5%    38.0 s       8.0 s
[2015-09-30T16:24Z] INFO  17:24:48,468 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:24Z] INFO  17:24:48,569 ProgressMeter -            done    398317.0    43.0 s     109.0 s       99.4%    43.0 s       0.0 s
[2015-09-30T16:24Z] INFO  17:24:48,570 ProgressMeter - Total runtime 43.75 secs, 0.73 min, 0.01 hours
[2015-09-30T16:24Z] INFO  17:24:48,570 MicroScheduler - 864 reads were filtered out during the traversal out of approximately 399181 total reads (0.22%)
[2015-09-30T16:24Z] INFO  17:24:48,570 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:24Z] INFO  17:24:48,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:24Z] INFO  17:24:48,571 MicroScheduler -   -> 864 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:24Z] INFO  17:24:49,574 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:24Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam
[2015-09-30T16:24Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam 3:186768754-198022430
[2015-09-30T16:24Z] GATK: RealignerTargetCreator
[2015-09-30T16:24Z] INFO  17:24:53,073 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:24Z] INFO  17:24:53,075 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:24Z] INFO  17:24:53,075 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:24Z] INFO  17:24:53,075 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:24Z] INFO  17:24:53,079 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpouto5T/2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign-realign.intervals -l INFO -L 3:186768754-198022430 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:24Z] INFO  17:24:53,084 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:24Z] INFO  17:24:53,084 HelpFormatter - Date/Time: 2015/09/30 17:24:53
[2015-09-30T16:24Z] INFO  17:24:53,085 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:24Z] INFO  17:24:53,085 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:24Z] INFO  17:24:53,144 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:24Z] INFO  17:24:53,339 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:24Z] INFO  17:24:53,346 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:24Z] INFO  17:24:53,390 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T16:24Z] INFO  17:24:53,638 IntervalUtils - Processing 11253677 bp from intervals
[2015-09-30T16:24Z] WARN  17:24:53,642 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:24Z] INFO  17:24:53,700 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:24Z] INFO  17:24:53,779 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:24Z] INFO  17:24:53,779 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:24Z] INFO  17:24:53,780 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:24Z] INFO  17:24:53,780 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:25Z] INFO  17:25:00,192 ProgressMeter -            done   1815567.0    89.0 s      49.0 s      100.0%    89.0 s       0.0 s
[2015-09-30T16:25Z] INFO  17:25:00,192 ProgressMeter - Total runtime 89.69 secs, 1.49 min, 0.02 hours
[2015-09-30T16:25Z] INFO  17:25:00,196 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1815567 total reads (0.00%)
[2015-09-30T16:25Z] INFO  17:25:00,196 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:25Z] INFO  17:25:00,196 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:25Z] INFO  17:25:00,196 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:25Z] INFO  17:25:01,338 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:25Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam
[2015-09-30T16:25Z] INFO  17:25:04,183 ProgressMeter -       4:2306821    200004.0    30.0 s       2.5 m        7.4%     6.7 m       6.2 m
[2015-09-30T16:25Z] GATK pre-alignment ('4', 31031389, 62067173) : syn3-tumor
[2015-09-30T16:25Z] INFO  17:25:06,704 ProgressMeter -            done   1.1253677E7    12.0 s       1.0 s      100.0%    12.0 s       0.0 s
[2015-09-30T16:25Z] INFO  17:25:06,704 ProgressMeter - Total runtime 12.92 secs, 0.22 min, 0.00 hours
[2015-09-30T16:25Z] INFO  17:25:06,707 MicroScheduler - 43952 reads were filtered out during the traversal out of approximately 401202 total reads (10.96%)
[2015-09-30T16:25Z] INFO  17:25:06,707 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:25Z] INFO  17:25:06,708 MicroScheduler -   -> 4563 reads (1.14% of total) failing BadMateFilter
[2015-09-30T16:25Z] INFO  17:25:06,708 MicroScheduler -   -> 17754 reads (4.43% of total) failing DuplicateReadFilter
[2015-09-30T16:25Z] INFO  17:25:06,708 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:25Z] INFO  17:25:06,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:25Z] INFO  17:25:06,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:25Z] INFO  17:25:06,709 MicroScheduler -   -> 21635 reads (5.39% of total) failing MappingQualityZeroFilter
[2015-09-30T16:25Z] INFO  17:25:06,709 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:25Z] INFO  17:25:06,709 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:25Z] INFO  17:25:06,710 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:25Z] INFO  17:25:07,757 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:25Z] GATK: realign ('3', 186768753, 198022430) : syn3-tumor
[2015-09-30T16:25Z] INFO  17:25:08,150 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:25Z] INFO  17:25:08,152 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:25Z] INFO  17:25:08,153 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:25Z] INFO  17:25:08,153 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:25Z] INFO  17:25:08,156 HelpFormatter - Program Args: -T PrintReads -L 4:31031390-62067173 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmprndoXE/2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam
[2015-09-30T16:25Z] INFO  17:25:08,162 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:25Z] INFO  17:25:08,162 HelpFormatter - Date/Time: 2015/09/30 17:25:08
[2015-09-30T16:25Z] INFO  17:25:08,162 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:25Z] INFO  17:25:08,162 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:25Z] INFO  17:25:08,270 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:25Z] INFO  17:25:09,354 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:25Z] INFO  17:25:09,404 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:25Z] INFO  17:25:09,412 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:25Z] INFO  17:25:09,427 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:25Z] INFO  17:25:09,440 IntervalUtils - Processing 31035784 bp from intervals
[2015-09-30T16:25Z] INFO  17:25:09,501 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:25Z] INFO  17:25:09,500 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:25Z] INFO  17:25:09,502 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:25Z] INFO  17:25:09,502 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:25Z] INFO  17:25:09,502 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:25Z] INFO  17:25:09,506 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep-prealign-realign.intervals -L 3:186768754-198022430 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/tx/tmpDEnVSs/2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam
[2015-09-30T16:25Z] INFO  17:25:09,512 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:25Z] INFO  17:25:09,512 HelpFormatter - Date/Time: 2015/09/30 17:25:09
[2015-09-30T16:25Z] INFO  17:25:09,512 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:25Z] INFO  17:25:09,512 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:25Z] INFO  17:25:09,618 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:25Z] INFO  17:25:09,690 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:25Z] INFO  17:25:09,692 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:25Z] INFO  17:25:09,692 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:25Z] INFO  17:25:09,692 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:25Z] INFO  17:25:09,692 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:25Z] INFO  17:25:09,698 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:25Z] INFO  17:25:09,704 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:25Z] INFO  17:25:09,714 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:25Z] INFO  17:25:09,899 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:25Z] INFO  17:25:09,942 IntervalUtils - Processing 11253677 bp from intervals
[2015-09-30T16:25Z] WARN  17:25:09,946 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:25Z] INFO  17:25:10,003 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:25Z] INFO  17:25:10,099 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:25Z] INFO  17:25:10,099 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:25Z] INFO  17:25:10,100 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:25Z] INFO  17:25:10,100 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:25Z] INFO  17:25:10,210 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:25Z] INFO  17:25:10,301 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:25Z] INFO  17:25:34,184 ProgressMeter -       4:7714462    500007.0    60.0 s     120.0 s       24.9%     4.0 m       3.0 m
[2015-09-30T16:25Z] INFO  17:25:34,210 ProgressMeter -            done    398317.0    24.0 s      60.0 s       99.4%    24.0 s       0.0 s
[2015-09-30T16:25Z] INFO  17:25:34,211 ProgressMeter - Total runtime 24.11 secs, 0.40 min, 0.01 hours
[2015-09-30T16:25Z] INFO  17:25:34,214 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 398317 total reads (0.00%)
[2015-09-30T16:25Z] INFO  17:25:34,214 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:25Z] INFO  17:25:34,214 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:25Z] INFO  17:25:34,215 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:25Z] INFO  17:25:35,291 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:25Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam
[2015-09-30T16:25Z] GATK pre-alignment ('4', 62292837, 93511697) : syn3-tumor
[2015-09-30T16:25Z] INFO  17:25:39,246 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:25Z] INFO  17:25:39,248 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:25Z] INFO  17:25:39,248 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:25Z] INFO  17:25:39,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:25Z] INFO  17:25:39,251 HelpFormatter - Program Args: -T PrintReads -L 4:62292838-93511697 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmp31HVTH/2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam
[2015-09-30T16:25Z] INFO  17:25:39,257 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:25Z] INFO  17:25:39,258 HelpFormatter - Date/Time: 2015/09/30 17:25:39
[2015-09-30T16:25Z] INFO  17:25:39,258 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:25Z] INFO  17:25:39,258 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:25Z] INFO  17:25:39,376 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:25Z] INFO  17:25:39,702 ProgressMeter -      4:48173771    200002.0    30.0 s       2.5 m       55.2%    54.0 s      24.0 s
[2015-09-30T16:25Z] INFO  17:25:40,072 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:25Z] INFO  17:25:40,123 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:25Z] INFO  17:25:40,130 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:25Z] INFO  17:25:40,145 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:25Z] INFO  17:25:40,158 IntervalUtils - Processing 31218860 bp from intervals
[2015-09-30T16:25Z] INFO  17:25:40,215 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:25Z] INFO  17:25:40,413 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:25Z] INFO  17:25:40,414 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:25Z] INFO  17:25:40,414 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:25Z] INFO  17:25:40,414 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:25Z] INFO  17:25:40,425 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:25Z] INFO  17:25:40,615 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:25Z] INFO  17:25:57,329 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:25Z] INFO  17:25:57,761 ProgressMeter -            done    451836.0    48.0 s     106.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T16:25Z] INFO  17:25:57,761 ProgressMeter - Total runtime 48.07 secs, 0.80 min, 0.01 hours
[2015-09-30T16:25Z] INFO  17:25:57,761 MicroScheduler - 2237 reads were filtered out during the traversal out of approximately 454073 total reads (0.49%)
[2015-09-30T16:25Z] INFO  17:25:57,762 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:25Z] INFO  17:25:57,762 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:25Z] INFO  17:25:57,762 MicroScheduler -   -> 2237 reads (0.49% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:25Z] INFO  17:25:58,811 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:26Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam
[2015-09-30T16:26Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam 4:31031390-62067173
[2015-09-30T16:26Z] GATK: RealignerTargetCreator
[2015-09-30T16:26Z] INFO  17:26:03,683 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:03,685 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:26Z] INFO  17:26:03,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:26Z] INFO  17:26:03,685 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:26Z] INFO  17:26:03,688 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpYn73XD/2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign-realign.intervals -l INFO -L 4:31031390-62067173 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:26Z] INFO  17:26:03,694 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:26Z] INFO  17:26:03,694 HelpFormatter - Date/Time: 2015/09/30 17:26:03
[2015-09-30T16:26Z] INFO  17:26:03,694 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:03,695 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:03,752 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:26Z] INFO  17:26:04,185 ProgressMeter -      4:25236114    800010.0    90.0 s     112.0 s       81.4%   110.0 s      20.0 s
[2015-09-30T16:26Z] INFO  17:26:04,763 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:26Z] INFO  17:26:04,771 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:26Z] INFO  17:26:04,819 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T16:26Z] INFO  17:26:05,075 IntervalUtils - Processing 31035784 bp from intervals
[2015-09-30T16:26Z] WARN  17:26:05,079 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:26Z] INFO  17:26:05,136 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:26Z] INFO  17:26:05,486 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:26Z] INFO  17:26:05,487 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:26Z] INFO  17:26:05,487 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:26Z] INFO  17:26:05,488 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:26Z] INFO  17:26:08,723 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:26Z] INFO  17:26:08,912 ProgressMeter -            done    921852.0    94.0 s     102.0 s      100.0%    94.0 s       0.0 s
[2015-09-30T16:26Z] INFO  17:26:08,913 ProgressMeter - Total runtime 94.73 secs, 1.58 min, 0.03 hours
[2015-09-30T16:26Z] INFO  17:26:08,913 MicroScheduler - 1920 reads were filtered out during the traversal out of approximately 923772 total reads (0.21%)
[2015-09-30T16:26Z] INFO  17:26:08,913 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:26Z] INFO  17:26:08,914 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:26Z] INFO  17:26:08,914 MicroScheduler -   -> 1920 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:26Z] INFO  17:26:10,016 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:26Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam
[2015-09-30T16:26Z] INFO  17:26:10,417 ProgressMeter -      4:76417037    200002.0    30.0 s       2.5 m       45.2%    66.0 s      36.0 s
[2015-09-30T16:26Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam 4:1-31018607
[2015-09-30T16:26Z] GATK: RealignerTargetCreator
[2015-09-30T16:26Z] INFO  17:26:14,130 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:14,133 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:26Z] INFO  17:26:14,133 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:26Z] INFO  17:26:14,133 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:26Z] INFO  17:26:14,137 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpZe9wlv/2_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign-realign.intervals -l INFO -L 4:1-31018607 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:26Z] INFO  17:26:14,142 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:26Z] INFO  17:26:14,143 HelpFormatter - Date/Time: 2015/09/30 17:26:14
[2015-09-30T16:26Z] INFO  17:26:14,143 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:14,143 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:14,203 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:26Z] INFO  17:26:14,328 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:26Z] INFO  17:26:14,336 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:26Z] INFO  17:26:14,354 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:26Z] INFO  17:26:15,098 IntervalUtils - Processing 31018607 bp from intervals
[2015-09-30T16:26Z] WARN  17:26:15,102 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:26Z] INFO  17:26:15,209 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:26Z] INFO  17:26:15,372 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:26Z] INFO  17:26:15,372 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:26Z] INFO  17:26:15,373 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:26Z] INFO  17:26:15,373 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:26Z] INFO  17:26:27,718 ProgressMeter -            done   3.1035784E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T16:26Z] INFO  17:26:27,719 ProgressMeter - Total runtime 22.23 secs, 0.37 min, 0.01 hours
[2015-09-30T16:26Z] INFO  17:26:27,722 MicroScheduler - 37623 reads were filtered out during the traversal out of approximately 454578 total reads (8.28%)
[2015-09-30T16:26Z] INFO  17:26:27,722 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:26Z] INFO  17:26:27,723 MicroScheduler -   -> 8225 reads (1.81% of total) failing BadMateFilter
[2015-09-30T16:26Z] INFO  17:26:27,723 MicroScheduler -   -> 17883 reads (3.93% of total) failing DuplicateReadFilter
[2015-09-30T16:26Z] INFO  17:26:27,723 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:26Z] INFO  17:26:27,723 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:26Z] INFO  17:26:27,724 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:26Z] INFO  17:26:27,724 MicroScheduler -   -> 11515 reads (2.53% of total) failing MappingQualityZeroFilter
[2015-09-30T16:26Z] INFO  17:26:27,724 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:26Z] INFO  17:26:27,724 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:26Z] INFO  17:26:27,724 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:26Z] INFO  17:26:28,714 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:26Z] GATK: realign ('4', 31031389, 62067173) : syn3-tumor
[2015-09-30T16:26Z] INFO  17:26:30,696 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:30,698 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:26Z] INFO  17:26:30,698 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:26Z] INFO  17:26:30,698 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:26Z] INFO  17:26:30,702 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep-prealign-realign.intervals -L 4:31031390-62067173 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmprW_F45/2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam
[2015-09-30T16:26Z] INFO  17:26:30,708 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:26Z] INFO  17:26:30,708 HelpFormatter - Date/Time: 2015/09/30 17:26:30
[2015-09-30T16:26Z] INFO  17:26:30,708 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:30,708 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:30,817 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:26Z] INFO  17:26:30,891 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:26Z] INFO  17:26:30,899 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:26Z] INFO  17:26:30,917 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:26Z] INFO  17:26:31,551 IntervalUtils - Processing 31035784 bp from intervals
[2015-09-30T16:26Z] WARN  17:26:31,555 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:26Z] INFO  17:26:31,611 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:26Z] INFO  17:26:31,751 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:26Z] INFO  17:26:31,752 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:26Z] INFO  17:26:31,752 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:26Z] INFO  17:26:31,752 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:26Z] INFO  17:26:31,896 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:26Z] INFO  17:26:32,081 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:26Z] INFO  17:26:40,417 ProgressMeter -      4:88056711    500006.0    60.0 s     120.0 s       82.5%    72.0 s      12.0 s
[2015-09-30T16:26Z] INFO  17:26:43,869 ProgressMeter -            done   3.1018607E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T16:26Z] INFO  17:26:43,870 ProgressMeter - Total runtime 28.50 secs, 0.47 min, 0.01 hours
[2015-09-30T16:26Z] INFO  17:26:43,873 MicroScheduler - 81656 reads were filtered out during the traversal out of approximately 926954 total reads (8.81%)
[2015-09-30T16:26Z] INFO  17:26:43,873 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:26Z] INFO  17:26:43,874 MicroScheduler -   -> 10827 reads (1.17% of total) failing BadMateFilter
[2015-09-30T16:26Z] INFO  17:26:43,874 MicroScheduler -   -> 45416 reads (4.90% of total) failing DuplicateReadFilter
[2015-09-30T16:26Z] INFO  17:26:43,874 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:26Z] INFO  17:26:43,874 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:26Z] INFO  17:26:43,875 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:26Z] INFO  17:26:43,875 MicroScheduler -   -> 25413 reads (2.74% of total) failing MappingQualityZeroFilter
[2015-09-30T16:26Z] INFO  17:26:43,875 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:26Z] INFO  17:26:43,875 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:26Z] INFO  17:26:43,876 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:26Z] INFO  17:26:44,853 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:26Z] GATK: realign ('4', 0, 31018607) : syn3-tumor
[2015-09-30T16:26Z] INFO  17:26:48,742 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:26Z] INFO  17:26:48,974 ProgressMeter -            done    627128.0    68.0 s     109.0 s      100.0%    68.0 s       0.0 s
[2015-09-30T16:26Z] INFO  17:26:48,975 ProgressMeter - Total runtime 68.56 secs, 1.14 min, 0.02 hours
[2015-09-30T16:26Z] INFO  17:26:48,975 MicroScheduler - 2101 reads were filtered out during the traversal out of approximately 629229 total reads (0.33%)
[2015-09-30T16:26Z] INFO  17:26:48,975 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:26Z] INFO  17:26:48,976 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:26Z] INFO  17:26:48,976 MicroScheduler -   -> 2101 reads (0.33% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:26Z] INFO  17:26:50,063 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:26Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam
[2015-09-30T16:26Z] INFO  17:26:51,886 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:51,888 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:26Z] INFO  17:26:51,888 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:26Z] INFO  17:26:51,889 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:26Z] INFO  17:26:51,892 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_0_31018607-prep-prealign-realign.intervals -L 4:1-31018607 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpOydVCg/2_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam
[2015-09-30T16:26Z] INFO  17:26:51,898 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:26Z] INFO  17:26:51,898 HelpFormatter - Date/Time: 2015/09/30 17:26:51
[2015-09-30T16:26Z] INFO  17:26:51,898 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:51,899 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam 4:62292838-93511697
[2015-09-30T16:26Z] GATK: RealignerTargetCreator
[2015-09-30T16:26Z] INFO  17:26:52,028 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:26Z] INFO  17:26:52,096 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:26Z] INFO  17:26:52,104 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:26Z] INFO  17:26:52,121 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:26Z] INFO  17:26:56,827 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:56,829 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:26Z] INFO  17:26:56,829 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:26Z] INFO  17:26:56,829 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:26Z] INFO  17:26:56,833 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpaO0P68/2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign-realign.intervals -l INFO -L 4:62292838-93511697 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:26Z] INFO  17:26:56,838 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:26Z] INFO  17:26:56,838 HelpFormatter - Date/Time: 2015/09/30 17:26:56
[2015-09-30T16:26Z] INFO  17:26:56,839 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:56,839 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:26Z] INFO  17:26:56,896 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:26Z] INFO  17:26:57,005 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:26Z] INFO  17:26:57,013 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:26Z] INFO  17:26:57,029 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:26Z] INFO  17:26:57,641 IntervalUtils - Processing 31018607 bp from intervals
[2015-09-30T16:26Z] WARN  17:26:57,645 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:26Z] INFO  17:26:57,702 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:26Z] INFO  17:26:57,844 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:26Z] INFO  17:26:57,845 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:26Z] INFO  17:26:57,845 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:26Z] INFO  17:26:57,846 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:26Z] INFO  17:26:57,990 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:26Z] INFO  17:26:58,178 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:26Z] INFO  17:26:58,527 IntervalUtils - Processing 31218860 bp from intervals
[2015-09-30T16:26Z] WARN  17:26:58,531 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:26Z] INFO  17:26:58,589 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:26Z] INFO  17:26:58,738 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:26Z] INFO  17:26:58,739 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:26Z] INFO  17:26:58,739 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:26Z] INFO  17:26:58,740 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:27Z] INFO  17:27:09,288 ProgressMeter -            done    451836.0    37.0 s      83.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T16:27Z] INFO  17:27:09,288 ProgressMeter - Total runtime 37.54 secs, 0.63 min, 0.01 hours
[2015-09-30T16:27Z] INFO  17:27:09,291 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 451836 total reads (0.00%)
[2015-09-30T16:27Z] INFO  17:27:09,291 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:27Z] INFO  17:27:09,291 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:27Z] INFO  17:27:09,292 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:27Z] INFO  17:27:10,415 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:27Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam
[2015-09-30T16:27Z] GATK pre-alignment ('4', 94005855, 125588163) : syn3-tumor
[2015-09-30T16:27Z] INFO  17:27:13,278 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:27Z] INFO  17:27:13,280 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:27Z] INFO  17:27:13,281 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:27Z] INFO  17:27:13,281 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:27Z] INFO  17:27:13,284 HelpFormatter - Program Args: -T PrintReads -L 4:94005856-125588163 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmp4ai4zn/2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam
[2015-09-30T16:27Z] INFO  17:27:13,290 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:27Z] INFO  17:27:13,290 HelpFormatter - Date/Time: 2015/09/30 17:27:13
[2015-09-30T16:27Z] INFO  17:27:13,290 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:27Z] INFO  17:27:13,290 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:27Z] INFO  17:27:13,395 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:27Z] INFO  17:27:15,407 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:27Z] INFO  17:27:15,457 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:27Z] INFO  17:27:15,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:27Z] INFO  17:27:15,479 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:27Z] INFO  17:27:15,493 IntervalUtils - Processing 31582308 bp from intervals
[2015-09-30T16:27Z] INFO  17:27:15,551 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:27Z] INFO  17:27:15,765 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:27Z] INFO  17:27:15,765 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:27Z] INFO  17:27:15,766 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:27Z] INFO  17:27:15,766 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:27Z] INFO  17:27:15,777 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:27Z] INFO  17:27:15,978 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:27Z] INFO  17:27:25,673 ProgressMeter -            done   3.121886E7    26.0 s       0.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T16:27Z] INFO  17:27:25,673 ProgressMeter - Total runtime 26.93 secs, 0.45 min, 0.01 hours
[2015-09-30T16:27Z] INFO  17:27:25,676 MicroScheduler - 47021 reads were filtered out during the traversal out of approximately 631011 total reads (7.45%)
[2015-09-30T16:27Z] INFO  17:27:25,677 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:27Z] INFO  17:27:25,677 MicroScheduler -   -> 9213 reads (1.46% of total) failing BadMateFilter
[2015-09-30T16:27Z] INFO  17:27:25,677 MicroScheduler -   -> 24660 reads (3.91% of total) failing DuplicateReadFilter
[2015-09-30T16:27Z] INFO  17:27:25,677 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:27Z] INFO  17:27:25,678 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:27Z] INFO  17:27:25,678 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:27Z] INFO  17:27:25,678 MicroScheduler -   -> 13148 reads (2.08% of total) failing MappingQualityZeroFilter
[2015-09-30T16:27Z] INFO  17:27:25,678 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:27Z] INFO  17:27:25,679 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:27Z] INFO  17:27:25,679 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:27Z] INFO  17:27:26,660 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:27Z] GATK: realign ('4', 62292837, 93511697) : syn3-tumor
[2015-09-30T16:27Z] INFO  17:27:27,848 ProgressMeter -       4:3478428    300005.0    30.0 s     100.0 s       11.2%     4.5 m       4.0 m
[2015-09-30T16:27Z] INFO  17:27:30,541 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:27Z] INFO  17:27:30,544 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:27Z] INFO  17:27:30,544 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:27Z] INFO  17:27:30,544 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:27Z] INFO  17:27:30,548 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep-prealign-realign.intervals -L 4:62292838-93511697 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmp2dAaJd/2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam
[2015-09-30T16:27Z] INFO  17:27:30,554 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:27Z] INFO  17:27:30,554 HelpFormatter - Date/Time: 2015/09/30 17:27:30
[2015-09-30T16:27Z] INFO  17:27:30,554 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:27Z] INFO  17:27:30,554 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:27Z] INFO  17:27:30,684 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:27Z] INFO  17:27:30,751 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:27Z] INFO  17:27:30,760 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:27Z] INFO  17:27:30,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:27Z] INFO  17:27:31,006 IntervalUtils - Processing 31218860 bp from intervals
[2015-09-30T16:27Z] WARN  17:27:31,010 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:27Z] INFO  17:27:31,070 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:27Z] INFO  17:27:31,211 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:27Z] INFO  17:27:31,212 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:27Z] INFO  17:27:31,212 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:27Z] INFO  17:27:31,213 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:27Z] INFO  17:27:31,361 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:27Z] INFO  17:27:31,548 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:27Z] INFO  17:27:46,040 ProgressMeter -     4:106181084    100001.0    30.0 s       5.0 m       38.6%    77.0 s      47.0 s
[2015-09-30T16:27Z] INFO  17:27:51,780 ProgressMeter -            done    921852.0    53.0 s      58.0 s      100.0%    53.0 s       0.0 s
[2015-09-30T16:27Z] INFO  17:27:51,781 ProgressMeter - Total runtime 53.94 secs, 0.90 min, 0.01 hours
[2015-09-30T16:27Z] INFO  17:27:51,784 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 921852 total reads (0.00%)
[2015-09-30T16:27Z] INFO  17:27:51,784 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:27Z] INFO  17:27:51,785 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:27Z] INFO  17:27:51,785 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:27Z] INFO  17:27:52,899 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:27Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam
[2015-09-30T16:27Z] GATK pre-alignment ('4', 125589908, 156618518) : syn3-tumor
[2015-09-30T16:27Z] INFO  17:27:57,148 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:27Z] INFO  17:27:57,150 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:27Z] INFO  17:27:57,150 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:27Z] INFO  17:27:57,150 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:27Z] INFO  17:27:57,154 HelpFormatter - Program Args: -T PrintReads -L 4:125589909-156618518 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpUgC6PG/2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam
[2015-09-30T16:27Z] INFO  17:27:57,159 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:27Z] INFO  17:27:57,159 HelpFormatter - Date/Time: 2015/09/30 17:27:57
[2015-09-30T16:27Z] INFO  17:27:57,160 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:27Z] INFO  17:27:57,160 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:27Z] INFO  17:27:57,263 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:27Z] INFO  17:27:58,950 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:27Z] INFO  17:27:58,999 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:27Z] INFO  17:27:59,007 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:27Z] INFO  17:27:59,021 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:27Z] INFO  17:27:59,034 IntervalUtils - Processing 31028610 bp from intervals
[2015-09-30T16:27Z] INFO  17:27:59,090 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:27Z] INFO  17:27:59,569 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:27Z] INFO  17:27:59,570 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:27Z] INFO  17:27:59,570 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:27Z] INFO  17:27:59,570 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:27Z] INFO  17:27:59,581 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:27Z] INFO  17:27:59,766 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:28Z] INFO  17:28:04,795 ProgressMeter -      4:85654307    400004.0    33.0 s      83.0 s       74.8%    44.0 s      11.0 s
[2015-09-30T16:28Z] INFO  17:28:09,089 ProgressMeter -            done    627128.0    37.0 s      60.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T16:28Z] INFO  17:28:09,089 ProgressMeter - Total runtime 37.88 secs, 0.63 min, 0.01 hours
[2015-09-30T16:28Z] INFO  17:28:09,092 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 627128 total reads (0.00%)
[2015-09-30T16:28Z] INFO  17:28:09,093 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:28Z] INFO  17:28:09,093 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:28Z] INFO  17:28:09,093 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:28Z] INFO  17:28:10,213 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:28Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam
[2015-09-30T16:28Z] GATK pre-alignment ('4', 156624795, 188926424) : syn3-tumor
[2015-09-30T16:28Z] INFO  17:28:14,277 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:14,279 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:28Z] INFO  17:28:14,279 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:28Z] INFO  17:28:14,279 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:28Z] INFO  17:28:14,283 HelpFormatter - Program Args: -T PrintReads -L 4:156624796-188926424 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmprdTDWn/2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam
[2015-09-30T16:28Z] INFO  17:28:14,288 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:28Z] INFO  17:28:14,288 HelpFormatter - Date/Time: 2015/09/30 17:28:14
[2015-09-30T16:28Z] INFO  17:28:14,288 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:14,289 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:14,414 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:28Z] INFO  17:28:14,782 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:28Z] INFO  17:28:14,906 ProgressMeter -            done    485720.0    59.0 s       2.0 m      100.0%    59.0 s       0.0 s
[2015-09-30T16:28Z] INFO  17:28:14,907 ProgressMeter - Total runtime 59.14 secs, 0.99 min, 0.02 hours
[2015-09-30T16:28Z] INFO  17:28:14,907 MicroScheduler - 1546 reads were filtered out during the traversal out of approximately 487266 total reads (0.32%)
[2015-09-30T16:28Z] INFO  17:28:14,907 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:28Z] INFO  17:28:14,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:28Z] INFO  17:28:14,908 MicroScheduler -   -> 1546 reads (0.32% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:28Z] INFO  17:28:15,234 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:28Z] INFO  17:28:15,282 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:28Z] INFO  17:28:15,290 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:28Z] INFO  17:28:15,304 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:28Z] INFO  17:28:15,317 IntervalUtils - Processing 32301629 bp from intervals
[2015-09-30T16:28Z] INFO  17:28:15,371 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:28Z] INFO  17:28:15,579 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:28Z] INFO  17:28:15,580 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:28Z] INFO  17:28:15,580 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:28Z] INFO  17:28:15,580 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:28Z] INFO  17:28:15,591 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:28Z] INFO  17:28:15,782 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:28Z] INFO  17:28:16,506 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:28Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam
[2015-09-30T16:28Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam 4:94005856-125588163
[2015-09-30T16:28Z] GATK: RealignerTargetCreator
[2015-09-30T16:28Z] INFO  17:28:19,435 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:19,437 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:28Z] INFO  17:28:19,437 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:28Z] INFO  17:28:19,437 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:28Z] INFO  17:28:19,441 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpzyYGO5/2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign-realign.intervals -l INFO -L 4:94005856-125588163 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:28Z] INFO  17:28:19,447 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:28Z] INFO  17:28:19,447 HelpFormatter - Date/Time: 2015/09/30 17:28:19
[2015-09-30T16:28Z] INFO  17:28:19,447 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:19,447 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:19,511 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:28Z] INFO  17:28:20,269 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:28Z] INFO  17:28:20,277 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:28Z] INFO  17:28:20,295 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:28Z] INFO  17:28:20,538 IntervalUtils - Processing 31582308 bp from intervals
[2015-09-30T16:28Z] WARN  17:28:20,542 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:28Z] INFO  17:28:20,603 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:28Z] INFO  17:28:20,754 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:28Z] INFO  17:28:20,754 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:28Z] INFO  17:28:20,755 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:28Z] INFO  17:28:20,755 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:28Z] INFO  17:28:29,598 ProgressMeter -     4:148493274    200003.0    30.0 s       2.5 m       73.8%    40.0 s      10.0 s
[2015-09-30T16:28Z] INFO  17:28:43,141 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:28Z] INFO  17:28:43,261 ProgressMeter -            done    401264.0    43.0 s     108.0 s      100.0%    43.0 s       0.0 s
[2015-09-30T16:28Z] INFO  17:28:43,261 ProgressMeter - Total runtime 43.69 secs, 0.73 min, 0.01 hours
[2015-09-30T16:28Z] INFO  17:28:43,262 MicroScheduler - 1471 reads were filtered out during the traversal out of approximately 402735 total reads (0.37%)
[2015-09-30T16:28Z] INFO  17:28:43,262 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:28Z] INFO  17:28:43,262 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:28Z] INFO  17:28:43,262 MicroScheduler -   -> 1471 reads (0.37% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:28Z] INFO  17:28:44,268 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:28Z] INFO  17:28:45,081 ProgressMeter -            done   3.1582308E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T16:28Z] INFO  17:28:45,082 ProgressMeter - Total runtime 24.33 secs, 0.41 min, 0.01 hours
[2015-09-30T16:28Z] INFO  17:28:45,085 MicroScheduler - 36596 reads were filtered out during the traversal out of approximately 488407 total reads (7.49%)
[2015-09-30T16:28Z] INFO  17:28:45,085 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:28Z] INFO  17:28:45,086 MicroScheduler -   -> 7809 reads (1.60% of total) failing BadMateFilter
[2015-09-30T16:28Z] INFO  17:28:45,086 MicroScheduler -   -> 18833 reads (3.86% of total) failing DuplicateReadFilter
[2015-09-30T16:28Z] INFO  17:28:45,086 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:28Z] INFO  17:28:45,087 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:28Z] INFO  17:28:45,087 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:28Z] INFO  17:28:45,087 MicroScheduler -   -> 9954 reads (2.04% of total) failing MappingQualityZeroFilter
[2015-09-30T16:28Z] INFO  17:28:45,087 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:28Z] INFO  17:28:45,087 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:28Z] INFO  17:28:45,088 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:28Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam
[2015-09-30T16:28Z] INFO  17:28:45,629 ProgressMeter -     4:183664012    200002.0    30.0 s       2.5 m       83.7%    35.0 s       5.0 s
[2015-09-30T16:28Z] INFO  17:28:46,030 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:28Z] GATK: realign ('4', 94005855, 125588163) : syn3-tumor
[2015-09-30T16:28Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam 4:125589909-156618518
[2015-09-30T16:28Z] GATK: RealignerTargetCreator
[2015-09-30T16:28Z] INFO  17:28:48,596 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:48,598 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:28Z] INFO  17:28:48,598 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:28Z] INFO  17:28:48,598 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:28Z] INFO  17:28:48,602 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep-prealign-realign.intervals -L 4:94005856-125588163 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmp5UkTvz/2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam
[2015-09-30T16:28Z] INFO  17:28:48,608 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:28Z] INFO  17:28:48,608 HelpFormatter - Date/Time: 2015/09/30 17:28:48
[2015-09-30T16:28Z] INFO  17:28:48,608 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:48,608 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:48,713 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:48,716 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:28Z] INFO  17:28:48,716 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:28Z] INFO  17:28:48,716 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:28Z] INFO  17:28:48,720 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:28Z] INFO  17:28:48,720 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpLn07F_/2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign-realign.intervals -l INFO -L 4:125589909-156618518 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:28Z] INFO  17:28:48,725 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:28Z] INFO  17:28:48,726 HelpFormatter - Date/Time: 2015/09/30 17:28:48
[2015-09-30T16:28Z] INFO  17:28:48,726 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:48,726 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:28Z] INFO  17:28:48,788 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:28Z] INFO  17:28:48,790 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:28Z] INFO  17:28:48,798 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:28Z] INFO  17:28:48,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:28Z] INFO  17:28:48,900 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:28Z] INFO  17:28:48,909 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:28Z] INFO  17:28:48,925 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:28Z] INFO  17:28:49,034 IntervalUtils - Processing 31582308 bp from intervals
[2015-09-30T16:28Z] WARN  17:28:49,038 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:28Z] INFO  17:28:49,095 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:28Z] INFO  17:28:49,254 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:28Z] INFO  17:28:49,254 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:28Z] INFO  17:28:49,255 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:28Z] INFO  17:28:49,255 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:28Z] INFO  17:28:49,395 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:28Z] INFO  17:28:49,585 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:28Z] INFO  17:28:49,706 IntervalUtils - Processing 31028610 bp from intervals
[2015-09-30T16:28Z] WARN  17:28:49,710 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:28Z] INFO  17:28:49,771 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:28Z] INFO  17:28:49,925 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:28Z] INFO  17:28:49,926 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:28Z] INFO  17:28:49,926 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:28Z] INFO  17:28:49,926 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:28Z] INFO  17:28:59,156 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:28Z] INFO  17:28:59,260 ProgressMeter -            done    410371.0    43.0 s     106.0 s      100.0%    43.0 s       0.0 s
[2015-09-30T16:28Z] INFO  17:28:59,261 ProgressMeter - Total runtime 43.68 secs, 0.73 min, 0.01 hours
[2015-09-30T16:28Z] INFO  17:28:59,261 MicroScheduler - 1465 reads were filtered out during the traversal out of approximately 411836 total reads (0.36%)
[2015-09-30T16:28Z] INFO  17:28:59,261 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:28Z] INFO  17:28:59,262 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:28Z] INFO  17:28:59,262 MicroScheduler -   -> 1465 reads (0.36% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:29Z] INFO  17:29:00,452 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:29Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam
[2015-09-30T16:29Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam 4:156624796-188926424
[2015-09-30T16:29Z] GATK: RealignerTargetCreator
[2015-09-30T16:29Z] INFO  17:29:03,286 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:03,288 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:29Z] INFO  17:29:03,288 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:29Z] INFO  17:29:03,288 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:29Z] INFO  17:29:03,292 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpIqG5rQ/2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign-realign.intervals -l INFO -L 4:156624796-188926424 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:29Z] INFO  17:29:03,298 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:29Z] INFO  17:29:03,298 HelpFormatter - Date/Time: 2015/09/30 17:29:03
[2015-09-30T16:29Z] INFO  17:29:03,299 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:03,299 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:03,357 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:29Z] INFO  17:29:04,052 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:29Z] INFO  17:29:04,060 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:29Z] INFO  17:29:04,075 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:29Z] INFO  17:29:04,571 IntervalUtils - Processing 32301629 bp from intervals
[2015-09-30T16:29Z] WARN  17:29:04,575 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:29Z] INFO  17:29:04,630 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:29Z] INFO  17:29:06,503 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:29Z] INFO  17:29:06,503 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:29Z] INFO  17:29:06,504 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:29Z] INFO  17:29:06,504 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:29Z] INFO  17:29:11,666 ProgressMeter -            done   3.102861E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T16:29Z] INFO  17:29:11,667 ProgressMeter - Total runtime 21.74 secs, 0.36 min, 0.01 hours
[2015-09-30T16:29Z] INFO  17:29:11,670 MicroScheduler - 31307 reads were filtered out during the traversal out of approximately 403634 total reads (7.76%)
[2015-09-30T16:29Z] INFO  17:29:11,671 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:29Z] INFO  17:29:11,671 MicroScheduler -   -> 7353 reads (1.82% of total) failing BadMateFilter
[2015-09-30T16:29Z] INFO  17:29:11,671 MicroScheduler -   -> 16230 reads (4.02% of total) failing DuplicateReadFilter
[2015-09-30T16:29Z] INFO  17:29:11,671 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:29Z] INFO  17:29:11,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:29Z] INFO  17:29:11,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:29Z] INFO  17:29:11,672 MicroScheduler -   -> 7724 reads (1.91% of total) failing MappingQualityZeroFilter
[2015-09-30T16:29Z] INFO  17:29:11,672 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:29Z] INFO  17:29:11,673 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:29Z] INFO  17:29:11,673 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:29Z] INFO  17:29:12,636 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:29Z] GATK: realign ('4', 125589908, 156618518) : syn3-tumor
[2015-09-30T16:29Z] INFO  17:29:14,587 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:14,589 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:29Z] INFO  17:29:14,589 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:29Z] INFO  17:29:14,590 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:29Z] INFO  17:29:14,593 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep-prealign-realign.intervals -L 4:125589909-156618518 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpnxssXq/2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam
[2015-09-30T16:29Z] INFO  17:29:14,599 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:29Z] INFO  17:29:14,599 HelpFormatter - Date/Time: 2015/09/30 17:29:14
[2015-09-30T16:29Z] INFO  17:29:14,599 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:14,599 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:15,163 ProgressMeter -            done    485720.0    25.0 s      53.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T16:29Z] INFO  17:29:15,164 ProgressMeter - Total runtime 25.91 secs, 0.43 min, 0.01 hours
[2015-09-30T16:29Z] INFO  17:29:15,167 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 485720 total reads (0.00%)
[2015-09-30T16:29Z] INFO  17:29:15,167 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:29Z] INFO  17:29:15,168 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:29Z] INFO  17:29:15,168 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:29Z] INFO  17:29:15,188 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:29Z] INFO  17:29:15,254 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:29Z] INFO  17:29:15,261 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:29Z] INFO  17:29:15,276 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:29Z] INFO  17:29:15,502 IntervalUtils - Processing 31028610 bp from intervals
[2015-09-30T16:29Z] WARN  17:29:15,505 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:29Z] INFO  17:29:15,560 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:29Z] INFO  17:29:15,713 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:29Z] INFO  17:29:15,713 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:29Z] INFO  17:29:15,714 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:29Z] INFO  17:29:15,714 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:29Z] INFO  17:29:15,859 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:16,041 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:16,283 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:29Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam
[2015-09-30T16:29Z] GATK pre-alignment ('4', 189012293, 191154276) : syn3-tumor
[2015-09-30T16:29Z] INFO  17:29:19,356 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:19,358 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:29Z] INFO  17:29:19,358 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:29Z] INFO  17:29:19,359 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:29Z] INFO  17:29:19,362 HelpFormatter - Program Args: -T PrintReads -L 4:189012294-191154276 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmp8lLhka/2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam
[2015-09-30T16:29Z] INFO  17:29:19,367 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:29Z] INFO  17:29:19,368 HelpFormatter - Date/Time: 2015/09/30 17:29:19
[2015-09-30T16:29Z] INFO  17:29:19,368 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:19,368 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:19,476 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:29Z] INFO  17:29:20,237 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:29Z] INFO  17:29:20,285 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:29Z] INFO  17:29:20,293 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:29Z] INFO  17:29:20,307 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:29Z] INFO  17:29:20,320 IntervalUtils - Processing 2141983 bp from intervals
[2015-09-30T16:29Z] INFO  17:29:20,377 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:29Z] INFO  17:29:20,485 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:29Z] INFO  17:29:20,485 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:29Z] INFO  17:29:20,485 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:29Z] INFO  17:29:20,486 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:29Z] INFO  17:29:20,496 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:20,514 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:24,277 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:29Z] INFO  17:29:24,334 ProgressMeter -            done     21384.0     3.0 s       3.0 m       93.4%     3.0 s       0.0 s
[2015-09-30T16:29Z] INFO  17:29:24,335 ProgressMeter - Total runtime 3.85 secs, 0.06 min, 0.00 hours
[2015-09-30T16:29Z] INFO  17:29:24,335 MicroScheduler - 131 reads were filtered out during the traversal out of approximately 21515 total reads (0.61%)
[2015-09-30T16:29Z] INFO  17:29:24,335 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:29Z] INFO  17:29:24,335 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:29Z] INFO  17:29:24,336 MicroScheduler -   -> 131 reads (0.61% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:29Z] INFO  17:29:25,528 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:29Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam
[2015-09-30T16:29Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam 4:189012294-191154276
[2015-09-30T16:29Z] GATK: RealignerTargetCreator
[2015-09-30T16:29Z] INFO  17:29:27,922 ProgressMeter -            done   3.2301629E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T16:29Z] INFO  17:29:27,923 ProgressMeter - Total runtime 21.42 secs, 0.36 min, 0.01 hours
[2015-09-30T16:29Z] INFO  17:29:27,926 MicroScheduler - 32440 reads were filtered out during the traversal out of approximately 413083 total reads (7.85%)
[2015-09-30T16:29Z] INFO  17:29:27,926 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:29Z] INFO  17:29:27,926 MicroScheduler -   -> 7858 reads (1.90% of total) failing BadMateFilter
[2015-09-30T16:29Z] INFO  17:29:27,927 MicroScheduler -   -> 16369 reads (3.96% of total) failing DuplicateReadFilter
[2015-09-30T16:29Z] INFO  17:29:27,927 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:29Z] INFO  17:29:27,927 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:29Z] INFO  17:29:27,927 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:29Z] INFO  17:29:27,928 MicroScheduler -   -> 8213 reads (1.99% of total) failing MappingQualityZeroFilter
[2015-09-30T16:29Z] INFO  17:29:27,928 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:29Z] INFO  17:29:27,928 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:29Z] INFO  17:29:27,928 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:29Z] INFO  17:29:28,777 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:28,779 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:29Z] INFO  17:29:28,779 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:29Z] INFO  17:29:28,779 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:29Z] INFO  17:29:28,783 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpQu1ORs/2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign-realign.intervals -l INFO -L 4:189012294-191154276 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:29Z] INFO  17:29:28,788 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:29Z] INFO  17:29:28,788 HelpFormatter - Date/Time: 2015/09/30 17:29:28
[2015-09-30T16:29Z] INFO  17:29:28,788 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:28,788 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:28,850 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:29Z] INFO  17:29:28,893 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:29Z] GATK: realign ('4', 156624795, 188926424) : syn3-tumor
[2015-09-30T16:29Z] INFO  17:29:28,956 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:29Z] INFO  17:29:28,964 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:29Z] INFO  17:29:28,980 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:29Z] INFO  17:29:29,565 IntervalUtils - Processing 2141983 bp from intervals
[2015-09-30T16:29Z] WARN  17:29:29,569 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:29Z] INFO  17:29:29,623 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:29Z] INFO  17:29:29,662 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:29Z] INFO  17:29:29,663 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:29Z] INFO  17:29:29,663 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:29Z] INFO  17:29:29,663 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:29Z] INFO  17:29:30,641 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:30,643 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:29Z] INFO  17:29:30,643 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:29Z] INFO  17:29:30,643 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:29Z] INFO  17:29:30,647 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep-prealign-realign.intervals -L 4:156624796-188926424 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmpUWBoAh/2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam
[2015-09-30T16:29Z] INFO  17:29:30,652 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:29Z] INFO  17:29:30,652 HelpFormatter - Date/Time: 2015/09/30 17:29:30
[2015-09-30T16:29Z] INFO  17:29:30,652 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:30,653 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:30,779 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:29Z] INFO  17:29:30,847 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:29Z] INFO  17:29:30,854 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:29Z] INFO  17:29:30,869 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:29Z] INFO  17:29:31,809 IntervalUtils - Processing 32301629 bp from intervals
[2015-09-30T16:29Z] WARN  17:29:31,813 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:29Z] INFO  17:29:31,907 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:29Z] INFO  17:29:32,239 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:29Z] INFO  17:29:32,239 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:29Z] INFO  17:29:32,239 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:29Z] INFO  17:29:32,240 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:29Z] INFO  17:29:32,387 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:32,571 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:33,347 ProgressMeter -            done   2141983.0     3.0 s       1.0 s      100.0%     3.0 s       0.0 s
[2015-09-30T16:29Z] INFO  17:29:33,347 ProgressMeter - Total runtime 3.68 secs, 0.06 min, 0.00 hours
[2015-09-30T16:29Z] INFO  17:29:33,350 MicroScheduler - 5712 reads were filtered out during the traversal out of approximately 21561 total reads (26.49%)
[2015-09-30T16:29Z] INFO  17:29:33,351 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:29Z] INFO  17:29:33,351 MicroScheduler -   -> 708 reads (3.28% of total) failing BadMateFilter
[2015-09-30T16:29Z] INFO  17:29:33,351 MicroScheduler -   -> 947 reads (4.39% of total) failing DuplicateReadFilter
[2015-09-30T16:29Z] INFO  17:29:33,351 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:29Z] INFO  17:29:33,352 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:29Z] INFO  17:29:33,352 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:29Z] INFO  17:29:33,352 MicroScheduler -   -> 4057 reads (18.82% of total) failing MappingQualityZeroFilter
[2015-09-30T16:29Z] INFO  17:29:33,352 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:29Z] INFO  17:29:33,352 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:29Z] INFO  17:29:33,353 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:29Z] INFO  17:29:34,694 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:29Z] GATK: realign ('4', 189012293, 191154276) : syn3-tumor
[2015-09-30T16:29Z] INFO  17:29:38,408 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:38,410 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:29Z] INFO  17:29:38,410 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:29Z] INFO  17:29:38,410 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:29Z] INFO  17:29:38,414 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep-prealign-realign.intervals -L 4:189012294-191154276 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/tx/tmp0ZkSSx/2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam
[2015-09-30T16:29Z] INFO  17:29:38,419 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:29Z] INFO  17:29:38,420 HelpFormatter - Date/Time: 2015/09/30 17:29:38
[2015-09-30T16:29Z] INFO  17:29:38,420 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:38,420 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:38,447 ProgressMeter -            done    401264.0    22.0 s      56.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T16:29Z] INFO  17:29:38,447 ProgressMeter - Total runtime 22.73 secs, 0.38 min, 0.01 hours
[2015-09-30T16:29Z] INFO  17:29:38,451 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 401264 total reads (0.00%)
[2015-09-30T16:29Z] INFO  17:29:38,451 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:29Z] INFO  17:29:38,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:29Z] INFO  17:29:38,452 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:29Z] INFO  17:29:38,532 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:29Z] INFO  17:29:38,604 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:29Z] INFO  17:29:38,612 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:29Z] INFO  17:29:38,628 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:29Z] INFO  17:29:38,851 IntervalUtils - Processing 2141983 bp from intervals
[2015-09-30T16:29Z] WARN  17:29:38,855 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:29Z] INFO  17:29:38,911 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:29Z] INFO  17:29:38,954 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:29Z] INFO  17:29:38,955 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:29Z] INFO  17:29:38,955 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:29Z] INFO  17:29:38,956 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:29Z] INFO  17:29:39,019 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:39,036 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:39,503 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:29Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam
[2015-09-30T16:29Z] GATK pre-alignment ('5', 0, 31268043) : syn3-tumor
[2015-09-30T16:29Z] INFO  17:29:41,671 ProgressMeter -            done     21384.0     2.0 s       2.1 m       93.4%     2.0 s       0.0 s
[2015-09-30T16:29Z] INFO  17:29:41,672 ProgressMeter - Total runtime 2.72 secs, 0.05 min, 0.00 hours
[2015-09-30T16:29Z] INFO  17:29:41,675 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 21384 total reads (0.00%)
[2015-09-30T16:29Z] INFO  17:29:41,675 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:29Z] INFO  17:29:41,676 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:29Z] INFO  17:29:41,676 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:29Z] INFO  17:29:42,669 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:29Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam
[2015-09-30T16:29Z] GATK pre-alignment ('5', 31293868, 62597714) : syn3-tumor
[2015-09-30T16:29Z] INFO  17:29:43,318 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:43,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:29Z] INFO  17:29:43,320 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:29Z] INFO  17:29:43,321 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:29Z] INFO  17:29:43,324 HelpFormatter - Program Args: -T PrintReads -L 5:1-31268043 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpXvR0c9/2_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam
[2015-09-30T16:29Z] INFO  17:29:43,330 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:29Z] INFO  17:29:43,330 HelpFormatter - Date/Time: 2015/09/30 17:29:43
[2015-09-30T16:29Z] INFO  17:29:43,330 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:43,331 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:43,436 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:29Z] INFO  17:29:44,335 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:44,337 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:29Z] INFO  17:29:44,337 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:29Z] INFO  17:29:44,337 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:29Z] INFO  17:29:44,341 HelpFormatter - Program Args: -T PrintReads -L 5:31293869-62597714 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpNPfF5Q/2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam
[2015-09-30T16:29Z] INFO  17:29:44,346 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:29Z] INFO  17:29:44,347 HelpFormatter - Date/Time: 2015/09/30 17:29:44
[2015-09-30T16:29Z] INFO  17:29:44,347 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:44,347 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:29Z] INFO  17:29:44,458 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:29Z] INFO  17:29:44,711 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:29Z] INFO  17:29:44,763 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:29Z] INFO  17:29:44,771 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:29Z] INFO  17:29:44,786 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:29Z] INFO  17:29:44,799 IntervalUtils - Processing 31268043 bp from intervals
[2015-09-30T16:29Z] INFO  17:29:44,858 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:29Z] INFO  17:29:45,040 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:29Z] INFO  17:29:45,040 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:29Z] INFO  17:29:45,040 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:29Z] INFO  17:29:45,041 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:29Z] INFO  17:29:45,051 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:45,241 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:45,630 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:29Z] INFO  17:29:45,678 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:29Z] INFO  17:29:45,685 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:29Z] INFO  17:29:45,700 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:29Z] INFO  17:29:45,712 IntervalUtils - Processing 31303846 bp from intervals
[2015-09-30T16:29Z] INFO  17:29:45,769 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:29Z] INFO  17:29:45,953 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:29Z] INFO  17:29:45,953 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:29Z] INFO  17:29:45,953 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:29Z] INFO  17:29:45,953 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:29Z] INFO  17:29:45,964 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:46,149 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:29Z] INFO  17:29:56,961 ProgressMeter -            done    410371.0    24.0 s      60.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T16:29Z] INFO  17:29:56,962 ProgressMeter - Total runtime 24.72 secs, 0.41 min, 0.01 hours
[2015-09-30T16:29Z] INFO  17:29:56,965 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 410371 total reads (0.00%)
[2015-09-30T16:29Z] INFO  17:29:56,965 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:29Z] INFO  17:29:56,965 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:29Z] INFO  17:29:56,966 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:29Z] INFO  17:29:58,072 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:29Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam
[2015-09-30T16:29Z] GATK pre-alignment ('5', 63256014, 94276127) : syn3-tumor
[2015-09-30T16:30Z] INFO  17:30:02,757 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:30Z] INFO  17:30:02,759 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:30Z] INFO  17:30:02,759 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:30Z] INFO  17:30:02,760 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:30Z] INFO  17:30:02,763 HelpFormatter - Program Args: -T PrintReads -L 5:63256015-94276127 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpwJVGdk/2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam
[2015-09-30T16:30Z] INFO  17:30:02,778 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:30Z] INFO  17:30:02,779 HelpFormatter - Date/Time: 2015/09/30 17:30:02
[2015-09-30T16:30Z] INFO  17:30:02,779 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:30Z] INFO  17:30:02,779 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:30Z] INFO  17:30:03,453 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:30Z] INFO  17:30:06,313 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:30Z] INFO  17:30:06,363 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:30Z] INFO  17:30:06,371 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:30Z] INFO  17:30:06,386 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:30Z] INFO  17:30:06,399 IntervalUtils - Processing 31020113 bp from intervals
[2015-09-30T16:30Z] INFO  17:30:06,456 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:30Z] INFO  17:30:06,860 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:30Z] INFO  17:30:06,861 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:30Z] INFO  17:30:06,861 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:30Z] INFO  17:30:06,861 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:30Z] INFO  17:30:06,872 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:30Z] INFO  17:30:07,074 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:30Z] INFO  17:30:15,168 ProgressMeter -       5:5468765    200002.0    30.0 s       2.5 m       17.5%     2.9 m       2.4 m
[2015-09-30T16:30Z] INFO  17:30:15,956 ProgressMeter -      5:37170086    200006.0    30.0 s       2.5 m       18.8%     2.7 m       2.2 m
[2015-09-30T16:30Z] INFO  17:30:36,864 ProgressMeter -      5:74032149    300004.0    30.0 s     100.0 s       34.7%    86.0 s      56.0 s
[2015-09-30T16:30Z] INFO  17:30:40,033 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:30Z] INFO  17:30:40,212 ProgressMeter -            done    501082.0    55.0 s     110.0 s      100.0%    55.0 s       0.0 s
[2015-09-30T16:30Z] INFO  17:30:40,212 ProgressMeter - Total runtime 55.17 secs, 0.92 min, 0.02 hours
[2015-09-30T16:30Z] INFO  17:30:40,212 MicroScheduler - 1206 reads were filtered out during the traversal out of approximately 502288 total reads (0.24%)
[2015-09-30T16:30Z] INFO  17:30:40,213 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:30Z] INFO  17:30:40,213 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:30Z] INFO  17:30:40,213 MicroScheduler -   -> 1206 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:30Z] INFO  17:30:41,198 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:30Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam
[2015-09-30T16:30Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam 5:1-31268043
[2015-09-30T16:30Z] GATK: RealignerTargetCreator
[2015-09-30T16:30Z] INFO  17:30:44,591 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:30Z] INFO  17:30:44,593 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:30Z] INFO  17:30:44,593 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:30Z] INFO  17:30:44,593 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:30Z] INFO  17:30:44,597 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmp4T3g8j/2_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign-realign.intervals -l INFO -L 5:1-31268043 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:30Z] INFO  17:30:44,603 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:30Z] INFO  17:30:44,603 HelpFormatter - Date/Time: 2015/09/30 17:30:44
[2015-09-30T16:30Z] INFO  17:30:44,603 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:30Z] INFO  17:30:44,603 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:30Z] INFO  17:30:44,669 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:30Z] INFO  17:30:44,784 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:30Z] INFO  17:30:44,792 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:30Z] INFO  17:30:44,807 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:30Z] INFO  17:30:45,042 IntervalUtils - Processing 31268043 bp from intervals
[2015-09-30T16:30Z] WARN  17:30:45,045 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:30Z] INFO  17:30:45,100 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:30Z] INFO  17:30:45,228 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:30Z] INFO  17:30:45,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:30Z] INFO  17:30:45,229 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:30Z] INFO  17:30:45,229 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:30Z] INFO  17:30:45,957 ProgressMeter -      5:57750952    500010.0    60.0 s     120.0 s       84.5%    70.0 s      10.0 s
[2015-09-30T16:30Z] INFO  17:30:51,573 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:30Z] INFO  17:30:51,975 ProgressMeter -            done    593029.0    66.0 s     111.0 s      100.0%    66.0 s       0.0 s
[2015-09-30T16:30Z] INFO  17:30:51,975 ProgressMeter - Total runtime 66.02 secs, 1.10 min, 0.02 hours
[2015-09-30T16:30Z] INFO  17:30:51,976 MicroScheduler - 1714 reads were filtered out during the traversal out of approximately 594743 total reads (0.29%)
[2015-09-30T16:30Z] INFO  17:30:51,976 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:30Z] INFO  17:30:51,976 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:30Z] INFO  17:30:51,976 MicroScheduler -   -> 1714 reads (0.29% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:30Z] INFO  17:30:53,028 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:30Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam
[2015-09-30T16:30Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam 5:31293869-62597714
[2015-09-30T16:30Z] GATK: RealignerTargetCreator
[2015-09-30T16:30Z] INFO  17:30:56,511 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:30Z] INFO  17:30:56,513 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:30Z] INFO  17:30:56,513 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:30Z] INFO  17:30:56,513 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:30Z] INFO  17:30:56,517 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpfyoDQ8/2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign-realign.intervals -l INFO -L 5:31293869-62597714 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:30Z] INFO  17:30:56,522 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:30Z] INFO  17:30:56,523 HelpFormatter - Date/Time: 2015/09/30 17:30:56
[2015-09-30T16:30Z] INFO  17:30:56,523 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:30Z] INFO  17:30:56,523 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:30Z] INFO  17:30:56,580 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:30Z] INFO  17:30:57,295 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:30Z] INFO  17:30:57,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:30Z] INFO  17:30:57,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:30Z] INFO  17:30:57,564 IntervalUtils - Processing 31303846 bp from intervals
[2015-09-30T16:30Z] WARN  17:30:57,567 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:30Z] INFO  17:30:57,623 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:30Z] INFO  17:30:57,751 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:30Z] INFO  17:30:57,752 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:30Z] INFO  17:30:57,752 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:30Z] INFO  17:30:57,753 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:31Z] INFO  17:31:01,942 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:31Z] INFO  17:31:02,104 ProgressMeter -            done    644513.0    55.0 s      85.0 s      100.0%    55.0 s       0.0 s
[2015-09-30T16:31Z] INFO  17:31:02,104 ProgressMeter - Total runtime 55.24 secs, 0.92 min, 0.02 hours
[2015-09-30T16:31Z] INFO  17:31:02,104 MicroScheduler - 2069 reads were filtered out during the traversal out of approximately 646582 total reads (0.32%)
[2015-09-30T16:31Z] INFO  17:31:02,104 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:31Z] INFO  17:31:02,105 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:31Z] INFO  17:31:02,105 MicroScheduler -   -> 2069 reads (0.32% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:31Z] INFO  17:31:03,045 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:31Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam
[2015-09-30T16:31Z] INFO  17:31:07,337 ProgressMeter -            done   3.1268043E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T16:31Z] INFO  17:31:07,337 ProgressMeter - Total runtime 22.11 secs, 0.37 min, 0.01 hours
[2015-09-30T16:31Z] INFO  17:31:07,340 MicroScheduler - 89816 reads were filtered out during the traversal out of approximately 503948 total reads (17.82%)
[2015-09-30T16:31Z] INFO  17:31:07,340 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:31Z] INFO  17:31:07,340 MicroScheduler -   -> 7447 reads (1.48% of total) failing BadMateFilter
[2015-09-30T16:31Z] INFO  17:31:07,341 MicroScheduler -   -> 21753 reads (4.32% of total) failing DuplicateReadFilter
[2015-09-30T16:31Z] INFO  17:31:07,341 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:31Z] INFO  17:31:07,341 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:31Z] INFO  17:31:07,341 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:31Z] INFO  17:31:07,342 MicroScheduler -   -> 60616 reads (12.03% of total) failing MappingQualityZeroFilter
[2015-09-30T16:31Z] INFO  17:31:07,342 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:31Z] INFO  17:31:07,342 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:31Z] INFO  17:31:07,342 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:31Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam 5:63256015-94276127
[2015-09-30T16:31Z] GATK: RealignerTargetCreator
[2015-09-30T16:31Z] INFO  17:31:08,302 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:31Z] GATK: realign ('5', 0, 31268043) : syn3-tumor
[2015-09-30T16:31Z] INFO  17:31:10,477 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:10,479 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:31Z] INFO  17:31:10,479 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:31Z] INFO  17:31:10,479 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:31Z] INFO  17:31:10,482 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmp2XJysX/2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign-realign.intervals -l INFO -L 5:63256015-94276127 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:31Z] INFO  17:31:10,488 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:31Z] INFO  17:31:10,488 HelpFormatter - Date/Time: 2015/09/30 17:31:10
[2015-09-30T16:31Z] INFO  17:31:10,489 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:10,489 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:10,550 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:31Z] INFO  17:31:10,663 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:31Z] INFO  17:31:10,671 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:31Z] INFO  17:31:10,688 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:31Z] INFO  17:31:11,139 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:11,142 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:31Z] INFO  17:31:11,142 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:31Z] INFO  17:31:11,142 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:31Z] INFO  17:31:11,146 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_0_31268043-prep-prealign-realign.intervals -L 5:1-31268043 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpZIkGzj/2_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam
[2015-09-30T16:31Z] INFO  17:31:11,151 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:31Z] INFO  17:31:11,151 HelpFormatter - Date/Time: 2015/09/30 17:31:11
[2015-09-30T16:31Z] INFO  17:31:11,152 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:11,152 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:11,497 IntervalUtils - Processing 31020113 bp from intervals
[2015-09-30T16:31Z] WARN  17:31:11,501 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:31Z] INFO  17:31:11,562 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:31Z] INFO  17:31:11,708 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:31Z] INFO  17:31:11,709 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:31Z] INFO  17:31:11,709 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:31Z] INFO  17:31:11,709 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:31Z] INFO  17:31:11,737 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:31Z] INFO  17:31:11,800 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:31Z] INFO  17:31:11,808 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:31Z] INFO  17:31:11,825 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:31Z] INFO  17:31:12,062 IntervalUtils - Processing 31268043 bp from intervals
[2015-09-30T16:31Z] WARN  17:31:12,066 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:31Z] INFO  17:31:12,538 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:31Z] INFO  17:31:12,683 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:31Z] INFO  17:31:12,684 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:31Z] INFO  17:31:12,684 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:31Z] INFO  17:31:12,684 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:31Z] INFO  17:31:12,829 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:31Z] INFO  17:31:13,017 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:31Z] INFO  17:31:20,476 ProgressMeter -            done   3.1303846E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T16:31Z] INFO  17:31:20,477 ProgressMeter - Total runtime 22.73 secs, 0.38 min, 0.01 hours
[2015-09-30T16:31Z] INFO  17:31:20,480 MicroScheduler - 46032 reads were filtered out during the traversal out of approximately 596340 total reads (7.72%)
[2015-09-30T16:31Z] INFO  17:31:20,480 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:31Z] INFO  17:31:20,480 MicroScheduler -   -> 8479 reads (1.42% of total) failing BadMateFilter
[2015-09-30T16:31Z] INFO  17:31:20,481 MicroScheduler -   -> 24041 reads (4.03% of total) failing DuplicateReadFilter
[2015-09-30T16:31Z] INFO  17:31:20,481 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:31Z] INFO  17:31:20,481 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:31Z] INFO  17:31:20,481 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:31Z] INFO  17:31:20,481 MicroScheduler -   -> 13512 reads (2.27% of total) failing MappingQualityZeroFilter
[2015-09-30T16:31Z] INFO  17:31:20,482 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:31Z] INFO  17:31:20,482 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:31Z] INFO  17:31:20,482 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:31Z] INFO  17:31:21,460 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:31Z] GATK: realign ('5', 31293868, 62597714) : syn3-tumor
[2015-09-30T16:31Z] INFO  17:31:23,562 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:23,564 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:31Z] INFO  17:31:23,564 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:31Z] INFO  17:31:23,564 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:31Z] INFO  17:31:23,568 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep-prealign-realign.intervals -L 5:31293869-62597714 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpe5dxrL/2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam
[2015-09-30T16:31Z] INFO  17:31:23,573 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:31Z] INFO  17:31:23,573 HelpFormatter - Date/Time: 2015/09/30 17:31:23
[2015-09-30T16:31Z] INFO  17:31:23,573 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:23,574 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:23,700 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:31Z] INFO  17:31:23,767 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:31Z] INFO  17:31:23,774 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:31Z] INFO  17:31:23,789 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:31Z] INFO  17:31:24,019 IntervalUtils - Processing 31303846 bp from intervals
[2015-09-30T16:31Z] WARN  17:31:24,022 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:31Z] INFO  17:31:24,077 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:31Z] INFO  17:31:24,202 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:31Z] INFO  17:31:24,202 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:31Z] INFO  17:31:24,203 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:31Z] INFO  17:31:24,203 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:31Z] INFO  17:31:24,341 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:31Z] INFO  17:31:24,519 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:31Z] INFO  17:31:36,393 ProgressMeter -            done   3.1020113E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T16:31Z] INFO  17:31:36,393 ProgressMeter - Total runtime 24.68 secs, 0.41 min, 0.01 hours
[2015-09-30T16:31Z] INFO  17:31:36,397 MicroScheduler - 117292 reads were filtered out during the traversal out of approximately 647950 total reads (18.10%)
[2015-09-30T16:31Z] INFO  17:31:36,397 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:31Z] INFO  17:31:36,397 MicroScheduler -   -> 8479 reads (1.31% of total) failing BadMateFilter
[2015-09-30T16:31Z] INFO  17:31:36,397 MicroScheduler -   -> 22666 reads (3.50% of total) failing DuplicateReadFilter
[2015-09-30T16:31Z] INFO  17:31:36,398 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:31Z] INFO  17:31:36,398 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:31Z] INFO  17:31:36,398 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:31Z] INFO  17:31:36,398 MicroScheduler -   -> 86147 reads (13.30% of total) failing MappingQualityZeroFilter
[2015-09-30T16:31Z] INFO  17:31:36,399 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:31Z] INFO  17:31:36,399 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:31Z] INFO  17:31:36,399 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:31Z] INFO  17:31:37,342 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:31Z] GATK: realign ('5', 63256014, 94276127) : syn3-tumor
[2015-09-30T16:31Z] INFO  17:31:39,268 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:39,270 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:31Z] INFO  17:31:39,270 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:31Z] INFO  17:31:39,270 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:31Z] INFO  17:31:39,273 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep-prealign-realign.intervals -L 5:63256015-94276127 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmp39FHvB/2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam
[2015-09-30T16:31Z] INFO  17:31:39,279 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:31Z] INFO  17:31:39,279 HelpFormatter - Date/Time: 2015/09/30 17:31:39
[2015-09-30T16:31Z] INFO  17:31:39,279 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:39,279 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:39,379 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:31Z] INFO  17:31:39,447 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:31Z] INFO  17:31:39,455 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:31Z] INFO  17:31:39,471 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:31Z] INFO  17:31:39,689 IntervalUtils - Processing 31020113 bp from intervals
[2015-09-30T16:31Z] WARN  17:31:39,693 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:31Z] INFO  17:31:39,746 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:31Z] INFO  17:31:39,879 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:31Z] INFO  17:31:39,880 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:31Z] INFO  17:31:39,880 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:31Z] INFO  17:31:39,881 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:31Z] INFO  17:31:40,017 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:31Z] INFO  17:31:40,197 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:31Z] INFO  17:31:41,092 ProgressMeter -            done    501082.0    28.0 s      56.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T16:31Z] INFO  17:31:41,092 ProgressMeter - Total runtime 28.41 secs, 0.47 min, 0.01 hours
[2015-09-30T16:31Z] INFO  17:31:41,095 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 501082 total reads (0.00%)
[2015-09-30T16:31Z] INFO  17:31:41,096 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:31Z] INFO  17:31:41,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:31Z] INFO  17:31:41,096 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:31Z] INFO  17:31:42,259 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:31Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam
[2015-09-30T16:31Z] GATK pre-alignment ('5', 94277739, 125696417) : syn3-tumor
[2015-09-30T16:31Z] INFO  17:31:47,891 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:47,893 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:31Z] INFO  17:31:47,893 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:31Z] INFO  17:31:47,893 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:31Z] INFO  17:31:47,897 HelpFormatter - Program Args: -T PrintReads -L 5:94277740-125696417 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmp4M8tlZ/2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam
[2015-09-30T16:31Z] INFO  17:31:47,902 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:31Z] INFO  17:31:47,903 HelpFormatter - Date/Time: 2015/09/30 17:31:47
[2015-09-30T16:31Z] INFO  17:31:47,903 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:47,903 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:31Z] INFO  17:31:48,608 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:31Z] INFO  17:31:49,910 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:31Z] INFO  17:31:49,960 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:31Z] INFO  17:31:49,968 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:31Z] INFO  17:31:49,983 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:31Z] INFO  17:31:49,996 IntervalUtils - Processing 31418678 bp from intervals
[2015-09-30T16:31Z] INFO  17:31:50,055 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:31Z] INFO  17:31:50,257 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:31Z] INFO  17:31:50,258 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:31Z] INFO  17:31:50,258 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:31Z] INFO  17:31:50,258 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:31Z] INFO  17:31:50,270 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:31Z] INFO  17:31:50,473 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:31Z] INFO  17:31:55,429 ProgressMeter -      5:60083455    500010.0    31.0 s      62.0 s       92.0%    33.0 s       2.0 s
[2015-09-30T16:31Z] INFO  17:31:57,014 ProgressMeter -            done    593029.0    32.0 s      55.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T16:31Z] INFO  17:31:57,015 ProgressMeter - Total runtime 32.81 secs, 0.55 min, 0.01 hours
[2015-09-30T16:31Z] INFO  17:31:57,018 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 593029 total reads (0.00%)
[2015-09-30T16:31Z] INFO  17:31:57,018 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:31Z] INFO  17:31:57,018 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:31Z] INFO  17:31:57,018 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:31Z] INFO  17:31:58,114 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:31Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam
[2015-09-30T16:32Z] GATK pre-alignment ('5', 125759062, 156781785) : syn3-tumor
[2015-09-30T16:32Z] INFO  17:32:01,500 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:01,502 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:32Z] INFO  17:32:01,502 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:32Z] INFO  17:32:01,502 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:32Z] INFO  17:32:01,505 HelpFormatter - Program Args: -T PrintReads -L 5:125759063-156781785 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmp1j6hga/2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam
[2015-09-30T16:32Z] INFO  17:32:01,511 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:32Z] INFO  17:32:01,511 HelpFormatter - Date/Time: 2015/09/30 17:32:01
[2015-09-30T16:32Z] INFO  17:32:01,511 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:01,511 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:01,606 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:32Z] INFO  17:32:02,768 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:32Z] INFO  17:32:02,814 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:32Z] INFO  17:32:02,821 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:32Z] INFO  17:32:02,835 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:32Z] INFO  17:32:02,847 IntervalUtils - Processing 31022723 bp from intervals
[2015-09-30T16:32Z] INFO  17:32:02,899 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:32Z] INFO  17:32:03,100 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:32Z] INFO  17:32:03,101 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:32Z] INFO  17:32:03,101 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:32Z] INFO  17:32:03,101 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:32Z] INFO  17:32:03,112 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:32Z] INFO  17:32:03,291 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:32Z] INFO  17:32:09,883 ProgressMeter -      5:85586619    500007.0    30.0 s      60.0 s       72.0%    41.0 s      11.0 s
[2015-09-30T16:32Z] INFO  17:32:12,731 ProgressMeter -            done    644513.0    32.0 s      50.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T16:32Z] INFO  17:32:12,731 ProgressMeter - Total runtime 32.85 secs, 0.55 min, 0.01 hours
[2015-09-30T16:32Z] INFO  17:32:12,734 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 644513 total reads (0.00%)
[2015-09-30T16:32Z] INFO  17:32:12,735 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:32Z] INFO  17:32:12,735 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:32Z] INFO  17:32:12,735 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:32Z] INFO  17:32:13,725 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:32Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam
[2015-09-30T16:32Z] GATK pre-alignment ('5', 156785743, 180915260) : syn3-tumor
[2015-09-30T16:32Z] INFO  17:32:17,429 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:17,431 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:32Z] INFO  17:32:17,431 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:32Z] INFO  17:32:17,431 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:32Z] INFO  17:32:17,435 HelpFormatter - Program Args: -T PrintReads -L 5:156785744-180915260 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpD7kwzx/2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam
[2015-09-30T16:32Z] INFO  17:32:17,440 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:32Z] INFO  17:32:17,441 HelpFormatter - Date/Time: 2015/09/30 17:32:17
[2015-09-30T16:32Z] INFO  17:32:17,441 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:17,441 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:17,548 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:32Z] INFO  17:32:20,105 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:32Z] INFO  17:32:20,154 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:32Z] INFO  17:32:20,161 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:32Z] INFO  17:32:20,176 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:32Z] INFO  17:32:20,189 IntervalUtils - Processing 24129517 bp from intervals
[2015-09-30T16:32Z] INFO  17:32:20,246 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:32Z] INFO  17:32:20,261 ProgressMeter -     5:118452142    200002.0    30.0 s       2.5 m       76.9%    38.0 s       8.0 s
[2015-09-30T16:32Z] INFO  17:32:20,439 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:32Z] INFO  17:32:20,440 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:32Z] INFO  17:32:20,440 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:32Z] INFO  17:32:20,440 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:32Z] INFO  17:32:20,451 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:32Z] INFO  17:32:20,607 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:32Z] INFO  17:32:25,151 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@2208e772
[2015-09-30T16:32Z] INFO  17:32:25,348 ProgressMeter -            done    351897.0    35.0 s      99.0 s      100.0%    35.0 s       0.0 s
[2015-09-30T16:32Z] INFO  17:32:25,348 ProgressMeter - Total runtime 35.09 secs, 0.58 min, 0.01 hours
[2015-09-30T16:32Z] INFO  17:32:25,349 MicroScheduler - 1302 reads were filtered out during the traversal out of approximately 353199 total reads (0.37%)
[2015-09-30T16:32Z] INFO  17:32:25,349 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:32Z] INFO  17:32:25,349 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:32Z] INFO  17:32:25,349 MicroScheduler -   -> 1302 reads (0.37% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:32Z] INFO  17:32:26,335 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:32Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam
[2015-09-30T16:32Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam 5:94277740-125696417
[2015-09-30T16:32Z] GATK: RealignerTargetCreator
[2015-09-30T16:32Z] INFO  17:32:28,822 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:28,824 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:32Z] INFO  17:32:28,824 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:32Z] INFO  17:32:28,825 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:32Z] INFO  17:32:28,828 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmphNfT4L/2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign-realign.intervals -l INFO -L 5:94277740-125696417 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:32Z] INFO  17:32:28,834 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:32Z] INFO  17:32:28,834 HelpFormatter - Date/Time: 2015/09/30 17:32:28
[2015-09-30T16:32Z] INFO  17:32:28,835 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:28,835 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:28,894 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:32Z] INFO  17:32:29,005 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:32Z] INFO  17:32:29,013 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:32Z] INFO  17:32:29,030 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:32Z] INFO  17:32:30,035 IntervalUtils - Processing 31418678 bp from intervals
[2015-09-30T16:32Z] WARN  17:32:30,039 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:32Z] INFO  17:32:30,095 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:32Z] INFO  17:32:30,414 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:32Z] INFO  17:32:30,415 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:32Z] INFO  17:32:30,415 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:32Z] INFO  17:32:30,415 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:32Z] INFO  17:32:33,103 ProgressMeter -     5:133476372    200003.0    30.0 s       2.5 m       24.9%   120.0 s      90.0 s
[2015-09-30T16:32Z] INFO  17:32:50,443 ProgressMeter -     5:171821373    200002.0    30.0 s       2.5 m       62.3%    48.0 s      18.0 s
[2015-09-30T16:32Z] INFO  17:32:51,525 ProgressMeter -            done   3.1418678E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T16:32Z] INFO  17:32:51,525 ProgressMeter - Total runtime 21.11 secs, 0.35 min, 0.01 hours
[2015-09-30T16:32Z] INFO  17:32:51,528 MicroScheduler - 29184 reads were filtered out during the traversal out of approximately 354185 total reads (8.24%)
[2015-09-30T16:32Z] INFO  17:32:51,529 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:32Z] INFO  17:32:51,529 MicroScheduler -   -> 7126 reads (2.01% of total) failing BadMateFilter
[2015-09-30T16:32Z] INFO  17:32:51,529 MicroScheduler -   -> 13631 reads (3.85% of total) failing DuplicateReadFilter
[2015-09-30T16:32Z] INFO  17:32:51,529 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:32Z] INFO  17:32:51,530 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:32Z] INFO  17:32:51,530 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:32Z] INFO  17:32:51,530 MicroScheduler -   -> 8427 reads (2.38% of total) failing MappingQualityZeroFilter
[2015-09-30T16:32Z] INFO  17:32:51,530 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:32Z] INFO  17:32:51,530 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:32Z] INFO  17:32:51,531 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:32Z] INFO  17:32:52,497 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:32Z] GATK: realign ('5', 94277739, 125696417) : syn3-tumor
[2015-09-30T16:32Z] INFO  17:32:54,654 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:54,656 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:32Z] INFO  17:32:54,656 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:32Z] INFO  17:32:54,657 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:32Z] INFO  17:32:54,660 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep-prealign-realign.intervals -L 5:94277740-125696417 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpc6n19p/2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam
[2015-09-30T16:32Z] INFO  17:32:54,667 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:32Z] INFO  17:32:54,667 HelpFormatter - Date/Time: 2015/09/30 17:32:54
[2015-09-30T16:32Z] INFO  17:32:54,668 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:54,668 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:32Z] INFO  17:32:54,800 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:32Z] INFO  17:32:54,868 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:32Z] INFO  17:32:54,876 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:32Z] INFO  17:32:54,891 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:32Z] INFO  17:32:55,545 IntervalUtils - Processing 31418678 bp from intervals
[2015-09-30T16:32Z] WARN  17:32:55,549 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:32Z] INFO  17:32:55,603 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:32Z] INFO  17:32:55,760 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:32Z] INFO  17:32:55,761 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:32Z] INFO  17:32:55,761 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:32Z] INFO  17:32:55,762 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:32Z] INFO  17:32:55,912 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:32Z] INFO  17:32:56,103 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:33Z] INFO  17:33:03,104 ProgressMeter -     5:139851903    500006.0    60.0 s     120.0 s       45.4%     2.2 m      72.0 s
[2015-09-30T16:33Z] INFO  17:33:18,116 ProgressMeter -            done    351897.0    22.0 s      63.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T16:33Z] INFO  17:33:18,116 ProgressMeter - Total runtime 22.36 secs, 0.37 min, 0.01 hours
[2015-09-30T16:33Z] INFO  17:33:18,119 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 351897 total reads (0.00%)
[2015-09-30T16:33Z] INFO  17:33:18,119 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:33Z] INFO  17:33:18,120 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:33Z] INFO  17:33:18,120 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:33Z] INFO  17:33:19,290 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:33Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam
[2015-09-30T16:33Z] GATK pre-alignment ('6', 0, 31080572) : syn3-tumor
[2015-09-30T16:33Z] INFO  17:33:20,463 ProgressMeter -     5:179012887    600008.0    60.0 s     100.0 s       92.1%    65.0 s       5.0 s
[2015-09-30T16:33Z] INFO  17:33:22,792 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:33Z] INFO  17:33:22,794 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:33Z] INFO  17:33:22,794 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:33Z] INFO  17:33:22,794 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:33Z] INFO  17:33:22,798 HelpFormatter - Program Args: -T PrintReads -L 6:1-31080572 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpy10hfU/2_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam
[2015-09-30T16:33Z] INFO  17:33:22,804 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:33Z] INFO  17:33:22,804 HelpFormatter - Date/Time: 2015/09/30 17:33:22
[2015-09-30T16:33Z] INFO  17:33:22,804 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:33Z] INFO  17:33:22,804 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:33Z] INFO  17:33:26,127 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:33Z] INFO  17:33:29,179 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:33Z] INFO  17:33:29,230 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:33Z] INFO  17:33:29,237 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:33Z] INFO  17:33:29,252 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:33Z] INFO  17:33:29,266 IntervalUtils - Processing 31080572 bp from intervals
[2015-09-30T16:33Z] INFO  17:33:29,324 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:33Z] INFO  17:33:29,522 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:33Z] INFO  17:33:29,522 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:33Z] INFO  17:33:29,522 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:33Z] INFO  17:33:29,523 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:33Z] INFO  17:33:29,534 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:33Z] INFO  17:33:29,733 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:33Z] INFO  17:33:30,357 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:33Z] INFO  17:33:30,549 ProgressMeter -            done    802525.0    70.0 s      87.0 s       99.9%    70.0 s       0.0 s
[2015-09-30T16:33Z] INFO  17:33:30,549 ProgressMeter - Total runtime 70.11 secs, 1.17 min, 0.02 hours
[2015-09-30T16:33Z] INFO  17:33:30,549 MicroScheduler - 1646 reads were filtered out during the traversal out of approximately 804171 total reads (0.20%)
[2015-09-30T16:33Z] INFO  17:33:30,550 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:33Z] INFO  17:33:30,550 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:33Z] INFO  17:33:30,550 MicroScheduler -   -> 1646 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:33Z] INFO  17:33:31,560 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:33Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam
[2015-09-30T16:33Z] INFO  17:33:33,105 ProgressMeter -     5:145612557    800009.0    90.0 s     112.0 s       64.0%     2.3 m      50.0 s
[2015-09-30T16:33Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam 5:156785744-180915260
[2015-09-30T16:33Z] GATK: RealignerTargetCreator
[2015-09-30T16:33Z] INFO  17:33:38,205 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:33Z] INFO  17:33:38,207 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:33Z] INFO  17:33:38,207 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:33Z] INFO  17:33:38,208 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:33Z] INFO  17:33:38,211 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpse8zvi/2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign-realign.intervals -l INFO -L 5:156785744-180915260 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:33Z] INFO  17:33:38,217 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:33Z] INFO  17:33:38,217 HelpFormatter - Date/Time: 2015/09/30 17:33:38
[2015-09-30T16:33Z] INFO  17:33:38,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:33Z] INFO  17:33:38,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:33Z] INFO  17:33:38,276 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:33Z] INFO  17:33:39,601 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:33Z] INFO  17:33:39,609 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:33Z] INFO  17:33:39,745 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2015-09-30T16:33Z] INFO  17:33:40,726 IntervalUtils - Processing 24129517 bp from intervals
[2015-09-30T16:33Z] WARN  17:33:40,730 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:33Z] INFO  17:33:40,792 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:33Z] INFO  17:33:40,915 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:33Z] INFO  17:33:40,915 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:33Z] INFO  17:33:40,916 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:33Z] INFO  17:33:40,916 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:33Z] INFO  17:33:59,525 ProgressMeter -      6:10419898    200003.0    30.0 s       2.5 m       33.5%    89.0 s      59.0 s
[2015-09-30T16:34Z] INFO  17:34:03,141 ProgressMeter -     5:150901160   1100012.0   120.0 s     109.0 s       81.0%     2.5 m      28.0 s
[2015-09-30T16:34Z] INFO  17:34:05,300 ProgressMeter -            done   2.4129517E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T16:34Z] INFO  17:34:05,300 ProgressMeter - Total runtime 24.39 secs, 0.41 min, 0.01 hours
[2015-09-30T16:34Z] INFO  17:34:05,303 MicroScheduler - 79427 reads were filtered out during the traversal out of approximately 807406 total reads (9.84%)
[2015-09-30T16:34Z] INFO  17:34:05,304 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:34Z] INFO  17:34:05,304 MicroScheduler -   -> 8856 reads (1.10% of total) failing BadMateFilter
[2015-09-30T16:34Z] INFO  17:34:05,304 MicroScheduler -   -> 38736 reads (4.80% of total) failing DuplicateReadFilter
[2015-09-30T16:34Z] INFO  17:34:05,304 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:34Z] INFO  17:34:05,305 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:34Z] INFO  17:34:05,305 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:34Z] INFO  17:34:05,305 MicroScheduler -   -> 31835 reads (3.94% of total) failing MappingQualityZeroFilter
[2015-09-30T16:34Z] INFO  17:34:05,305 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:34Z] INFO  17:34:05,306 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:34Z] INFO  17:34:05,306 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:34Z] INFO  17:34:06,392 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:34Z] GATK: realign ('5', 156785743, 180915260) : syn3-tumor
[2015-09-30T16:34Z] INFO  17:34:08,393 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:08,395 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:34Z] INFO  17:34:08,395 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:34Z] INFO  17:34:08,396 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:34Z] INFO  17:34:08,399 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep-prealign-realign.intervals -L 5:156785744-180915260 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpKPbWje/2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam
[2015-09-30T16:34Z] INFO  17:34:08,405 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:34Z] INFO  17:34:08,405 HelpFormatter - Date/Time: 2015/09/30 17:34:08
[2015-09-30T16:34Z] INFO  17:34:08,405 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:08,405 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:08,533 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:34Z] INFO  17:34:08,594 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:34Z] INFO  17:34:08,601 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:34Z] INFO  17:34:08,617 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:34Z] INFO  17:34:08,848 IntervalUtils - Processing 24129517 bp from intervals
[2015-09-30T16:34Z] WARN  17:34:08,852 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:34Z] INFO  17:34:08,903 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:34Z] INFO  17:34:09,022 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:34Z] INFO  17:34:09,022 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:34Z] INFO  17:34:09,023 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:34Z] INFO  17:34:09,023 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:34Z] INFO  17:34:09,161 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:34Z] INFO  17:34:09,305 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:34Z] INFO  17:34:15,413 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:34Z] INFO  17:34:15,798 ProgressMeter -            done   1282402.0     2.2 m     103.0 s      100.0%     2.2 m       0.0 s
[2015-09-30T16:34Z] INFO  17:34:15,798 ProgressMeter - Total runtime 132.70 secs, 2.21 min, 0.04 hours
[2015-09-30T16:34Z] INFO  17:34:15,799 MicroScheduler - 2625 reads were filtered out during the traversal out of approximately 1285027 total reads (0.20%)
[2015-09-30T16:34Z] INFO  17:34:15,799 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:34Z] INFO  17:34:15,799 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:34Z] INFO  17:34:15,799 MicroScheduler -   -> 2625 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:34Z] INFO  17:34:16,837 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:34Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam
[2015-09-30T16:34Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam 5:125759063-156781785
[2015-09-30T16:34Z] GATK: RealignerTargetCreator
[2015-09-30T16:34Z] INFO  17:34:24,888 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:24,890 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:34Z] INFO  17:34:24,890 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:34Z] INFO  17:34:24,890 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:34Z] INFO  17:34:24,893 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpifsFHP/2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign-realign.intervals -l INFO -L 5:125759063-156781785 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:34Z] INFO  17:34:24,899 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:34Z] INFO  17:34:24,899 HelpFormatter - Date/Time: 2015/09/30 17:34:24
[2015-09-30T16:34Z] INFO  17:34:24,900 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:24,900 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:24,954 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:34Z] INFO  17:34:25,057 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:34Z] INFO  17:34:25,064 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:34Z] INFO  17:34:25,079 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:34Z] INFO  17:34:25,735 IntervalUtils - Processing 31022723 bp from intervals
[2015-09-30T16:34Z] WARN  17:34:25,739 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:34Z] INFO  17:34:25,794 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:34Z] INFO  17:34:25,939 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:34Z] INFO  17:34:25,940 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:34Z] INFO  17:34:25,940 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:34Z] INFO  17:34:25,941 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:34Z] INFO  17:34:29,862 ProgressMeter -      6:26422047    500008.0    60.0 s     120.0 s       85.0%    70.0 s      10.0 s
[2015-09-30T16:34Z] INFO  17:34:40,214 ProgressMeter -     5:176831953    400005.0    31.0 s      77.0 s       83.1%    37.0 s       6.0 s
[2015-09-30T16:34Z] INFO  17:34:50,460 ProgressMeter -            done    802525.0    41.0 s      51.0 s       99.9%    41.0 s       0.0 s
[2015-09-30T16:34Z] INFO  17:34:50,460 ProgressMeter - Total runtime 41.44 secs, 0.69 min, 0.01 hours
[2015-09-30T16:34Z] INFO  17:34:50,463 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 802525 total reads (0.00%)
[2015-09-30T16:34Z] INFO  17:34:50,463 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:34Z] INFO  17:34:50,464 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:34Z] INFO  17:34:50,464 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:34Z] INFO  17:34:50,547 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@2208e772
[2015-09-30T16:34Z] INFO  17:34:50,604 ProgressMeter -            done    866123.0    81.0 s      93.0 s      100.0%    81.0 s       0.0 s
[2015-09-30T16:34Z] INFO  17:34:50,604 ProgressMeter - Total runtime 81.08 secs, 1.35 min, 0.02 hours
[2015-09-30T16:34Z] INFO  17:34:50,605 MicroScheduler - 2217 reads were filtered out during the traversal out of approximately 868340 total reads (0.26%)
[2015-09-30T16:34Z] INFO  17:34:50,605 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:34Z] INFO  17:34:50,606 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:34Z] INFO  17:34:50,606 MicroScheduler -   -> 2217 reads (0.26% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:34Z] INFO  17:34:51,577 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:34Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam
[2015-09-30T16:34Z] INFO  17:34:52,443 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:34Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam
[2015-09-30T16:34Z] GATK pre-alignment ('6', 31082315, 62284583) : syn3-tumor
[2015-09-30T16:34Z] INFO  17:34:55,259 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:55,261 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:34Z] INFO  17:34:55,262 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:34Z] INFO  17:34:55,262 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:34Z] INFO  17:34:55,265 HelpFormatter - Program Args: -T PrintReads -L 6:31082316-62284583 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpjZxst7/2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam
[2015-09-30T16:34Z] INFO  17:34:55,270 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:34Z] INFO  17:34:55,271 HelpFormatter - Date/Time: 2015/09/30 17:34:55
[2015-09-30T16:34Z] INFO  17:34:55,271 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:55,271 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:55,372 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:34Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam 6:1-31080572
[2015-09-30T16:34Z] GATK: RealignerTargetCreator
[2015-09-30T16:34Z] INFO  17:34:55,943 ProgressMeter -     5:150946293   2.518673E7    30.0 s       1.0 s       81.2%    36.0 s       6.0 s
[2015-09-30T16:34Z] INFO  17:34:58,827 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:34Z] INFO  17:34:58,877 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:34Z] INFO  17:34:58,885 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:34Z] INFO  17:34:58,900 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:34Z] INFO  17:34:58,913 IntervalUtils - Processing 31202268 bp from intervals
[2015-09-30T16:34Z] INFO  17:34:58,970 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:34Z] INFO  17:34:59,138 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:59,140 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:34Z] INFO  17:34:59,140 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:34Z] INFO  17:34:59,141 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:34Z] INFO  17:34:59,144 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmprChiSG/2_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign-realign.intervals -l INFO -L 6:1-31080572 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:34Z] INFO  17:34:59,150 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:34Z] INFO  17:34:59,150 HelpFormatter - Date/Time: 2015/09/30 17:34:59
[2015-09-30T16:34Z] INFO  17:34:59,150 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:59,150 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:34Z] INFO  17:34:59,173 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:34Z] INFO  17:34:59,173 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:34Z] INFO  17:34:59,174 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:34Z] INFO  17:34:59,174 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:34Z] INFO  17:34:59,185 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:34Z] INFO  17:34:59,206 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:34Z] INFO  17:34:59,374 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:35Z] INFO  17:35:00,668 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:35Z] INFO  17:35:00,676 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:35Z] INFO  17:35:00,693 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:35Z] INFO  17:35:00,946 IntervalUtils - Processing 31080572 bp from intervals
[2015-09-30T16:35Z] WARN  17:35:00,949 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:35Z] INFO  17:35:01,006 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:35Z] INFO  17:35:01,141 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:35Z] INFO  17:35:01,142 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:35Z] INFO  17:35:01,142 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:35Z] INFO  17:35:01,142 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:35Z] INFO  17:35:01,959 ProgressMeter -            done   3.1022723E7    36.0 s       1.0 s      100.0%    36.0 s       0.0 s
[2015-09-30T16:35Z] INFO  17:35:01,960 ProgressMeter - Total runtime 36.02 secs, 0.60 min, 0.01 hours
[2015-09-30T16:35Z] INFO  17:35:01,963 MicroScheduler - 96212 reads were filtered out during the traversal out of approximately 1290281 total reads (7.46%)
[2015-09-30T16:35Z] INFO  17:35:01,963 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:35Z] INFO  17:35:01,964 MicroScheduler -   -> 13216 reads (1.02% of total) failing BadMateFilter
[2015-09-30T16:35Z] INFO  17:35:01,964 MicroScheduler -   -> 59373 reads (4.60% of total) failing DuplicateReadFilter
[2015-09-30T16:35Z] INFO  17:35:01,964 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:35Z] INFO  17:35:01,965 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:35Z] INFO  17:35:01,965 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:35Z] INFO  17:35:01,965 MicroScheduler -   -> 23623 reads (1.83% of total) failing MappingQualityZeroFilter
[2015-09-30T16:35Z] INFO  17:35:01,965 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:35Z] INFO  17:35:01,966 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:35Z] INFO  17:35:01,966 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:35Z] INFO  17:35:03,021 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:35Z] GATK: realign ('5', 125759062, 156781785) : syn3-tumor
[2015-09-30T16:35Z] INFO  17:35:08,558 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:35Z] INFO  17:35:08,560 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:35Z] INFO  17:35:08,560 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:35Z] INFO  17:35:08,560 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:35Z] INFO  17:35:08,564 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep-prealign-realign.intervals -L 5:125759063-156781785 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/tx/tmpu43Dkt/2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam
[2015-09-30T16:35Z] INFO  17:35:08,569 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:35Z] INFO  17:35:08,569 HelpFormatter - Date/Time: 2015/09/30 17:35:08
[2015-09-30T16:35Z] INFO  17:35:08,569 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:35Z] INFO  17:35:08,570 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:35Z] INFO  17:35:08,702 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:35Z] INFO  17:35:08,767 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:35Z] INFO  17:35:08,775 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:35Z] INFO  17:35:08,790 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:35Z] INFO  17:35:10,247 IntervalUtils - Processing 31022723 bp from intervals
[2015-09-30T16:35Z] WARN  17:35:10,251 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:35Z] INFO  17:35:10,309 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:35Z] INFO  17:35:10,465 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:35Z] INFO  17:35:10,466 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:35Z] INFO  17:35:10,466 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:35Z] INFO  17:35:10,467 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:35Z] INFO  17:35:13,369 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:35Z] INFO  17:35:13,608 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:35Z] INFO  17:35:29,481 ProgressMeter -      6:32015192    100002.0    30.0 s       5.1 m        3.0%    16.7 m      16.2 m
[2015-09-30T16:35Z] INFO  17:35:31,145 ProgressMeter -      6:30887441   3.088384E7    30.0 s       0.0 s       99.4%    30.0 s       0.0 s
[2015-09-30T16:35Z] INFO  17:35:31,658 ProgressMeter -            done   3.1080572E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T16:35Z] INFO  17:35:31,659 ProgressMeter - Total runtime 30.52 secs, 0.51 min, 0.01 hours
[2015-09-30T16:35Z] INFO  17:35:31,662 MicroScheduler - 69295 reads were filtered out during the traversal out of approximately 870895 total reads (7.96%)
[2015-09-30T16:35Z] INFO  17:35:31,662 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:35Z] INFO  17:35:31,663 MicroScheduler -   -> 11281 reads (1.30% of total) failing BadMateFilter
[2015-09-30T16:35Z] INFO  17:35:31,663 MicroScheduler -   -> 39281 reads (4.51% of total) failing DuplicateReadFilter
[2015-09-30T16:35Z] INFO  17:35:31,663 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:35Z] INFO  17:35:31,663 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:35Z] INFO  17:35:31,663 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:35Z] INFO  17:35:31,664 MicroScheduler -   -> 18733 reads (2.15% of total) failing MappingQualityZeroFilter
[2015-09-30T16:35Z] INFO  17:35:31,664 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:35Z] INFO  17:35:31,664 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:35Z] INFO  17:35:31,664 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:35Z] INFO  17:35:32,670 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:35Z] GATK: realign ('6', 0, 31080572) : syn3-tumor
[2015-09-30T16:35Z] INFO  17:35:34,668 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:35Z] INFO  17:35:34,669 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:35Z] INFO  17:35:34,670 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:35Z] INFO  17:35:34,670 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:35Z] INFO  17:35:34,673 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_0_31080572-prep-prealign-realign.intervals -L 6:1-31080572 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpxQ7ohv/2_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam
[2015-09-30T16:35Z] INFO  17:35:34,678 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:35Z] INFO  17:35:34,679 HelpFormatter - Date/Time: 2015/09/30 17:35:34
[2015-09-30T16:35Z] INFO  17:35:34,679 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:35Z] INFO  17:35:34,679 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:35Z] INFO  17:35:34,806 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:35Z] INFO  17:35:34,866 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:35Z] INFO  17:35:34,873 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:35Z] INFO  17:35:34,889 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:35Z] INFO  17:35:35,730 IntervalUtils - Processing 31080572 bp from intervals
[2015-09-30T16:35Z] WARN  17:35:35,734 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:35Z] INFO  17:35:35,788 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:35Z] INFO  17:35:35,922 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:35Z] INFO  17:35:35,922 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:35Z] INFO  17:35:35,922 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:35Z] INFO  17:35:35,923 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:35Z] INFO  17:35:36,078 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:35Z] INFO  17:35:36,260 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:35Z] INFO  17:35:40,580 ProgressMeter -     5:137424897    300004.0    30.0 s     100.0 s       37.6%    79.0 s      49.0 s
[2015-09-30T16:35Z] INFO  17:35:59,500 ProgressMeter -      6:35444806    500007.0    60.0 s     120.0 s       14.0%     7.2 m       6.2 m
[2015-09-30T16:36Z] INFO  17:36:06,949 ProgressMeter -      6:24651231    400007.0    31.0 s      77.0 s       79.3%    39.0 s       8.0 s
[2015-09-30T16:36Z] INFO  17:36:11,478 ProgressMeter -     5:150481009   1100012.0    61.0 s      55.0 s       79.7%    76.0 s      15.0 s
[2015-09-30T16:36Z] INFO  17:36:17,449 ProgressMeter -            done   1282402.0    66.0 s      52.0 s      100.0%    66.0 s       0.0 s
[2015-09-30T16:36Z] INFO  17:36:17,450 ProgressMeter - Total runtime 66.98 secs, 1.12 min, 0.02 hours
[2015-09-30T16:36Z] INFO  17:36:17,453 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1282402 total reads (0.00%)
[2015-09-30T16:36Z] INFO  17:36:17,454 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:36Z] INFO  17:36:17,454 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:36Z] INFO  17:36:17,454 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:36Z] INFO  17:36:18,578 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:36Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam
[2015-09-30T16:36Z] INFO  17:36:21,375 ProgressMeter -            done    866123.0    45.0 s      52.0 s      100.0%    45.0 s       0.0 s
[2015-09-30T16:36Z] INFO  17:36:21,376 ProgressMeter - Total runtime 45.45 secs, 0.76 min, 0.01 hours
[2015-09-30T16:36Z] INFO  17:36:21,379 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 866123 total reads (0.00%)
[2015-09-30T16:36Z] INFO  17:36:21,379 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:36Z] INFO  17:36:21,380 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:36Z] INFO  17:36:21,380 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:36Z] GATK pre-alignment ('6', 62389878, 93953543) : syn3-tumor
[2015-09-30T16:36Z] INFO  17:36:22,612 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:36Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam
[2015-09-30T16:36Z] GATK pre-alignment ('6', 93954776, 124979769) : syn3-tumor
[2015-09-30T16:36Z] INFO  17:36:25,936 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:36Z] INFO  17:36:25,938 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:36Z] INFO  17:36:25,938 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:36Z] INFO  17:36:25,938 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:36Z] INFO  17:36:25,942 HelpFormatter - Program Args: -T PrintReads -L 6:62389879-93953543 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpqyXKnV/2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam
[2015-09-30T16:36Z] INFO  17:36:25,948 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:36Z] INFO  17:36:25,948 HelpFormatter - Date/Time: 2015/09/30 17:36:25
[2015-09-30T16:36Z] INFO  17:36:25,948 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:36Z] INFO  17:36:25,948 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:36Z] INFO  17:36:26,059 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:36Z] INFO  17:36:29,355 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:36Z] INFO  17:36:29,405 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:36Z] INFO  17:36:29,412 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:36Z] INFO  17:36:29,427 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:36Z] INFO  17:36:29,441 IntervalUtils - Processing 31563665 bp from intervals
[2015-09-30T16:36Z] INFO  17:36:29,500 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:36Z] INFO  17:36:29,501 ProgressMeter -      6:41752650    900014.0    90.0 s     100.0 s       34.2%     4.4 m       2.9 m
[2015-09-30T16:36Z] INFO  17:36:29,694 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:36Z] INFO  17:36:29,694 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:36Z] INFO  17:36:29,694 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:36Z] INFO  17:36:29,695 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:36Z] INFO  17:36:29,706 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:36Z] INFO  17:36:29,905 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:36Z] INFO  17:36:30,133 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:36Z] INFO  17:36:30,136 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:36Z] INFO  17:36:30,136 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:36Z] INFO  17:36:30,136 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:36Z] INFO  17:36:30,139 HelpFormatter - Program Args: -T PrintReads -L 6:93954777-124979769 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpU9OsXT/2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam
[2015-09-30T16:36Z] INFO  17:36:30,145 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:36Z] INFO  17:36:30,145 HelpFormatter - Date/Time: 2015/09/30 17:36:30
[2015-09-30T16:36Z] INFO  17:36:30,145 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:36Z] INFO  17:36:30,145 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:36Z] INFO  17:36:30,248 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:36Z] INFO  17:36:31,407 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:36Z] INFO  17:36:31,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:36Z] INFO  17:36:31,463 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:36Z] INFO  17:36:31,477 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:36Z] INFO  17:36:31,491 IntervalUtils - Processing 31024993 bp from intervals
[2015-09-30T16:36Z] INFO  17:36:31,551 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:36Z] INFO  17:36:31,741 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:36Z] INFO  17:36:31,742 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:36Z] INFO  17:36:31,742 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:36Z] INFO  17:36:31,742 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:36Z] INFO  17:36:31,754 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:36Z] INFO  17:36:31,943 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:36Z] INFO  17:36:59,536 ProgressMeter -      6:47624093   1300019.0   120.0 s      92.0 s       53.0%     3.8 m     106.0 s
[2015-09-30T16:36Z] INFO  17:36:59,697 ProgressMeter -      6:84419102    200008.0    30.0 s       2.5 m       69.8%    42.0 s      12.0 s
[2015-09-30T16:37Z] INFO  17:37:01,895 ProgressMeter -     6:111700970    200002.0    30.0 s       2.5 m       57.2%    52.0 s      22.0 s
[2015-09-30T16:37Z] INFO  17:37:12,195 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:37Z] INFO  17:37:12,274 ProgressMeter -            done    444055.0    42.0 s      95.0 s      100.0%    42.0 s       0.0 s
[2015-09-30T16:37Z] INFO  17:37:12,274 ProgressMeter - Total runtime 42.58 secs, 0.71 min, 0.01 hours
[2015-09-30T16:37Z] INFO  17:37:12,274 MicroScheduler - 1361 reads were filtered out during the traversal out of approximately 445416 total reads (0.31%)
[2015-09-30T16:37Z] INFO  17:37:12,275 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:37Z] INFO  17:37:12,275 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:37Z] INFO  17:37:12,275 MicroScheduler -   -> 1361 reads (0.31% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:37Z] INFO  17:37:13,237 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:37Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam
[2015-09-30T16:37Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam 6:62389879-93953543
[2015-09-30T16:37Z] GATK: RealignerTargetCreator
[2015-09-30T16:37Z] INFO  17:37:15,869 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7e2705ea
[2015-09-30T16:37Z] INFO  17:37:15,992 ProgressMeter -            done    488150.0    44.0 s      90.0 s      100.0%    44.0 s       0.0 s
[2015-09-30T16:37Z] INFO  17:37:15,992 ProgressMeter - Total runtime 44.25 secs, 0.74 min, 0.01 hours
[2015-09-30T16:37Z] INFO  17:37:15,992 MicroScheduler - 1533 reads were filtered out during the traversal out of approximately 489683 total reads (0.31%)
[2015-09-30T16:37Z] INFO  17:37:15,993 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:37Z] INFO  17:37:15,993 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:37Z] INFO  17:37:15,993 MicroScheduler -   -> 1533 reads (0.31% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:37Z] INFO  17:37:16,008 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:16,011 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:37Z] INFO  17:37:16,011 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:37Z] INFO  17:37:16,011 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:37Z] INFO  17:37:16,014 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpkOnzUt/2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign-realign.intervals -l INFO -L 6:62389879-93953543 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:37Z] INFO  17:37:16,021 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:37Z] INFO  17:37:16,021 HelpFormatter - Date/Time: 2015/09/30 17:37:16
[2015-09-30T16:37Z] INFO  17:37:16,022 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:16,022 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:16,091 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:37Z] INFO  17:37:16,207 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:37Z] INFO  17:37:16,215 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:37Z] INFO  17:37:16,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:37Z] INFO  17:37:16,473 IntervalUtils - Processing 31563665 bp from intervals
[2015-09-30T16:37Z] WARN  17:37:16,477 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:37Z] INFO  17:37:16,532 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:37Z] INFO  17:37:16,708 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:37Z] INFO  17:37:16,709 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:37Z] INFO  17:37:16,709 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:37Z] INFO  17:37:16,710 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:37Z] INFO  17:37:17,003 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:37Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam
[2015-09-30T16:37Z] INFO  17:37:17,293 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:37Z] INFO  17:37:17,673 ProgressMeter -            done   1557085.0     2.3 m      88.0 s      100.0%     2.3 m       0.0 s
[2015-09-30T16:37Z] INFO  17:37:17,673 ProgressMeter - Total runtime 138.50 secs, 2.31 min, 0.04 hours
[2015-09-30T16:37Z] INFO  17:37:17,673 MicroScheduler - 2591 reads were filtered out during the traversal out of approximately 1559676 total reads (0.17%)
[2015-09-30T16:37Z] INFO  17:37:17,674 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:37Z] INFO  17:37:17,674 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:37Z] INFO  17:37:17,674 MicroScheduler -   -> 2591 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:37Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam 6:93954777-124979769
[2015-09-30T16:37Z] GATK: RealignerTargetCreator
[2015-09-30T16:37Z] INFO  17:37:18,690 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:37Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam
[2015-09-30T16:37Z] INFO  17:37:19,889 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:19,892 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:37Z] INFO  17:37:19,892 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:37Z] INFO  17:37:19,892 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:37Z] INFO  17:37:19,896 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmptrUatC/2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign-realign.intervals -l INFO -L 6:93954777-124979769 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:37Z] INFO  17:37:19,919 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:37Z] INFO  17:37:19,919 HelpFormatter - Date/Time: 2015/09/30 17:37:19
[2015-09-30T16:37Z] INFO  17:37:19,919 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:19,919 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:19,978 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:37Z] INFO  17:37:20,086 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:37Z] INFO  17:37:20,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:37Z] INFO  17:37:20,156 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:37Z] INFO  17:37:20,421 IntervalUtils - Processing 31024993 bp from intervals
[2015-09-30T16:37Z] WARN  17:37:20,425 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:37Z] INFO  17:37:20,484 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:37Z] INFO  17:37:20,929 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:37Z] INFO  17:37:20,930 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:37Z] INFO  17:37:20,930 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:37Z] INFO  17:37:20,930 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:37Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam 6:31082316-62284583
[2015-09-30T16:37Z] GATK: RealignerTargetCreator
[2015-09-30T16:37Z] INFO  17:37:26,482 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:26,484 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:37Z] INFO  17:37:26,485 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:37Z] INFO  17:37:26,485 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:37Z] INFO  17:37:26,488 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpAJquHp/2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign-realign.intervals -l INFO -L 6:31082316-62284583 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:37Z] INFO  17:37:26,494 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:37Z] INFO  17:37:26,494 HelpFormatter - Date/Time: 2015/09/30 17:37:26
[2015-09-30T16:37Z] INFO  17:37:26,494 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:26,495 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:26,554 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:37Z] INFO  17:37:26,666 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:37Z] INFO  17:37:26,674 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:37Z] INFO  17:37:26,690 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:37Z] INFO  17:37:26,937 IntervalUtils - Processing 31202268 bp from intervals
[2015-09-30T16:37Z] WARN  17:37:26,941 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:37Z] INFO  17:37:27,000 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:37Z] INFO  17:37:27,139 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:37Z] INFO  17:37:27,139 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:37Z] INFO  17:37:27,140 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:37Z] INFO  17:37:27,140 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:37Z] INFO  17:37:39,804 ProgressMeter -            done   3.1563665E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T16:37Z] INFO  17:37:39,804 ProgressMeter - Total runtime 23.10 secs, 0.38 min, 0.01 hours
[2015-09-30T16:37Z] INFO  17:37:39,807 MicroScheduler - 33383 reads were filtered out during the traversal out of approximately 446373 total reads (7.48%)
[2015-09-30T16:37Z] INFO  17:37:39,808 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:37Z] INFO  17:37:39,808 MicroScheduler -   -> 7531 reads (1.69% of total) failing BadMateFilter
[2015-09-30T16:37Z] INFO  17:37:39,808 MicroScheduler -   -> 17221 reads (3.86% of total) failing DuplicateReadFilter
[2015-09-30T16:37Z] INFO  17:37:39,808 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:37Z] INFO  17:37:39,809 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:37Z] INFO  17:37:39,809 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:37Z] INFO  17:37:39,809 MicroScheduler -   -> 8631 reads (1.93% of total) failing MappingQualityZeroFilter
[2015-09-30T16:37Z] INFO  17:37:39,809 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:37Z] INFO  17:37:39,809 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:37Z] INFO  17:37:39,810 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:37Z] INFO  17:37:40,805 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:37Z] GATK: realign ('6', 62389878, 93953543) : syn3-tumor
[2015-09-30T16:37Z] INFO  17:37:42,911 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:42,913 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:37Z] INFO  17:37:42,914 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:37Z] INFO  17:37:42,914 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:37Z] INFO  17:37:42,917 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep-prealign-realign.intervals -L 6:62389879-93953543 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmphEFT2p/2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam
[2015-09-30T16:37Z] INFO  17:37:42,923 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:37Z] INFO  17:37:42,923 HelpFormatter - Date/Time: 2015/09/30 17:37:42
[2015-09-30T16:37Z] INFO  17:37:42,923 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:42,924 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:43,693 ProgressMeter -            done   3.1024993E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T16:37Z] INFO  17:37:43,693 ProgressMeter - Total runtime 22.76 secs, 0.38 min, 0.01 hours
[2015-09-30T16:37Z] INFO  17:37:43,696 MicroScheduler - 36429 reads were filtered out during the traversal out of approximately 491164 total reads (7.42%)
[2015-09-30T16:37Z] INFO  17:37:43,696 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:37Z] INFO  17:37:43,697 MicroScheduler -   -> 7883 reads (1.60% of total) failing BadMateFilter
[2015-09-30T16:37Z] INFO  17:37:43,697 MicroScheduler -   -> 19725 reads (4.02% of total) failing DuplicateReadFilter
[2015-09-30T16:37Z] INFO  17:37:43,697 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:37Z] INFO  17:37:43,697 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:37Z] INFO  17:37:43,697 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:37Z] INFO  17:37:43,698 MicroScheduler -   -> 8821 reads (1.80% of total) failing MappingQualityZeroFilter
[2015-09-30T16:37Z] INFO  17:37:43,698 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:37Z] INFO  17:37:43,698 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:37Z] INFO  17:37:43,698 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:37Z] INFO  17:37:44,164 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:37Z] INFO  17:37:44,264 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:37Z] INFO  17:37:44,271 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:37Z] INFO  17:37:44,388 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2015-09-30T16:37Z] INFO  17:37:44,684 IntervalUtils - Processing 31563665 bp from intervals
[2015-09-30T16:37Z] INFO  17:37:44,687 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:37Z] WARN  17:37:44,688 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:37Z] INFO  17:37:44,780 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:37Z] INFO  17:37:45,175 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:37Z] INFO  17:37:45,175 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:37Z] INFO  17:37:45,176 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:37Z] INFO  17:37:45,176 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:37Z] INFO  17:37:45,318 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:37Z] INFO  17:37:45,508 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:37Z] GATK: realign ('6', 93954776, 124979769) : syn3-tumor
[2015-09-30T16:37Z] INFO  17:37:48,344 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:48,346 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:37Z] INFO  17:37:48,346 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:37Z] INFO  17:37:48,346 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:37Z] INFO  17:37:48,350 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep-prealign-realign.intervals -L 6:93954777-124979769 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpzbmhZ4/2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam
[2015-09-30T16:37Z] INFO  17:37:48,356 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:37Z] INFO  17:37:48,356 HelpFormatter - Date/Time: 2015/09/30 17:37:48
[2015-09-30T16:37Z] INFO  17:37:48,356 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:48,356 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:37Z] INFO  17:37:48,464 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:37Z] INFO  17:37:48,531 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:37Z] INFO  17:37:48,539 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:37Z] INFO  17:37:48,555 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:37Z] INFO  17:37:48,786 IntervalUtils - Processing 31024993 bp from intervals
[2015-09-30T16:37Z] WARN  17:37:48,790 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:37Z] INFO  17:37:48,849 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:37Z] INFO  17:37:48,991 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:37Z] INFO  17:37:48,991 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:37Z] INFO  17:37:48,992 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:37Z] INFO  17:37:48,992 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:37Z] INFO  17:37:49,141 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:37Z] INFO  17:37:49,323 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:37Z] INFO  17:37:57,142 ProgressMeter -      6:51666753   2.0576437E7    30.0 s       1.0 s       66.0%    45.0 s      15.0 s
[2015-09-30T16:38Z] INFO  17:38:04,478 ProgressMeter -            done   3.1202268E7    37.0 s       1.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T16:38Z] INFO  17:38:04,479 ProgressMeter - Total runtime 37.34 secs, 0.62 min, 0.01 hours
[2015-09-30T16:38Z] INFO  17:38:04,482 MicroScheduler - 142329 reads were filtered out during the traversal out of approximately 1566690 total reads (9.08%)
[2015-09-30T16:38Z] INFO  17:38:04,482 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:38Z] INFO  17:38:04,482 MicroScheduler -   -> 14931 reads (0.95% of total) failing BadMateFilter
[2015-09-30T16:38Z] INFO  17:38:04,483 MicroScheduler -   -> 74222 reads (4.74% of total) failing DuplicateReadFilter
[2015-09-30T16:38Z] INFO  17:38:04,483 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:38Z] INFO  17:38:04,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:38Z] INFO  17:38:04,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:38Z] INFO  17:38:04,484 MicroScheduler -   -> 53176 reads (3.39% of total) failing MappingQualityZeroFilter
[2015-09-30T16:38Z] INFO  17:38:04,484 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:38Z] INFO  17:38:04,484 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:38Z] INFO  17:38:04,484 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:38Z] INFO  17:38:05,428 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:38Z] GATK: realign ('6', 31082315, 62284583) : syn3-tumor
[2015-09-30T16:38Z] INFO  17:38:07,661 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:38Z] INFO  17:38:07,663 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:38Z] INFO  17:38:07,663 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:38Z] INFO  17:38:07,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:38Z] INFO  17:38:07,667 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep-prealign-realign.intervals -L 6:31082316-62284583 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpwD7xE6/2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam
[2015-09-30T16:38Z] INFO  17:38:07,673 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:38Z] INFO  17:38:07,673 HelpFormatter - Date/Time: 2015/09/30 17:38:07
[2015-09-30T16:38Z] INFO  17:38:07,673 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:38Z] INFO  17:38:07,673 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:38Z] INFO  17:38:07,802 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:38Z] INFO  17:38:07,865 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:38Z] INFO  17:38:07,873 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:38Z] INFO  17:38:07,889 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:38Z] INFO  17:38:08,539 IntervalUtils - Processing 31202268 bp from intervals
[2015-09-30T16:38Z] WARN  17:38:08,543 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:38Z] INFO  17:38:08,598 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:38Z] INFO  17:38:08,740 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:38Z] INFO  17:38:08,741 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:38Z] INFO  17:38:08,741 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:38Z] INFO  17:38:08,741 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:38Z] INFO  17:38:08,887 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:38Z] INFO  17:38:09,072 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:38Z] INFO  17:38:11,789 ProgressMeter -            done    444055.0    26.0 s      59.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T16:38Z] INFO  17:38:11,789 ProgressMeter - Total runtime 26.61 secs, 0.44 min, 0.01 hours
[2015-09-30T16:38Z] INFO  17:38:11,792 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 444055 total reads (0.00%)
[2015-09-30T16:38Z] INFO  17:38:11,793 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:38Z] INFO  17:38:11,793 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:38Z] INFO  17:38:11,793 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:38Z] INFO  17:38:12,919 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:38Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam
[2015-09-30T16:38Z] GATK pre-alignment ('6', 125064552, 156268261) : syn3-tumor
[2015-09-30T16:38Z] INFO  17:38:16,937 ProgressMeter -            done    488150.0    27.0 s      57.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T16:38Z] INFO  17:38:16,937 ProgressMeter - Total runtime 27.95 secs, 0.47 min, 0.01 hours
[2015-09-30T16:38Z] INFO  17:38:16,940 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 488150 total reads (0.00%)
[2015-09-30T16:38Z] INFO  17:38:16,941 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:38Z] INFO  17:38:16,941 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:38Z] INFO  17:38:16,941 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:38Z] INFO  17:38:17,298 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:38Z] INFO  17:38:17,300 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:38Z] INFO  17:38:17,300 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:38Z] INFO  17:38:17,300 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:38Z] INFO  17:38:17,304 HelpFormatter - Program Args: -T PrintReads -L 6:125064553-156268261 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpYIcZXi/2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam
[2015-09-30T16:38Z] INFO  17:38:17,309 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:38Z] INFO  17:38:17,309 HelpFormatter - Date/Time: 2015/09/30 17:38:17
[2015-09-30T16:38Z] INFO  17:38:17,310 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:38Z] INFO  17:38:17,310 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:38Z] INFO  17:38:17,413 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:38Z] INFO  17:38:18,119 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:38Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam
[2015-09-30T16:38Z] INFO  17:38:18,413 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:38Z] INFO  17:38:18,464 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:38Z] INFO  17:38:18,472 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:38Z] INFO  17:38:18,487 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:38Z] INFO  17:38:18,500 IntervalUtils - Processing 31203709 bp from intervals
[2015-09-30T16:38Z] INFO  17:38:18,580 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:38Z] INFO  17:38:18,811 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:38Z] INFO  17:38:18,811 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:38Z] INFO  17:38:18,812 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:38Z] INFO  17:38:18,812 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:38Z] INFO  17:38:18,823 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:38Z] INFO  17:38:19,013 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:38Z] GATK pre-alignment ('6', 156275378, 171115067) : syn3-tumor
[2015-09-30T16:38Z] INFO  17:38:21,119 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:38Z] INFO  17:38:21,121 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:38Z] INFO  17:38:21,122 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:38Z] INFO  17:38:21,122 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:38Z] INFO  17:38:21,125 HelpFormatter - Program Args: -T PrintReads -L 6:156275379-171115067 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpQpPqHT/2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam
[2015-09-30T16:38Z] INFO  17:38:21,131 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:38Z] INFO  17:38:21,132 HelpFormatter - Date/Time: 2015/09/30 17:38:21
[2015-09-30T16:38Z] INFO  17:38:21,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:38Z] INFO  17:38:21,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:38Z] INFO  17:38:21,249 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:38Z] INFO  17:38:22,305 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:38Z] INFO  17:38:22,355 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:38Z] INFO  17:38:22,362 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:38Z] INFO  17:38:22,380 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:38Z] INFO  17:38:22,392 IntervalUtils - Processing 14839689 bp from intervals
[2015-09-30T16:38Z] INFO  17:38:22,450 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:38Z] INFO  17:38:22,718 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:38Z] INFO  17:38:22,719 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:38Z] INFO  17:38:22,719 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:38Z] INFO  17:38:22,719 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:38Z] INFO  17:38:22,730 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:38Z] INFO  17:38:22,840 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:38Z] INFO  17:38:39,240 ProgressMeter -      6:33400207    400006.0    30.0 s      76.0 s        7.4%     6.7 m       6.2 m
[2015-09-30T16:38Z] INFO  17:38:48,814 ProgressMeter -     6:136665087    200002.0    30.0 s       2.5 m       37.2%    80.0 s      50.0 s
[2015-09-30T16:38Z] INFO  17:38:52,722 ProgressMeter -     6:161552193    200002.0    30.0 s       2.5 m       35.6%    84.0 s      54.0 s
[2015-09-30T16:39Z] INFO  17:39:09,274 ProgressMeter -      6:43310604   1100016.0    60.0 s      55.0 s       39.2%     2.6 m      93.0 s
[2015-09-30T16:39Z] INFO  17:39:10,292 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:39Z] INFO  17:39:10,435 ProgressMeter -            done    445442.0    47.0 s     107.0 s       99.6%    47.0 s       0.0 s
[2015-09-30T16:39Z] INFO  17:39:10,435 ProgressMeter - Total runtime 47.72 secs, 0.80 min, 0.01 hours
[2015-09-30T16:39Z] INFO  17:39:10,436 MicroScheduler - 953 reads were filtered out during the traversal out of approximately 446395 total reads (0.21%)
[2015-09-30T16:39Z] INFO  17:39:10,436 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:39Z] INFO  17:39:10,436 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:39Z] INFO  17:39:10,436 MicroScheduler -   -> 953 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:39Z] INFO  17:39:11,407 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:39Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam
[2015-09-30T16:39Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam 6:156275379-171115067
[2015-09-30T16:39Z] GATK: RealignerTargetCreator
[2015-09-30T16:39Z] INFO  17:39:14,265 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:14,267 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:39Z] INFO  17:39:14,267 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:39Z] INFO  17:39:14,267 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:39Z] INFO  17:39:14,270 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpoxDB0s/2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign-realign.intervals -l INFO -L 6:156275379-171115067 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:39Z] INFO  17:39:14,277 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:39Z] INFO  17:39:14,277 HelpFormatter - Date/Time: 2015/09/30 17:39:14
[2015-09-30T16:39Z] INFO  17:39:14,277 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:14,277 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:14,339 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:39Z] INFO  17:39:14,450 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:39Z] INFO  17:39:14,458 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:39Z] INFO  17:39:14,478 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:39Z] INFO  17:39:15,517 IntervalUtils - Processing 14839689 bp from intervals
[2015-09-30T16:39Z] WARN  17:39:15,521 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:39Z] INFO  17:39:15,577 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:39Z] INFO  17:39:15,673 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:39Z] INFO  17:39:15,673 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:39Z] INFO  17:39:15,673 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:39Z] INFO  17:39:15,674 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:39Z] INFO  17:39:18,815 ProgressMeter -     6:151936812    500005.0    60.0 s     120.0 s       86.1%    69.0 s       9.0 s
[2015-09-30T16:39Z] INFO  17:39:26,777 ProgressMeter -            done   1557085.0    78.0 s      50.0 s      100.0%    78.0 s       0.0 s
[2015-09-30T16:39Z] INFO  17:39:26,778 ProgressMeter - Total runtime 78.04 secs, 1.30 min, 0.02 hours
[2015-09-30T16:39Z] INFO  17:39:26,781 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1557085 total reads (0.00%)
[2015-09-30T16:39Z] INFO  17:39:26,781 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:39Z] INFO  17:39:26,781 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:39Z] INFO  17:39:26,782 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:39Z] INFO  17:39:28,018 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:39Z] INFO  17:39:28,687 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:39Z] INFO  17:39:28,751 ProgressMeter -            done    678378.0    69.0 s     103.0 s      100.0%    69.0 s       0.0 s
[2015-09-30T16:39Z] INFO  17:39:28,752 ProgressMeter - Total runtime 69.94 secs, 1.17 min, 0.02 hours
[2015-09-30T16:39Z] INFO  17:39:28,752 MicroScheduler - 1969 reads were filtered out during the traversal out of approximately 680347 total reads (0.29%)
[2015-09-30T16:39Z] INFO  17:39:28,752 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:39Z] INFO  17:39:28,753 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:39Z] INFO  17:39:28,753 MicroScheduler -   -> 1969 reads (0.29% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:39Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam
[2015-09-30T16:39Z] INFO  17:39:29,749 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:39Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam
[2015-09-30T16:39Z] INFO  17:39:30,338 ProgressMeter -            done   1.4839689E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2015-09-30T16:39Z] INFO  17:39:30,338 ProgressMeter - Total runtime 14.67 secs, 0.24 min, 0.00 hours
[2015-09-30T16:39Z] INFO  17:39:30,341 MicroScheduler - 61018 reads were filtered out during the traversal out of approximately 448251 total reads (13.61%)
[2015-09-30T16:39Z] INFO  17:39:30,342 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:39Z] INFO  17:39:30,342 MicroScheduler -   -> 5343 reads (1.19% of total) failing BadMateFilter
[2015-09-30T16:39Z] INFO  17:39:30,342 MicroScheduler -   -> 19714 reads (4.40% of total) failing DuplicateReadFilter
[2015-09-30T16:39Z] INFO  17:39:30,342 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:39Z] INFO  17:39:30,343 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:39Z] INFO  17:39:30,343 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:39Z] INFO  17:39:30,343 MicroScheduler -   -> 35961 reads (8.02% of total) failing MappingQualityZeroFilter
[2015-09-30T16:39Z] INFO  17:39:30,343 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:39Z] INFO  17:39:30,343 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:39Z] INFO  17:39:30,344 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:39Z] INFO  17:39:31,325 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:39Z] GATK: realign ('6', 156275378, 171115067) : syn3-tumor
[2015-09-30T16:39Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam 6:125064553-156268261
[2015-09-30T16:39Z] GATK: RealignerTargetCreator
[2015-09-30T16:39Z] GATK pre-alignment ('7', 0, 31019109) : syn3-tumor
[2015-09-30T16:39Z] INFO  17:39:32,930 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:32,932 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:39Z] INFO  17:39:32,932 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:39Z] INFO  17:39:32,932 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:39Z] INFO  17:39:32,935 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep-prealign-realign.intervals -L 6:156275379-171115067 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpwd3RNt/2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam
[2015-09-30T16:39Z] INFO  17:39:32,941 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:39Z] INFO  17:39:32,941 HelpFormatter - Date/Time: 2015/09/30 17:39:32
[2015-09-30T16:39Z] INFO  17:39:32,941 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:32,941 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:33,065 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:39Z] INFO  17:39:33,127 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:39Z] INFO  17:39:33,134 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:39Z] INFO  17:39:33,150 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:39Z] INFO  17:39:33,214 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:33,216 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:39Z] INFO  17:39:33,216 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:39Z] INFO  17:39:33,216 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:39Z] INFO  17:39:33,219 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmp4Hdm9K/2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign-realign.intervals -l INFO -L 6:125064553-156268261 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:39Z] INFO  17:39:33,225 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:39Z] INFO  17:39:33,226 HelpFormatter - Date/Time: 2015/09/30 17:39:33
[2015-09-30T16:39Z] INFO  17:39:33,226 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:33,226 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:33,293 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:39Z] INFO  17:39:34,569 IntervalUtils - Processing 14839689 bp from intervals
[2015-09-30T16:39Z] WARN  17:39:34,573 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:39Z] INFO  17:39:35,017 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:39Z] INFO  17:39:35,055 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:39Z] INFO  17:39:35,063 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:39Z] INFO  17:39:35,079 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:39Z] INFO  17:39:35,124 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:39Z] INFO  17:39:35,124 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:39Z] INFO  17:39:35,125 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:39Z] INFO  17:39:35,125 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:39Z] INFO  17:39:35,256 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:39Z] INFO  17:39:35,321 IntervalUtils - Processing 31203709 bp from intervals
[2015-09-30T16:39Z] WARN  17:39:35,325 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:39Z] INFO  17:39:35,368 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:39Z] INFO  17:39:35,382 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:39Z] INFO  17:39:35,536 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:39Z] INFO  17:39:35,536 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:39Z] INFO  17:39:35,537 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:39Z] INFO  17:39:35,537 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:39Z] INFO  17:39:38,423 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:38,425 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:39Z] INFO  17:39:38,425 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:39Z] INFO  17:39:38,426 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:39Z] INFO  17:39:38,429 HelpFormatter - Program Args: -T PrintReads -L 7:1-31019109 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmppDPZDY/2_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam
[2015-09-30T16:39Z] INFO  17:39:38,435 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:39Z] INFO  17:39:38,436 HelpFormatter - Date/Time: 2015/09/30 17:39:38
[2015-09-30T16:39Z] INFO  17:39:38,436 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:38,436 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:39Z] INFO  17:39:38,545 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:39Z] INFO  17:39:40,177 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:39Z] INFO  17:39:40,230 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:39Z] INFO  17:39:40,237 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:39Z] INFO  17:39:40,253 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:39Z] INFO  17:39:40,266 IntervalUtils - Processing 31019109 bp from intervals
[2015-09-30T16:39Z] INFO  17:39:40,329 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:39Z] INFO  17:39:40,529 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:39Z] INFO  17:39:40,530 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:39Z] INFO  17:39:40,530 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:39Z] INFO  17:39:40,530 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:39Z] INFO  17:39:40,542 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:39Z] INFO  17:39:40,749 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:40Z] INFO  17:40:00,769 ProgressMeter -            done   3.1203709E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T16:40Z] INFO  17:40:00,769 ProgressMeter - Total runtime 25.23 secs, 0.42 min, 0.01 hours
[2015-09-30T16:40Z] INFO  17:40:00,772 MicroScheduler - 52788 reads were filtered out during the traversal out of approximately 683049 total reads (7.73%)
[2015-09-30T16:40Z] INFO  17:40:00,772 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:40Z] INFO  17:40:00,773 MicroScheduler -   -> 9892 reads (1.45% of total) failing BadMateFilter
[2015-09-30T16:40Z] INFO  17:40:00,773 MicroScheduler -   -> 27835 reads (4.08% of total) failing DuplicateReadFilter
[2015-09-30T16:40Z] INFO  17:40:00,773 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:40Z] INFO  17:40:00,773 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:40Z] INFO  17:40:00,774 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:40Z] INFO  17:40:00,774 MicroScheduler -   -> 15061 reads (2.20% of total) failing MappingQualityZeroFilter
[2015-09-30T16:40Z] INFO  17:40:00,774 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:40Z] INFO  17:40:00,774 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:40Z] INFO  17:40:00,774 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:40Z] INFO  17:40:01,737 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:40Z] GATK: realign ('6', 125064552, 156268261) : syn3-tumor
[2015-09-30T16:40Z] INFO  17:40:01,927 ProgressMeter -            done    445442.0    26.0 s      60.0 s       99.6%    26.0 s       0.0 s
[2015-09-30T16:40Z] INFO  17:40:01,928 ProgressMeter - Total runtime 26.80 secs, 0.45 min, 0.01 hours
[2015-09-30T16:40Z] INFO  17:40:01,931 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 445442 total reads (0.00%)
[2015-09-30T16:40Z] INFO  17:40:01,931 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:40Z] INFO  17:40:01,931 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:40Z] INFO  17:40:01,932 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:40Z] INFO  17:40:02,928 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:40Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam
[2015-09-30T16:40Z] INFO  17:40:03,536 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:40Z] INFO  17:40:03,540 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:40Z] INFO  17:40:03,540 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:40Z] INFO  17:40:03,540 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:40Z] INFO  17:40:03,546 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep-prealign-realign.intervals -L 6:125064553-156268261 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/tx/tmpnMtxz7/2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam
[2015-09-30T16:40Z] INFO  17:40:03,553 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:40Z] INFO  17:40:03,553 HelpFormatter - Date/Time: 2015/09/30 17:40:03
[2015-09-30T16:40Z] INFO  17:40:03,554 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:40Z] INFO  17:40:03,554 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:40Z] INFO  17:40:03,685 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:40Z] INFO  17:40:03,756 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:40Z] INFO  17:40:03,763 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:40Z] INFO  17:40:03,791 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T16:40Z] INFO  17:40:04,019 IntervalUtils - Processing 31203709 bp from intervals
[2015-09-30T16:40Z] WARN  17:40:04,023 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:40Z] INFO  17:40:04,078 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:40Z] GATK pre-alignment ('7', 31022897, 62585293) : syn3-tumor
[2015-09-30T16:40Z] INFO  17:40:04,224 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:40Z] INFO  17:40:04,224 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:40Z] INFO  17:40:04,225 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:40Z] INFO  17:40:04,225 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:40Z] INFO  17:40:04,372 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:40Z] INFO  17:40:04,564 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:40Z] INFO  17:40:06,636 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:40Z] INFO  17:40:06,639 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:40Z] INFO  17:40:06,639 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:40Z] INFO  17:40:06,639 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:40Z] INFO  17:40:06,642 HelpFormatter - Program Args: -T PrintReads -L 7:31022898-62585293 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmps6EkyD/2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam
[2015-09-30T16:40Z] INFO  17:40:06,648 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:40Z] INFO  17:40:06,648 HelpFormatter - Date/Time: 2015/09/30 17:40:06
[2015-09-30T16:40Z] INFO  17:40:06,648 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:40Z] INFO  17:40:06,648 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:40Z] INFO  17:40:08,226 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:40Z] INFO  17:40:09,348 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:40Z] INFO  17:40:09,397 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:40Z] INFO  17:40:09,404 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:40Z] INFO  17:40:09,420 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:40Z] INFO  17:40:09,432 IntervalUtils - Processing 31562396 bp from intervals
[2015-09-30T16:40Z] INFO  17:40:09,488 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:40Z] INFO  17:40:09,687 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:40Z] INFO  17:40:09,688 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:40Z] INFO  17:40:09,688 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:40Z] INFO  17:40:09,688 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:40Z] INFO  17:40:09,699 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:40Z] INFO  17:40:09,906 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:40Z] INFO  17:40:10,548 ProgressMeter -       7:4824749    200002.0    30.0 s       2.5 m       15.6%     3.2 m       2.7 m
[2015-09-30T16:40Z] INFO  17:40:36,125 ProgressMeter -     6:150003852    400004.0    31.0 s      79.0 s       79.9%    38.0 s       7.0 s
[2015-09-30T16:40Z] INFO  17:40:39,990 ProgressMeter -      7:44096973    200002.0    30.0 s       2.5 m       41.4%    72.0 s      42.0 s
[2015-09-30T16:40Z] INFO  17:40:40,549 ProgressMeter -      7:21659389    600007.0    60.0 s     100.0 s       69.8%    85.0 s      25.0 s
[2015-09-30T16:40Z] INFO  17:40:42,320 ProgressMeter -            done    678378.0    38.0 s      56.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T16:40Z] INFO  17:40:42,320 ProgressMeter - Total runtime 38.10 secs, 0.63 min, 0.01 hours
[2015-09-30T16:40Z] INFO  17:40:42,323 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 678378 total reads (0.00%)
[2015-09-30T16:40Z] INFO  17:40:42,324 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:40Z] INFO  17:40:42,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:40Z] INFO  17:40:42,324 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:40Z] INFO  17:40:43,423 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:40Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam
[2015-09-30T16:40Z] GATK pre-alignment ('7', 62708318, 93925745) : syn3-tumor
[2015-09-30T16:40Z] INFO  17:40:46,998 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:40Z] INFO  17:40:47,001 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:40Z] INFO  17:40:47,001 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:40Z] INFO  17:40:47,001 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:40Z] INFO  17:40:47,004 HelpFormatter - Program Args: -T PrintReads -L 7:62708319-93925745 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpmQ3eyp/2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam
[2015-09-30T16:40Z] INFO  17:40:47,010 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:40Z] INFO  17:40:47,010 HelpFormatter - Date/Time: 2015/09/30 17:40:46
[2015-09-30T16:40Z] INFO  17:40:47,010 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:40Z] INFO  17:40:47,010 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:40Z] INFO  17:40:47,101 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:40Z] INFO  17:40:48,017 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:40Z] INFO  17:40:48,066 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:40Z] INFO  17:40:48,074 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:40Z] INFO  17:40:48,088 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:40Z] INFO  17:40:48,237 IntervalUtils - Processing 31217427 bp from intervals
[2015-09-30T16:40Z] INFO  17:40:48,294 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:40Z] INFO  17:40:48,505 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:40Z] INFO  17:40:48,505 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:40Z] INFO  17:40:48,505 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:40Z] INFO  17:40:48,505 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:40Z] INFO  17:40:48,516 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:40Z] INFO  17:40:48,728 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:41Z] INFO  17:41:00,883 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@fb5265f
[2015-09-30T16:41Z] INFO  17:41:00,981 ProgressMeter -            done    944287.0    80.0 s      85.0 s      100.0%    80.0 s       0.0 s
[2015-09-30T16:41Z] INFO  17:41:00,981 ProgressMeter - Total runtime 80.45 secs, 1.34 min, 0.02 hours
[2015-09-30T16:41Z] INFO  17:41:00,982 MicroScheduler - 2003 reads were filtered out during the traversal out of approximately 946290 total reads (0.21%)
[2015-09-30T16:41Z] INFO  17:41:00,982 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:41Z] INFO  17:41:00,982 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:41Z] INFO  17:41:00,982 MicroScheduler -   -> 2003 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:41Z] INFO  17:41:02,039 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:41Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam
[2015-09-30T16:41Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam 7:1-31019109
[2015-09-30T16:41Z] GATK: RealignerTargetCreator
[2015-09-30T16:41Z] INFO  17:41:06,259 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:06,261 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:41Z] INFO  17:41:06,261 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:41Z] INFO  17:41:06,261 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:41Z] INFO  17:41:06,265 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpMJQ4dp/2_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign-realign.intervals -l INFO -L 7:1-31019109 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:41Z] INFO  17:41:06,271 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:41Z] INFO  17:41:06,271 HelpFormatter - Date/Time: 2015/09/30 17:41:06
[2015-09-30T16:41Z] INFO  17:41:06,271 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:06,271 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:06,343 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:41Z] INFO  17:41:06,472 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:41Z] INFO  17:41:06,480 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:41Z] INFO  17:41:06,497 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:41Z] INFO  17:41:06,747 IntervalUtils - Processing 31019109 bp from intervals
[2015-09-30T16:41Z] WARN  17:41:06,751 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:41Z] INFO  17:41:06,811 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:41Z] INFO  17:41:06,956 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:41Z] INFO  17:41:06,957 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:41Z] INFO  17:41:06,957 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:41Z] INFO  17:41:06,957 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:41Z] INFO  17:41:09,991 ProgressMeter -      7:57085544    600009.0    60.0 s     100.0 s       82.6%    72.0 s      12.0 s
[2015-09-30T16:41Z] INFO  17:41:11,164 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:41Z] INFO  17:41:11,424 ProgressMeter -            done    697529.0    61.0 s      88.0 s      100.0%    61.0 s       0.0 s
[2015-09-30T16:41Z] INFO  17:41:11,424 ProgressMeter - Total runtime 61.74 secs, 1.03 min, 0.02 hours
[2015-09-30T16:41Z] INFO  17:41:11,425 MicroScheduler - 1776 reads were filtered out during the traversal out of approximately 699305 total reads (0.25%)
[2015-09-30T16:41Z] INFO  17:41:11,425 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:41Z] INFO  17:41:11,425 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:41Z] INFO  17:41:11,425 MicroScheduler -   -> 1776 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:41Z] INFO  17:41:12,469 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:41Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam
[2015-09-30T16:41Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam 7:31022898-62585293
[2015-09-30T16:41Z] GATK: RealignerTargetCreator
[2015-09-30T16:41Z] INFO  17:41:16,617 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:16,619 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:41Z] INFO  17:41:16,619 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:41Z] INFO  17:41:16,619 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:41Z] INFO  17:41:16,623 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpa6Ipmb/2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign-realign.intervals -l INFO -L 7:31022898-62585293 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:41Z] INFO  17:41:16,628 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:41Z] INFO  17:41:16,629 HelpFormatter - Date/Time: 2015/09/30 17:41:16
[2015-09-30T16:41Z] INFO  17:41:16,629 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:16,629 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:16,687 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:41Z] INFO  17:41:17,236 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:41Z] INFO  17:41:17,243 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:41Z] INFO  17:41:17,266 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:41Z] INFO  17:41:17,518 IntervalUtils - Processing 31562396 bp from intervals
[2015-09-30T16:41Z] WARN  17:41:17,522 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:41Z] INFO  17:41:17,581 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:41Z] INFO  17:41:17,741 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:41Z] INFO  17:41:17,741 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:41Z] INFO  17:41:17,742 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:41Z] INFO  17:41:17,742 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:41Z] INFO  17:41:18,508 ProgressMeter -      7:72730264    200003.0    30.0 s       2.5 m       32.1%    93.0 s      63.0 s
[2015-09-30T16:41Z] INFO  17:41:35,078 ProgressMeter -            done   3.1019109E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T16:41Z] INFO  17:41:35,079 ProgressMeter - Total runtime 28.12 secs, 0.47 min, 0.01 hours
[2015-09-30T16:41Z] INFO  17:41:35,082 MicroScheduler - 90993 reads were filtered out during the traversal out of approximately 949551 total reads (9.58%)
[2015-09-30T16:41Z] INFO  17:41:35,082 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:41Z] INFO  17:41:35,082 MicroScheduler -   -> 10905 reads (1.15% of total) failing BadMateFilter
[2015-09-30T16:41Z] INFO  17:41:35,083 MicroScheduler -   -> 44642 reads (4.70% of total) failing DuplicateReadFilter
[2015-09-30T16:41Z] INFO  17:41:35,083 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:41Z] INFO  17:41:35,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:41Z] INFO  17:41:35,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:41Z] INFO  17:41:35,084 MicroScheduler -   -> 35446 reads (3.73% of total) failing MappingQualityZeroFilter
[2015-09-30T16:41Z] INFO  17:41:35,085 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:41Z] INFO  17:41:35,085 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:41Z] INFO  17:41:35,086 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:41Z] INFO  17:41:36,079 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:41Z] GATK: realign ('7', 0, 31019109) : syn3-tumor
[2015-09-30T16:41Z] INFO  17:41:39,339 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:39,341 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:41Z] INFO  17:41:39,341 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:41Z] INFO  17:41:39,341 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:41Z] INFO  17:41:39,345 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_0_31019109-prep-prealign-realign.intervals -L 7:1-31019109 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpoaDr1q/2_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam
[2015-09-30T16:41Z] INFO  17:41:39,351 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:41Z] INFO  17:41:39,351 HelpFormatter - Date/Time: 2015/09/30 17:41:39
[2015-09-30T16:41Z] INFO  17:41:39,351 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:39,351 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:39,818 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:41Z] INFO  17:41:39,888 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:41Z] INFO  17:41:39,896 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:41Z] INFO  17:41:39,914 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:41Z] INFO  17:41:40,142 IntervalUtils - Processing 31019109 bp from intervals
[2015-09-30T16:41Z] WARN  17:41:40,150 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:41Z] INFO  17:41:40,212 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:41Z] INFO  17:41:40,355 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:41Z] INFO  17:41:40,355 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:41Z] INFO  17:41:40,356 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:41Z] INFO  17:41:40,356 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:41Z] INFO  17:41:40,500 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:41Z] INFO  17:41:40,693 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:41Z] INFO  17:41:42,902 ProgressMeter -            done   3.1562396E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T16:41Z] INFO  17:41:42,903 ProgressMeter - Total runtime 25.16 secs, 0.42 min, 0.01 hours
[2015-09-30T16:41Z] INFO  17:41:42,906 MicroScheduler - 73192 reads were filtered out during the traversal out of approximately 701372 total reads (10.44%)
[2015-09-30T16:41Z] INFO  17:41:42,906 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:41Z] INFO  17:41:42,906 MicroScheduler -   -> 9528 reads (1.36% of total) failing BadMateFilter
[2015-09-30T16:41Z] INFO  17:41:42,907 MicroScheduler -   -> 31206 reads (4.45% of total) failing DuplicateReadFilter
[2015-09-30T16:41Z] INFO  17:41:42,907 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:41Z] INFO  17:41:42,907 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:41Z] INFO  17:41:42,907 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:41Z] INFO  17:41:42,907 MicroScheduler -   -> 32458 reads (4.63% of total) failing MappingQualityZeroFilter
[2015-09-30T16:41Z] INFO  17:41:42,908 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:41Z] INFO  17:41:42,908 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:41Z] INFO  17:41:42,908 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:41Z] INFO  17:41:43,868 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:41Z] GATK: realign ('7', 31022897, 62585293) : syn3-tumor
[2015-09-30T16:41Z] INFO  17:41:45,681 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:45,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:41Z] INFO  17:41:45,684 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:41Z] INFO  17:41:45,684 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:41Z] INFO  17:41:45,687 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep-prealign-realign.intervals -L 7:31022898-62585293 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpHpZyjf/2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam
[2015-09-30T16:41Z] INFO  17:41:45,693 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:41Z] INFO  17:41:45,693 HelpFormatter - Date/Time: 2015/09/30 17:41:45
[2015-09-30T16:41Z] INFO  17:41:45,693 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:45,694 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:41Z] INFO  17:41:46,364 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:41Z] INFO  17:41:46,430 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:41Z] INFO  17:41:46,437 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:41Z] INFO  17:41:46,454 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:41Z] INFO  17:41:46,686 IntervalUtils - Processing 31562396 bp from intervals
[2015-09-30T16:41Z] WARN  17:41:46,690 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:41Z] INFO  17:41:46,745 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:41Z] INFO  17:41:46,877 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:41Z] INFO  17:41:46,877 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:41Z] INFO  17:41:46,878 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:41Z] INFO  17:41:46,878 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:41Z] INFO  17:41:47,011 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:41Z] INFO  17:41:47,201 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:41Z] INFO  17:41:48,566 ProgressMeter -      7:76033799    500007.0    60.0 s     120.0 s       42.7%     2.3 m      80.0 s
[2015-09-30T16:42Z] INFO  17:42:10,474 ProgressMeter -       7:8301756    500006.0    30.0 s      60.0 s       26.8%   112.0 s      82.0 s
[2015-09-30T16:42Z] INFO  17:42:17,109 ProgressMeter -      7:50450711    500008.0    30.0 s      60.0 s       61.6%    48.0 s      18.0 s
[2015-09-30T16:42Z] INFO  17:42:20,647 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:42Z] INFO  17:42:21,030 ProgressMeter -            done    884631.0    92.0 s     104.0 s      100.0%    92.0 s       0.0 s
[2015-09-30T16:42Z] INFO  17:42:21,030 ProgressMeter - Total runtime 92.53 secs, 1.54 min, 0.03 hours
[2015-09-30T16:42Z] INFO  17:42:21,031 MicroScheduler - 2496 reads were filtered out during the traversal out of approximately 887127 total reads (0.28%)
[2015-09-30T16:42Z] INFO  17:42:21,031 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:42Z] INFO  17:42:21,031 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:42Z] INFO  17:42:21,031 MicroScheduler -   -> 2496 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:42Z] INFO  17:42:21,059 ProgressMeter -            done    697529.0    34.0 s      49.0 s      100.0%    34.0 s       0.0 s
[2015-09-30T16:42Z] INFO  17:42:21,060 ProgressMeter - Total runtime 34.18 secs, 0.57 min, 0.01 hours
[2015-09-30T16:42Z] INFO  17:42:21,063 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 697529 total reads (0.00%)
[2015-09-30T16:42Z] INFO  17:42:21,063 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:42Z] INFO  17:42:21,063 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:42Z] INFO  17:42:21,064 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:42Z] INFO  17:42:22,081 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:42Z] INFO  17:42:22,115 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:42Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam
[2015-09-30T16:42Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam
[2015-09-30T16:42Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam 7:62708319-93925745
[2015-09-30T16:42Z] GATK: RealignerTargetCreator
[2015-09-30T16:42Z] GATK pre-alignment ('7', 94024041, 125680568) : syn3-tumor
[2015-09-30T16:42Z] INFO  17:42:25,988 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:25,990 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:42Z] INFO  17:42:25,990 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:42Z] INFO  17:42:25,991 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:42Z] INFO  17:42:25,994 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmp_FBMPa/2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign-realign.intervals -l INFO -L 7:62708319-93925745 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:42Z] INFO  17:42:25,999 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:42Z] INFO  17:42:26,000 HelpFormatter - Date/Time: 2015/09/30 17:42:25
[2015-09-30T16:42Z] INFO  17:42:26,000 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:26,000 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:26,048 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:26,050 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:42Z] INFO  17:42:26,051 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:42Z] INFO  17:42:26,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:42Z] INFO  17:42:26,054 HelpFormatter - Program Args: -T PrintReads -L 7:94024042-125680568 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmp1K3pSL/2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam
[2015-09-30T16:42Z] INFO  17:42:26,056 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:42Z] INFO  17:42:26,060 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:42Z] INFO  17:42:26,060 HelpFormatter - Date/Time: 2015/09/30 17:42:26
[2015-09-30T16:42Z] INFO  17:42:26,060 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:26,060 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:26,281 ProgressMeter -            done    944287.0    45.0 s      48.0 s      100.0%    45.0 s       0.0 s
[2015-09-30T16:42Z] INFO  17:42:26,281 ProgressMeter - Total runtime 45.93 secs, 0.77 min, 0.01 hours
[2015-09-30T16:42Z] INFO  17:42:26,285 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 944287 total reads (0.00%)
[2015-09-30T16:42Z] INFO  17:42:26,285 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:42Z] INFO  17:42:26,286 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:42Z] INFO  17:42:26,286 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:42Z] INFO  17:42:27,141 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:42Z] INFO  17:42:27,149 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:42Z] INFO  17:42:27,165 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:42Z] INFO  17:42:27,182 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:42Z] INFO  17:42:27,392 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:42Z] INFO  17:42:27,408 IntervalUtils - Processing 31217427 bp from intervals
[2015-09-30T16:42Z] WARN  17:42:27,412 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:42Z] INFO  17:42:27,469 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:42Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam
[2015-09-30T16:42Z] INFO  17:42:27,772 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:42Z] INFO  17:42:27,772 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:42Z] INFO  17:42:27,772 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:42Z] INFO  17:42:27,773 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:42Z] INFO  17:42:27,871 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:42Z] INFO  17:42:27,921 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:42Z] INFO  17:42:27,929 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:42Z] INFO  17:42:27,944 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:42Z] INFO  17:42:27,957 IntervalUtils - Processing 31656527 bp from intervals
[2015-09-30T16:42Z] INFO  17:42:28,029 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:42Z] INFO  17:42:28,287 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:42Z] INFO  17:42:28,287 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:42Z] INFO  17:42:28,288 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:42Z] INFO  17:42:28,288 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:42Z] INFO  17:42:28,299 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:42Z] INFO  17:42:28,661 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:42Z] GATK pre-alignment ('7', 126078434, 157151579) : syn3-tumor
[2015-09-30T16:42Z] INFO  17:42:31,553 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:31,555 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:42Z] INFO  17:42:31,555 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:42Z] INFO  17:42:31,555 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:42Z] INFO  17:42:31,558 HelpFormatter - Program Args: -T PrintReads -L 7:126078435-157151579 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpvcjvMZ/2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam
[2015-09-30T16:42Z] INFO  17:42:31,564 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:42Z] INFO  17:42:31,564 HelpFormatter - Date/Time: 2015/09/30 17:42:31
[2015-09-30T16:42Z] INFO  17:42:31,565 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:31,565 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:31,675 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:42Z] INFO  17:42:33,063 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:42Z] INFO  17:42:33,113 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:42Z] INFO  17:42:33,121 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:42Z] INFO  17:42:33,135 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:42Z] INFO  17:42:33,149 IntervalUtils - Processing 31073145 bp from intervals
[2015-09-30T16:42Z] INFO  17:42:33,205 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:42Z] INFO  17:42:33,582 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:42Z] INFO  17:42:33,583 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:42Z] INFO  17:42:33,583 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:42Z] INFO  17:42:33,583 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:42Z] INFO  17:42:33,595 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:42Z] INFO  17:42:33,821 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:42Z] INFO  17:42:55,108 ProgressMeter -            done   3.1217427E7    27.0 s       0.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T16:42Z] INFO  17:42:55,109 ProgressMeter - Total runtime 27.34 secs, 0.46 min, 0.01 hours
[2015-09-30T16:42Z] INFO  17:42:55,112 MicroScheduler - 203719 reads were filtered out during the traversal out of approximately 889340 total reads (22.91%)
[2015-09-30T16:42Z] INFO  17:42:55,112 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:42Z] INFO  17:42:55,112 MicroScheduler -   -> 9942 reads (1.12% of total) failing BadMateFilter
[2015-09-30T16:42Z] INFO  17:42:55,112 MicroScheduler -   -> 33046 reads (3.72% of total) failing DuplicateReadFilter
[2015-09-30T16:42Z] INFO  17:42:55,113 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:42Z] INFO  17:42:55,113 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:42Z] INFO  17:42:55,113 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:42Z] INFO  17:42:55,113 MicroScheduler -   -> 160731 reads (18.07% of total) failing MappingQualityZeroFilter
[2015-09-30T16:42Z] INFO  17:42:55,114 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:42Z] INFO  17:42:55,114 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:42Z] INFO  17:42:55,114 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:42Z] INFO  17:42:56,066 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:42Z] GATK: realign ('7', 62708318, 93925745) : syn3-tumor
[2015-09-30T16:42Z] INFO  17:42:57,649 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:57,651 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:42Z] INFO  17:42:57,651 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:42Z] INFO  17:42:57,651 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:42Z] INFO  17:42:57,655 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep-prealign-realign.intervals -L 7:62708319-93925745 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpZh15RG/2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam
[2015-09-30T16:42Z] INFO  17:42:57,660 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:42Z] INFO  17:42:57,661 HelpFormatter - Date/Time: 2015/09/30 17:42:57
[2015-09-30T16:42Z] INFO  17:42:57,661 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:57,661 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:42Z] INFO  17:42:57,764 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:42Z] INFO  17:42:57,831 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:42Z] INFO  17:42:57,838 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:42Z] INFO  17:42:57,854 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:42Z] INFO  17:42:58,077 IntervalUtils - Processing 31217427 bp from intervals
[2015-09-30T16:42Z] WARN  17:42:58,081 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:42Z] INFO  17:42:58,136 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:42Z] INFO  17:42:58,274 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:42Z] INFO  17:42:58,274 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:42Z] INFO  17:42:58,275 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:42Z] INFO  17:42:58,275 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:42Z] INFO  17:42:58,419 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:42Z] INFO  17:42:58,508 ProgressMeter -      7:99425715    200002.0    30.0 s       2.5 m       17.1%     2.9 m       2.4 m
[2015-09-30T16:42Z] INFO  17:42:58,602 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:43Z] INFO  17:43:03,596 ProgressMeter -     7:130417617    200003.0    30.0 s       2.5 m       14.0%     3.6 m       3.1 m
[2015-09-30T16:43Z] INFO  17:43:28,390 ProgressMeter -      7:75166599    400006.0    30.0 s      75.0 s       39.9%    75.0 s      45.0 s
[2015-09-30T16:43Z] INFO  17:43:28,668 ProgressMeter -     7:100884540    500007.0    60.0 s     120.0 s       21.7%     4.6 m       3.6 m
[2015-09-30T16:43Z] INFO  17:43:33,597 ProgressMeter -     7:141137982    500008.0    60.0 s     120.0 s       48.5%     2.1 m      63.0 s
[2015-09-30T16:43Z] INFO  17:43:43,085 ProgressMeter -            done    884631.0    44.0 s      50.0 s      100.0%    44.0 s       0.0 s
[2015-09-30T16:43Z] INFO  17:43:43,085 ProgressMeter - Total runtime 44.81 secs, 0.75 min, 0.01 hours
[2015-09-30T16:43Z] INFO  17:43:43,088 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 884631 total reads (0.00%)
[2015-09-30T16:43Z] INFO  17:43:43,089 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:43Z] INFO  17:43:43,089 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:43Z] INFO  17:43:43,089 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:43Z] INFO  17:43:44,225 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:43Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam
[2015-09-30T16:43Z] GATK pre-alignment ('7', 157155595, 159138663) : syn3-tumor
[2015-09-30T16:43Z] INFO  17:43:48,655 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:43Z] INFO  17:43:48,657 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:43Z] INFO  17:43:48,657 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:43Z] INFO  17:43:48,657 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:43Z] INFO  17:43:48,661 HelpFormatter - Program Args: -T PrintReads -L 7:157155596-159138663 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpVkBGAt/2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam
[2015-09-30T16:43Z] INFO  17:43:48,666 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:43Z] INFO  17:43:48,666 HelpFormatter - Date/Time: 2015/09/30 17:43:48
[2015-09-30T16:43Z] INFO  17:43:48,666 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:43Z] INFO  17:43:48,666 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:43Z] INFO  17:43:48,771 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:43Z] INFO  17:43:49,552 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:43Z] INFO  17:43:49,606 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:43Z] INFO  17:43:49,614 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:43Z] INFO  17:43:49,628 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:43Z] INFO  17:43:49,640 IntervalUtils - Processing 1983068 bp from intervals
[2015-09-30T16:43Z] INFO  17:43:49,695 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:43Z] INFO  17:43:49,810 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:43Z] INFO  17:43:49,810 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:43Z] INFO  17:43:49,811 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:43Z] INFO  17:43:49,811 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:43Z] INFO  17:43:49,821 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:43Z] INFO  17:43:49,838 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:43Z] INFO  17:43:58,669 ProgressMeter -     7:106921497    800011.0    90.0 s     112.0 s       40.7%     3.7 m       2.2 m
[2015-09-30T16:43Z] INFO  17:43:59,526 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:43Z] INFO  17:43:59,603 ProgressMeter -            done     77572.0     9.0 s       2.1 m       89.9%    10.0 s       1.0 s
[2015-09-30T16:43Z] INFO  17:43:59,603 ProgressMeter - Total runtime 9.79 secs, 0.16 min, 0.00 hours
[2015-09-30T16:43Z] INFO  17:43:59,603 MicroScheduler - 211 reads were filtered out during the traversal out of approximately 77783 total reads (0.27%)
[2015-09-30T16:43Z] INFO  17:43:59,604 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:43Z] INFO  17:43:59,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:43Z] INFO  17:43:59,604 MicroScheduler -   -> 211 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:44Z] INFO  17:44:00,596 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:44Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam
[2015-09-30T16:44Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam 7:157155596-159138663
[2015-09-30T16:44Z] GATK: RealignerTargetCreator
[2015-09-30T16:44Z] INFO  17:44:02,482 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:02,484 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:44Z] INFO  17:44:02,484 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:44Z] INFO  17:44:02,484 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:44Z] INFO  17:44:02,488 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpBROoFE/2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign-realign.intervals -l INFO -L 7:157155596-159138663 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:44Z] INFO  17:44:02,492 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:44Z] INFO  17:44:02,493 HelpFormatter - Date/Time: 2015/09/30 17:44:02
[2015-09-30T16:44Z] INFO  17:44:02,493 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:02,493 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:02,545 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:44Z] INFO  17:44:02,650 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:44Z] INFO  17:44:02,657 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:44Z] INFO  17:44:02,672 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:44Z] INFO  17:44:02,909 IntervalUtils - Processing 1983068 bp from intervals
[2015-09-30T16:44Z] WARN  17:44:02,913 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:44Z] INFO  17:44:02,966 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:44Z] INFO  17:44:03,318 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:44Z] INFO  17:44:03,318 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:44Z] INFO  17:44:03,319 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:44Z] INFO  17:44:03,319 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:44Z] INFO  17:44:04,369 ProgressMeter -     7:148709339    800011.0    90.0 s     113.0 s       72.8%     2.1 m      33.0 s
[2015-09-30T16:44Z] INFO  17:44:07,426 ProgressMeter -            done   1983068.0     4.0 s       2.0 s      100.0%     4.0 s       0.0 s
[2015-09-30T16:44Z] INFO  17:44:07,426 ProgressMeter - Total runtime 4.11 secs, 0.07 min, 0.00 hours
[2015-09-30T16:44Z] INFO  17:44:07,429 MicroScheduler - 6740 reads were filtered out during the traversal out of approximately 77887 total reads (8.65%)
[2015-09-30T16:44Z] INFO  17:44:07,429 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:44Z] INFO  17:44:07,430 MicroScheduler -   -> 868 reads (1.11% of total) failing BadMateFilter
[2015-09-30T16:44Z] INFO  17:44:07,430 MicroScheduler -   -> 3585 reads (4.60% of total) failing DuplicateReadFilter
[2015-09-30T16:44Z] INFO  17:44:07,430 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:44Z] INFO  17:44:07,430 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:44Z] INFO  17:44:07,430 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:44Z] INFO  17:44:07,431 MicroScheduler -   -> 2287 reads (2.94% of total) failing MappingQualityZeroFilter
[2015-09-30T16:44Z] INFO  17:44:07,431 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:44Z] INFO  17:44:07,431 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:44Z] INFO  17:44:07,431 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:44Z] INFO  17:44:08,385 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:44Z] GATK: realign ('7', 157155595, 159138663) : syn3-tumor
[2015-09-30T16:44Z] INFO  17:44:10,171 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:10,174 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:44Z] INFO  17:44:10,174 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:44Z] INFO  17:44:10,174 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:44Z] INFO  17:44:10,178 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep-prealign-realign.intervals -L 7:157155596-159138663 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpnTVjeB/2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam
[2015-09-30T16:44Z] INFO  17:44:10,183 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:44Z] INFO  17:44:10,183 HelpFormatter - Date/Time: 2015/09/30 17:44:10
[2015-09-30T16:44Z] INFO  17:44:10,184 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:10,184 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:10,290 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:44Z] INFO  17:44:10,367 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:44Z] INFO  17:44:10,375 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:44Z] INFO  17:44:10,393 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:44Z] INFO  17:44:10,610 IntervalUtils - Processing 1983068 bp from intervals
[2015-09-30T16:44Z] WARN  17:44:10,614 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:44Z] INFO  17:44:10,668 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:44Z] INFO  17:44:10,726 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:44Z] INFO  17:44:10,727 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:44Z] INFO  17:44:10,727 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:44Z] INFO  17:44:10,728 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:44Z] INFO  17:44:10,784 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:44Z] INFO  17:44:10,800 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:44Z] INFO  17:44:16,136 ProgressMeter -            done     77572.0     5.0 s      69.0 s       89.9%     5.0 s       0.0 s
[2015-09-30T16:44Z] INFO  17:44:16,136 ProgressMeter - Total runtime 5.41 secs, 0.09 min, 0.00 hours
[2015-09-30T16:44Z] INFO  17:44:16,139 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 77572 total reads (0.00%)
[2015-09-30T16:44Z] INFO  17:44:16,140 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:44Z] INFO  17:44:16,140 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:44Z] INFO  17:44:16,140 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:44Z] INFO  17:44:17,144 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:44Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam
[2015-09-30T16:44Z] GATK pre-alignment ('8', 0, 31024990) : syn3-tumor
[2015-09-30T16:44Z] INFO  17:44:19,448 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:19,451 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:44Z] INFO  17:44:19,451 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:44Z] INFO  17:44:19,451 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:44Z] INFO  17:44:19,454 HelpFormatter - Program Args: -T PrintReads -L 8:1-31024990 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmp3hxn85/2_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam
[2015-09-30T16:44Z] INFO  17:44:19,462 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:44Z] INFO  17:44:19,462 HelpFormatter - Date/Time: 2015/09/30 17:44:19
[2015-09-30T16:44Z] INFO  17:44:19,463 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:19,463 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:19,874 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:44Z] INFO  17:44:20,561 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:44Z] INFO  17:44:20,611 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:44Z] INFO  17:44:20,619 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:44Z] INFO  17:44:20,634 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:44Z] INFO  17:44:20,647 IntervalUtils - Processing 31024990 bp from intervals
[2015-09-30T16:44Z] INFO  17:44:20,706 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:44Z] INFO  17:44:20,908 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:44Z] INFO  17:44:20,909 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:44Z] INFO  17:44:20,909 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:44Z] INFO  17:44:20,909 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:44Z] INFO  17:44:20,920 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:44Z] INFO  17:44:21,120 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:44Z] INFO  17:44:26,082 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:44Z] INFO  17:44:26,274 ProgressMeter -            done   1175888.0   117.0 s     100.0 s      100.0%   117.0 s       0.0 s
[2015-09-30T16:44Z] INFO  17:44:26,275 ProgressMeter - Total runtime 117.99 secs, 1.97 min, 0.03 hours
[2015-09-30T16:44Z] INFO  17:44:26,275 MicroScheduler - 3029 reads were filtered out during the traversal out of approximately 1178917 total reads (0.26%)
[2015-09-30T16:44Z] INFO  17:44:26,275 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:44Z] INFO  17:44:26,275 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:44Z] INFO  17:44:26,276 MicroScheduler -   -> 3029 reads (0.26% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:44Z] INFO  17:44:27,314 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:44Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam
[2015-09-30T16:44Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam 7:94024042-125680568
[2015-09-30T16:44Z] GATK: RealignerTargetCreator
[2015-09-30T16:44Z] INFO  17:44:31,915 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:31,917 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:44Z] INFO  17:44:31,917 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:44Z] INFO  17:44:31,917 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:44Z] INFO  17:44:31,921 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpTgyDac/2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign-realign.intervals -l INFO -L 7:94024042-125680568 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:44Z] INFO  17:44:31,926 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:44Z] INFO  17:44:31,927 HelpFormatter - Date/Time: 2015/09/30 17:44:31
[2015-09-30T16:44Z] INFO  17:44:31,927 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:31,927 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:31,984 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:44Z] INFO  17:44:32,093 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:44Z] INFO  17:44:32,100 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:44Z] INFO  17:44:32,116 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:44Z] INFO  17:44:32,370 IntervalUtils - Processing 31656527 bp from intervals
[2015-09-30T16:44Z] WARN  17:44:32,374 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:44Z] INFO  17:44:32,431 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:44Z] INFO  17:44:32,826 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:44Z] INFO  17:44:32,826 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:44Z] INFO  17:44:32,827 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:44Z] INFO  17:44:32,827 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:44Z] INFO  17:44:34,461 ProgressMeter -     7:152520814   1200015.0   120.0 s     100.0 s       85.1%     2.4 m      21.0 s
[2015-09-30T16:44Z] INFO  17:44:42,865 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:44Z] INFO  17:44:43,066 ProgressMeter -            done   1297808.0     2.2 m      99.0 s      100.0%     2.2 m       0.0 s
[2015-09-30T16:44Z] INFO  17:44:43,067 ProgressMeter - Total runtime 129.48 secs, 2.16 min, 0.04 hours
[2015-09-30T16:44Z] INFO  17:44:43,067 MicroScheduler - 2598 reads were filtered out during the traversal out of approximately 1300406 total reads (0.20%)
[2015-09-30T16:44Z] INFO  17:44:43,067 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:44Z] INFO  17:44:43,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:44Z] INFO  17:44:43,068 MicroScheduler -   -> 2598 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:44Z] INFO  17:44:44,084 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:44Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam
[2015-09-30T16:44Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam 7:126078435-157151579
[2015-09-30T16:44Z] GATK: RealignerTargetCreator
[2015-09-30T16:44Z] INFO  17:44:48,991 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:48,993 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:44Z] INFO  17:44:48,993 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:44Z] INFO  17:44:48,993 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:44Z] INFO  17:44:48,997 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpuef2mO/2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign-realign.intervals -l INFO -L 7:126078435-157151579 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:44Z] INFO  17:44:49,002 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:44Z] INFO  17:44:49,003 HelpFormatter - Date/Time: 2015/09/30 17:44:48
[2015-09-30T16:44Z] INFO  17:44:49,003 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:49,003 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:44Z] INFO  17:44:49,058 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:44Z] INFO  17:44:49,166 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:44Z] INFO  17:44:49,173 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:44Z] INFO  17:44:49,188 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:44Z] INFO  17:44:50,350 IntervalUtils - Processing 31073145 bp from intervals
[2015-09-30T16:44Z] WARN  17:44:50,354 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:44Z] INFO  17:44:50,412 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:44Z] INFO  17:44:50,608 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:44Z] INFO  17:44:50,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:44Z] INFO  17:44:50,609 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:44Z] INFO  17:44:50,609 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:44Z] INFO  17:44:50,937 ProgressMeter -      8:11281666    200002.0    30.0 s       2.5 m       36.4%    82.0 s      52.0 s
[2015-09-30T16:45Z] INFO  17:45:02,831 ProgressMeter -     7:123045041   2.9019799E7    30.0 s       1.0 s       91.7%    32.0 s       2.0 s
[2015-09-30T16:45Z] INFO  17:45:04,579 ProgressMeter -            done   3.1656527E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T16:45Z] INFO  17:45:04,580 ProgressMeter - Total runtime 31.75 secs, 0.53 min, 0.01 hours
[2015-09-30T16:45Z] INFO  17:45:04,580 MicroScheduler - 186496 reads were filtered out during the traversal out of approximately 1182863 total reads (15.77%)
[2015-09-30T16:45Z] INFO  17:45:04,580 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:45Z] INFO  17:45:04,581 MicroScheduler -   -> 13059 reads (1.10% of total) failing BadMateFilter
[2015-09-30T16:45Z] INFO  17:45:04,581 MicroScheduler -   -> 51602 reads (4.36% of total) failing DuplicateReadFilter
[2015-09-30T16:45Z] INFO  17:45:04,581 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:45Z] INFO  17:45:04,581 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:45Z] INFO  17:45:04,582 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:45Z] INFO  17:45:04,582 MicroScheduler -   -> 121835 reads (10.30% of total) failing MappingQualityZeroFilter
[2015-09-30T16:45Z] INFO  17:45:04,582 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:45Z] INFO  17:45:04,582 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:45Z] INFO  17:45:04,582 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:45Z] INFO  17:45:05,639 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:45Z] GATK: realign ('7', 94024041, 125680568) : syn3-tumor
[2015-09-30T16:45Z] INFO  17:45:07,181 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:45Z] INFO  17:45:07,183 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:45Z] INFO  17:45:07,183 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:45Z] INFO  17:45:07,183 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:45Z] INFO  17:45:07,187 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep-prealign-realign.intervals -L 7:94024042-125680568 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmphDmPAb/2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam
[2015-09-30T16:45Z] INFO  17:45:07,192 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:45Z] INFO  17:45:07,192 HelpFormatter - Date/Time: 2015/09/30 17:45:07
[2015-09-30T16:45Z] INFO  17:45:07,193 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:45Z] INFO  17:45:07,193 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:45Z] INFO  17:45:07,627 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:45Z] INFO  17:45:07,691 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:45Z] INFO  17:45:07,698 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:45Z] INFO  17:45:07,714 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:45Z] INFO  17:45:07,941 IntervalUtils - Processing 31656527 bp from intervals
[2015-09-30T16:45Z] WARN  17:45:07,945 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:45Z] INFO  17:45:08,000 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:45Z] INFO  17:45:08,151 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:45Z] INFO  17:45:08,151 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:45Z] INFO  17:45:08,152 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:45Z] INFO  17:45:08,152 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:45Z] INFO  17:45:08,295 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:45Z] INFO  17:45:08,479 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:45Z] INFO  17:45:20,612 ProgressMeter -     7:151432529   2.5342494E7    30.0 s       1.0 s       81.6%    36.0 s       6.0 s
[2015-09-30T16:45Z] INFO  17:45:20,965 ProgressMeter -      8:22443310    500006.0    60.0 s     120.0 s       72.3%    82.0 s      22.0 s
[2015-09-30T16:45Z] INFO  17:45:25,806 ProgressMeter -            done   3.1073145E7    35.0 s       1.0 s      100.0%    35.0 s       0.0 s
[2015-09-30T16:45Z] INFO  17:45:25,806 ProgressMeter - Total runtime 35.20 secs, 0.59 min, 0.01 hours
[2015-09-30T16:45Z] INFO  17:45:25,809 MicroScheduler - 152172 reads were filtered out during the traversal out of approximately 1306377 total reads (11.65%)
[2015-09-30T16:45Z] INFO  17:45:25,810 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:45Z] INFO  17:45:25,810 MicroScheduler -   -> 13250 reads (1.01% of total) failing BadMateFilter
[2015-09-30T16:45Z] INFO  17:45:25,810 MicroScheduler -   -> 59479 reads (4.55% of total) failing DuplicateReadFilter
[2015-09-30T16:45Z] INFO  17:45:25,810 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:45Z] INFO  17:45:25,811 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:45Z] INFO  17:45:25,811 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:45Z] INFO  17:45:25,811 MicroScheduler -   -> 79443 reads (6.08% of total) failing MappingQualityZeroFilter
[2015-09-30T16:45Z] INFO  17:45:25,811 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:45Z] INFO  17:45:25,811 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:45Z] INFO  17:45:25,812 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:45Z] INFO  17:45:26,784 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:45Z] GATK: realign ('7', 126078434, 157151579) : syn3-tumor
[2015-09-30T16:45Z] INFO  17:45:28,997 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:45Z] INFO  17:45:28,999 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:45Z] INFO  17:45:28,999 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:45Z] INFO  17:45:28,999 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:45Z] INFO  17:45:29,002 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep-prealign-realign.intervals -L 7:126078435-157151579 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/tx/tmpil5Lxz/2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam
[2015-09-30T16:45Z] INFO  17:45:29,008 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:45Z] INFO  17:45:29,008 HelpFormatter - Date/Time: 2015/09/30 17:45:28
[2015-09-30T16:45Z] INFO  17:45:29,008 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:45Z] INFO  17:45:29,008 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:45Z] INFO  17:45:29,135 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:45Z] INFO  17:45:29,601 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:45Z] INFO  17:45:29,608 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:45Z] INFO  17:45:29,623 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:45Z] INFO  17:45:29,846 IntervalUtils - Processing 31073145 bp from intervals
[2015-09-30T16:45Z] WARN  17:45:29,850 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:45Z] INFO  17:45:29,974 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:45Z] INFO  17:45:30,169 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:45Z] INFO  17:45:30,169 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:45Z] INFO  17:45:30,170 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:45Z] INFO  17:45:30,170 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:45Z] INFO  17:45:30,312 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:45Z] INFO  17:45:30,508 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:45Z] INFO  17:45:40,171 ProgressMeter -     7:100642217    400004.0    32.0 s      80.0 s       20.9%     2.6 m       2.0 m
[2015-09-30T16:45Z] INFO  17:45:51,212 ProgressMeter -      8:30890312    900011.0    90.0 s     100.0 s       99.6%    90.0 s       0.0 s
[2015-09-30T16:45Z] INFO  17:45:51,843 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:45Z] INFO  17:45:52,061 ProgressMeter -            done    933719.0    91.0 s      97.0 s      100.0%    91.0 s       0.0 s
[2015-09-30T16:45Z] INFO  17:45:52,061 ProgressMeter - Total runtime 91.15 secs, 1.52 min, 0.03 hours
[2015-09-30T16:45Z] INFO  17:45:52,061 MicroScheduler - 2190 reads were filtered out during the traversal out of approximately 935909 total reads (0.23%)
[2015-09-30T16:45Z] INFO  17:45:52,062 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:45Z] INFO  17:45:52,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:45Z] INFO  17:45:52,062 MicroScheduler -   -> 2190 reads (0.23% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:45Z] INFO  17:45:53,050 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:45Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam
[2015-09-30T16:45Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam 8:1-31024990
[2015-09-30T16:45Z] GATK: RealignerTargetCreator
[2015-09-30T16:45Z] INFO  17:45:58,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:45Z] INFO  17:45:58,086 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:45Z] INFO  17:45:58,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:45Z] INFO  17:45:58,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:45Z] INFO  17:45:58,090 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpynyjcx/2_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign-realign.intervals -l INFO -L 8:1-31024990 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:45Z] INFO  17:45:58,095 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:45Z] INFO  17:45:58,096 HelpFormatter - Date/Time: 2015/09/30 17:45:58
[2015-09-30T16:45Z] INFO  17:45:58,096 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:45Z] INFO  17:45:58,096 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:45Z] INFO  17:45:58,155 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:45Z] INFO  17:45:58,264 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:45Z] INFO  17:45:58,275 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:45Z] INFO  17:45:58,290 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:45Z] INFO  17:45:58,550 IntervalUtils - Processing 31024990 bp from intervals
[2015-09-30T16:45Z] WARN  17:45:58,554 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:45Z] INFO  17:45:58,611 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:45Z] INFO  17:45:58,762 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:45Z] INFO  17:45:58,762 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:45Z] INFO  17:45:58,763 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:45Z] INFO  17:45:58,763 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:46Z] INFO  17:46:01,457 ProgressMeter -     7:141414086    500008.0    31.0 s      62.0 s       49.4%    62.0 s      31.0 s
[2015-09-30T16:46Z] INFO  17:46:06,522 ProgressMeter -            done   1175888.0    58.0 s      49.0 s      100.0%    58.0 s       0.0 s
[2015-09-30T16:46Z] INFO  17:46:06,522 ProgressMeter - Total runtime 58.37 secs, 0.97 min, 0.02 hours
[2015-09-30T16:46Z] INFO  17:46:06,525 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1175888 total reads (0.00%)
[2015-09-30T16:46Z] INFO  17:46:06,526 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:46Z] INFO  17:46:06,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:46Z] INFO  17:46:06,526 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:46Z] INFO  17:46:07,684 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:46Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam
[2015-09-30T16:46Z] GATK pre-alignment ('8', 31030285, 62213090) : syn3-tumor
[2015-09-30T16:46Z] INFO  17:46:12,528 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:46Z] INFO  17:46:12,531 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:46Z] INFO  17:46:12,531 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:46Z] INFO  17:46:12,531 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:46Z] INFO  17:46:12,535 HelpFormatter - Program Args: -T PrintReads -L 8:31030286-62213090 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmp6ojMc2/2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam
[2015-09-30T16:46Z] INFO  17:46:12,540 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:46Z] INFO  17:46:12,540 HelpFormatter - Date/Time: 2015/09/30 17:46:12
[2015-09-30T16:46Z] INFO  17:46:12,541 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:46Z] INFO  17:46:12,541 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:46Z] INFO  17:46:13,607 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:46Z] INFO  17:46:14,312 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:46Z] INFO  17:46:14,362 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:46Z] INFO  17:46:14,370 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:46Z] INFO  17:46:14,385 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:46Z] INFO  17:46:14,398 IntervalUtils - Processing 31182805 bp from intervals
[2015-09-30T16:46Z] INFO  17:46:14,457 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:46Z] INFO  17:46:14,653 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:46Z] INFO  17:46:14,654 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:46Z] INFO  17:46:14,654 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:46Z] INFO  17:46:14,654 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:46Z] INFO  17:46:14,665 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:46Z] INFO  17:46:14,854 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:46Z] INFO  17:46:28,280 ProgressMeter -            done   3.102499E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T16:46Z] INFO  17:46:28,281 ProgressMeter - Total runtime 29.52 secs, 0.49 min, 0.01 hours
[2015-09-30T16:46Z] INFO  17:46:28,284 MicroScheduler - 135253 reads were filtered out during the traversal out of approximately 940388 total reads (14.38%)
[2015-09-30T16:46Z] INFO  17:46:28,284 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:46Z] INFO  17:46:28,284 MicroScheduler -   -> 10667 reads (1.13% of total) failing BadMateFilter
[2015-09-30T16:46Z] INFO  17:46:28,285 MicroScheduler -   -> 40427 reads (4.30% of total) failing DuplicateReadFilter
[2015-09-30T16:46Z] INFO  17:46:28,285 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:46Z] INFO  17:46:28,285 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:46Z] INFO  17:46:28,285 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:46Z] INFO  17:46:28,286 MicroScheduler -   -> 84159 reads (8.95% of total) failing MappingQualityZeroFilter
[2015-09-30T16:46Z] INFO  17:46:28,286 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:46Z] INFO  17:46:28,286 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:46Z] INFO  17:46:28,286 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:46Z] INFO  17:46:29,286 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:46Z] GATK: realign ('8', 0, 31024990) : syn3-tumor
[2015-09-30T16:46Z] INFO  17:46:30,323 ProgressMeter -            done   1297808.0    60.0 s      46.0 s      100.0%    60.0 s       0.0 s
[2015-09-30T16:46Z] INFO  17:46:30,323 ProgressMeter - Total runtime 60.15 secs, 1.00 min, 0.02 hours
[2015-09-30T16:46Z] INFO  17:46:30,326 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1297808 total reads (0.00%)
[2015-09-30T16:46Z] INFO  17:46:30,327 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:46Z] INFO  17:46:30,327 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:46Z] INFO  17:46:30,327 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:46Z] INFO  17:46:31,151 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:46Z] INFO  17:46:31,153 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:46Z] INFO  17:46:31,153 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:46Z] INFO  17:46:31,153 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:46Z] INFO  17:46:31,157 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_0_31024990-prep-prealign-realign.intervals -L 8:1-31024990 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmprsCAkq/2_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam
[2015-09-30T16:46Z] INFO  17:46:31,162 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:46Z] INFO  17:46:31,162 HelpFormatter - Date/Time: 2015/09/30 17:46:31
[2015-09-30T16:46Z] INFO  17:46:31,162 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:46Z] INFO  17:46:31,163 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:46Z] INFO  17:46:31,287 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:46Z] INFO  17:46:31,353 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:46Z] INFO  17:46:31,361 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:46Z] INFO  17:46:31,378 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:46Z] INFO  17:46:31,448 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:46Z] INFO  17:46:31,600 IntervalUtils - Processing 31024990 bp from intervals
[2015-09-30T16:46Z] WARN  17:46:31,604 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:46Z] INFO  17:46:31,663 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:46Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam
[2015-09-30T16:46Z] INFO  17:46:31,817 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:46Z] INFO  17:46:31,818 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:46Z] INFO  17:46:31,818 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:46Z] INFO  17:46:31,819 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:46Z] INFO  17:46:31,989 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:46Z] INFO  17:46:32,193 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:46Z] GATK pre-alignment ('8', 62288979, 93648031) : syn3-tumor
[2015-09-30T16:46Z] INFO  17:46:37,039 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:46Z] INFO  17:46:37,042 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:46Z] INFO  17:46:37,042 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:46Z] INFO  17:46:37,042 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:46Z] INFO  17:46:37,045 HelpFormatter - Program Args: -T PrintReads -L 8:62288980-93648031 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpH1dfjG/2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam
[2015-09-30T16:46Z] INFO  17:46:37,051 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:46Z] INFO  17:46:37,051 HelpFormatter - Date/Time: 2015/09/30 17:46:37
[2015-09-30T16:46Z] INFO  17:46:37,052 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:46Z] INFO  17:46:37,052 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:46Z] INFO  17:46:37,161 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:46Z] INFO  17:46:39,092 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:46Z] INFO  17:46:39,142 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:46Z] INFO  17:46:39,149 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:46Z] INFO  17:46:41,009 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 1.86
[2015-09-30T16:46Z] INFO  17:46:41,028 IntervalUtils - Processing 31359052 bp from intervals
[2015-09-30T16:46Z] INFO  17:46:41,084 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:46Z] INFO  17:46:43,838 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:46Z] INFO  17:46:43,838 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:46Z] INFO  17:46:43,838 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:46Z] INFO  17:46:43,839 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:46Z] INFO  17:46:43,850 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:46Z] INFO  17:46:44,035 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:46Z] INFO  17:46:45,094 ProgressMeter -      8:41393739    200002.0    30.0 s       2.5 m       33.2%    90.0 s      60.0 s
[2015-09-30T16:47Z] INFO  17:47:01,821 ProgressMeter -      8:21998950    500006.0    30.0 s      60.0 s       70.9%    42.0 s      12.0 s
[2015-09-30T16:47Z] INFO  17:47:13,841 ProgressMeter -      8:79610378    200002.0    30.0 s       2.5 m       55.2%    54.0 s      24.0 s
[2015-09-30T16:47Z] INFO  17:47:15,098 ProgressMeter -      8:62212693    500006.0    60.0 s     120.0 s      100.0%    60.0 s       0.0 s
[2015-09-30T16:47Z] INFO  17:47:15,110 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:47Z] INFO  17:47:15,243 ProgressMeter -            done    521518.0    60.0 s     116.0 s      100.0%    60.0 s       0.0 s
[2015-09-30T16:47Z] INFO  17:47:15,243 ProgressMeter - Total runtime 60.59 secs, 1.01 min, 0.02 hours
[2015-09-30T16:47Z] INFO  17:47:15,244 MicroScheduler - 1524 reads were filtered out during the traversal out of approximately 523042 total reads (0.29%)
[2015-09-30T16:47Z] INFO  17:47:15,244 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:47Z] INFO  17:47:15,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:47Z] INFO  17:47:15,244 MicroScheduler -   -> 1524 reads (0.29% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:47Z] INFO  17:47:16,269 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:47Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam
[2015-09-30T16:47Z] INFO  17:47:17,121 ProgressMeter -            done    933719.0    45.0 s      48.0 s      100.0%    45.0 s       0.0 s
[2015-09-30T16:47Z] INFO  17:47:17,122 ProgressMeter - Total runtime 45.30 secs, 0.76 min, 0.01 hours
[2015-09-30T16:47Z] INFO  17:47:17,125 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 933719 total reads (0.00%)
[2015-09-30T16:47Z] INFO  17:47:17,125 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:47Z] INFO  17:47:17,126 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:47Z] INFO  17:47:17,126 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:47Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam 8:31030286-62213090
[2015-09-30T16:47Z] GATK: RealignerTargetCreator
[2015-09-30T16:47Z] INFO  17:47:18,278 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:47Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam
[2015-09-30T16:47Z] INFO  17:47:19,276 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:19,278 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:47Z] INFO  17:47:19,279 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:47Z] INFO  17:47:19,279 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:47Z] INFO  17:47:19,282 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmplSjiUa/2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign-realign.intervals -l INFO -L 8:31030286-62213090 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:47Z] INFO  17:47:19,288 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:47Z] INFO  17:47:19,289 HelpFormatter - Date/Time: 2015/09/30 17:47:19
[2015-09-30T16:47Z] INFO  17:47:19,289 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:19,289 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:19,360 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:47Z] INFO  17:47:19,506 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:47Z] INFO  17:47:19,514 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:47Z] INFO  17:47:19,530 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:47Z] INFO  17:47:20,165 IntervalUtils - Processing 31182805 bp from intervals
[2015-09-30T16:47Z] WARN  17:47:20,176 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:47Z] INFO  17:47:20,235 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:47Z] INFO  17:47:20,367 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:47Z] INFO  17:47:20,367 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:47Z] INFO  17:47:20,368 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:47Z] INFO  17:47:20,368 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:47Z] GATK pre-alignment ('8', 93896832, 124968568) : syn3-tumor
[2015-09-30T16:47Z] INFO  17:47:22,414 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:22,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:47Z] INFO  17:47:22,417 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:47Z] INFO  17:47:22,417 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:47Z] INFO  17:47:22,420 HelpFormatter - Program Args: -T PrintReads -L 8:93896833-124968568 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpmuZHc7/2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam
[2015-09-30T16:47Z] INFO  17:47:22,426 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:47Z] INFO  17:47:22,426 HelpFormatter - Date/Time: 2015/09/30 17:47:22
[2015-09-30T16:47Z] INFO  17:47:22,426 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:22,426 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:22,530 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:47Z] INFO  17:47:23,571 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:47Z] INFO  17:47:23,623 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:47Z] INFO  17:47:23,631 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:47Z] INFO  17:47:23,647 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:47Z] INFO  17:47:23,660 IntervalUtils - Processing 31071736 bp from intervals
[2015-09-30T16:47Z] INFO  17:47:23,721 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:47Z] INFO  17:47:23,929 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:47Z] INFO  17:47:23,930 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:47Z] INFO  17:47:23,930 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:47Z] INFO  17:47:23,930 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:47Z] INFO  17:47:23,942 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:47Z] INFO  17:47:24,147 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:47Z] INFO  17:47:42,420 ProgressMeter -            done   3.1182805E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T16:47Z] INFO  17:47:42,420 ProgressMeter - Total runtime 22.05 secs, 0.37 min, 0.01 hours
[2015-09-30T16:47Z] INFO  17:47:42,423 MicroScheduler - 41709 reads were filtered out during the traversal out of approximately 524474 total reads (7.95%)
[2015-09-30T16:47Z] INFO  17:47:42,424 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:47Z] INFO  17:47:42,424 MicroScheduler -   -> 8678 reads (1.65% of total) failing BadMateFilter
[2015-09-30T16:47Z] INFO  17:47:42,424 MicroScheduler -   -> 22729 reads (4.33% of total) failing DuplicateReadFilter
[2015-09-30T16:47Z] INFO  17:47:42,425 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:47Z] INFO  17:47:42,425 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:47Z] INFO  17:47:42,425 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:47Z] INFO  17:47:42,425 MicroScheduler -   -> 10302 reads (1.96% of total) failing MappingQualityZeroFilter
[2015-09-30T16:47Z] INFO  17:47:42,425 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:47Z] INFO  17:47:42,426 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:47Z] INFO  17:47:42,426 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:47Z] INFO  17:47:43,115 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:47Z] INFO  17:47:43,315 ProgressMeter -            done    573713.0    59.0 s     103.0 s      100.0%    59.0 s       0.0 s
[2015-09-30T16:47Z] INFO  17:47:43,315 ProgressMeter - Total runtime 59.48 secs, 0.99 min, 0.02 hours
[2015-09-30T16:47Z] INFO  17:47:43,315 MicroScheduler - 1553 reads were filtered out during the traversal out of approximately 575266 total reads (0.27%)
[2015-09-30T16:47Z] INFO  17:47:43,316 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:47Z] INFO  17:47:43,316 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:47Z] INFO  17:47:43,316 MicroScheduler -   -> 1553 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:47Z] INFO  17:47:43,454 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:47Z] GATK: realign ('8', 31030285, 62213090) : syn3-tumor
[2015-09-30T16:47Z] INFO  17:47:44,323 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:47Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam
[2015-09-30T16:47Z] INFO  17:47:45,173 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:45,175 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:47Z] INFO  17:47:45,176 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:47Z] INFO  17:47:45,176 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:47Z] INFO  17:47:45,179 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep-prealign-realign.intervals -L 8:31030286-62213090 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmp88x6B3/2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam
[2015-09-30T16:47Z] INFO  17:47:45,184 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:47Z] INFO  17:47:45,185 HelpFormatter - Date/Time: 2015/09/30 17:47:45
[2015-09-30T16:47Z] INFO  17:47:45,185 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:45,185 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:45,285 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:47Z] INFO  17:47:45,383 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:47Z] INFO  17:47:45,390 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:47Z] INFO  17:47:45,406 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:47Z] INFO  17:47:45,622 IntervalUtils - Processing 31182805 bp from intervals
[2015-09-30T16:47Z] WARN  17:47:45,625 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:47Z] INFO  17:47:45,677 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:47Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam 8:62288980-93648031
[2015-09-30T16:47Z] GATK: RealignerTargetCreator
[2015-09-30T16:47Z] INFO  17:47:45,819 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:47Z] INFO  17:47:45,819 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:47Z] INFO  17:47:45,820 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:47Z] INFO  17:47:45,820 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:47Z] INFO  17:47:45,953 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:47Z] INFO  17:47:46,130 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:47Z] INFO  17:47:47,654 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:47,657 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:47Z] INFO  17:47:47,657 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:47Z] INFO  17:47:47,657 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:47Z] INFO  17:47:47,660 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpewUNWb/2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign-realign.intervals -l INFO -L 8:62288980-93648031 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:47Z] INFO  17:47:47,666 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:47Z] INFO  17:47:47,666 HelpFormatter - Date/Time: 2015/09/30 17:47:47
[2015-09-30T16:47Z] INFO  17:47:47,667 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:47,667 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:47Z] INFO  17:47:47,724 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:47Z] INFO  17:47:50,162 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:47Z] INFO  17:47:50,170 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:47Z] INFO  17:47:50,187 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:47Z] INFO  17:47:50,660 IntervalUtils - Processing 31359052 bp from intervals
[2015-09-30T16:47Z] WARN  17:47:50,664 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:47Z] INFO  17:47:50,722 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:47Z] INFO  17:47:50,863 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:47Z] INFO  17:47:50,863 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:47Z] INFO  17:47:50,863 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:47Z] INFO  17:47:50,864 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:47Z] INFO  17:47:53,933 ProgressMeter -     8:103224586    200002.0    30.0 s       2.5 m       30.0%    99.0 s      69.0 s
[2015-09-30T16:48Z] INFO  17:48:12,444 ProgressMeter -            done   3.1359052E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T16:48Z] INFO  17:48:12,445 ProgressMeter - Total runtime 21.58 secs, 0.36 min, 0.01 hours
[2015-09-30T16:48Z] INFO  17:48:12,445 MicroScheduler - 206902 reads were filtered out during the traversal out of approximately 576890 total reads (35.87%)
[2015-09-30T16:48Z] INFO  17:48:12,446 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:48Z] INFO  17:48:12,446 MicroScheduler -   -> 7365 reads (1.28% of total) failing BadMateFilter
[2015-09-30T16:48Z] INFO  17:48:12,446 MicroScheduler -   -> 16067 reads (2.79% of total) failing DuplicateReadFilter
[2015-09-30T16:48Z] INFO  17:48:12,447 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:48Z] INFO  17:48:12,447 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:48Z] INFO  17:48:12,447 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:48Z] INFO  17:48:12,447 MicroScheduler -   -> 183470 reads (31.80% of total) failing MappingQualityZeroFilter
[2015-09-30T16:48Z] INFO  17:48:12,448 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:48Z] INFO  17:48:12,448 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:48Z] INFO  17:48:12,448 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:48Z] INFO  17:48:13,407 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:48Z] GATK: realign ('8', 62288979, 93648031) : syn3-tumor
[2015-09-30T16:48Z] INFO  17:48:15,089 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:15,091 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:48Z] INFO  17:48:15,091 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:48Z] INFO  17:48:15,091 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:48Z] INFO  17:48:15,095 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep-prealign-realign.intervals -L 8:62288980-93648031 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpCKQHvs/2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam
[2015-09-30T16:48Z] INFO  17:48:15,101 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:48Z] INFO  17:48:15,101 HelpFormatter - Date/Time: 2015/09/30 17:48:15
[2015-09-30T16:48Z] INFO  17:48:15,101 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:15,101 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:15,208 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:48Z] INFO  17:48:15,275 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:48Z] INFO  17:48:15,283 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:48Z] INFO  17:48:15,299 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:48Z] INFO  17:48:15,532 IntervalUtils - Processing 31359052 bp from intervals
[2015-09-30T16:48Z] WARN  17:48:15,536 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:48Z] INFO  17:48:15,592 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:48Z] INFO  17:48:15,841 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:48Z] INFO  17:48:15,841 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:48Z] INFO  17:48:15,842 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:48Z] INFO  17:48:15,842 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:48Z] INFO  17:48:16,123 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:48Z] INFO  17:48:16,310 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:48Z] INFO  17:48:16,790 ProgressMeter -      8:62213134    500006.0    30.0 s      61.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T16:48Z] INFO  17:48:17,356 ProgressMeter -            done    521518.0    31.0 s      60.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T16:48Z] INFO  17:48:17,356 ProgressMeter - Total runtime 31.54 secs, 0.53 min, 0.01 hours
[2015-09-30T16:48Z] INFO  17:48:17,359 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 521518 total reads (0.00%)
[2015-09-30T16:48Z] INFO  17:48:17,359 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:48Z] INFO  17:48:17,360 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:48Z] INFO  17:48:17,360 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:48Z] INFO  17:48:18,486 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:48Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam
[2015-09-30T16:48Z] GATK pre-alignment ('8', 124975213, 146364022) : syn3-tumor
[2015-09-30T16:48Z] INFO  17:48:20,710 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T16:48Z] INFO  17:48:20,848 ProgressMeter -            done    515962.0    56.0 s     110.0 s      100.0%    56.0 s       0.0 s
[2015-09-30T16:48Z] INFO  17:48:20,848 ProgressMeter - Total runtime 56.92 secs, 0.95 min, 0.02 hours
[2015-09-30T16:48Z] INFO  17:48:20,849 MicroScheduler - 1707 reads were filtered out during the traversal out of approximately 517669 total reads (0.33%)
[2015-09-30T16:48Z] INFO  17:48:20,849 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:48Z] INFO  17:48:20,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:48Z] INFO  17:48:20,850 MicroScheduler -   -> 1707 reads (0.33% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:48Z] INFO  17:48:21,645 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:21,647 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:48Z] INFO  17:48:21,647 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:48Z] INFO  17:48:21,647 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:48Z] INFO  17:48:21,651 HelpFormatter - Program Args: -T PrintReads -L 8:124975214-146364022 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpTZu3Hr/2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam
[2015-09-30T16:48Z] INFO  17:48:21,656 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:48Z] INFO  17:48:21,657 HelpFormatter - Date/Time: 2015/09/30 17:48:21
[2015-09-30T16:48Z] INFO  17:48:21,657 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:21,657 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:21,765 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:48Z] INFO  17:48:21,908 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:48Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam
[2015-09-30T16:48Z] INFO  17:48:23,391 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:48Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam 8:93896833-124968568
[2015-09-30T16:48Z] GATK: RealignerTargetCreator
[2015-09-30T16:48Z] INFO  17:48:23,446 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:48Z] INFO  17:48:23,454 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:48Z] INFO  17:48:23,470 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:48Z] INFO  17:48:23,483 IntervalUtils - Processing 21388809 bp from intervals
[2015-09-30T16:48Z] INFO  17:48:23,543 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:48Z] INFO  17:48:23,723 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:48Z] INFO  17:48:23,723 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:48Z] INFO  17:48:23,723 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:48Z] INFO  17:48:23,724 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:48Z] INFO  17:48:23,735 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:48Z] INFO  17:48:23,880 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:48Z] INFO  17:48:25,735 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:25,738 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:48Z] INFO  17:48:25,738 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:48Z] INFO  17:48:25,738 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:48Z] INFO  17:48:25,741 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpyv9Fpv/2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign-realign.intervals -l INFO -L 8:93896833-124968568 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:48Z] INFO  17:48:25,747 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:48Z] INFO  17:48:25,747 HelpFormatter - Date/Time: 2015/09/30 17:48:25
[2015-09-30T16:48Z] INFO  17:48:25,748 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:25,748 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:25,818 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:48Z] INFO  17:48:25,940 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:48Z] INFO  17:48:25,947 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:48Z] INFO  17:48:25,963 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:48Z] INFO  17:48:26,215 IntervalUtils - Processing 31071736 bp from intervals
[2015-09-30T16:48Z] WARN  17:48:26,219 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:48Z] INFO  17:48:26,277 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:48Z] INFO  17:48:26,419 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:48Z] INFO  17:48:26,420 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:48Z] INFO  17:48:26,420 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:48Z] INFO  17:48:26,420 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:48Z] INFO  17:48:45,844 ProgressMeter -      8:92170844    500008.0    30.0 s      60.0 s       95.3%    31.0 s       1.0 s
[2015-09-30T16:48Z] INFO  17:48:46,499 ProgressMeter -            done    573713.0    30.0 s      53.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T16:48Z] INFO  17:48:46,499 ProgressMeter - Total runtime 30.66 secs, 0.51 min, 0.01 hours
[2015-09-30T16:48Z] INFO  17:48:46,502 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 573713 total reads (0.00%)
[2015-09-30T16:48Z] INFO  17:48:46,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:48Z] INFO  17:48:46,503 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:48Z] INFO  17:48:46,503 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:48Z] INFO  17:48:47,493 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:48Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam
[2015-09-30T16:48Z] GATK pre-alignment ('9', 0, 32405837) : syn3-tumor
[2015-09-30T16:48Z] INFO  17:48:49,078 ProgressMeter -            done   3.1071736E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T16:48Z] INFO  17:48:49,078 ProgressMeter - Total runtime 22.66 secs, 0.38 min, 0.01 hours
[2015-09-30T16:48Z] INFO  17:48:49,081 MicroScheduler - 38173 reads were filtered out during the traversal out of approximately 519540 total reads (7.35%)
[2015-09-30T16:48Z] INFO  17:48:49,082 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:48Z] INFO  17:48:49,082 MicroScheduler -   -> 8547 reads (1.65% of total) failing BadMateFilter
[2015-09-30T16:48Z] INFO  17:48:49,082 MicroScheduler -   -> 20526 reads (3.95% of total) failing DuplicateReadFilter
[2015-09-30T16:48Z] INFO  17:48:49,083 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:48Z] INFO  17:48:49,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:48Z] INFO  17:48:49,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:48Z] INFO  17:48:49,083 MicroScheduler -   -> 9100 reads (1.75% of total) failing MappingQualityZeroFilter
[2015-09-30T16:48Z] INFO  17:48:49,083 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:48Z] INFO  17:48:49,084 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:48Z] INFO  17:48:49,084 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:48Z] INFO  17:48:50,066 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:48Z] GATK: realign ('8', 93896832, 124968568) : syn3-tumor
[2015-09-30T16:48Z] INFO  17:48:50,547 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:50,549 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:48Z] INFO  17:48:50,549 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:48Z] INFO  17:48:50,549 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:48Z] INFO  17:48:50,553 HelpFormatter - Program Args: -T PrintReads -L 9:1-32405837 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpZSw8B9/2_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam
[2015-09-30T16:48Z] INFO  17:48:50,558 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:48Z] INFO  17:48:50,558 HelpFormatter - Date/Time: 2015/09/30 17:48:50
[2015-09-30T16:48Z] INFO  17:48:50,558 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:50,558 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:50,656 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:48Z] INFO  17:48:51,968 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:48Z] INFO  17:48:52,016 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:48Z] INFO  17:48:52,023 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:48Z] INFO  17:48:52,037 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:48Z] INFO  17:48:52,049 IntervalUtils - Processing 32405837 bp from intervals
[2015-09-30T16:48Z] INFO  17:48:52,104 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:48Z] INFO  17:48:52,395 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:52,397 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:48Z] INFO  17:48:52,397 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:48Z] INFO  17:48:52,397 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:48Z] INFO  17:48:52,400 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep-prealign-realign.intervals -L 8:93896833-124968568 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpp8QeFm/2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam
[2015-09-30T16:48Z] INFO  17:48:52,405 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:48Z] INFO  17:48:52,406 HelpFormatter - Date/Time: 2015/09/30 17:48:52
[2015-09-30T16:48Z] INFO  17:48:52,406 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:52,406 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:48Z] INFO  17:48:52,527 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:48Z] INFO  17:48:52,586 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:48Z] INFO  17:48:52,593 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:48Z] INFO  17:48:52,608 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:48Z] INFO  17:48:52,825 IntervalUtils - Processing 31071736 bp from intervals
[2015-09-30T16:48Z] WARN  17:48:52,828 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:48Z] INFO  17:48:52,878 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:48Z] INFO  17:48:53,726 ProgressMeter -     8:134292086    200012.0    30.0 s       2.5 m       43.6%    68.0 s      38.0 s
[2015-09-30T16:48Z] INFO  17:48:54,072 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:48Z] INFO  17:48:54,073 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:48Z] INFO  17:48:54,073 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:48Z] INFO  17:48:54,073 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:48Z] INFO  17:48:54,083 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:48Z] INFO  17:48:54,272 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:48Z] INFO  17:48:54,374 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:48Z] INFO  17:48:54,374 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:48Z] INFO  17:48:54,375 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:48Z] INFO  17:48:54,375 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:48Z] INFO  17:48:54,517 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:48Z] INFO  17:48:54,698 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:49Z] INFO  17:49:20,962 ProgressMeter -            done    515962.0    26.0 s      51.0 s      100.0%    26.0 s       0.0 s
[2015-09-30T16:49Z] INFO  17:49:20,962 ProgressMeter - Total runtime 26.59 secs, 0.44 min, 0.01 hours
[2015-09-30T16:49Z] INFO  17:49:20,965 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 515962 total reads (0.00%)
[2015-09-30T16:49Z] INFO  17:49:20,965 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:49Z] INFO  17:49:20,966 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:49Z] INFO  17:49:20,966 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:49Z] INFO  17:49:22,126 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:49Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam
[2015-09-30T16:49Z] GATK pre-alignment ('9', 32406980, 65488652) : syn3-tumor
[2015-09-30T16:49Z] INFO  17:49:23,747 ProgressMeter -     8:144920745    500017.0    60.0 s     120.0 s       93.3%    64.0 s       4.0 s
[2015-09-30T16:49Z] INFO  17:49:24,105 ProgressMeter -      9:14842290    200003.0    30.0 s       2.5 m       45.8%    65.0 s      35.0 s
[2015-09-30T16:49Z] INFO  17:49:25,162 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:49Z] INFO  17:49:25,164 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:49Z] INFO  17:49:25,164 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:49Z] INFO  17:49:25,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:49Z] INFO  17:49:25,168 HelpFormatter - Program Args: -T PrintReads -L 9:32406981-65488652 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpO3gvE9/2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam
[2015-09-30T16:49Z] INFO  17:49:25,174 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:49Z] INFO  17:49:25,174 HelpFormatter - Date/Time: 2015/09/30 17:49:25
[2015-09-30T16:49Z] INFO  17:49:25,174 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:49Z] INFO  17:49:25,175 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:49Z] INFO  17:49:25,280 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:49Z] INFO  17:49:26,544 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:49Z] INFO  17:49:26,595 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:49Z] INFO  17:49:26,603 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:49Z] INFO  17:49:26,618 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:49Z] INFO  17:49:26,630 IntervalUtils - Processing 33081672 bp from intervals
[2015-09-30T16:49Z] INFO  17:49:26,689 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:49Z] INFO  17:49:26,851 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:49Z] INFO  17:49:26,851 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:49Z] INFO  17:49:26,851 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:49Z] INFO  17:49:26,851 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:49Z] INFO  17:49:26,862 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:49Z] INFO  17:49:27,027 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:49Z] INFO  17:49:41,412 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:49Z] INFO  17:49:41,496 ProgressMeter -            done    767677.0    77.0 s     101.0 s       99.6%    77.0 s       0.0 s
[2015-09-30T16:49Z] INFO  17:49:41,496 ProgressMeter - Total runtime 77.77 secs, 1.30 min, 0.02 hours
[2015-09-30T16:49Z] INFO  17:49:41,496 MicroScheduler - 4747 reads were filtered out during the traversal out of approximately 772424 total reads (0.61%)
[2015-09-30T16:49Z] INFO  17:49:41,497 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:49Z] INFO  17:49:41,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:49Z] INFO  17:49:41,497 MicroScheduler -   -> 4747 reads (0.61% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:49Z] INFO  17:49:42,462 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:49Z] INFO  17:49:42,581 ProgressMeter -            done    470804.0    48.0 s     103.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T16:49Z] INFO  17:49:42,581 ProgressMeter - Total runtime 48.51 secs, 0.81 min, 0.01 hours
[2015-09-30T16:49Z] INFO  17:49:42,583 MicroScheduler - 1645 reads were filtered out during the traversal out of approximately 472449 total reads (0.35%)
[2015-09-30T16:49Z] INFO  17:49:42,583 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:49Z] INFO  17:49:42,583 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:49Z] INFO  17:49:42,583 MicroScheduler -   -> 1645 reads (0.35% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:49Z] INFO  17:49:42,708 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:49Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam
[2015-09-30T16:49Z] INFO  17:49:43,574 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:49Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam
[2015-09-30T16:49Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam 8:124975214-146364022
[2015-09-30T16:49Z] GATK: RealignerTargetCreator
[2015-09-30T16:49Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam 9:1-32405837
[2015-09-30T16:49Z] GATK: RealignerTargetCreator
[2015-09-30T16:49Z] INFO  17:49:46,064 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:49Z] INFO  17:49:46,066 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:49Z] INFO  17:49:46,066 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:49Z] INFO  17:49:46,067 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:49Z] INFO  17:49:46,070 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpk4qScO/2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign-realign.intervals -l INFO -L 8:124975214-146364022 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:49Z] INFO  17:49:46,075 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:49Z] INFO  17:49:46,076 HelpFormatter - Date/Time: 2015/09/30 17:49:46
[2015-09-30T16:49Z] INFO  17:49:46,076 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:49Z] INFO  17:49:46,076 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:49Z] INFO  17:49:46,134 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:49Z] INFO  17:49:46,241 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:49Z] INFO  17:49:46,249 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:49Z] INFO  17:49:46,265 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:49Z] INFO  17:49:46,509 IntervalUtils - Processing 21388809 bp from intervals
[2015-09-30T16:49Z] WARN  17:49:46,513 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:49Z] INFO  17:49:46,570 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:49Z] INFO  17:49:46,683 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:49Z] INFO  17:49:46,683 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:49Z] INFO  17:49:46,684 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:49Z] INFO  17:49:46,684 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:49Z] INFO  17:49:46,715 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:49Z] INFO  17:49:46,717 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:49Z] INFO  17:49:46,717 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:49Z] INFO  17:49:46,717 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:49Z] INFO  17:49:46,721 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmps8DtwM/2_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign-realign.intervals -l INFO -L 9:1-32405837 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:49Z] INFO  17:49:46,726 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:49Z] INFO  17:49:46,727 HelpFormatter - Date/Time: 2015/09/30 17:49:46
[2015-09-30T16:49Z] INFO  17:49:46,727 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:49Z] INFO  17:49:46,727 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:49Z] INFO  17:49:46,784 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:49Z] INFO  17:49:47,415 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:49Z] INFO  17:49:47,423 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:49Z] INFO  17:49:47,439 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:49Z] INFO  17:49:47,689 IntervalUtils - Processing 32405837 bp from intervals
[2015-09-30T16:49Z] WARN  17:49:47,693 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:49Z] INFO  17:49:47,750 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:49Z] INFO  17:49:47,909 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:49Z] INFO  17:49:47,910 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:49Z] INFO  17:49:47,910 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:49Z] INFO  17:49:47,911 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:49Z] INFO  17:49:56,854 ProgressMeter -      9:35471627    200003.0    30.0 s       2.5 m        9.3%     5.4 m       4.9 m
[2015-09-30T16:50Z] INFO  17:50:08,607 ProgressMeter -            done   2.1388809E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T16:50Z] INFO  17:50:08,607 ProgressMeter - Total runtime 21.92 secs, 0.37 min, 0.01 hours
[2015-09-30T16:50Z] INFO  17:50:08,608 MicroScheduler - 87322 reads were filtered out during the traversal out of approximately 771264 total reads (11.32%)
[2015-09-30T16:50Z] INFO  17:50:08,608 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:50Z] INFO  17:50:08,608 MicroScheduler -   -> 17095 reads (2.22% of total) failing BadMateFilter
[2015-09-30T16:50Z] INFO  17:50:08,608 MicroScheduler -   -> 39240 reads (5.09% of total) failing DuplicateReadFilter
[2015-09-30T16:50Z] INFO  17:50:08,609 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:50Z] INFO  17:50:08,609 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:50Z] INFO  17:50:08,609 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:50Z] INFO  17:50:08,609 MicroScheduler -   -> 30987 reads (4.02% of total) failing MappingQualityZeroFilter
[2015-09-30T16:50Z] INFO  17:50:08,609 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:50Z] INFO  17:50:08,610 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:50Z] INFO  17:50:08,610 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:50Z] INFO  17:50:09,682 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:50Z] GATK: realign ('8', 124975213, 146364022) : syn3-tumor
[2015-09-30T16:50Z] INFO  17:50:10,062 ProgressMeter -            done   3.2405837E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T16:50Z] INFO  17:50:10,062 ProgressMeter - Total runtime 22.15 secs, 0.37 min, 0.01 hours
[2015-09-30T16:50Z] INFO  17:50:10,065 MicroScheduler - 44066 reads were filtered out during the traversal out of approximately 473961 total reads (9.30%)
[2015-09-30T16:50Z] INFO  17:50:10,065 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:50Z] INFO  17:50:10,066 MicroScheduler -   -> 8062 reads (1.70% of total) failing BadMateFilter
[2015-09-30T16:50Z] INFO  17:50:10,066 MicroScheduler -   -> 19254 reads (4.06% of total) failing DuplicateReadFilter
[2015-09-30T16:50Z] INFO  17:50:10,066 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:50Z] INFO  17:50:10,066 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:50Z] INFO  17:50:10,067 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:50Z] INFO  17:50:10,067 MicroScheduler -   -> 16750 reads (3.53% of total) failing MappingQualityZeroFilter
[2015-09-30T16:50Z] INFO  17:50:10,067 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:50Z] INFO  17:50:10,067 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:50Z] INFO  17:50:10,068 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:50Z] INFO  17:50:11,033 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:50Z] GATK: realign ('9', 0, 32405837) : syn3-tumor
[2015-09-30T16:50Z] INFO  17:50:11,512 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:11,514 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:50Z] INFO  17:50:11,515 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:50Z] INFO  17:50:11,515 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:50Z] INFO  17:50:11,518 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep-prealign-realign.intervals -L 8:124975214-146364022 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/tx/tmpWowDAO/2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam
[2015-09-30T16:50Z] INFO  17:50:11,524 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:50Z] INFO  17:50:11,524 HelpFormatter - Date/Time: 2015/09/30 17:50:11
[2015-09-30T16:50Z] INFO  17:50:11,524 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:11,524 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:11,648 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:50Z] INFO  17:50:11,711 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:50Z] INFO  17:50:11,718 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:50Z] INFO  17:50:11,734 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:50Z] INFO  17:50:11,960 IntervalUtils - Processing 21388809 bp from intervals
[2015-09-30T16:50Z] WARN  17:50:11,964 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:50Z] INFO  17:50:12,016 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:50Z] INFO  17:50:12,127 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:50Z] INFO  17:50:12,128 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:50Z] INFO  17:50:12,128 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:50Z] INFO  17:50:12,129 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:50Z] INFO  17:50:12,266 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:50Z] INFO  17:50:12,418 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:50Z] INFO  17:50:12,755 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:12,757 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:50Z] INFO  17:50:12,757 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:50Z] INFO  17:50:12,757 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:50Z] INFO  17:50:12,760 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_0_32405837-prep-prealign-realign.intervals -L 9:1-32405837 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpcH64wE/2_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam
[2015-09-30T16:50Z] INFO  17:50:12,766 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:50Z] INFO  17:50:12,766 HelpFormatter - Date/Time: 2015/09/30 17:50:12
[2015-09-30T16:50Z] INFO  17:50:12,766 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:12,766 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:14,393 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:50Z] INFO  17:50:15,068 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:50Z] INFO  17:50:15,076 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:50Z] INFO  17:50:15,093 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:50Z] INFO  17:50:15,322 IntervalUtils - Processing 32405837 bp from intervals
[2015-09-30T16:50Z] WARN  17:50:15,326 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:50Z] INFO  17:50:15,382 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:50Z] INFO  17:50:15,562 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:50Z] INFO  17:50:15,562 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:50Z] INFO  17:50:15,563 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:50Z] INFO  17:50:15,563 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:50Z] INFO  17:50:15,700 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:50Z] INFO  17:50:15,891 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:50Z] INFO  17:50:27,663 ProgressMeter -      9:44115196    500007.0    60.0 s       2.0 m       35.4%     2.8 m     109.0 s
[2015-09-30T16:50Z] INFO  17:50:30,407 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:50Z] INFO  17:50:30,637 ProgressMeter -            done    571728.0    63.0 s     111.0 s      100.0%    63.0 s       0.0 s
[2015-09-30T16:50Z] INFO  17:50:30,637 ProgressMeter - Total runtime 63.79 secs, 1.06 min, 0.02 hours
[2015-09-30T16:50Z] INFO  17:50:30,637 MicroScheduler - 1173 reads were filtered out during the traversal out of approximately 572901 total reads (0.20%)
[2015-09-30T16:50Z] INFO  17:50:30,638 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:50Z] INFO  17:50:30,638 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:50Z] INFO  17:50:30,638 MicroScheduler -   -> 1173 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:50Z] INFO  17:50:32,056 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:50Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam
[2015-09-30T16:50Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam 9:32406981-65488652
[2015-09-30T16:50Z] GATK: RealignerTargetCreator
[2015-09-30T16:50Z] INFO  17:50:35,827 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:35,829 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:50Z] INFO  17:50:35,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:50Z] INFO  17:50:35,830 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:50Z] INFO  17:50:35,833 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpFy3Rmt/2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign-realign.intervals -l INFO -L 9:32406981-65488652 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:50Z] INFO  17:50:35,839 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:50Z] INFO  17:50:35,839 HelpFormatter - Date/Time: 2015/09/30 17:50:35
[2015-09-30T16:50Z] INFO  17:50:35,840 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:35,840 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:35,899 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:50Z] INFO  17:50:36,446 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:50Z] INFO  17:50:36,454 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:50Z] INFO  17:50:36,470 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:50Z] INFO  17:50:36,707 IntervalUtils - Processing 33081672 bp from intervals
[2015-09-30T16:50Z] WARN  17:50:36,711 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:50Z] INFO  17:50:36,769 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:50Z] INFO  17:50:36,862 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:50Z] INFO  17:50:36,862 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:50Z] INFO  17:50:36,862 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:50Z] INFO  17:50:36,863 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:50Z] INFO  17:50:42,820 ProgressMeter -     8:144820742    500017.0    30.0 s      61.0 s       92.8%    32.0 s       2.0 s
[2015-09-30T16:50Z] INFO  17:50:43,682 ProgressMeter -            done    470804.0    28.0 s      59.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T16:50Z] INFO  17:50:43,683 ProgressMeter - Total runtime 28.12 secs, 0.47 min, 0.01 hours
[2015-09-30T16:50Z] INFO  17:50:43,685 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 470804 total reads (0.00%)
[2015-09-30T16:50Z] INFO  17:50:43,686 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:50Z] INFO  17:50:43,686 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:50Z] INFO  17:50:43,686 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:50Z] INFO  17:50:44,731 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:50Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam
[2015-09-30T16:50Z] GATK pre-alignment ('9', 65505265, 96581951) : syn3-tumor
[2015-09-30T16:50Z] INFO  17:50:48,628 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:48,630 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:50Z] INFO  17:50:48,630 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:50Z] INFO  17:50:48,630 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:50Z] INFO  17:50:48,634 HelpFormatter - Program Args: -T PrintReads -L 9:65505266-96581951 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmp_y79LL/2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam
[2015-09-30T16:50Z] INFO  17:50:48,639 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:50Z] INFO  17:50:48,639 HelpFormatter - Date/Time: 2015/09/30 17:50:48
[2015-09-30T16:50Z] INFO  17:50:48,639 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:48,640 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:50Z] INFO  17:50:48,750 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:50Z] INFO  17:50:49,714 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:50Z] INFO  17:50:49,761 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:50Z] INFO  17:50:49,769 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:50Z] INFO  17:50:49,783 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:50Z] INFO  17:50:49,795 IntervalUtils - Processing 31076686 bp from intervals
[2015-09-30T16:50Z] INFO  17:50:49,850 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:50Z] INFO  17:50:50,038 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:50Z] INFO  17:50:50,039 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:50Z] INFO  17:50:50,039 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:50Z] INFO  17:50:50,039 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:50Z] INFO  17:50:50,050 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:50Z] INFO  17:50:50,233 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:50Z] INFO  17:50:50,784 ProgressMeter -            done    767677.0    38.0 s      50.0 s       99.6%    38.0 s       0.0 s
[2015-09-30T16:50Z] INFO  17:50:50,784 ProgressMeter - Total runtime 38.66 secs, 0.64 min, 0.01 hours
[2015-09-30T16:50Z] INFO  17:50:50,787 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 767677 total reads (0.00%)
[2015-09-30T16:50Z] INFO  17:50:50,788 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:50Z] INFO  17:50:50,788 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:50Z] INFO  17:50:50,788 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:50Z] INFO  17:50:51,851 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:50Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam
[2015-09-30T16:50Z] GATK pre-alignment ('9', 96714155, 127734373) : syn3-tumor
[2015-09-30T16:51Z] INFO  17:51:01,926 ProgressMeter -            done   3.3081672E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T16:51Z] INFO  17:51:01,927 ProgressMeter - Total runtime 25.06 secs, 0.42 min, 0.01 hours
[2015-09-30T16:51Z] INFO  17:51:01,930 MicroScheduler - 113493 reads were filtered out during the traversal out of approximately 574857 total reads (19.74%)
[2015-09-30T16:51Z] INFO  17:51:01,930 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:51Z] INFO  17:51:01,930 MicroScheduler -   -> 4587 reads (0.80% of total) failing BadMateFilter
[2015-09-30T16:51Z] INFO  17:51:01,930 MicroScheduler -   -> 23867 reads (4.15% of total) failing DuplicateReadFilter
[2015-09-30T16:51Z] INFO  17:51:01,931 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:51Z] INFO  17:51:01,931 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:51Z] INFO  17:51:01,931 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:51Z] INFO  17:51:01,931 MicroScheduler -   -> 85039 reads (14.79% of total) failing MappingQualityZeroFilter
[2015-09-30T16:51Z] INFO  17:51:01,932 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:51Z] INFO  17:51:01,932 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:51Z] INFO  17:51:01,932 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:51Z] INFO  17:51:02,130 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:51Z] INFO  17:51:02,132 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:51Z] INFO  17:51:02,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:51Z] INFO  17:51:02,132 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:51Z] INFO  17:51:02,136 HelpFormatter - Program Args: -T PrintReads -L 9:96714156-127734373 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmprVusNP/2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam
[2015-09-30T16:51Z] INFO  17:51:02,141 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:51Z] INFO  17:51:02,141 HelpFormatter - Date/Time: 2015/09/30 17:51:02
[2015-09-30T16:51Z] INFO  17:51:02,142 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:51Z] INFO  17:51:02,142 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:51Z] INFO  17:51:02,249 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:51Z] INFO  17:51:02,955 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:51Z] INFO  17:51:03,007 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:51Z] INFO  17:51:03,015 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:51Z] INFO  17:51:03,023 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:51Z] INFO  17:51:03,031 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:51Z] INFO  17:51:03,045 IntervalUtils - Processing 31020218 bp from intervals
[2015-09-30T16:51Z] GATK: realign ('9', 32406980, 65488652) : syn3-tumor
[2015-09-30T16:51Z] INFO  17:51:03,107 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:51Z] INFO  17:51:03,311 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:51Z] INFO  17:51:03,312 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:51Z] INFO  17:51:03,312 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:51Z] INFO  17:51:03,312 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:51Z] INFO  17:51:03,324 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:51Z] INFO  17:51:03,527 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:51Z] INFO  17:51:06,210 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:51Z] INFO  17:51:06,212 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:51Z] INFO  17:51:06,212 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:51Z] INFO  17:51:06,212 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:51Z] INFO  17:51:06,216 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep-prealign-realign.intervals -L 9:32406981-65488652 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpWGVElw/2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam
[2015-09-30T16:51Z] INFO  17:51:06,221 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:51Z] INFO  17:51:06,221 HelpFormatter - Date/Time: 2015/09/30 17:51:06
[2015-09-30T16:51Z] INFO  17:51:06,222 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:51Z] INFO  17:51:06,222 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:51Z] INFO  17:51:07,073 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:51Z] INFO  17:51:07,138 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:51Z] INFO  17:51:07,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:51Z] INFO  17:51:07,162 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:51Z] INFO  17:51:07,396 IntervalUtils - Processing 33081672 bp from intervals
[2015-09-30T16:51Z] WARN  17:51:07,400 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:51Z] INFO  17:51:07,456 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:51Z] INFO  17:51:07,647 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:51Z] INFO  17:51:07,648 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:51Z] INFO  17:51:07,648 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:51Z] INFO  17:51:07,649 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:51Z] INFO  17:51:07,893 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:51Z] INFO  17:51:08,069 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:51Z] INFO  17:51:20,522 ProgressMeter -      9:72901141    200003.0    30.0 s       2.5 m       23.8%     2.1 m      96.0 s
[2015-09-30T16:51Z] INFO  17:51:33,315 ProgressMeter -     9:101803883    200002.0    30.0 s       2.5 m       16.4%     3.0 m       2.5 m
[2015-09-30T16:51Z] INFO  17:51:37,901 ProgressMeter -            done    571728.0    30.0 s      52.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T16:51Z] INFO  17:51:37,901 ProgressMeter - Total runtime 30.25 secs, 0.50 min, 0.01 hours
[2015-09-30T16:51Z] INFO  17:51:37,904 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 571728 total reads (0.00%)
[2015-09-30T16:51Z] INFO  17:51:37,904 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:51Z] INFO  17:51:37,904 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:51Z] INFO  17:51:37,905 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:51Z] INFO  17:51:39,071 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:51Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam
[2015-09-30T16:51Z] GATK pre-alignment ('9', 127737328, 141213431) : syn3-tumor
[2015-09-30T16:51Z] INFO  17:51:44,347 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:51Z] INFO  17:51:44,350 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:51Z] INFO  17:51:44,350 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:51Z] INFO  17:51:44,350 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:51Z] INFO  17:51:44,353 HelpFormatter - Program Args: -T PrintReads -L 9:127737329-141213431 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpxtUhoT/2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam
[2015-09-30T16:51Z] INFO  17:51:44,359 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:51Z] INFO  17:51:44,359 HelpFormatter - Date/Time: 2015/09/30 17:51:44
[2015-09-30T16:51Z] INFO  17:51:44,359 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:51Z] INFO  17:51:44,359 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:51Z] INFO  17:51:44,466 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:51Z] INFO  17:51:45,158 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:51Z] INFO  17:51:45,208 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:51Z] INFO  17:51:45,216 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:51Z] INFO  17:51:45,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:51Z] INFO  17:51:45,244 IntervalUtils - Processing 13476103 bp from intervals
[2015-09-30T16:51Z] INFO  17:51:45,301 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:51Z] INFO  17:51:45,468 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:51Z] INFO  17:51:45,468 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:51Z] INFO  17:51:45,469 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:51Z] INFO  17:51:45,469 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:51Z] INFO  17:51:45,480 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:51Z] INFO  17:51:45,574 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:51Z] INFO  17:51:50,523 ProgressMeter -      9:90537767    500007.0    60.0 s     120.0 s       80.6%    74.0 s      14.0 s
[2015-09-30T16:52Z] INFO  17:52:03,483 ProgressMeter -     9:114842785    500006.0    60.0 s     120.0 s       58.4%   102.0 s      42.0 s
[2015-09-30T16:52Z] INFO  17:52:09,952 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:52Z] INFO  17:52:10,047 ProgressMeter -            done    749625.0    80.0 s     106.0 s      100.0%    80.0 s       0.0 s
[2015-09-30T16:52Z] INFO  17:52:10,047 ProgressMeter - Total runtime 80.01 secs, 1.33 min, 0.02 hours
[2015-09-30T16:52Z] INFO  17:52:10,047 MicroScheduler - 2467 reads were filtered out during the traversal out of approximately 752092 total reads (0.33%)
[2015-09-30T16:52Z] INFO  17:52:10,048 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:52Z] INFO  17:52:10,048 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:52Z] INFO  17:52:10,048 MicroScheduler -   -> 2467 reads (0.33% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:52Z] INFO  17:52:11,168 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:52Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam
[2015-09-30T16:52Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam 9:65505266-96581951
[2015-09-30T16:52Z] GATK: RealignerTargetCreator
[2015-09-30T16:52Z] INFO  17:52:14,765 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:52Z] INFO  17:52:14,767 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:52Z] INFO  17:52:14,767 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:52Z] INFO  17:52:14,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:52Z] INFO  17:52:14,771 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmphjQaB0/2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign-realign.intervals -l INFO -L 9:65505266-96581951 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:52Z] INFO  17:52:14,776 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:52Z] INFO  17:52:14,776 HelpFormatter - Date/Time: 2015/09/30 17:52:14
[2015-09-30T16:52Z] INFO  17:52:14,776 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:52Z] INFO  17:52:14,776 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:52Z] INFO  17:52:14,830 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:52Z] INFO  17:52:14,930 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:52Z] INFO  17:52:14,938 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:52Z] INFO  17:52:14,953 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:52Z] INFO  17:52:15,471 ProgressMeter -     9:130898080    200005.0    30.0 s       2.5 m       23.5%     2.1 m      97.0 s
[2015-09-30T16:52Z] INFO  17:52:15,673 IntervalUtils - Processing 31076686 bp from intervals
[2015-09-30T16:52Z] WARN  17:52:15,677 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:52Z] INFO  17:52:15,733 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:52Z] INFO  17:52:15,871 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:52Z] INFO  17:52:15,871 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:52Z] INFO  17:52:15,871 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:52Z] INFO  17:52:15,872 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:52Z] INFO  17:52:33,484 ProgressMeter -     9:123857197    800013.0    90.0 s     112.0 s       87.5%   102.0 s      12.0 s
[2015-09-30T16:52Z] INFO  17:52:39,660 ProgressMeter -            done   3.1076686E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T16:52Z] INFO  17:52:39,661 ProgressMeter - Total runtime 23.79 secs, 0.40 min, 0.01 hours
[2015-09-30T16:52Z] INFO  17:52:39,664 MicroScheduler - 134110 reads were filtered out during the traversal out of approximately 753284 total reads (17.80%)
[2015-09-30T16:52Z] INFO  17:52:39,664 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:52Z] INFO  17:52:39,664 MicroScheduler -   -> 10640 reads (1.41% of total) failing BadMateFilter
[2015-09-30T16:52Z] INFO  17:52:39,665 MicroScheduler -   -> 30435 reads (4.04% of total) failing DuplicateReadFilter
[2015-09-30T16:52Z] INFO  17:52:39,665 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:52Z] INFO  17:52:39,665 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:52Z] INFO  17:52:39,665 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:52Z] INFO  17:52:39,666 MicroScheduler -   -> 93035 reads (12.35% of total) failing MappingQualityZeroFilter
[2015-09-30T16:52Z] INFO  17:52:39,666 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:52Z] INFO  17:52:39,666 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:52Z] INFO  17:52:39,666 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:52Z] INFO  17:52:40,620 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:52Z] GATK: realign ('9', 65505265, 96581951) : syn3-tumor
[2015-09-30T16:52Z] INFO  17:52:42,148 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:52Z] INFO  17:52:42,150 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:52Z] INFO  17:52:42,150 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:52Z] INFO  17:52:42,150 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:52Z] INFO  17:52:42,153 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep-prealign-realign.intervals -L 9:65505266-96581951 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmp9jA0RO/2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam
[2015-09-30T16:52Z] INFO  17:52:42,159 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:52Z] INFO  17:52:42,159 HelpFormatter - Date/Time: 2015/09/30 17:52:42
[2015-09-30T16:52Z] INFO  17:52:42,159 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:52Z] INFO  17:52:42,159 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:52Z] INFO  17:52:42,281 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:52Z] INFO  17:52:42,344 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:52Z] INFO  17:52:42,352 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:52Z] INFO  17:52:42,367 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:52Z] INFO  17:52:42,723 IntervalUtils - Processing 31076686 bp from intervals
[2015-09-30T16:52Z] WARN  17:52:42,726 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:52Z] INFO  17:52:42,781 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:52Z] INFO  17:52:42,926 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:52Z] INFO  17:52:42,926 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:52Z] INFO  17:52:42,926 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:52Z] INFO  17:52:42,927 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:52Z] INFO  17:52:43,065 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:52Z] INFO  17:52:43,241 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:52Z] INFO  17:52:45,472 ProgressMeter -     9:133282078    500011.0    60.0 s     120.0 s       41.1%     2.4 m      85.0 s
[2015-09-30T16:52Z] INFO  17:52:52,883 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:52Z] INFO  17:52:53,005 ProgressMeter -            done   1068302.0   109.0 s     102.0 s      100.0%   109.0 s       0.0 s
[2015-09-30T16:52Z] INFO  17:52:53,005 ProgressMeter - Total runtime 109.69 secs, 1.83 min, 0.03 hours
[2015-09-30T16:52Z] INFO  17:52:53,006 MicroScheduler - 2217 reads were filtered out during the traversal out of approximately 1070519 total reads (0.21%)
[2015-09-30T16:52Z] INFO  17:52:53,006 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:52Z] INFO  17:52:53,006 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:52Z] INFO  17:52:53,006 MicroScheduler -   -> 2217 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:52Z] INFO  17:52:53,975 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:52Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam
[2015-09-30T16:52Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam 9:96714156-127734373
[2015-09-30T16:52Z] GATK: RealignerTargetCreator
[2015-09-30T16:52Z] INFO  17:52:59,403 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:52Z] INFO  17:52:59,406 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:52Z] INFO  17:52:59,406 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:52Z] INFO  17:52:59,406 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:52Z] INFO  17:52:59,409 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpVtZcUB/2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign-realign.intervals -l INFO -L 9:96714156-127734373 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:52Z] INFO  17:52:59,415 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:52Z] INFO  17:52:59,416 HelpFormatter - Date/Time: 2015/09/30 17:52:59
[2015-09-30T16:52Z] INFO  17:52:59,416 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:52Z] INFO  17:52:59,416 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:52Z] INFO  17:52:59,482 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:52Z] INFO  17:52:59,594 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:52Z] INFO  17:52:59,602 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:52Z] INFO  17:52:59,616 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:52Z] INFO  17:52:59,854 IntervalUtils - Processing 31020218 bp from intervals
[2015-09-30T16:52Z] WARN  17:52:59,858 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:52Z] INFO  17:52:59,911 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:53Z] INFO  17:53:00,056 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:53Z] INFO  17:53:00,056 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:53Z] INFO  17:53:00,056 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:53Z] INFO  17:53:00,057 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:53Z] INFO  17:53:12,929 ProgressMeter -      9:73391473    200003.0    30.0 s       2.5 m       25.4%   118.0 s      88.0 s
[2015-09-30T16:53Z] INFO  17:53:15,473 ProgressMeter -     9:136339603    800015.0    90.0 s     112.0 s       63.8%     2.3 m      50.0 s
[2015-09-30T16:53Z] INFO  17:53:30,059 ProgressMeter -     9:127226961   3.0507605E7    30.0 s       0.0 s       98.4%    30.0 s       0.0 s
[2015-09-30T16:53Z] INFO  17:53:31,111 ProgressMeter -            done   3.1020218E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T16:53Z] INFO  17:53:31,112 ProgressMeter - Total runtime 31.06 secs, 0.52 min, 0.01 hours
[2015-09-30T16:53Z] INFO  17:53:31,115 MicroScheduler - 86267 reads were filtered out during the traversal out of approximately 1074342 total reads (8.03%)
[2015-09-30T16:53Z] INFO  17:53:31,115 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:53Z] INFO  17:53:31,116 MicroScheduler -   -> 12073 reads (1.12% of total) failing BadMateFilter
[2015-09-30T16:53Z] INFO  17:53:31,116 MicroScheduler -   -> 48915 reads (4.55% of total) failing DuplicateReadFilter
[2015-09-30T16:53Z] INFO  17:53:31,116 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:53Z] INFO  17:53:31,116 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:53Z] INFO  17:53:31,117 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:53Z] INFO  17:53:31,117 MicroScheduler -   -> 25279 reads (2.35% of total) failing MappingQualityZeroFilter
[2015-09-30T16:53Z] INFO  17:53:31,117 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:53Z] INFO  17:53:31,117 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:53Z] INFO  17:53:31,117 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:53Z] INFO  17:53:32,086 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:53Z] GATK: realign ('9', 96714155, 127734373) : syn3-tumor
[2015-09-30T16:53Z] INFO  17:53:33,006 ProgressMeter -            done    749625.0    50.0 s      66.0 s      100.0%    50.0 s       0.0 s
[2015-09-30T16:53Z] INFO  17:53:33,007 ProgressMeter - Total runtime 50.08 secs, 0.83 min, 0.01 hours
[2015-09-30T16:53Z] INFO  17:53:33,010 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 749625 total reads (0.00%)
[2015-09-30T16:53Z] INFO  17:53:33,010 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:53Z] INFO  17:53:33,011 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:53Z] INFO  17:53:33,011 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:53Z] INFO  17:53:34,146 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:53Z] INFO  17:53:34,285 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:53Z] INFO  17:53:34,287 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:53Z] INFO  17:53:34,287 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:53Z] INFO  17:53:34,287 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:53Z] INFO  17:53:34,290 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep-prealign-realign.intervals -L 9:96714156-127734373 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpM8p75S/2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam
[2015-09-30T16:53Z] INFO  17:53:34,296 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:53Z] INFO  17:53:34,296 HelpFormatter - Date/Time: 2015/09/30 17:53:34
[2015-09-30T16:53Z] INFO  17:53:34,296 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:53Z] INFO  17:53:34,296 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:53Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam
[2015-09-30T16:53Z] INFO  17:53:34,435 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:53Z] INFO  17:53:34,528 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:53Z] INFO  17:53:34,535 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:53Z] INFO  17:53:34,567 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T16:53Z] INFO  17:53:34,813 IntervalUtils - Processing 31020218 bp from intervals
[2015-09-30T16:53Z] WARN  17:53:34,817 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:53Z] INFO  17:53:34,884 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:53Z] INFO  17:53:35,030 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:53Z] INFO  17:53:35,030 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:53Z] INFO  17:53:35,031 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:53Z] INFO  17:53:35,031 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:53Z] INFO  17:53:35,185 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:53Z] INFO  17:53:35,381 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:53Z] GATK pre-alignment ('10', 0, 31134673) : syn3-tumor
[2015-09-30T16:53Z] INFO  17:53:38,001 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:53Z] INFO  17:53:38,003 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:53Z] INFO  17:53:38,003 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:53Z] INFO  17:53:38,003 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:53Z] INFO  17:53:38,007 HelpFormatter - Program Args: -T PrintReads -L 10:1-31134673 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpF8cs4D/2_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam
[2015-09-30T16:53Z] INFO  17:53:38,012 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:53Z] INFO  17:53:38,013 HelpFormatter - Date/Time: 2015/09/30 17:53:38
[2015-09-30T16:53Z] INFO  17:53:38,013 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:53Z] INFO  17:53:38,013 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:53Z] INFO  17:53:38,395 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:53Z] INFO  17:53:39,310 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:53Z] INFO  17:53:39,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:53Z] INFO  17:53:39,368 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:53Z] INFO  17:53:39,383 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:53Z] INFO  17:53:39,396 IntervalUtils - Processing 31134673 bp from intervals
[2015-09-30T16:53Z] INFO  17:53:39,455 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:53Z] INFO  17:53:39,673 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:53Z] INFO  17:53:39,674 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:53Z] INFO  17:53:39,674 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:53Z] INFO  17:53:39,674 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:53Z] INFO  17:53:39,685 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:53Z] INFO  17:53:39,891 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:53Z] INFO  17:53:55,474 ProgressMeter -     9:140008203   1200020.0     2.2 m     108.0 s       91.1%     2.4 m      12.0 s
[2015-09-30T16:54Z] INFO  17:54:05,033 ProgressMeter -     9:115480682    500006.0    30.0 s      60.0 s       60.5%    49.0 s      19.0 s
[2015-09-30T16:54Z] INFO  17:54:09,846 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T16:54Z] INFO  17:54:09,852 ProgressMeter -      10:7763598    200003.0    30.0 s       2.5 m       24.9%   120.0 s      90.0 s
[2015-09-30T16:54Z] INFO  17:54:10,218 ProgressMeter -            done   1440512.0     2.4 m     100.0 s       99.4%     2.4 m       0.0 s
[2015-09-30T16:54Z] INFO  17:54:10,218 ProgressMeter - Total runtime 144.75 secs, 2.41 min, 0.04 hours
[2015-09-30T16:54Z] INFO  17:54:10,219 MicroScheduler - 1826 reads were filtered out during the traversal out of approximately 1442338 total reads (0.13%)
[2015-09-30T16:54Z] INFO  17:54:10,219 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:54Z] INFO  17:54:10,219 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:54Z] INFO  17:54:10,219 MicroScheduler -   -> 1826 reads (0.13% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:54Z] INFO  17:54:11,491 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:54Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam
[2015-09-30T16:54Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam 9:127737329-141213431
[2015-09-30T16:54Z] GATK: RealignerTargetCreator
[2015-09-30T16:54Z] INFO  17:54:18,279 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:54Z] INFO  17:54:18,280 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:54Z] INFO  17:54:18,281 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:54Z] INFO  17:54:18,281 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:54Z] INFO  17:54:18,285 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpMEVlxJ/2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign-realign.intervals -l INFO -L 9:127737329-141213431 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:54Z] INFO  17:54:18,294 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:54Z] INFO  17:54:18,295 HelpFormatter - Date/Time: 2015/09/30 17:54:18
[2015-09-30T16:54Z] INFO  17:54:18,295 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:54Z] INFO  17:54:18,295 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:54Z] INFO  17:54:18,354 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:54Z] INFO  17:54:18,566 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:54Z] INFO  17:54:18,574 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:54Z] INFO  17:54:18,590 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:54Z] INFO  17:54:18,831 IntervalUtils - Processing 13476103 bp from intervals
[2015-09-30T16:54Z] WARN  17:54:18,835 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:54Z] INFO  17:54:18,893 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:54Z] INFO  17:54:18,990 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:54Z] INFO  17:54:18,991 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:54Z] INFO  17:54:18,991 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:54Z] INFO  17:54:18,991 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:54Z] INFO  17:54:23,320 ProgressMeter -            done   1068302.0    48.0 s      45.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T16:54Z] INFO  17:54:23,320 ProgressMeter - Total runtime 48.29 secs, 0.80 min, 0.01 hours
[2015-09-30T16:54Z] INFO  17:54:23,324 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1068302 total reads (0.00%)
[2015-09-30T16:54Z] INFO  17:54:23,324 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:54Z] INFO  17:54:23,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:54Z] INFO  17:54:23,325 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:54Z] INFO  17:54:24,628 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:54Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam
[2015-09-30T16:54Z] GATK pre-alignment ('10', 31137165, 62208748) : syn3-tumor
[2015-09-30T16:54Z] INFO  17:54:28,965 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:54Z] INFO  17:54:28,967 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:54Z] INFO  17:54:28,967 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:54Z] INFO  17:54:28,968 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:54Z] INFO  17:54:28,971 HelpFormatter - Program Args: -T PrintReads -L 10:31137166-62208748 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpcZNKPZ/2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam
[2015-09-30T16:54Z] INFO  17:54:28,976 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:54Z] INFO  17:54:28,977 HelpFormatter - Date/Time: 2015/09/30 17:54:28
[2015-09-30T16:54Z] INFO  17:54:28,977 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:54Z] INFO  17:54:28,977 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:54Z] INFO  17:54:29,093 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:54Z] INFO  17:54:29,772 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:54Z] INFO  17:54:29,819 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:54Z] INFO  17:54:29,826 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:54Z] INFO  17:54:29,840 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:54Z] INFO  17:54:29,852 IntervalUtils - Processing 31071583 bp from intervals
[2015-09-30T16:54Z] INFO  17:54:29,905 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:54Z] INFO  17:54:30,101 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:54Z] INFO  17:54:30,101 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:54Z] INFO  17:54:30,101 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:54Z] INFO  17:54:30,102 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:54Z] INFO  17:54:30,113 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:54Z] INFO  17:54:30,320 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:54Z] INFO  17:54:39,889 ProgressMeter -     10:21309516    500017.0    60.0 s     120.0 s       68.4%    87.0 s      27.0 s
[2015-09-30T16:54Z] INFO  17:54:46,666 ProgressMeter -            done   1.3476103E7    27.0 s       2.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T16:54Z] INFO  17:54:46,667 ProgressMeter - Total runtime 27.68 secs, 0.46 min, 0.01 hours
[2015-09-30T16:54Z] INFO  17:54:46,670 MicroScheduler - 121111 reads were filtered out during the traversal out of approximately 1448844 total reads (8.36%)
[2015-09-30T16:54Z] INFO  17:54:46,670 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:54Z] INFO  17:54:46,671 MicroScheduler -   -> 10737 reads (0.74% of total) failing BadMateFilter
[2015-09-30T16:54Z] INFO  17:54:46,671 MicroScheduler -   -> 77099 reads (5.32% of total) failing DuplicateReadFilter
[2015-09-30T16:54Z] INFO  17:54:46,671 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:54Z] INFO  17:54:46,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:54Z] INFO  17:54:46,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:54Z] INFO  17:54:46,672 MicroScheduler -   -> 33275 reads (2.30% of total) failing MappingQualityZeroFilter
[2015-09-30T16:54Z] INFO  17:54:46,672 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:54Z] INFO  17:54:46,672 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:54Z] INFO  17:54:46,673 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:54Z] INFO  17:54:47,623 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:54Z] GATK: realign ('9', 127737328, 141213431) : syn3-tumor
[2015-09-30T16:54Z] INFO  17:54:49,369 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:54Z] INFO  17:54:49,371 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:54Z] INFO  17:54:49,371 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:54Z] INFO  17:54:49,371 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:54Z] INFO  17:54:49,375 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep-prealign-realign.intervals -L 9:127737329-141213431 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/tx/tmpDKDQo4/2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam
[2015-09-30T16:54Z] INFO  17:54:49,380 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:54Z] INFO  17:54:49,381 HelpFormatter - Date/Time: 2015/09/30 17:54:49
[2015-09-30T16:54Z] INFO  17:54:49,381 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:54Z] INFO  17:54:49,381 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:54Z] INFO  17:54:49,846 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:54Z] INFO  17:54:49,915 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:54Z] INFO  17:54:49,923 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:54Z] INFO  17:54:49,939 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:54Z] INFO  17:54:50,167 IntervalUtils - Processing 13476103 bp from intervals
[2015-09-30T16:54Z] WARN  17:54:50,171 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:54Z] INFO  17:54:50,226 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:54Z] INFO  17:54:50,372 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:54Z] INFO  17:54:50,373 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:54Z] INFO  17:54:50,373 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:54Z] INFO  17:54:50,373 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:54Z] INFO  17:54:50,502 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:54Z] INFO  17:54:50,600 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:55Z] INFO  17:55:00,304 ProgressMeter -     10:46251909    200002.0    30.0 s       2.5 m       48.6%    61.0 s      31.0 s
[2015-09-30T16:55Z] INFO  17:55:00,824 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:55Z] INFO  17:55:00,955 ProgressMeter -            done    760537.0    81.0 s     106.0 s      100.0%    81.0 s       0.0 s
[2015-09-30T16:55Z] INFO  17:55:00,956 ProgressMeter - Total runtime 81.28 secs, 1.35 min, 0.02 hours
[2015-09-30T16:55Z] INFO  17:55:00,956 MicroScheduler - 2147 reads were filtered out during the traversal out of approximately 762684 total reads (0.28%)
[2015-09-30T16:55Z] INFO  17:55:00,956 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:55Z] INFO  17:55:00,956 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:55Z] INFO  17:55:00,957 MicroScheduler -   -> 2147 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:55Z] INFO  17:55:01,989 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:55Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam
[2015-09-30T16:55Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam 10:1-31134673
[2015-09-30T16:55Z] GATK: RealignerTargetCreator
[2015-09-30T16:55Z] INFO  17:55:05,541 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:55Z] INFO  17:55:05,543 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:55Z] INFO  17:55:05,543 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:55Z] INFO  17:55:05,543 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:55Z] INFO  17:55:05,547 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmp_OLp2i/2_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign-realign.intervals -l INFO -L 10:1-31134673 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:55Z] INFO  17:55:05,552 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:55Z] INFO  17:55:05,553 HelpFormatter - Date/Time: 2015/09/30 17:55:05
[2015-09-30T16:55Z] INFO  17:55:05,553 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:55Z] INFO  17:55:05,553 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:55Z] INFO  17:55:05,610 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:55Z] INFO  17:55:05,718 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:55Z] INFO  17:55:05,726 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:55Z] INFO  17:55:05,742 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:55Z] INFO  17:55:06,127 IntervalUtils - Processing 31134673 bp from intervals
[2015-09-30T16:55Z] WARN  17:55:06,131 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:55Z] INFO  17:55:06,251 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:55Z] INFO  17:55:06,393 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:55Z] INFO  17:55:06,393 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:55Z] INFO  17:55:06,394 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:55Z] INFO  17:55:06,394 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:55Z] INFO  17:55:20,915 ProgressMeter -     9:133972439    500011.0    30.0 s      61.0 s       46.3%    64.0 s      34.0 s
[2015-09-30T16:55Z] INFO  17:55:30,331 ProgressMeter -     10:53898653    500007.0    60.0 s     120.0 s       73.3%    81.0 s      21.0 s
[2015-09-30T16:55Z] INFO  17:55:33,928 ProgressMeter -            done   3.1134673E7    27.0 s       0.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T16:55Z] INFO  17:55:33,929 ProgressMeter - Total runtime 27.54 secs, 0.46 min, 0.01 hours
[2015-09-30T16:55Z] INFO  17:55:33,932 MicroScheduler - 68442 reads were filtered out during the traversal out of approximately 765640 total reads (8.94%)
[2015-09-30T16:55Z] INFO  17:55:33,932 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:55Z] INFO  17:55:33,932 MicroScheduler -   -> 11173 reads (1.46% of total) failing BadMateFilter
[2015-09-30T16:55Z] INFO  17:55:33,933 MicroScheduler -   -> 32562 reads (4.25% of total) failing DuplicateReadFilter
[2015-09-30T16:55Z] INFO  17:55:33,933 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:55Z] INFO  17:55:33,933 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:55Z] INFO  17:55:33,933 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:55Z] INFO  17:55:33,934 MicroScheduler -   -> 24707 reads (3.23% of total) failing MappingQualityZeroFilter
[2015-09-30T16:55Z] INFO  17:55:33,934 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:55Z] INFO  17:55:33,934 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:55Z] INFO  17:55:33,934 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:55Z] INFO  17:55:35,046 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:55Z] GATK: realign ('10', 0, 31134673) : syn3-tumor
[2015-09-30T16:55Z] INFO  17:55:36,403 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:55Z] INFO  17:55:36,590 ProgressMeter -            done    636453.0    66.0 s     104.0 s      100.0%    66.0 s       0.0 s
[2015-09-30T16:55Z] INFO  17:55:36,590 ProgressMeter - Total runtime 66.49 secs, 1.11 min, 0.02 hours
[2015-09-30T16:55Z] INFO  17:55:36,590 MicroScheduler - 2505 reads were filtered out during the traversal out of approximately 638958 total reads (0.39%)
[2015-09-30T16:55Z] INFO  17:55:36,590 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:55Z] INFO  17:55:36,591 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:55Z] INFO  17:55:36,591 MicroScheduler -   -> 2505 reads (0.39% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:55Z] INFO  17:55:36,823 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:55Z] INFO  17:55:36,825 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:55Z] INFO  17:55:36,825 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:55Z] INFO  17:55:36,825 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:55Z] INFO  17:55:36,829 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_0_31134673-prep-prealign-realign.intervals -L 10:1-31134673 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpQsf1WC/2_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam
[2015-09-30T16:55Z] INFO  17:55:36,835 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:55Z] INFO  17:55:36,835 HelpFormatter - Date/Time: 2015/09/30 17:55:36
[2015-09-30T16:55Z] INFO  17:55:36,835 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:55Z] INFO  17:55:36,835 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:55Z] INFO  17:55:36,960 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:55Z] INFO  17:55:37,028 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:55Z] INFO  17:55:37,036 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:55Z] INFO  17:55:37,052 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:55Z] INFO  17:55:37,287 IntervalUtils - Processing 31134673 bp from intervals
[2015-09-30T16:55Z] WARN  17:55:37,292 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:55Z] INFO  17:55:37,350 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:55Z] INFO  17:55:37,490 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:55Z] INFO  17:55:37,491 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:55Z] INFO  17:55:37,491 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:55Z] INFO  17:55:37,492 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:55Z] INFO  17:55:37,596 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:55Z] INFO  17:55:37,638 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:55Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam
[2015-09-30T16:55Z] INFO  17:55:37,846 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:55Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam 10:31137166-62208748
[2015-09-30T16:55Z] GATK: RealignerTargetCreator
[2015-09-30T16:55Z] INFO  17:55:42,293 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:55Z] INFO  17:55:42,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:55Z] INFO  17:55:42,296 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:55Z] INFO  17:55:42,296 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:55Z] INFO  17:55:42,300 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmp0D5ONG/2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign-realign.intervals -l INFO -L 10:31137166-62208748 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:55Z] INFO  17:55:42,306 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:55Z] INFO  17:55:42,306 HelpFormatter - Date/Time: 2015/09/30 17:55:42
[2015-09-30T16:55Z] INFO  17:55:42,306 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:55Z] INFO  17:55:42,306 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:55Z] INFO  17:55:42,508 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:55Z] INFO  17:55:42,679 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:55Z] INFO  17:55:42,687 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:55Z] INFO  17:55:42,780 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2015-09-30T16:55Z] INFO  17:55:43,249 IntervalUtils - Processing 31071583 bp from intervals
[2015-09-30T16:55Z] WARN  17:55:43,253 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:55Z] INFO  17:55:43,311 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:55Z] INFO  17:55:44,090 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:55Z] INFO  17:55:44,091 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:55Z] INFO  17:55:44,091 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:55Z] INFO  17:55:44,091 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:55Z] INFO  17:55:50,916 ProgressMeter -     9:140251381   1300021.0    60.0 s      46.0 s       92.9%    64.0 s       4.0 s
[2015-09-30T16:55Z] INFO  17:55:54,036 ProgressMeter -            done   1440512.0    63.0 s      44.0 s       99.4%    63.0 s       0.0 s
[2015-09-30T16:55Z] INFO  17:55:54,036 ProgressMeter - Total runtime 63.66 secs, 1.06 min, 0.02 hours
[2015-09-30T16:55Z] INFO  17:55:54,039 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1440512 total reads (0.00%)
[2015-09-30T16:55Z] INFO  17:55:54,039 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:55Z] INFO  17:55:54,039 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:55Z] INFO  17:55:54,040 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:55Z] INFO  17:55:55,173 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:55Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam
[2015-09-30T16:55Z] GATK pre-alignment ('10', 62267938, 93388847) : syn3-tumor
[2015-09-30T16:56Z] INFO  17:56:00,641 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:00,643 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:56Z] INFO  17:56:00,643 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:56Z] INFO  17:56:00,643 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:56Z] INFO  17:56:00,647 HelpFormatter - Program Args: -T PrintReads -L 10:62267939-93388847 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpzkxjkb/2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam
[2015-09-30T16:56Z] INFO  17:56:00,652 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:56Z] INFO  17:56:00,653 HelpFormatter - Date/Time: 2015/09/30 17:56:00
[2015-09-30T16:56Z] INFO  17:56:00,653 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:00,653 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:00,759 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:56Z] INFO  17:56:01,767 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:56Z] INFO  17:56:01,816 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:56Z] INFO  17:56:01,824 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:56Z] INFO  17:56:01,838 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:56Z] INFO  17:56:01,852 IntervalUtils - Processing 31120909 bp from intervals
[2015-09-30T16:56Z] INFO  17:56:01,909 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:56Z] INFO  17:56:02,137 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:56Z] INFO  17:56:02,138 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:56Z] INFO  17:56:02,138 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:56Z] INFO  17:56:02,138 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:56Z] INFO  17:56:02,149 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:56Z] INFO  17:56:02,344 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:56Z] INFO  17:56:07,494 ProgressMeter -     10:18955657    500017.0    30.0 s      60.0 s       60.9%    49.0 s      19.0 s
[2015-09-30T16:56Z] INFO  17:56:07,588 ProgressMeter -            done   3.1071583E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T16:56Z] INFO  17:56:07,588 ProgressMeter - Total runtime 23.50 secs, 0.39 min, 0.01 hours
[2015-09-30T16:56Z] INFO  17:56:07,591 MicroScheduler - 142287 reads were filtered out during the traversal out of approximately 640652 total reads (22.21%)
[2015-09-30T16:56Z] INFO  17:56:07,592 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:56Z] INFO  17:56:07,592 MicroScheduler -   -> 9274 reads (1.45% of total) failing BadMateFilter
[2015-09-30T16:56Z] INFO  17:56:07,592 MicroScheduler -   -> 24113 reads (3.76% of total) failing DuplicateReadFilter
[2015-09-30T16:56Z] INFO  17:56:07,593 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:56Z] INFO  17:56:07,593 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:56Z] INFO  17:56:07,593 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:56Z] INFO  17:56:07,593 MicroScheduler -   -> 108900 reads (17.00% of total) failing MappingQualityZeroFilter
[2015-09-30T16:56Z] INFO  17:56:07,593 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:56Z] INFO  17:56:07,594 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:56Z] INFO  17:56:07,594 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:56Z] INFO  17:56:08,701 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:56Z] GATK: realign ('10', 31137165, 62208748) : syn3-tumor
[2015-09-30T16:56Z] INFO  17:56:10,582 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:10,584 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:56Z] INFO  17:56:10,584 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:56Z] INFO  17:56:10,585 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:56Z] INFO  17:56:10,588 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep-prealign-realign.intervals -L 10:31137166-62208748 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpOuZEQm/2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam
[2015-09-30T16:56Z] INFO  17:56:10,593 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:56Z] INFO  17:56:10,594 HelpFormatter - Date/Time: 2015/09/30 17:56:10
[2015-09-30T16:56Z] INFO  17:56:10,594 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:10,594 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:11,190 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:56Z] INFO  17:56:11,319 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:56Z] INFO  17:56:11,327 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:56Z] INFO  17:56:11,452 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2015-09-30T16:56Z] INFO  17:56:11,792 IntervalUtils - Processing 31071583 bp from intervals
[2015-09-30T16:56Z] WARN  17:56:11,796 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:56Z] INFO  17:56:12,054 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:56Z] INFO  17:56:12,442 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:56Z] INFO  17:56:12,442 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:56Z] INFO  17:56:12,443 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:56Z] INFO  17:56:12,443 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:56Z] INFO  17:56:12,677 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:56Z] INFO  17:56:12,875 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:56Z] INFO  17:56:16,499 ProgressMeter -            done    760537.0    39.0 s      51.0 s      100.0%    39.0 s       0.0 s
[2015-09-30T16:56Z] INFO  17:56:16,499 ProgressMeter - Total runtime 39.01 secs, 0.65 min, 0.01 hours
[2015-09-30T16:56Z] INFO  17:56:16,503 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 760537 total reads (0.00%)
[2015-09-30T16:56Z] INFO  17:56:16,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:56Z] INFO  17:56:16,503 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:56Z] INFO  17:56:16,504 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:56Z] INFO  17:56:17,692 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:56Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam
[2015-09-30T16:56Z] GATK pre-alignment ('10', 93389481, 124436664) : syn3-tumor
[2015-09-30T16:56Z] INFO  17:56:21,251 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:21,253 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:56Z] INFO  17:56:21,253 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:56Z] INFO  17:56:21,254 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:56Z] INFO  17:56:21,257 HelpFormatter - Program Args: -T PrintReads -L 10:93389482-124436664 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpshgBiQ/2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam
[2015-09-30T16:56Z] INFO  17:56:21,264 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:56Z] INFO  17:56:21,265 HelpFormatter - Date/Time: 2015/09/30 17:56:21
[2015-09-30T16:56Z] INFO  17:56:21,265 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:21,265 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:21,369 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:56Z] INFO  17:56:22,373 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:56Z] INFO  17:56:22,421 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:56Z] INFO  17:56:22,429 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:56Z] INFO  17:56:22,443 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:56Z] INFO  17:56:22,456 IntervalUtils - Processing 31047183 bp from intervals
[2015-09-30T16:56Z] INFO  17:56:22,512 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:56Z] INFO  17:56:22,740 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:56Z] INFO  17:56:22,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:56Z] INFO  17:56:22,740 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:56Z] INFO  17:56:22,741 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:56Z] INFO  17:56:22,751 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:56Z] INFO  17:56:22,955 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:56Z] INFO  17:56:32,145 ProgressMeter -     10:72327439    200005.0    30.0 s       2.5 m       32.3%    92.0 s      62.0 s
[2015-09-30T16:56Z] INFO  17:56:43,404 ProgressMeter -     10:61833549    600009.0    30.0 s      51.0 s       98.8%    30.0 s       0.0 s
[2015-09-30T16:56Z] INFO  17:56:44,887 ProgressMeter -            done    636453.0    32.0 s      50.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T16:56Z] INFO  17:56:44,888 ProgressMeter - Total runtime 32.45 secs, 0.54 min, 0.01 hours
[2015-09-30T16:56Z] INFO  17:56:44,891 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 636453 total reads (0.00%)
[2015-09-30T16:56Z] INFO  17:56:44,891 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:56Z] INFO  17:56:44,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:56Z] INFO  17:56:44,892 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:56Z] INFO  17:56:45,946 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:56Z] INFO  17:56:52,743 ProgressMeter -     10:98745630    200003.0    30.0 s       2.5 m       17.3%     2.9 m       2.4 m
[2015-09-30T16:56Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam
[2015-09-30T16:56Z] GATK pre-alignment ('10', 124438084, 135534747) : syn3-tumor
[2015-09-30T16:56Z] INFO  17:56:59,863 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:59,865 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:56Z] INFO  17:56:59,865 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:56Z] INFO  17:56:59,865 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:56Z] INFO  17:56:59,869 HelpFormatter - Program Args: -T PrintReads -L 10:124438085-135534747 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpf50wqh/2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam
[2015-09-30T16:56Z] INFO  17:56:59,874 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:56Z] INFO  17:56:59,874 HelpFormatter - Date/Time: 2015/09/30 17:56:59
[2015-09-30T16:56Z] INFO  17:56:59,875 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:59,875 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:56Z] INFO  17:56:59,980 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:57Z] INFO  17:57:00,685 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:57Z] INFO  17:57:00,733 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:57Z] INFO  17:57:00,740 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:57Z] INFO  17:57:00,755 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:57Z] INFO  17:57:00,767 IntervalUtils - Processing 11096663 bp from intervals
[2015-09-30T16:57Z] INFO  17:57:00,823 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:57Z] INFO  17:57:01,074 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:57Z] INFO  17:57:01,074 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:57Z] INFO  17:57:01,074 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:57Z] INFO  17:57:01,075 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:57Z] INFO  17:57:01,085 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:57Z] INFO  17:57:01,163 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:57Z] INFO  17:57:02,196 ProgressMeter -     10:77167125    500009.0    60.0 s     120.0 s       47.9%     2.1 m      65.0 s
[2015-09-30T16:57Z] INFO  17:57:23,304 ProgressMeter -    10:103543221    500010.0    60.0 s       2.0 m       32.7%     3.1 m       2.1 m
[2015-09-30T16:57Z] INFO  17:57:31,077 ProgressMeter -    10:134018150    200004.0    30.0 s       2.5 m       86.3%    34.0 s       4.0 s
[2015-09-30T16:57Z] INFO  17:57:35,094 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:57Z] INFO  17:57:35,253 ProgressMeter -            done    927311.0    93.0 s     100.0 s      100.0%    93.0 s       0.0 s
[2015-09-30T16:57Z] INFO  17:57:35,254 ProgressMeter - Total runtime 93.12 secs, 1.55 min, 0.03 hours
[2015-09-30T16:57Z] INFO  17:57:35,254 MicroScheduler - 1954 reads were filtered out during the traversal out of approximately 929265 total reads (0.21%)
[2015-09-30T16:57Z] INFO  17:57:35,254 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:57Z] INFO  17:57:35,255 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:57Z] INFO  17:57:35,255 MicroScheduler -   -> 1954 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:57Z] INFO  17:57:36,331 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:57Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam
[2015-09-30T16:57Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam 10:62267939-93388847
[2015-09-30T16:57Z] GATK: RealignerTargetCreator
[2015-09-30T16:57Z] INFO  17:57:40,649 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:57Z] INFO  17:57:40,651 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:57Z] INFO  17:57:40,651 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:57Z] INFO  17:57:40,651 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:57Z] INFO  17:57:40,655 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpEmQrki/2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign-realign.intervals -l INFO -L 10:62267939-93388847 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:57Z] INFO  17:57:40,729 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:57Z] INFO  17:57:40,729 HelpFormatter - Date/Time: 2015/09/30 17:57:40
[2015-09-30T16:57Z] INFO  17:57:40,729 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:57Z] INFO  17:57:40,729 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:57Z] INFO  17:57:40,932 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:57Z] INFO  17:57:41,109 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:57Z] INFO  17:57:41,117 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:57Z] INFO  17:57:41,187 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2015-09-30T16:57Z] INFO  17:57:41,606 IntervalUtils - Processing 31120909 bp from intervals
[2015-09-30T16:57Z] WARN  17:57:41,610 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:57Z] INFO  17:57:41,682 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:57Z] INFO  17:57:42,047 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:57Z] INFO  17:57:42,047 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:57Z] INFO  17:57:42,048 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:57Z] INFO  17:57:42,048 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:57Z] INFO  17:57:46,429 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:57Z] INFO  17:57:46,513 ProgressMeter -            done    439342.0    45.0 s     103.0 s       99.8%    45.0 s       0.0 s
[2015-09-30T16:57Z] INFO  17:57:46,514 ProgressMeter - Total runtime 45.44 secs, 0.76 min, 0.01 hours
[2015-09-30T16:57Z] INFO  17:57:46,514 MicroScheduler - 831 reads were filtered out during the traversal out of approximately 440173 total reads (0.19%)
[2015-09-30T16:57Z] INFO  17:57:46,514 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:57Z] INFO  17:57:46,515 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:57Z] INFO  17:57:46,515 MicroScheduler -   -> 831 reads (0.19% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:57Z] INFO  17:57:47,447 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:57Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam
[2015-09-30T16:57Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam 10:124438085-135534747
[2015-09-30T16:57Z] GATK: RealignerTargetCreator
[2015-09-30T16:57Z] INFO  17:57:50,122 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:57Z] INFO  17:57:50,124 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:57Z] INFO  17:57:50,124 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:57Z] INFO  17:57:50,124 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:57Z] INFO  17:57:50,127 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpFr2QWO/2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign-realign.intervals -l INFO -L 10:124438085-135534747 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:57Z] INFO  17:57:50,133 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:57Z] INFO  17:57:50,134 HelpFormatter - Date/Time: 2015/09/30 17:57:50
[2015-09-30T16:57Z] INFO  17:57:50,134 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:57Z] INFO  17:57:50,134 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:57Z] INFO  17:57:50,192 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:57Z] INFO  17:57:50,628 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:57Z] INFO  17:57:50,636 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:57Z] INFO  17:57:50,652 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:57Z] INFO  17:57:50,894 IntervalUtils - Processing 11096663 bp from intervals
[2015-09-30T16:57Z] WARN  17:57:50,898 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:57Z] INFO  17:57:50,954 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:57Z] INFO  17:57:51,035 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:57Z] INFO  17:57:51,035 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:57Z] INFO  17:57:51,036 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:57Z] INFO  17:57:51,036 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:58Z] INFO  17:58:03,305 ProgressMeter -    10:115897064    900018.0   100.0 s     111.0 s       72.5%     2.3 m      37.0 s
[2015-09-30T16:58Z] INFO  17:58:03,877 ProgressMeter -            done   1.1096663E7    12.0 s       1.0 s      100.0%    12.0 s       0.0 s
[2015-09-30T16:58Z] INFO  17:58:03,877 ProgressMeter - Total runtime 12.84 secs, 0.21 min, 0.00 hours
[2015-09-30T16:58Z] INFO  17:58:03,880 MicroScheduler - 38643 reads were filtered out during the traversal out of approximately 441369 total reads (8.76%)
[2015-09-30T16:58Z] INFO  17:58:03,881 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:58Z] INFO  17:58:03,881 MicroScheduler -   -> 4608 reads (1.04% of total) failing BadMateFilter
[2015-09-30T16:58Z] INFO  17:58:03,881 MicroScheduler -   -> 22245 reads (5.04% of total) failing DuplicateReadFilter
[2015-09-30T16:58Z] INFO  17:58:03,882 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:58Z] INFO  17:58:03,882 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:58Z] INFO  17:58:03,882 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:58Z] INFO  17:58:03,882 MicroScheduler -   -> 11790 reads (2.67% of total) failing MappingQualityZeroFilter
[2015-09-30T16:58Z] INFO  17:58:03,883 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:58Z] INFO  17:58:03,883 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:58Z] INFO  17:58:03,883 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:58Z] INFO  17:58:04,857 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:58Z] GATK: realign ('10', 124438084, 135534747) : syn3-tumor
[2015-09-30T16:58Z] INFO  17:58:06,883 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:06,885 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:58Z] INFO  17:58:06,885 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:58Z] INFO  17:58:06,885 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:58Z] INFO  17:58:06,888 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep-prealign-realign.intervals -L 10:124438085-135534747 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpfwPhsi/2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam
[2015-09-30T16:58Z] INFO  17:58:06,894 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:58Z] INFO  17:58:06,895 HelpFormatter - Date/Time: 2015/09/30 17:58:06
[2015-09-30T16:58Z] INFO  17:58:06,895 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:06,895 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:07,020 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:58Z] INFO  17:58:07,083 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:58Z] INFO  17:58:07,091 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:58Z] INFO  17:58:07,106 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:58Z] INFO  17:58:07,336 IntervalUtils - Processing 11096663 bp from intervals
[2015-09-30T16:58Z] WARN  17:58:07,339 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:58Z] INFO  17:58:07,395 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:58Z] INFO  17:58:07,472 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:58Z] INFO  17:58:07,473 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:58Z] INFO  17:58:07,473 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:58Z] INFO  17:58:07,473 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:58Z] INFO  17:58:07,577 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:58Z] INFO  17:58:07,663 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:58Z] INFO  17:58:09,130 ProgressMeter -            done   3.1120909E7    27.0 s       0.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T16:58Z] INFO  17:58:09,130 ProgressMeter - Total runtime 27.08 secs, 0.45 min, 0.01 hours
[2015-09-30T16:58Z] INFO  17:58:09,133 MicroScheduler - 85233 reads were filtered out during the traversal out of approximately 932811 total reads (9.14%)
[2015-09-30T16:58Z] INFO  17:58:09,134 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:58Z] INFO  17:58:09,134 MicroScheduler -   -> 10899 reads (1.17% of total) failing BadMateFilter
[2015-09-30T16:58Z] INFO  17:58:09,134 MicroScheduler -   -> 42777 reads (4.59% of total) failing DuplicateReadFilter
[2015-09-30T16:58Z] INFO  17:58:09,134 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:58Z] INFO  17:58:09,135 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:58Z] INFO  17:58:09,135 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:58Z] INFO  17:58:09,135 MicroScheduler -   -> 31557 reads (3.38% of total) failing MappingQualityZeroFilter
[2015-09-30T16:58Z] INFO  17:58:09,135 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:58Z] INFO  17:58:09,135 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:58Z] INFO  17:58:09,136 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:58Z] INFO  17:58:10,087 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:58Z] GATK: realign ('10', 62267938, 93388847) : syn3-tumor
[2015-09-30T16:58Z] INFO  17:58:11,860 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:11,862 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:58Z] INFO  17:58:11,862 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:58Z] INFO  17:58:11,862 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:58Z] INFO  17:58:11,866 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep-prealign-realign.intervals -L 10:62267939-93388847 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpgeusTK/2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam
[2015-09-30T16:58Z] INFO  17:58:11,871 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:58Z] INFO  17:58:11,872 HelpFormatter - Date/Time: 2015/09/30 17:58:11
[2015-09-30T16:58Z] INFO  17:58:11,872 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:11,872 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:12,608 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:58Z] INFO  17:58:12,767 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:58Z] INFO  17:58:12,775 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:58Z] INFO  17:58:12,925 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
[2015-09-30T16:58Z] INFO  17:58:13,345 IntervalUtils - Processing 31120909 bp from intervals
[2015-09-30T16:58Z] WARN  17:58:13,354 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:58Z] INFO  17:58:13,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:58Z] INFO  17:58:14,859 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:58Z] INFO  17:58:14,860 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:58Z] INFO  17:58:14,860 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:58Z] INFO  17:58:14,861 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:58Z] INFO  17:58:15,133 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:58Z] INFO  17:58:15,317 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:58Z] INFO  17:58:32,710 ProgressMeter -            done    439342.0    25.0 s      57.0 s       99.8%    25.0 s       0.0 s
[2015-09-30T16:58Z] INFO  17:58:32,711 ProgressMeter - Total runtime 25.24 secs, 0.42 min, 0.01 hours
[2015-09-30T16:58Z] INFO  17:58:32,714 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 439342 total reads (0.00%)
[2015-09-30T16:58Z] INFO  17:58:32,714 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:58Z] INFO  17:58:32,714 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:58Z] INFO  17:58:32,714 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:58Z] INFO  17:58:33,045 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T16:58Z] INFO  17:58:33,169 ProgressMeter -            done   1301131.0     2.2 m     100.0 s      100.0%     2.2 m       0.0 s
[2015-09-30T16:58Z] INFO  17:58:33,170 ProgressMeter - Total runtime 130.43 secs, 2.17 min, 0.04 hours
[2015-09-30T16:58Z] INFO  17:58:33,170 MicroScheduler - 2709 reads were filtered out during the traversal out of approximately 1303840 total reads (0.21%)
[2015-09-30T16:58Z] INFO  17:58:33,170 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:58Z] INFO  17:58:33,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:58Z] INFO  17:58:33,171 MicroScheduler -   -> 2709 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:58Z] INFO  17:58:33,693 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:58Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam
[2015-09-30T16:58Z] INFO  17:58:34,137 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:58Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam
[2015-09-30T16:58Z] GATK pre-alignment ('11', 0, 31082819) : syn3-tumor
[2015-09-30T16:58Z] INFO  17:58:36,557 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:36,558 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:58Z] INFO  17:58:36,559 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:58Z] INFO  17:58:36,559 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:58Z] INFO  17:58:36,562 HelpFormatter - Program Args: -T PrintReads -L 11:1-31082819 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpOdTmEb/2_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam
[2015-09-30T16:58Z] INFO  17:58:36,567 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:58Z] INFO  17:58:36,567 HelpFormatter - Date/Time: 2015/09/30 17:58:36
[2015-09-30T16:58Z] INFO  17:58:36,568 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:36,568 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:36,671 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:58Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam 10:93389482-124436664
[2015-09-30T16:58Z] GATK: RealignerTargetCreator
[2015-09-30T16:58Z] INFO  17:58:37,871 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:58Z] INFO  17:58:37,920 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:58Z] INFO  17:58:37,928 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:58Z] INFO  17:58:37,942 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:58Z] INFO  17:58:37,955 IntervalUtils - Processing 31082819 bp from intervals
[2015-09-30T16:58Z] INFO  17:58:38,012 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:58Z] INFO  17:58:38,215 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:58Z] INFO  17:58:38,215 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:58Z] INFO  17:58:38,215 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:58Z] INFO  17:58:38,215 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:58Z] INFO  17:58:38,226 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:58Z] INFO  17:58:38,422 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:58Z] INFO  17:58:39,352 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:39,354 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:58Z] INFO  17:58:39,354 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:58Z] INFO  17:58:39,354 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:58Z] INFO  17:58:39,358 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpAWVxqG/2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign-realign.intervals -l INFO -L 10:93389482-124436664 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T16:58Z] INFO  17:58:39,364 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:58Z] INFO  17:58:39,364 HelpFormatter - Date/Time: 2015/09/30 17:58:39
[2015-09-30T16:58Z] INFO  17:58:39,364 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:39,364 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:58Z] INFO  17:58:39,425 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:58Z] INFO  17:58:39,534 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T16:58Z] INFO  17:58:39,542 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:58Z] INFO  17:58:39,558 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:58Z] INFO  17:58:39,814 IntervalUtils - Processing 31047183 bp from intervals
[2015-09-30T16:58Z] WARN  17:58:39,818 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:58Z] INFO  17:58:39,876 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:58Z] INFO  17:58:40,024 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:58Z] INFO  17:58:40,025 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:58Z] INFO  17:58:40,025 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:58Z] INFO  17:58:40,025 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T16:58Z] INFO  17:58:45,234 ProgressMeter -     10:75613005    500009.0    30.0 s      60.0 s       42.9%    69.0 s      39.0 s
[2015-09-30T16:59Z] INFO  17:59:01,099 ProgressMeter -            done    927311.0    46.0 s      49.0 s      100.0%    46.0 s       0.0 s
[2015-09-30T16:59Z] INFO  17:59:01,099 ProgressMeter - Total runtime 46.24 secs, 0.77 min, 0.01 hours
[2015-09-30T16:59Z] INFO  17:59:01,102 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 927311 total reads (0.00%)
[2015-09-30T16:59Z] INFO  17:59:01,103 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:59Z] INFO  17:59:01,103 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:59Z] INFO  17:59:01,103 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:59Z] INFO  17:59:02,226 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:59Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam
[2015-09-30T16:59Z] GATK pre-alignment ('11', 31085657, 62105890) : syn3-tumor
[2015-09-30T16:59Z] INFO  17:59:06,468 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:59Z] INFO  17:59:06,470 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:59Z] INFO  17:59:06,470 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:59Z] INFO  17:59:06,470 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:59Z] INFO  17:59:06,474 HelpFormatter - Program Args: -T PrintReads -L 11:31085658-62105890 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmp_DjOLg/2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam
[2015-09-30T16:59Z] INFO  17:59:06,479 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:59Z] INFO  17:59:06,480 HelpFormatter - Date/Time: 2015/09/30 17:59:06
[2015-09-30T16:59Z] INFO  17:59:06,480 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:59Z] INFO  17:59:06,480 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:59Z] INFO  17:59:06,973 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:59Z] INFO  17:59:07,668 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T16:59Z] INFO  17:59:07,716 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T16:59Z] INFO  17:59:07,724 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:59Z] INFO  17:59:07,738 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T16:59Z] INFO  17:59:07,752 IntervalUtils - Processing 31020233 bp from intervals
[2015-09-30T16:59Z] INFO  17:59:07,810 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:59Z] INFO  17:59:08,012 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:59Z] INFO  17:59:08,013 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:59Z] INFO  17:59:08,013 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:59Z] INFO  17:59:08,013 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:59Z] INFO  17:59:08,024 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:59Z] INFO  17:59:08,218 ProgressMeter -      11:1271386    200002.0    30.0 s       2.5 m        4.1%    12.2 m      11.7 m
[2015-09-30T16:59Z] INFO  17:59:08,222 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:59Z] INFO  17:59:10,028 ProgressMeter -    10:118641245   2.5247063E7    30.0 s       1.0 s       81.3%    36.0 s       6.0 s
[2015-09-30T16:59Z] INFO  17:59:16,300 ProgressMeter -            done   3.1047183E7    36.0 s       1.0 s      100.0%    36.0 s       0.0 s
[2015-09-30T16:59Z] INFO  17:59:16,301 ProgressMeter - Total runtime 36.28 secs, 0.60 min, 0.01 hours
[2015-09-30T16:59Z] INFO  17:59:16,304 MicroScheduler - 104075 reads were filtered out during the traversal out of approximately 1308471 total reads (7.95%)
[2015-09-30T16:59Z] INFO  17:59:16,304 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T16:59Z] INFO  17:59:16,305 MicroScheduler -   -> 13997 reads (1.07% of total) failing BadMateFilter
[2015-09-30T16:59Z] INFO  17:59:16,305 MicroScheduler -   -> 59148 reads (4.52% of total) failing DuplicateReadFilter
[2015-09-30T16:59Z] INFO  17:59:16,305 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T16:59Z] INFO  17:59:16,305 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T16:59Z] INFO  17:59:16,306 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T16:59Z] INFO  17:59:16,306 MicroScheduler -   -> 30930 reads (2.36% of total) failing MappingQualityZeroFilter
[2015-09-30T16:59Z] INFO  17:59:16,306 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T16:59Z] INFO  17:59:16,306 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T16:59Z] INFO  17:59:16,307 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T16:59Z] INFO  17:59:17,292 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T16:59Z] GATK: realign ('10', 93389481, 124436664) : syn3-tumor
[2015-09-30T16:59Z] INFO  17:59:19,212 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:59Z] INFO  17:59:19,214 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T16:59Z] INFO  17:59:19,214 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T16:59Z] INFO  17:59:19,214 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T16:59Z] INFO  17:59:19,218 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep-prealign-realign.intervals -L 10:93389482-124436664 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/tx/tmpZYvwwd/2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam
[2015-09-30T16:59Z] INFO  17:59:19,223 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T16:59Z] INFO  17:59:19,223 HelpFormatter - Date/Time: 2015/09/30 17:59:19
[2015-09-30T16:59Z] INFO  17:59:19,224 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:59Z] INFO  17:59:19,224 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T16:59Z] INFO  17:59:19,351 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T16:59Z] INFO  17:59:19,416 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T16:59Z] INFO  17:59:19,423 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T16:59Z] INFO  17:59:19,439 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T16:59Z] INFO  17:59:19,945 IntervalUtils - Processing 31047183 bp from intervals
[2015-09-30T16:59Z] WARN  17:59:19,949 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T16:59Z] INFO  17:59:20,005 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T16:59Z] INFO  17:59:20,333 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T16:59Z] INFO  17:59:20,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T16:59Z] INFO  17:59:20,333 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T16:59Z] INFO  17:59:20,334 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T16:59Z] INFO  17:59:20,493 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T16:59Z] INFO  17:59:20,683 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T16:59Z] INFO  17:59:38,015 ProgressMeter -     11:45265488    200003.0    30.0 s       2.5 m       45.7%    65.0 s      35.0 s
[2015-09-30T16:59Z] INFO  17:59:38,219 ProgressMeter -      11:5656185    500005.0    60.0 s     120.0 s       18.2%     5.5 m       4.5 m
[2015-09-30T16:59Z] INFO  17:59:51,531 ProgressMeter -    10:103609007    500010.0    31.0 s      62.0 s       32.9%    94.0 s      63.0 s
[2015-09-30T17:00Z] INFO  18:00:08,016 ProgressMeter -     11:55072048    500007.0    60.0 s     120.0 s       77.3%    77.0 s      17.0 s
[2015-09-30T17:00Z] INFO  18:00:08,543 ProgressMeter -     11:11362459    900010.0    90.0 s     100.0 s       36.6%     4.1 m       2.6 m
[2015-09-30T17:00Z] INFO  18:00:21,532 ProgressMeter -    10:124436742   1300025.0    61.0 s      47.0 s      100.0%    61.0 s       0.0 s
[2015-09-30T17:00Z] INFO  18:00:21,649 ProgressMeter -            done   1301131.0    61.0 s      47.0 s      100.0%    61.0 s       0.0 s
[2015-09-30T17:00Z] INFO  18:00:21,649 ProgressMeter - Total runtime 61.32 secs, 1.02 min, 0.02 hours
[2015-09-30T17:00Z] INFO  18:00:21,652 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1301131 total reads (0.00%)
[2015-09-30T17:00Z] INFO  18:00:21,652 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:00Z] INFO  18:00:21,653 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:00Z] INFO  18:00:21,653 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:00Z] INFO  18:00:22,843 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:00Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam
[2015-09-30T17:00Z] GATK pre-alignment ('11', 62123540, 93141822) : syn3-tumor
[2015-09-30T17:00Z] INFO  18:00:27,932 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:00Z] INFO  18:00:27,934 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:00Z] INFO  18:00:27,934 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:00Z] INFO  18:00:27,934 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:00Z] INFO  18:00:27,938 HelpFormatter - Program Args: -T PrintReads -L 11:62123541-93141822 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpOKk0ZM/2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam
[2015-09-30T17:00Z] INFO  18:00:27,944 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:00Z] INFO  18:00:27,944 HelpFormatter - Date/Time: 2015/09/30 18:00:27
[2015-09-30T17:00Z] INFO  18:00:27,944 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:00Z] INFO  18:00:27,944 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:00Z] INFO  18:00:28,062 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:00Z] INFO  18:00:29,177 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:00Z] INFO  18:00:29,227 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:00Z] INFO  18:00:29,235 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:00Z] INFO  18:00:29,249 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:00Z] INFO  18:00:29,263 IntervalUtils - Processing 31018282 bp from intervals
[2015-09-30T17:00Z] INFO  18:00:29,320 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:00Z] INFO  18:00:29,542 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:00Z] INFO  18:00:29,542 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:00Z] INFO  18:00:29,543 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:00Z] INFO  18:00:29,543 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:00Z] INFO  18:00:29,554 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:00Z] INFO  18:00:29,769 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:00Z] INFO  18:00:38,017 ProgressMeter -     11:60980401    800010.0    90.0 s     112.0 s       96.4%    93.0 s       3.0 s
[2015-09-30T17:00Z] INFO  18:00:38,544 ProgressMeter -     11:20058229   1200014.0   120.0 s     100.0 s       64.5%     3.1 m      65.0 s
[2015-09-30T17:00Z] INFO  18:00:48,945 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:00Z] INFO  18:00:49,220 ProgressMeter -            done   1357245.0     2.2 m      96.0 s      100.0%     2.2 m       0.0 s
[2015-09-30T17:00Z] INFO  18:00:49,220 ProgressMeter - Total runtime 131.01 secs, 2.18 min, 0.04 hours
[2015-09-30T17:00Z] INFO  18:00:49,221 MicroScheduler - 2662 reads were filtered out during the traversal out of approximately 1359907 total reads (0.20%)
[2015-09-30T17:00Z] INFO  18:00:49,221 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:00Z] INFO  18:00:49,221 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:00Z] INFO  18:00:49,221 MicroScheduler -   -> 2662 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:00Z] INFO  18:00:50,363 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:00Z] INFO  18:00:50,447 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:00Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam
[2015-09-30T17:00Z] INFO  18:00:50,537 ProgressMeter -            done   1020618.0   102.0 s     100.0 s      100.0%   102.0 s       0.0 s
[2015-09-30T17:00Z] INFO  18:00:50,537 ProgressMeter - Total runtime 102.52 secs, 1.71 min, 0.03 hours
[2015-09-30T17:00Z] INFO  18:00:50,537 MicroScheduler - 2475 reads were filtered out during the traversal out of approximately 1023093 total reads (0.24%)
[2015-09-30T17:00Z] INFO  18:00:50,538 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:00Z] INFO  18:00:50,538 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:00Z] INFO  18:00:50,538 MicroScheduler -   -> 2475 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:00Z] INFO  18:00:51,542 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:00Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam
[2015-09-30T17:00Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam 11:31085658-62105890
[2015-09-30T17:00Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam 11:1-31082819
[2015-09-30T17:00Z] GATK: RealignerTargetCreator
[2015-09-30T17:00Z] GATK: RealignerTargetCreator
[2015-09-30T17:00Z] INFO  18:00:58,454 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:00Z] INFO  18:00:58,456 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:00Z] INFO  18:00:58,456 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:00Z] INFO  18:00:58,456 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:00Z] INFO  18:00:58,460 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpklq7UJ/2_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign-realign.intervals -l INFO -L 11:1-31082819 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:00Z] INFO  18:00:58,463 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:00Z] INFO  18:00:58,465 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:00Z] INFO  18:00:58,465 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:00Z] INFO  18:00:58,466 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:00Z] INFO  18:00:58,465 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:00Z] INFO  18:00:58,466 HelpFormatter - Date/Time: 2015/09/30 18:00:58
[2015-09-30T17:00Z] INFO  18:00:58,466 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:00Z] INFO  18:00:58,466 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:00Z] INFO  18:00:58,469 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmphptBKs/2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign-realign.intervals -l INFO -L 11:31085658-62105890 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:00Z] INFO  18:00:58,474 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:00Z] INFO  18:00:58,474 HelpFormatter - Date/Time: 2015/09/30 18:00:58
[2015-09-30T17:00Z] INFO  18:00:58,474 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:00Z] INFO  18:00:58,474 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:00Z] INFO  18:00:58,523 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:00Z] INFO  18:00:58,531 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:00Z] INFO  18:00:58,815 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:00Z] INFO  18:00:58,818 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:00Z] INFO  18:00:58,823 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:00Z] INFO  18:00:58,825 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:00Z] INFO  18:00:58,839 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:00Z] INFO  18:00:58,841 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:00Z] INFO  18:00:59,082 IntervalUtils - Processing 31082819 bp from intervals
[2015-09-30T17:00Z] WARN  18:00:59,086 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:00Z] INFO  18:00:59,146 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:00Z] INFO  18:00:59,149 IntervalUtils - Processing 31020233 bp from intervals
[2015-09-30T17:00Z] WARN  18:00:59,153 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:00Z] INFO  18:00:59,210 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:00Z] INFO  18:00:59,288 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:00Z] INFO  18:00:59,289 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:00Z] INFO  18:00:59,289 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:00Z] INFO  18:00:59,290 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:00Z] INFO  18:00:59,346 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:00Z] INFO  18:00:59,346 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:00Z] INFO  18:00:59,347 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:00Z] INFO  18:00:59,347 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:00Z] INFO  18:00:59,563 ProgressMeter -     11:64332359    200002.0    30.0 s       2.5 m        7.1%     7.0 m       6.5 m
[2015-09-30T17:01Z] INFO  18:01:28,500 ProgressMeter -            done   3.1020233E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T17:01Z] INFO  18:01:28,501 ProgressMeter - Total runtime 29.15 secs, 0.49 min, 0.01 hours
[2015-09-30T17:01Z] INFO  18:01:28,504 MicroScheduler - 84863 reads were filtered out during the traversal out of approximately 1026932 total reads (8.26%)
[2015-09-30T17:01Z] INFO  18:01:28,504 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:01Z] INFO  18:01:28,505 MicroScheduler -   -> 11130 reads (1.08% of total) failing BadMateFilter
[2015-09-30T17:01Z] INFO  18:01:28,505 MicroScheduler -   -> 47932 reads (4.67% of total) failing DuplicateReadFilter
[2015-09-30T17:01Z] INFO  18:01:28,505 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:01Z] INFO  18:01:28,505 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:01Z] INFO  18:01:28,506 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:01Z] INFO  18:01:28,506 MicroScheduler -   -> 25801 reads (2.51% of total) failing MappingQualityZeroFilter
[2015-09-30T17:01Z] INFO  18:01:28,506 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:01Z] INFO  18:01:28,506 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:01Z] INFO  18:01:28,506 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:01Z] INFO  18:01:29,292 ProgressMeter -     11:22400129   2.2396928E7    30.0 s       1.0 s       72.1%    41.0 s      11.0 s
[2015-09-30T17:01Z] INFO  18:01:29,475 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:01Z] GATK: realign ('11', 31085657, 62105890) : syn3-tumor
[2015-09-30T17:01Z] INFO  18:01:29,585 ProgressMeter -     11:65835442    500005.0    60.0 s     120.0 s       12.0%     8.4 m       7.4 m
[2015-09-30T17:01Z] INFO  18:01:31,464 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:01Z] INFO  18:01:31,466 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:01Z] INFO  18:01:31,466 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:01Z] INFO  18:01:31,466 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:01Z] INFO  18:01:31,470 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep-prealign-realign.intervals -L 11:31085658-62105890 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmprjyJiO/2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam
[2015-09-30T17:01Z] INFO  18:01:31,476 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:01Z] INFO  18:01:31,476 HelpFormatter - Date/Time: 2015/09/30 18:01:31
[2015-09-30T17:01Z] INFO  18:01:31,476 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:01Z] INFO  18:01:31,476 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:01Z] INFO  18:01:31,581 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:01Z] INFO  18:01:31,647 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:01Z] INFO  18:01:31,655 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:01Z] INFO  18:01:31,671 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:01Z] INFO  18:01:31,892 IntervalUtils - Processing 31020233 bp from intervals
[2015-09-30T17:01Z] WARN  18:01:31,896 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:01Z] INFO  18:01:31,950 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:01Z] INFO  18:01:32,079 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:01Z] INFO  18:01:32,080 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:01Z] INFO  18:01:32,080 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:01Z] INFO  18:01:32,081 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:01Z] INFO  18:01:32,218 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:01Z] INFO  18:01:32,391 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:01Z] INFO  18:01:34,277 ProgressMeter -            done   3.1082819E7    34.0 s       1.0 s      100.0%    34.0 s       0.0 s
[2015-09-30T17:01Z] INFO  18:01:34,278 ProgressMeter - Total runtime 34.99 secs, 0.58 min, 0.01 hours
[2015-09-30T17:01Z] INFO  18:01:34,278 MicroScheduler - 115731 reads were filtered out during the traversal out of approximately 1364693 total reads (8.48%)
[2015-09-30T17:01Z] INFO  18:01:34,278 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:01Z] INFO  18:01:34,279 MicroScheduler -   -> 13195 reads (0.97% of total) failing BadMateFilter
[2015-09-30T17:01Z] INFO  18:01:34,279 MicroScheduler -   -> 68677 reads (5.03% of total) failing DuplicateReadFilter
[2015-09-30T17:01Z] INFO  18:01:34,279 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:01Z] INFO  18:01:34,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:01Z] INFO  18:01:34,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:01Z] INFO  18:01:34,280 MicroScheduler -   -> 33859 reads (2.48% of total) failing MappingQualityZeroFilter
[2015-09-30T17:01Z] INFO  18:01:34,280 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:01Z] INFO  18:01:34,280 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:01Z] INFO  18:01:34,280 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:01Z] INFO  18:01:35,284 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:01Z] GATK: realign ('11', 0, 31082819) : syn3-tumor
[2015-09-30T17:01Z] INFO  18:01:37,094 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:01Z] INFO  18:01:37,096 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:01Z] INFO  18:01:37,096 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:01Z] INFO  18:01:37,097 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:01Z] INFO  18:01:37,100 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_0_31082819-prep-prealign-realign.intervals -L 11:1-31082819 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpUq4KTd/2_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam
[2015-09-30T17:01Z] INFO  18:01:37,106 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:01Z] INFO  18:01:37,106 HelpFormatter - Date/Time: 2015/09/30 18:01:37
[2015-09-30T17:01Z] INFO  18:01:37,106 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:01Z] INFO  18:01:37,106 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:01Z] INFO  18:01:37,230 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:01Z] INFO  18:01:37,295 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:01Z] INFO  18:01:37,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:01Z] INFO  18:01:37,318 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:01Z] INFO  18:01:37,542 IntervalUtils - Processing 31082819 bp from intervals
[2015-09-30T17:01Z] WARN  18:01:37,546 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:01Z] INFO  18:01:37,601 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:01Z] INFO  18:01:37,748 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:01Z] INFO  18:01:37,748 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:01Z] INFO  18:01:37,748 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:01Z] INFO  18:01:37,749 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:01Z] INFO  18:01:37,893 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:01Z] INFO  18:01:38,088 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:01Z] INFO  18:01:59,586 ProgressMeter -     11:68453370    800009.0    90.0 s     112.0 s       20.4%     7.4 m       5.9 m
[2015-09-30T17:02Z] INFO  18:02:02,229 ProgressMeter -     11:49071690    500007.0    30.0 s      60.0 s       58.0%    51.0 s      21.0 s
[2015-09-30T17:02Z] INFO  18:02:09,119 ProgressMeter -      11:5535612    500005.0    31.0 s      62.0 s       17.8%     2.9 m       2.4 m
[2015-09-30T17:02Z] INFO  18:02:19,359 ProgressMeter -            done   1020618.0    47.0 s      46.0 s      100.0%    47.0 s       0.0 s
[2015-09-30T17:02Z] INFO  18:02:19,360 ProgressMeter - Total runtime 47.28 secs, 0.79 min, 0.01 hours
[2015-09-30T17:02Z] INFO  18:02:19,363 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1020618 total reads (0.00%)
[2015-09-30T17:02Z] INFO  18:02:19,363 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:02Z] INFO  18:02:19,364 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:02Z] INFO  18:02:19,364 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:02Z] INFO  18:02:20,450 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:02Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam
[2015-09-30T17:02Z] GATK pre-alignment ('11', 93147865, 124180877) : syn3-tumor
[2015-09-30T17:02Z] INFO  18:02:24,676 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:02Z] INFO  18:02:24,678 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:02Z] INFO  18:02:24,678 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:02Z] INFO  18:02:24,678 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:02Z] INFO  18:02:24,682 HelpFormatter - Program Args: -T PrintReads -L 11:93147866-124180877 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmp5ExNCP/2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam
[2015-09-30T17:02Z] INFO  18:02:24,687 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:02Z] INFO  18:02:24,688 HelpFormatter - Date/Time: 2015/09/30 18:02:24
[2015-09-30T17:02Z] INFO  18:02:24,688 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:02Z] INFO  18:02:24,688 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:02Z] INFO  18:02:25,344 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:02Z] INFO  18:02:26,058 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:02Z] INFO  18:02:26,106 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:02Z] INFO  18:02:26,113 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:02Z] INFO  18:02:26,127 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:02Z] INFO  18:02:26,140 IntervalUtils - Processing 31033012 bp from intervals
[2015-09-30T17:02Z] INFO  18:02:26,195 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:02Z] INFO  18:02:26,398 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:02Z] INFO  18:02:26,399 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:02Z] INFO  18:02:26,399 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:02Z] INFO  18:02:26,399 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:02Z] INFO  18:02:26,410 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:02Z] INFO  18:02:26,615 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:02Z] INFO  18:02:29,587 ProgressMeter -     11:73309536   1100013.0   120.0 s     109.0 s       36.1%     5.5 m       3.5 m
[2015-09-30T17:02Z] INFO  18:02:39,522 ProgressMeter -     11:27114457   1300015.0    61.0 s      47.0 s       87.2%    69.0 s       8.0 s
[2015-09-30T17:02Z] INFO  18:02:42,092 ProgressMeter -            done   1357245.0    64.0 s      47.0 s      100.0%    64.0 s       0.0 s
[2015-09-30T17:02Z] INFO  18:02:42,092 ProgressMeter - Total runtime 64.34 secs, 1.07 min, 0.02 hours
[2015-09-30T17:02Z] INFO  18:02:42,096 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1357245 total reads (0.00%)
[2015-09-30T17:02Z] INFO  18:02:42,096 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:02Z] INFO  18:02:42,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:02Z] INFO  18:02:42,096 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:02Z] INFO  18:02:43,183 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:02Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam
[2015-09-30T17:02Z] GATK pre-alignment ('11', 124188917, 135006516) : syn3-tumor
[2015-09-30T17:02Z] INFO  18:02:52,000 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:02Z] INFO  18:02:52,001 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:02Z] INFO  18:02:52,002 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:02Z] INFO  18:02:52,002 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:02Z] INFO  18:02:52,005 HelpFormatter - Program Args: -T PrintReads -L 11:124188918-135006516 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpzkSmoN/2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam
[2015-09-30T17:02Z] INFO  18:02:52,010 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:02Z] INFO  18:02:52,011 HelpFormatter - Date/Time: 2015/09/30 18:02:51
[2015-09-30T17:02Z] INFO  18:02:52,011 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:02Z] INFO  18:02:52,011 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:02Z] INFO  18:02:52,123 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:02Z] INFO  18:02:53,110 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:02Z] INFO  18:02:53,160 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:02Z] INFO  18:02:53,168 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:02Z] INFO  18:02:53,182 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:02Z] INFO  18:02:53,195 IntervalUtils - Processing 10817599 bp from intervals
[2015-09-30T17:02Z] INFO  18:02:53,253 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:02Z] INFO  18:02:53,400 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:02Z] INFO  18:02:53,400 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:02Z] INFO  18:02:53,401 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:02Z] INFO  18:02:53,401 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:02Z] INFO  18:02:53,411 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:02Z] INFO  18:02:53,490 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:02Z] INFO  18:02:56,401 ProgressMeter -    11:107880420    200002.0    30.0 s       2.5 m       47.5%    63.0 s      33.0 s
[2015-09-30T17:02Z] INFO  18:02:59,587 ProgressMeter -     11:78574463   1400017.0     2.5 m     107.0 s       53.0%     4.7 m       2.2 m
[2015-09-30T17:03Z] INFO  18:03:19,097 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:03Z] INFO  18:03:19,224 ProgressMeter -            done   1691625.0     2.8 m     100.0 s      100.0%     2.8 m       0.0 s
[2015-09-30T17:03Z] INFO  18:03:19,225 ProgressMeter - Total runtime 169.68 secs, 2.83 min, 0.05 hours
[2015-09-30T17:03Z] INFO  18:03:19,225 MicroScheduler - 2543 reads were filtered out during the traversal out of approximately 1694168 total reads (0.15%)
[2015-09-30T17:03Z] INFO  18:03:19,225 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:03Z] INFO  18:03:19,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:03Z] INFO  18:03:19,226 MicroScheduler -   -> 2543 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:03Z] INFO  18:03:20,320 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:03Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam
[2015-09-30T17:03Z] INFO  18:03:23,435 ProgressMeter -    11:132811629    200002.0    30.0 s       2.5 m       79.7%    37.0 s       7.0 s
[2015-09-30T17:03Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam 11:62123541-93141822
[2015-09-30T17:03Z] GATK: RealignerTargetCreator
[2015-09-30T17:03Z] INFO  18:03:26,299 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:03Z] INFO  18:03:26,301 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:03Z] INFO  18:03:26,301 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:03Z] INFO  18:03:26,302 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:03Z] INFO  18:03:26,305 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpPYb9TL/2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign-realign.intervals -l INFO -L 11:62123541-93141822 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:03Z] INFO  18:03:26,311 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:03Z] INFO  18:03:26,311 HelpFormatter - Date/Time: 2015/09/30 18:03:26
[2015-09-30T17:03Z] INFO  18:03:26,312 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:03Z] INFO  18:03:26,312 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:03Z] INFO  18:03:26,368 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:03Z] INFO  18:03:26,402 ProgressMeter -    11:117078817    500005.0    60.0 s     120.0 s       77.1%    77.0 s      17.0 s
[2015-09-30T17:03Z] INFO  18:03:26,479 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:03Z] INFO  18:03:26,488 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:03Z] INFO  18:03:26,503 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:03Z] INFO  18:03:26,742 IntervalUtils - Processing 31018282 bp from intervals
[2015-09-30T17:03Z] WARN  18:03:26,746 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:03Z] INFO  18:03:26,801 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:03Z] INFO  18:03:26,945 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:03Z] INFO  18:03:26,946 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:03Z] INFO  18:03:26,946 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:03Z] INFO  18:03:26,947 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:03Z] INFO  18:03:29,519 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:03Z] INFO  18:03:29,578 ProgressMeter -            done    334194.0    36.0 s     108.0 s       96.3%    37.0 s       1.0 s
[2015-09-30T17:03Z] INFO  18:03:29,578 ProgressMeter - Total runtime 36.18 secs, 0.60 min, 0.01 hours
[2015-09-30T17:03Z] INFO  18:03:29,579 MicroScheduler - 592 reads were filtered out during the traversal out of approximately 334786 total reads (0.18%)
[2015-09-30T17:03Z] INFO  18:03:29,579 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:03Z] INFO  18:03:29,579 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:03Z] INFO  18:03:29,580 MicroScheduler -   -> 592 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:03Z] INFO  18:03:30,580 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:03Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam
[2015-09-30T17:03Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam 11:124188918-135006516
[2015-09-30T17:03Z] GATK: RealignerTargetCreator
[2015-09-30T17:03Z] INFO  18:03:33,088 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:03Z] INFO  18:03:33,090 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:03Z] INFO  18:03:33,090 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:03Z] INFO  18:03:33,090 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:03Z] INFO  18:03:33,094 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpZWkV0H/2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign-realign.intervals -l INFO -L 11:124188918-135006516 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:03Z] INFO  18:03:33,099 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:03Z] INFO  18:03:33,099 HelpFormatter - Date/Time: 2015/09/30 18:03:33
[2015-09-30T17:03Z] INFO  18:03:33,100 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:03Z] INFO  18:03:33,100 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:03Z] INFO  18:03:33,157 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:03Z] INFO  18:03:33,265 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:03Z] INFO  18:03:33,273 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:03Z] INFO  18:03:33,288 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:03Z] INFO  18:03:33,924 IntervalUtils - Processing 10817599 bp from intervals
[2015-09-30T17:03Z] WARN  18:03:33,928 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:03Z] INFO  18:03:33,984 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:03Z] INFO  18:03:34,063 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:03Z] INFO  18:03:34,063 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:03Z] INFO  18:03:34,063 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:03Z] INFO  18:03:34,064 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:03Z] INFO  18:03:45,347 ProgressMeter -            done   1.0817599E7    11.0 s       1.0 s      100.0%    11.0 s       0.0 s
[2015-09-30T17:03Z] INFO  18:03:45,348 ProgressMeter - Total runtime 11.28 secs, 0.19 min, 0.00 hours
[2015-09-30T17:03Z] INFO  18:03:45,351 MicroScheduler - 25947 reads were filtered out during the traversal out of approximately 335864 total reads (7.73%)
[2015-09-30T17:03Z] INFO  18:03:45,351 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:03Z] INFO  18:03:45,351 MicroScheduler -   -> 3848 reads (1.15% of total) failing BadMateFilter
[2015-09-30T17:03Z] INFO  18:03:45,352 MicroScheduler -   -> 15914 reads (4.74% of total) failing DuplicateReadFilter
[2015-09-30T17:03Z] INFO  18:03:45,352 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:03Z] INFO  18:03:45,352 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:03Z] INFO  18:03:45,352 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:03Z] INFO  18:03:45,353 MicroScheduler -   -> 6185 reads (1.84% of total) failing MappingQualityZeroFilter
[2015-09-30T17:03Z] INFO  18:03:45,353 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:03Z] INFO  18:03:45,353 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:03Z] INFO  18:03:45,353 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:03Z] INFO  18:03:46,314 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:03Z] GATK: realign ('11', 124188917, 135006516) : syn3-tumor
[2015-09-30T17:03Z] INFO  18:03:48,471 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:03Z] INFO  18:03:48,473 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:03Z] INFO  18:03:48,473 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:03Z] INFO  18:03:48,473 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:03Z] INFO  18:03:48,476 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep-prealign-realign.intervals -L 11:124188918-135006516 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmp2CiQkX/2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam
[2015-09-30T17:03Z] INFO  18:03:48,482 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:03Z] INFO  18:03:48,482 HelpFormatter - Date/Time: 2015/09/30 18:03:48
[2015-09-30T17:03Z] INFO  18:03:48,482 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:03Z] INFO  18:03:48,483 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:03Z] INFO  18:03:48,610 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:03Z] INFO  18:03:48,676 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:03Z] INFO  18:03:48,684 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:03Z] INFO  18:03:48,700 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:03Z] INFO  18:03:49,176 IntervalUtils - Processing 10817599 bp from intervals
[2015-09-30T17:03Z] WARN  18:03:49,180 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:03Z] INFO  18:03:49,236 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:03Z] INFO  18:03:49,610 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:03Z] INFO  18:03:49,610 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:03Z] INFO  18:03:49,611 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:03Z] INFO  18:03:49,611 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:03Z] INFO  18:03:49,711 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:03Z] INFO  18:03:49,795 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:03Z] INFO  18:03:56,410 ProgressMeter -    11:120291104    800008.0    90.0 s     112.0 s       87.5%   102.0 s      12.0 s
[2015-09-30T17:03Z] INFO  18:03:56,949 ProgressMeter -     11:78766889   1.6634348E7    30.0 s       1.0 s       53.7%    55.0 s      25.0 s
[2015-09-30T17:04Z] INFO  18:04:06,467 ProgressMeter -            done   3.1018282E7    39.0 s       1.0 s      100.0%    39.0 s       0.0 s
[2015-09-30T17:04Z] INFO  18:04:06,468 ProgressMeter - Total runtime 39.52 secs, 0.66 min, 0.01 hours
[2015-09-30T17:04Z] INFO  18:04:06,471 MicroScheduler - 152423 reads were filtered out during the traversal out of approximately 1701226 total reads (8.96%)
[2015-09-30T17:04Z] INFO  18:04:06,472 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:04Z] INFO  18:04:06,472 MicroScheduler -   -> 15438 reads (0.91% of total) failing BadMateFilter
[2015-09-30T17:04Z] INFO  18:04:06,472 MicroScheduler -   -> 85314 reads (5.01% of total) failing DuplicateReadFilter
[2015-09-30T17:04Z] INFO  18:04:06,472 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:04Z] INFO  18:04:06,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:04Z] INFO  18:04:06,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:04Z] INFO  18:04:06,473 MicroScheduler -   -> 51671 reads (3.04% of total) failing MappingQualityZeroFilter
[2015-09-30T17:04Z] INFO  18:04:06,473 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:04Z] INFO  18:04:06,473 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:04Z] INFO  18:04:06,473 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:04Z] INFO  18:04:07,331 ProgressMeter -            done    334194.0    17.0 s      53.0 s       96.3%    17.0 s       0.0 s
[2015-09-30T17:04Z] INFO  18:04:07,332 ProgressMeter - Total runtime 17.72 secs, 0.30 min, 0.00 hours
[2015-09-30T17:04Z] INFO  18:04:07,335 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 334194 total reads (0.00%)
[2015-09-30T17:04Z] INFO  18:04:07,335 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:04Z] INFO  18:04:07,335 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:04Z] INFO  18:04:07,335 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:04Z] INFO  18:04:07,457 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:04Z] GATK: realign ('11', 62123540, 93141822) : syn3-tumor
[2015-09-30T17:04Z] INFO  18:04:08,490 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:04Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam
[2015-09-30T17:04Z] INFO  18:04:08,774 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:04Z] INFO  18:04:08,899 ProgressMeter -            done   1008372.0   102.0 s     101.0 s      100.0%   102.0 s       0.0 s
[2015-09-30T17:04Z] INFO  18:04:08,900 ProgressMeter - Total runtime 102.50 secs, 1.71 min, 0.03 hours
[2015-09-30T17:04Z] INFO  18:04:08,900 MicroScheduler - 2225 reads were filtered out during the traversal out of approximately 1010597 total reads (0.22%)
[2015-09-30T17:04Z] INFO  18:04:08,900 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:04Z] INFO  18:04:08,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:04Z] INFO  18:04:08,900 MicroScheduler -   -> 2225 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:04Z] INFO  18:04:09,120 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:09,122 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:04Z] INFO  18:04:09,122 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:04Z] INFO  18:04:09,122 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:04Z] INFO  18:04:09,126 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep-prealign-realign.intervals -L 11:62123541-93141822 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpuJkmd2/2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam
[2015-09-30T17:04Z] INFO  18:04:09,132 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:04Z] INFO  18:04:09,132 HelpFormatter - Date/Time: 2015/09/30 18:04:09
[2015-09-30T17:04Z] INFO  18:04:09,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:09,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] GATK pre-alignment ('12', 0, 31107241) : syn3-tumor
[2015-09-30T17:04Z] INFO  18:04:09,576 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:04Z] INFO  18:04:09,649 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:04Z] INFO  18:04:09,664 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:04Z] INFO  18:04:09,806 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
[2015-09-30T17:04Z] INFO  18:04:10,239 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:04Z] INFO  18:04:10,329 IntervalUtils - Processing 31018282 bp from intervals
[2015-09-30T17:04Z] WARN  18:04:10,340 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:04Z] INFO  18:04:10,420 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:04Z] INFO  18:04:10,825 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:04Z] INFO  18:04:10,826 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:04Z] INFO  18:04:10,826 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:04Z] INFO  18:04:10,827 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:04Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam
[2015-09-30T17:04Z] INFO  18:04:11,085 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:04Z] INFO  18:04:11,109 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:11,112 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:04Z] INFO  18:04:11,112 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:04Z] INFO  18:04:11,112 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:04Z] INFO  18:04:11,115 HelpFormatter - Program Args: -T PrintReads -L 12:1-31107241 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpthW5Qi/2_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam
[2015-09-30T17:04Z] INFO  18:04:11,120 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:04Z] INFO  18:04:11,121 HelpFormatter - Date/Time: 2015/09/30 18:04:11
[2015-09-30T17:04Z] INFO  18:04:11,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:11,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:11,224 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:04Z] INFO  18:04:11,270 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:04Z] INFO  18:04:12,234 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:04Z] INFO  18:04:12,286 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:04Z] INFO  18:04:12,294 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:04Z] INFO  18:04:12,368 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2015-09-30T17:04Z] INFO  18:04:12,453 IntervalUtils - Processing 31107241 bp from intervals
[2015-09-30T17:04Z] INFO  18:04:12,628 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:04Z] INFO  18:04:13,076 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:04Z] INFO  18:04:13,077 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:04Z] INFO  18:04:13,077 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:04Z] INFO  18:04:13,077 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:04Z] INFO  18:04:13,088 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:04Z] INFO  18:04:13,291 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:04Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam 11:93147866-124180877
[2015-09-30T17:04Z] GATK: RealignerTargetCreator
[2015-09-30T17:04Z] INFO  18:04:16,256 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:16,258 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:04Z] INFO  18:04:16,258 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:04Z] INFO  18:04:16,258 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:04Z] INFO  18:04:16,262 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpDakDAR/2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign-realign.intervals -l INFO -L 11:93147866-124180877 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:04Z] INFO  18:04:16,267 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:04Z] INFO  18:04:16,268 HelpFormatter - Date/Time: 2015/09/30 18:04:16
[2015-09-30T17:04Z] INFO  18:04:16,268 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:16,268 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:16,332 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:04Z] INFO  18:04:16,458 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:04Z] INFO  18:04:16,466 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:04Z] INFO  18:04:16,482 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:04Z] INFO  18:04:16,717 IntervalUtils - Processing 31033012 bp from intervals
[2015-09-30T17:04Z] WARN  18:04:16,720 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:04Z] INFO  18:04:16,776 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:04Z] INFO  18:04:16,959 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:04Z] INFO  18:04:16,960 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:04Z] INFO  18:04:16,960 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:04Z] INFO  18:04:16,960 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:04Z] INFO  18:04:40,832 ProgressMeter -     11:66133517    500005.0    30.0 s      60.0 s       12.9%     3.9 m       3.4 m
[2015-09-30T17:04Z] INFO  18:04:43,081 ProgressMeter -      12:4627627    200003.0    30.0 s       2.5 m       14.9%     3.4 m       2.9 m
[2015-09-30T17:04Z] INFO  18:04:46,963 ProgressMeter -    11:123774037   3.0616871E7    30.0 s       0.0 s       98.7%    30.0 s       0.0 s
[2015-09-30T17:04Z] INFO  18:04:47,702 ProgressMeter -            done   3.1033012E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T17:04Z] INFO  18:04:47,702 ProgressMeter - Total runtime 30.74 secs, 0.51 min, 0.01 hours
[2015-09-30T17:04Z] INFO  18:04:47,706 MicroScheduler - 76855 reads were filtered out during the traversal out of approximately 1014865 total reads (7.57%)
[2015-09-30T17:04Z] INFO  18:04:47,706 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:04Z] INFO  18:04:47,706 MicroScheduler -   -> 11756 reads (1.16% of total) failing BadMateFilter
[2015-09-30T17:04Z] INFO  18:04:47,707 MicroScheduler -   -> 45801 reads (4.51% of total) failing DuplicateReadFilter
[2015-09-30T17:04Z] INFO  18:04:47,707 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:04Z] INFO  18:04:47,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:04Z] INFO  18:04:47,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:04Z] INFO  18:04:47,707 MicroScheduler -   -> 19298 reads (1.90% of total) failing MappingQualityZeroFilter
[2015-09-30T17:04Z] INFO  18:04:47,708 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:04Z] INFO  18:04:47,708 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:04Z] INFO  18:04:47,708 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:04Z] INFO  18:04:48,703 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:04Z] GATK: realign ('11', 93147865, 124180877) : syn3-tumor
[2015-09-30T17:04Z] INFO  18:04:50,755 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:50,758 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:04Z] INFO  18:04:50,758 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:04Z] INFO  18:04:50,758 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:04Z] INFO  18:04:50,761 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep-prealign-realign.intervals -L 11:93147866-124180877 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/tx/tmpWgcj5g/2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam
[2015-09-30T17:04Z] INFO  18:04:50,767 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:04Z] INFO  18:04:50,767 HelpFormatter - Date/Time: 2015/09/30 18:04:50
[2015-09-30T17:04Z] INFO  18:04:50,767 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:50,768 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:04Z] INFO  18:04:50,887 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:04Z] INFO  18:04:50,950 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:04Z] INFO  18:04:50,957 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:04Z] INFO  18:04:50,973 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:04Z] INFO  18:04:51,324 IntervalUtils - Processing 31033012 bp from intervals
[2015-09-30T17:04Z] WARN  18:04:51,327 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:04Z] INFO  18:04:51,383 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:04Z] INFO  18:04:51,653 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:04Z] INFO  18:04:51,653 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:04Z] INFO  18:04:51,653 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:04Z] INFO  18:04:51,654 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:04Z] INFO  18:04:51,802 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:04Z] INFO  18:04:51,992 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:05Z] INFO  18:05:10,833 ProgressMeter -     11:75143796   1200014.0    60.0 s      50.0 s       42.0%     2.4 m      82.0 s
[2015-09-30T17:05Z] INFO  18:05:13,083 ProgressMeter -      12:8083812    500006.0    60.0 s     120.0 s       26.0%     3.8 m       2.8 m
[2015-09-30T17:05Z] INFO  18:05:22,068 ProgressMeter -    11:116691549    500005.0    30.0 s      60.0 s       75.9%    39.0 s       9.0 s
[2015-09-30T17:05Z] INFO  18:05:25,204 ProgressMeter -            done   1691625.0    74.0 s      43.0 s      100.0%    74.0 s       0.0 s
[2015-09-30T17:05Z] INFO  18:05:25,204 ProgressMeter - Total runtime 74.38 secs, 1.24 min, 0.02 hours
[2015-09-30T17:05Z] INFO  18:05:25,208 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1691625 total reads (0.00%)
[2015-09-30T17:05Z] INFO  18:05:25,208 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:05Z] INFO  18:05:25,208 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:05Z] INFO  18:05:25,209 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:05Z] INFO  18:05:26,516 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:05Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam
[2015-09-30T17:05Z] GATK pre-alignment ('12', 31116488, 62142833) : syn3-tumor
[2015-09-30T17:05Z] INFO  18:05:33,051 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:05Z] INFO  18:05:33,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:05Z] INFO  18:05:33,053 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:05Z] INFO  18:05:33,053 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:05Z] INFO  18:05:33,056 HelpFormatter - Program Args: -T PrintReads -L 12:31116489-62142833 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpRorole/2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam
[2015-09-30T17:05Z] INFO  18:05:33,062 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:05Z] INFO  18:05:33,062 HelpFormatter - Date/Time: 2015/09/30 18:05:33
[2015-09-30T17:05Z] INFO  18:05:33,063 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:05Z] INFO  18:05:33,063 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:05Z] INFO  18:05:33,160 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:05Z] INFO  18:05:33,824 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:05Z] INFO  18:05:33,873 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:05Z] INFO  18:05:33,880 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:05Z] INFO  18:05:33,895 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:05Z] INFO  18:05:33,908 IntervalUtils - Processing 31026345 bp from intervals
[2015-09-30T17:05Z] INFO  18:05:33,964 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:05Z] INFO  18:05:34,184 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:05Z] INFO  18:05:34,184 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:05Z] INFO  18:05:34,184 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:05Z] INFO  18:05:34,185 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:05Z] INFO  18:05:34,195 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:05Z] INFO  18:05:34,392 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:05Z] INFO  18:05:40,664 ProgressMeter -            done   1008372.0    49.0 s      48.0 s      100.0%    49.0 s       0.0 s
[2015-09-30T17:05Z] INFO  18:05:40,664 ProgressMeter - Total runtime 49.01 secs, 0.82 min, 0.01 hours
[2015-09-30T17:05Z] INFO  18:05:40,667 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1008372 total reads (0.00%)
[2015-09-30T17:05Z] INFO  18:05:40,668 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:05Z] INFO  18:05:40,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:05Z] INFO  18:05:40,668 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:05Z] INFO  18:05:41,740 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:05Z] INFO  18:05:43,092 ProgressMeter -     12:15273599    800009.0    90.0 s     112.0 s       49.1%     3.1 m      93.0 s
[2015-09-30T17:05Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam
[2015-09-30T17:05Z] GATK pre-alignment ('12', 62147092, 93167456) : syn3-tumor
[2015-09-30T17:05Z] INFO  18:05:48,852 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:05Z] INFO  18:05:48,854 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:05Z] INFO  18:05:48,854 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:05Z] INFO  18:05:48,855 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:05Z] INFO  18:05:48,858 HelpFormatter - Program Args: -T PrintReads -L 12:62147093-93167456 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpS5k5Uf/2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam
[2015-09-30T17:05Z] INFO  18:05:48,864 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:05Z] INFO  18:05:48,864 HelpFormatter - Date/Time: 2015/09/30 18:05:48
[2015-09-30T17:05Z] INFO  18:05:48,864 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:05Z] INFO  18:05:48,865 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:05Z] INFO  18:05:48,973 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:05Z] INFO  18:05:49,928 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:05Z] INFO  18:05:49,977 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:05Z] INFO  18:05:49,985 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:05Z] INFO  18:05:50,000 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:05Z] INFO  18:05:50,014 IntervalUtils - Processing 31020364 bp from intervals
[2015-09-30T17:05Z] INFO  18:05:50,075 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:05Z] INFO  18:05:50,895 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:05Z] INFO  18:05:50,896 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:05Z] INFO  18:05:50,896 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:05Z] INFO  18:05:50,896 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:05Z] INFO  18:05:50,910 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:05Z] INFO  18:05:51,116 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:06Z] INFO  18:06:04,187 ProgressMeter -     12:48096595    200002.0    30.0 s       2.5 m       54.7%    54.0 s      24.0 s
[2015-09-30T17:06Z] INFO  18:06:08,625 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:06Z] INFO  18:06:09,023 ProgressMeter -            done   1148473.0   115.0 s     100.0 s      100.0%   115.0 s       0.0 s
[2015-09-30T17:06Z] INFO  18:06:09,023 ProgressMeter - Total runtime 115.95 secs, 1.93 min, 0.03 hours
[2015-09-30T17:06Z] INFO  18:06:09,023 MicroScheduler - 2560 reads were filtered out during the traversal out of approximately 1151033 total reads (0.22%)
[2015-09-30T17:06Z] INFO  18:06:09,024 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:06Z] INFO  18:06:09,024 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:06Z] INFO  18:06:09,024 MicroScheduler -   -> 2560 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:06Z] INFO  18:06:10,300 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:06Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam
[2015-09-30T17:06Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam 12:1-31107241
[2015-09-30T17:06Z] GATK: RealignerTargetCreator
[2015-09-30T17:06Z] INFO  18:06:14,803 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:06Z] INFO  18:06:14,805 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:06Z] INFO  18:06:14,805 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:06Z] INFO  18:06:14,806 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:06Z] INFO  18:06:14,809 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpjtag9g/2_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign-realign.intervals -l INFO -L 12:1-31107241 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:06Z] INFO  18:06:14,815 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:06Z] INFO  18:06:14,815 HelpFormatter - Date/Time: 2015/09/30 18:06:14
[2015-09-30T17:06Z] INFO  18:06:14,815 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:06Z] INFO  18:06:14,815 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:06Z] INFO  18:06:14,871 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:06Z] INFO  18:06:15,323 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:06Z] INFO  18:06:15,330 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:06Z] INFO  18:06:15,346 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:06Z] INFO  18:06:15,599 IntervalUtils - Processing 31107241 bp from intervals
[2015-09-30T17:06Z] WARN  18:06:15,603 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:06Z] INFO  18:06:15,658 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:06Z] INFO  18:06:15,812 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:06Z] INFO  18:06:15,812 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:06Z] INFO  18:06:15,813 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:06Z] INFO  18:06:15,813 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:06Z] INFO  18:06:20,900 ProgressMeter -     12:72290156    200002.0    30.0 s       2.5 m       32.7%    91.0 s      61.0 s
[2015-09-30T17:06Z] INFO  18:06:34,188 ProgressMeter -     12:51139962    500006.0    60.0 s     120.0 s       64.5%    92.0 s      32.0 s
[2015-09-30T17:06Z] INFO  18:06:40,337 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:06Z] INFO  18:06:40,650 ProgressMeter -            done    453827.0    49.0 s     109.0 s      100.0%    49.0 s       0.0 s
[2015-09-30T17:06Z] INFO  18:06:40,650 ProgressMeter - Total runtime 49.75 secs, 0.83 min, 0.01 hours
[2015-09-30T17:06Z] INFO  18:06:40,651 MicroScheduler - 1631 reads were filtered out during the traversal out of approximately 455458 total reads (0.36%)
[2015-09-30T17:06Z] INFO  18:06:40,651 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:06Z] INFO  18:06:40,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:06Z] INFO  18:06:40,651 MicroScheduler -   -> 1631 reads (0.36% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:06Z] INFO  18:06:41,655 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:06Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam
[2015-09-30T17:06Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam 12:62147093-93167456
[2015-09-30T17:06Z] GATK: RealignerTargetCreator
[2015-09-30T17:06Z] INFO  18:06:44,622 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:06Z] INFO  18:06:44,624 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:06Z] INFO  18:06:44,625 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:06Z] INFO  18:06:44,625 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:06Z] INFO  18:06:44,628 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpXQfNIt/2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign-realign.intervals -l INFO -L 12:62147093-93167456 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:06Z] INFO  18:06:44,634 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:06Z] INFO  18:06:44,634 HelpFormatter - Date/Time: 2015/09/30 18:06:44
[2015-09-30T17:06Z] INFO  18:06:44,635 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:06Z] INFO  18:06:44,635 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:06Z] INFO  18:06:44,694 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:06Z] INFO  18:06:44,799 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:06Z] INFO  18:06:44,807 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:06Z] INFO  18:06:44,824 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:06Z] INFO  18:06:45,290 IntervalUtils - Processing 31020364 bp from intervals
[2015-09-30T17:06Z] WARN  18:06:45,294 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:06Z] INFO  18:06:45,351 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:06Z] INFO  18:06:45,815 ProgressMeter -     12:28359721   2.834432E7    30.0 s       1.0 s       91.2%    32.0 s       2.0 s
[2015-09-30T17:06Z] INFO  18:06:45,893 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:06Z] INFO  18:06:45,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:06Z] INFO  18:06:45,894 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:06Z] INFO  18:06:45,895 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:06Z] INFO  18:06:47,915 ProgressMeter -            done   3.1107241E7    32.0 s       1.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T17:06Z] INFO  18:06:47,916 ProgressMeter - Total runtime 32.10 secs, 0.54 min, 0.01 hours
[2015-09-30T17:06Z] INFO  18:06:47,919 MicroScheduler - 98647 reads were filtered out during the traversal out of approximately 1155352 total reads (8.54%)
[2015-09-30T17:06Z] INFO  18:06:47,919 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:06Z] INFO  18:06:47,920 MicroScheduler -   -> 12591 reads (1.09% of total) failing BadMateFilter
[2015-09-30T17:06Z] INFO  18:06:47,920 MicroScheduler -   -> 51008 reads (4.41% of total) failing DuplicateReadFilter
[2015-09-30T17:06Z] INFO  18:06:47,920 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:06Z] INFO  18:06:47,920 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:06Z] INFO  18:06:47,921 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:06Z] INFO  18:06:47,921 MicroScheduler -   -> 35048 reads (3.03% of total) failing MappingQualityZeroFilter
[2015-09-30T17:06Z] INFO  18:06:47,921 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:06Z] INFO  18:06:47,921 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:06Z] INFO  18:06:47,922 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:06Z] INFO  18:06:48,890 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:06Z] GATK: realign ('12', 0, 31107241) : syn3-tumor
[2015-09-30T17:06Z] INFO  18:06:50,556 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:06Z] INFO  18:06:50,558 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:06Z] INFO  18:06:50,558 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:06Z] INFO  18:06:50,558 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:06Z] INFO  18:06:50,562 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_0_31107241-prep-prealign-realign.intervals -L 12:1-31107241 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpOSPDGg/2_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam
[2015-09-30T17:06Z] INFO  18:06:50,567 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:06Z] INFO  18:06:50,568 HelpFormatter - Date/Time: 2015/09/30 18:06:50
[2015-09-30T17:06Z] INFO  18:06:50,568 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:06Z] INFO  18:06:50,568 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:06Z] INFO  18:06:50,966 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:06Z] INFO  18:06:51,030 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:06Z] INFO  18:06:51,038 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:06Z] INFO  18:06:51,054 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:06Z] INFO  18:06:51,283 IntervalUtils - Processing 31107241 bp from intervals
[2015-09-30T17:06Z] WARN  18:06:51,287 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:06Z] INFO  18:06:51,353 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:06Z] INFO  18:06:51,494 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:06Z] INFO  18:06:51,494 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:06Z] INFO  18:06:51,495 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:06Z] INFO  18:06:51,495 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:06Z] INFO  18:06:51,635 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:06Z] INFO  18:06:51,813 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:07Z] INFO  18:07:04,695 ProgressMeter -     12:53775941    800010.0    90.0 s     113.0 s       73.0%     2.1 m      33.0 s
[2015-09-30T17:07Z] INFO  18:07:07,816 ProgressMeter -            done   3.1020364E7    21.0 s       0.0 s      100.0%    21.0 s       0.0 s
[2015-09-30T17:07Z] INFO  18:07:07,816 ProgressMeter - Total runtime 21.92 secs, 0.37 min, 0.01 hours
[2015-09-30T17:07Z] INFO  18:07:07,820 MicroScheduler - 34465 reads were filtered out during the traversal out of approximately 456141 total reads (7.56%)
[2015-09-30T17:07Z] INFO  18:07:07,820 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:07Z] INFO  18:07:07,820 MicroScheduler -   -> 8046 reads (1.76% of total) failing BadMateFilter
[2015-09-30T17:07Z] INFO  18:07:07,821 MicroScheduler -   -> 17635 reads (3.87% of total) failing DuplicateReadFilter
[2015-09-30T17:07Z] INFO  18:07:07,821 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:07Z] INFO  18:07:07,821 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:07Z] INFO  18:07:07,821 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:07Z] INFO  18:07:07,822 MicroScheduler -   -> 8784 reads (1.93% of total) failing MappingQualityZeroFilter
[2015-09-30T17:07Z] INFO  18:07:07,822 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:07Z] INFO  18:07:07,822 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:07Z] INFO  18:07:07,822 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:07Z] INFO  18:07:08,892 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:07Z] GATK: realign ('12', 62147092, 93167456) : syn3-tumor
[2015-09-30T17:07Z] INFO  18:07:12,327 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:07Z] INFO  18:07:12,329 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:07Z] INFO  18:07:12,329 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:07Z] INFO  18:07:12,329 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:07Z] INFO  18:07:12,332 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep-prealign-realign.intervals -L 12:62147093-93167456 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmp9D5eNC/2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam
[2015-09-30T17:07Z] INFO  18:07:12,338 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:07Z] INFO  18:07:12,339 HelpFormatter - Date/Time: 2015/09/30 18:07:12
[2015-09-30T17:07Z] INFO  18:07:12,339 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:07Z] INFO  18:07:12,339 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:07Z] INFO  18:07:12,469 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:07Z] INFO  18:07:12,534 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:07Z] INFO  18:07:12,541 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:07Z] INFO  18:07:12,558 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:07Z] INFO  18:07:13,084 IntervalUtils - Processing 31020364 bp from intervals
[2015-09-30T17:07Z] WARN  18:07:13,088 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:07Z] INFO  18:07:13,145 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:07Z] INFO  18:07:13,286 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:07Z] INFO  18:07:13,286 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:07Z] INFO  18:07:13,286 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:07Z] INFO  18:07:13,287 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:07Z] INFO  18:07:13,433 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:07Z] INFO  18:07:13,621 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:07Z] INFO  18:07:22,617 ProgressMeter -      12:8211837    500006.0    31.0 s      62.0 s       26.4%   117.0 s      86.0 s
[2015-09-30T17:07Z] INFO  18:07:35,573 ProgressMeter -     12:57011565   1200015.0     2.0 m     101.0 s       83.5%     2.4 m      23.0 s
[2015-09-30T17:07Z] INFO  18:07:36,321 ProgressMeter -            done    453827.0    23.0 s      50.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T17:07Z] INFO  18:07:36,322 ProgressMeter - Total runtime 23.04 secs, 0.38 min, 0.01 hours
[2015-09-30T17:07Z] INFO  18:07:36,324 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 453827 total reads (0.00%)
[2015-09-30T17:07Z] INFO  18:07:36,325 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:07Z] INFO  18:07:36,325 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:07Z] INFO  18:07:36,325 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:07Z] INFO  18:07:37,455 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:07Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam
[2015-09-30T17:07Z] GATK pre-alignment ('12', 93169109, 124189486) : syn3-tumor
[2015-09-30T17:07Z] INFO  18:07:43,927 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:07Z] INFO  18:07:43,932 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:07Z] INFO  18:07:43,932 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:07Z] INFO  18:07:43,932 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:07Z] INFO  18:07:43,936 HelpFormatter - Program Args: -T PrintReads -L 12:93169110-124189486 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpSTYnHx/2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam
[2015-09-30T17:07Z] INFO  18:07:43,942 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:07Z] INFO  18:07:43,942 HelpFormatter - Date/Time: 2015/09/30 18:07:43
[2015-09-30T17:07Z] INFO  18:07:43,942 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:07Z] INFO  18:07:43,942 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:07Z] INFO  18:07:44,048 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:07Z] INFO  18:07:46,363 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:07Z] INFO  18:07:46,416 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:07Z] INFO  18:07:46,424 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:07Z] INFO  18:07:46,503 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2015-09-30T17:07Z] INFO  18:07:46,518 IntervalUtils - Processing 31020377 bp from intervals
[2015-09-30T17:07Z] INFO  18:07:46,570 ProgressMeter -            done   1148473.0    55.0 s      47.0 s      100.0%    55.0 s       0.0 s
[2015-09-30T17:07Z] INFO  18:07:46,571 ProgressMeter - Total runtime 55.08 secs, 0.92 min, 0.02 hours
[2015-09-30T17:07Z] INFO  18:07:46,574 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1148473 total reads (0.00%)
[2015-09-30T17:07Z] INFO  18:07:46,574 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:07Z] INFO  18:07:46,574 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:07Z] INFO  18:07:46,574 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:07Z] INFO  18:07:46,578 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:07Z] INFO  18:07:46,797 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:07Z] INFO  18:07:46,797 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:07Z] INFO  18:07:46,798 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:07Z] INFO  18:07:46,798 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:07Z] INFO  18:07:46,809 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:07Z] INFO  18:07:47,024 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:07Z] INFO  18:07:47,699 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:07Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam
[2015-09-30T17:07Z] GATK pre-alignment ('12', 124191013, 133851895) : syn3-tumor
[2015-09-30T17:07Z] INFO  18:07:54,583 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:07Z] INFO  18:07:54,583 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:07Z] INFO  18:07:54,589 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:07Z] INFO  18:07:54,590 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:07Z] INFO  18:07:54,592 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:07Z] INFO  18:07:54,596 HelpFormatter - Program Args: -T PrintReads -L 12:124191014-133851895 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpALKrBc/2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam
[2015-09-30T17:07Z] INFO  18:07:54,607 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:07Z] INFO  18:07:54,608 HelpFormatter - Date/Time: 2015/09/30 18:07:54
[2015-09-30T17:07Z] INFO  18:07:54,608 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:07Z] INFO  18:07:54,608 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:07Z] INFO  18:07:54,725 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:07Z] INFO  18:07:54,749 ProgressMeter -            done   1428960.0     2.3 m      98.0 s      100.0%     2.3 m       0.0 s
[2015-09-30T17:07Z] INFO  18:07:54,749 ProgressMeter - Total runtime 140.57 secs, 2.34 min, 0.04 hours
[2015-09-30T17:07Z] INFO  18:07:54,749 MicroScheduler - 2551 reads were filtered out during the traversal out of approximately 1431511 total reads (0.18%)
[2015-09-30T17:07Z] INFO  18:07:54,750 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:07Z] INFO  18:07:54,750 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:07Z] INFO  18:07:54,750 MicroScheduler -   -> 2551 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:07Z] INFO  18:07:56,327 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:07Z] INFO  18:07:56,378 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:07Z] INFO  18:07:56,386 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:07Z] INFO  18:07:56,401 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:07Z] INFO  18:07:56,415 IntervalUtils - Processing 9660882 bp from intervals
[2015-09-30T17:07Z] INFO  18:07:56,472 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:07Z] INFO  18:07:56,698 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:07Z] INFO  18:07:56,952 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:07Z] INFO  18:07:56,953 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:07Z] INFO  18:07:56,953 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:07Z] INFO  18:07:56,954 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:07Z] INFO  18:07:56,965 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:07Z] INFO  18:07:57,039 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:07Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam
[2015-09-30T17:08Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam 12:31116489-62142833
[2015-09-30T17:08Z] GATK: RealignerTargetCreator
[2015-09-30T17:08Z] INFO  18:08:03,602 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:03,604 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:08Z] INFO  18:08:03,604 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:08Z] INFO  18:08:03,604 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:08Z] INFO  18:08:03,608 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpXE25zL/2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign-realign.intervals -l INFO -L 12:31116489-62142833 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:08Z] INFO  18:08:03,614 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:08Z] INFO  18:08:03,614 HelpFormatter - Date/Time: 2015/09/30 18:08:03
[2015-09-30T17:08Z] INFO  18:08:03,614 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:03,614 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:03,675 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:08Z] INFO  18:08:05,279 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:08Z] INFO  18:08:05,625 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:08Z] INFO  18:08:05,642 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:08Z] INFO  18:08:05,896 IntervalUtils - Processing 31026345 bp from intervals
[2015-09-30T17:08Z] WARN  18:08:05,900 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:08Z] INFO  18:08:05,961 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:08Z] INFO  18:08:06,124 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:08Z] INFO  18:08:06,124 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:08Z] INFO  18:08:06,124 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:08Z] INFO  18:08:06,125 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:08Z] INFO  18:08:17,164 ProgressMeter -    12:101510287    200002.0    30.0 s       2.5 m       26.9%   111.0 s      81.0 s
[2015-09-30T17:08Z] INFO  18:08:26,956 ProgressMeter -    12:132627733    200003.0    30.0 s       2.5 m       87.3%    34.0 s       4.0 s
[2015-09-30T17:08Z] INFO  18:08:34,110 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:08Z] INFO  18:08:34,169 ProgressMeter -            done    376150.0    37.0 s      98.0 s       99.6%    37.0 s       0.0 s
[2015-09-30T17:08Z] INFO  18:08:34,169 ProgressMeter - Total runtime 37.22 secs, 0.62 min, 0.01 hours
[2015-09-30T17:08Z] INFO  18:08:34,170 MicroScheduler - 686 reads were filtered out during the traversal out of approximately 376836 total reads (0.18%)
[2015-09-30T17:08Z] INFO  18:08:34,170 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:08Z] INFO  18:08:34,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:08Z] INFO  18:08:34,170 MicroScheduler -   -> 686 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:08Z] INFO  18:08:35,227 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:08Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam
[2015-09-30T17:08Z] INFO  18:08:36,127 ProgressMeter -     12:56716525   2.5588536E7    30.0 s       1.0 s       82.5%    36.0 s       6.0 s
[2015-09-30T17:08Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam 12:124191014-133851895
[2015-09-30T17:08Z] GATK: RealignerTargetCreator
[2015-09-30T17:08Z] INFO  18:08:38,106 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:38,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:08Z] INFO  18:08:38,108 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:08Z] INFO  18:08:38,108 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:08Z] INFO  18:08:38,112 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpMEiDLk/2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign-realign.intervals -l INFO -L 12:124191014-133851895 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:08Z] INFO  18:08:38,118 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:08Z] INFO  18:08:38,118 HelpFormatter - Date/Time: 2015/09/30 18:08:38
[2015-09-30T17:08Z] INFO  18:08:38,119 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:38,119 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:39,250 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:08Z] INFO  18:08:39,421 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:08Z] INFO  18:08:39,428 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:08Z] INFO  18:08:39,561 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2015-09-30T17:08Z] INFO  18:08:39,971 IntervalUtils - Processing 9660882 bp from intervals
[2015-09-30T17:08Z] WARN  18:08:39,975 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:08Z] INFO  18:08:40,033 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:08Z] INFO  18:08:40,749 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:08Z] INFO  18:08:40,750 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:08Z] INFO  18:08:40,750 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:08Z] INFO  18:08:40,751 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:08Z] INFO  18:08:43,450 ProgressMeter -            done   3.1026345E7    37.0 s       1.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T17:08Z] INFO  18:08:43,450 ProgressMeter - Total runtime 37.33 secs, 0.62 min, 0.01 hours
[2015-09-30T17:08Z] INFO  18:08:43,454 MicroScheduler - 113080 reads were filtered out during the traversal out of approximately 1437105 total reads (7.87%)
[2015-09-30T17:08Z] INFO  18:08:43,454 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:08Z] INFO  18:08:43,454 MicroScheduler -   -> 14084 reads (0.98% of total) failing BadMateFilter
[2015-09-30T17:08Z] INFO  18:08:43,454 MicroScheduler -   -> 68350 reads (4.76% of total) failing DuplicateReadFilter
[2015-09-30T17:08Z] INFO  18:08:43,455 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:08Z] INFO  18:08:43,455 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:08Z] INFO  18:08:43,455 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:08Z] INFO  18:08:43,455 MicroScheduler -   -> 30646 reads (2.13% of total) failing MappingQualityZeroFilter
[2015-09-30T17:08Z] INFO  18:08:43,456 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:08Z] INFO  18:08:43,456 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:08Z] INFO  18:08:43,456 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:08Z] INFO  18:08:44,401 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:08Z] GATK: realign ('12', 31116488, 62142833) : syn3-tumor
[2015-09-30T17:08Z] INFO  18:08:46,843 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:46,845 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:08Z] INFO  18:08:46,845 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:08Z] INFO  18:08:46,845 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:08Z] INFO  18:08:46,849 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep-prealign-realign.intervals -L 12:31116489-62142833 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpm_mMLj/2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam
[2015-09-30T17:08Z] INFO  18:08:46,854 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:08Z] INFO  18:08:46,854 HelpFormatter - Date/Time: 2015/09/30 18:08:46
[2015-09-30T17:08Z] INFO  18:08:46,855 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:46,855 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:46,976 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:08Z] INFO  18:08:47,039 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:08Z] INFO  18:08:47,047 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:08Z] INFO  18:08:47,062 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:08Z] INFO  18:08:47,289 IntervalUtils - Processing 31026345 bp from intervals
[2015-09-30T17:08Z] WARN  18:08:47,293 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:08Z] INFO  18:08:47,326 ProgressMeter -    12:109274200    500005.0    60.0 s       2.0 m       51.9%   115.0 s      55.0 s
[2015-09-30T17:08Z] INFO  18:08:47,348 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:08Z] INFO  18:08:47,494 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:08Z] INFO  18:08:47,495 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:08Z] INFO  18:08:47,495 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:08Z] INFO  18:08:47,495 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:08Z] INFO  18:08:47,633 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:08Z] INFO  18:08:47,825 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:08Z] INFO  18:08:53,364 ProgressMeter -            done   9660882.0    12.0 s       1.0 s      100.0%    12.0 s       0.0 s
[2015-09-30T17:08Z] INFO  18:08:53,364 ProgressMeter - Total runtime 12.61 secs, 0.21 min, 0.00 hours
[2015-09-30T17:08Z] INFO  18:08:53,367 MicroScheduler - 33238 reads were filtered out during the traversal out of approximately 378200 total reads (8.79%)
[2015-09-30T17:08Z] INFO  18:08:53,367 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:08Z] INFO  18:08:53,368 MicroScheduler -   -> 3986 reads (1.05% of total) failing BadMateFilter
[2015-09-30T17:08Z] INFO  18:08:53,368 MicroScheduler -   -> 19605 reads (5.18% of total) failing DuplicateReadFilter
[2015-09-30T17:08Z] INFO  18:08:53,368 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:08Z] INFO  18:08:53,368 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:08Z] INFO  18:08:53,369 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:08Z] INFO  18:08:53,369 MicroScheduler -   -> 9647 reads (2.55% of total) failing MappingQualityZeroFilter
[2015-09-30T17:08Z] INFO  18:08:53,369 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:08Z] INFO  18:08:53,369 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:08Z] INFO  18:08:53,370 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:08Z] INFO  18:08:54,362 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:08Z] GATK: realign ('12', 124191013, 133851895) : syn3-tumor
[2015-09-30T17:08Z] INFO  18:08:56,558 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:56,560 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:08Z] INFO  18:08:56,560 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:08Z] INFO  18:08:56,561 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:08Z] INFO  18:08:56,564 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep-prealign-realign.intervals -L 12:124191014-133851895 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmp6XM1bc/2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam
[2015-09-30T17:08Z] INFO  18:08:56,570 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:08Z] INFO  18:08:56,570 HelpFormatter - Date/Time: 2015/09/30 18:08:56
[2015-09-30T17:08Z] INFO  18:08:56,570 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:56,570 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:08Z] INFO  18:08:56,694 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:08Z] INFO  18:08:56,757 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:08Z] INFO  18:08:56,765 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:08Z] INFO  18:08:56,781 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:08Z] INFO  18:08:57,285 IntervalUtils - Processing 9660882 bp from intervals
[2015-09-30T17:08Z] WARN  18:08:57,289 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:08Z] INFO  18:08:57,486 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:08Z] INFO  18:08:57,572 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:08Z] INFO  18:08:57,573 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:08Z] INFO  18:08:57,573 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:08Z] INFO  18:08:57,574 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:08Z] INFO  18:08:57,681 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:08Z] INFO  18:08:57,754 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:09Z] INFO  18:09:17,362 ProgressMeter -    12:112672661    800011.0    90.0 s     113.0 s       62.9%     2.4 m      53.0 s
[2015-09-30T17:09Z] INFO  18:09:17,498 ProgressMeter -     12:51493174    500006.0    30.0 s      60.0 s       65.7%    45.0 s      15.0 s
[2015-09-30T17:09Z] INFO  18:09:18,115 ProgressMeter -            done    376150.0    20.0 s      54.0 s       99.6%    20.0 s       0.0 s
[2015-09-30T17:09Z] INFO  18:09:18,116 ProgressMeter - Total runtime 20.54 secs, 0.34 min, 0.01 hours
[2015-09-30T17:09Z] INFO  18:09:18,118 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 376150 total reads (0.00%)
[2015-09-30T17:09Z] INFO  18:09:18,119 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:09Z] INFO  18:09:18,119 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:09Z] INFO  18:09:18,119 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:09Z] INFO  18:09:19,195 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:09Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam
[2015-09-30T17:09Z] GATK pre-alignment ('13', 0, 31036104) : syn3-tumor
[2015-09-30T17:09Z] INFO  18:09:22,058 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:09Z] INFO  18:09:22,061 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:09Z] INFO  18:09:22,061 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:09Z] INFO  18:09:22,061 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:09Z] INFO  18:09:22,064 HelpFormatter - Program Args: -T PrintReads -L 13:1-31036104 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpRpRPpc/2_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam
[2015-09-30T17:09Z] INFO  18:09:22,071 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:09Z] INFO  18:09:22,071 HelpFormatter - Date/Time: 2015/09/30 18:09:22
[2015-09-30T17:09Z] INFO  18:09:22,071 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:09Z] INFO  18:09:22,071 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:09Z] INFO  18:09:22,181 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:09Z] INFO  18:09:22,873 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:09Z] INFO  18:09:22,922 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:09Z] INFO  18:09:22,929 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:09Z] INFO  18:09:22,943 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:09Z] INFO  18:09:22,956 IntervalUtils - Processing 31036104 bp from intervals
[2015-09-30T17:09Z] INFO  18:09:23,012 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:09Z] INFO  18:09:23,335 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:09Z] INFO  18:09:23,335 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:09Z] INFO  18:09:23,335 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:09Z] INFO  18:09:23,336 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:09Z] INFO  18:09:23,346 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:09Z] INFO  18:09:23,414 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:09Z] INFO  18:09:47,363 ProgressMeter -    12:120574054   1100015.0   120.0 s     109.0 s       88.3%     2.3 m      15.0 s
[2015-09-30T17:09Z] INFO  18:09:47,499 ProgressMeter -     12:57989132   1300016.0    60.0 s      46.0 s       86.6%    69.0 s       9.0 s
[2015-09-30T17:09Z] INFO  18:09:49,744 ProgressMeter -            done   1428960.0    62.0 s      43.0 s      100.0%    62.0 s       0.0 s
[2015-09-30T17:09Z] INFO  18:09:49,744 ProgressMeter - Total runtime 62.25 secs, 1.04 min, 0.02 hours
[2015-09-30T17:09Z] INFO  18:09:49,748 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1428960 total reads (0.00%)
[2015-09-30T17:09Z] INFO  18:09:49,748 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:09Z] INFO  18:09:49,748 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:09Z] INFO  18:09:49,748 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:09Z] INFO  18:09:50,833 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:09Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam
[2015-09-30T17:09Z] INFO  18:09:53,347 ProgressMeter -     13:28624465    200002.0    30.0 s       2.5 m       92.2%    32.0 s       2.0 s
[2015-09-30T17:09Z] GATK pre-alignment ('13', 31036377, 62334609) : syn3-tumor
[2015-09-30T17:09Z] INFO  18:09:57,262 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:09Z] INFO  18:09:57,264 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:09Z] INFO  18:09:57,264 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:09Z] INFO  18:09:57,264 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:09Z] INFO  18:09:57,268 HelpFormatter - Program Args: -T PrintReads -L 13:31036378-62334609 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpNpPDxU/2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam
[2015-09-30T17:09Z] INFO  18:09:57,274 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:09Z] INFO  18:09:57,274 HelpFormatter - Date/Time: 2015/09/30 18:09:57
[2015-09-30T17:09Z] INFO  18:09:57,274 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:09Z] INFO  18:09:57,274 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:09Z] INFO  18:09:57,383 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:09Z] INFO  18:09:58,262 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:09Z] INFO  18:09:58,431 ProgressMeter -            done    329386.0    35.0 s     106.0 s      100.0%    35.0 s       0.0 s
[2015-09-30T17:09Z] INFO  18:09:58,432 ProgressMeter - Total runtime 35.10 secs, 0.58 min, 0.01 hours
[2015-09-30T17:09Z] INFO  18:09:58,432 MicroScheduler - 946 reads were filtered out during the traversal out of approximately 330332 total reads (0.29%)
[2015-09-30T17:09Z] INFO  18:09:58,432 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:09Z] INFO  18:09:58,432 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:09Z] INFO  18:09:58,433 MicroScheduler -   -> 946 reads (0.29% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:09Z] INFO  18:09:58,729 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:09Z] INFO  18:09:58,780 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:09Z] INFO  18:09:58,788 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:09Z] INFO  18:09:58,803 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:09Z] INFO  18:09:58,817 IntervalUtils - Processing 31298232 bp from intervals
[2015-09-30T17:09Z] INFO  18:09:58,875 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:09Z] INFO  18:09:59,078 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:09Z] INFO  18:09:59,079 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:09Z] INFO  18:09:59,079 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:09Z] INFO  18:09:59,079 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:09Z] INFO  18:09:59,090 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:09Z] INFO  18:09:59,290 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:09Z] INFO  18:09:59,474 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:09Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam
[2015-09-30T17:10Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam 13:1-31036104
[2015-09-30T17:10Z] GATK: RealignerTargetCreator
[2015-09-30T17:10Z] INFO  18:10:02,998 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:03,000 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:10Z] INFO  18:10:03,000 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:10Z] INFO  18:10:03,000 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:10Z] INFO  18:10:03,003 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmptOeYCl/2_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign-realign.intervals -l INFO -L 13:1-31036104 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:10Z] INFO  18:10:03,009 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:10Z] INFO  18:10:03,009 HelpFormatter - Date/Time: 2015/09/30 18:10:02
[2015-09-30T17:10Z] INFO  18:10:03,009 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:03,009 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:03,066 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:10Z] INFO  18:10:03,166 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:10Z] INFO  18:10:03,173 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:10Z] INFO  18:10:03,188 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:10Z] INFO  18:10:03,423 IntervalUtils - Processing 31036104 bp from intervals
[2015-09-30T17:10Z] WARN  18:10:03,426 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:10Z] INFO  18:10:03,483 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:10Z] INFO  18:10:03,653 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:10Z] INFO  18:10:03,653 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:10Z] INFO  18:10:03,653 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:10Z] INFO  18:10:03,654 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:10Z] INFO  18:10:17,364 ProgressMeter -    12:123749297   1400019.0     2.5 m     107.0 s       98.6%     2.5 m       2.0 s
[2015-09-30T17:10Z] INFO  18:10:21,218 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:10Z] INFO  18:10:21,424 ProgressMeter -            done   1481462.0     2.6 m     104.0 s      100.0%     2.6 m       0.0 s
[2015-09-30T17:10Z] INFO  18:10:21,425 ProgressMeter - Total runtime 154.63 secs, 2.58 min, 0.04 hours
[2015-09-30T17:10Z] INFO  18:10:21,425 MicroScheduler - 3155 reads were filtered out during the traversal out of approximately 1484617 total reads (0.21%)
[2015-09-30T17:10Z] INFO  18:10:21,425 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:10Z] INFO  18:10:21,426 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:10Z] INFO  18:10:21,426 MicroScheduler -   -> 3155 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:10Z] INFO  18:10:22,144 ProgressMeter -            done   3.1036104E7    18.0 s       0.0 s      100.0%    18.0 s       0.0 s
[2015-09-30T17:10Z] INFO  18:10:22,145 ProgressMeter - Total runtime 18.49 secs, 0.31 min, 0.01 hours
[2015-09-30T17:10Z] INFO  18:10:22,148 MicroScheduler - 26547 reads were filtered out during the traversal out of approximately 331190 total reads (8.02%)
[2015-09-30T17:10Z] INFO  18:10:22,148 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:10Z] INFO  18:10:22,149 MicroScheduler -   -> 4603 reads (1.39% of total) failing BadMateFilter
[2015-09-30T17:10Z] INFO  18:10:22,149 MicroScheduler -   -> 13861 reads (4.19% of total) failing DuplicateReadFilter
[2015-09-30T17:10Z] INFO  18:10:22,149 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:10Z] INFO  18:10:22,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:10Z] INFO  18:10:22,150 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:10Z] INFO  18:10:22,150 MicroScheduler -   -> 8083 reads (2.44% of total) failing MappingQualityZeroFilter
[2015-09-30T17:10Z] INFO  18:10:22,150 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:10Z] INFO  18:10:22,150 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:10Z] INFO  18:10:22,151 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:10Z] INFO  18:10:22,473 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:10Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam
[2015-09-30T17:10Z] INFO  18:10:23,111 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:10Z] GATK: realign ('13', 0, 31036104) : syn3-tumor
[2015-09-30T17:10Z] INFO  18:10:24,977 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:24,979 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:10Z] INFO  18:10:24,979 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:10Z] INFO  18:10:24,979 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:10Z] INFO  18:10:24,983 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_0_31036104-prep-prealign-realign.intervals -L 13:1-31036104 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmp5uz1s0/2_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam
[2015-09-30T17:10Z] INFO  18:10:24,988 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:10Z] INFO  18:10:24,988 HelpFormatter - Date/Time: 2015/09/30 18:10:24
[2015-09-30T17:10Z] INFO  18:10:24,989 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:24,989 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:25,132 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:10Z] INFO  18:10:25,211 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:10Z] INFO  18:10:25,219 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:10Z] INFO  18:10:25,235 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:10Z] INFO  18:10:25,470 IntervalUtils - Processing 31036104 bp from intervals
[2015-09-30T17:10Z] WARN  18:10:25,474 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:10Z] INFO  18:10:25,528 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:10Z] INFO  18:10:25,717 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:10Z] INFO  18:10:25,717 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:10Z] INFO  18:10:25,718 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:10Z] INFO  18:10:25,718 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:10Z] INFO  18:10:25,838 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:10Z] INFO  18:10:25,910 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:10Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam 12:93169110-124189486
[2015-09-30T17:10Z] GATK: RealignerTargetCreator
[2015-09-30T17:10Z] INFO  18:10:27,836 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:27,838 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:10Z] INFO  18:10:27,838 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:10Z] INFO  18:10:27,838 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:10Z] INFO  18:10:27,842 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmp80nVXJ/2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign-realign.intervals -l INFO -L 12:93169110-124189486 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:10Z] INFO  18:10:27,847 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:10Z] INFO  18:10:27,847 HelpFormatter - Date/Time: 2015/09/30 18:10:27
[2015-09-30T17:10Z] INFO  18:10:27,848 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:27,848 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:27,906 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:10Z] INFO  18:10:28,103 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:10Z] INFO  18:10:28,110 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:10Z] INFO  18:10:28,126 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:10Z] INFO  18:10:28,375 IntervalUtils - Processing 31020377 bp from intervals
[2015-09-30T17:10Z] WARN  18:10:28,379 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:10Z] INFO  18:10:28,433 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:10Z] INFO  18:10:28,580 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:10Z] INFO  18:10:28,580 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:10Z] INFO  18:10:28,581 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:10Z] INFO  18:10:28,581 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:10Z] INFO  18:10:29,082 ProgressMeter -     13:42097514    200002.0    30.0 s       2.5 m       35.3%    84.0 s      54.0 s
[2015-09-30T17:10Z] INFO  18:10:45,610 ProgressMeter -            done    329386.0    19.0 s      60.0 s      100.0%    19.0 s       0.0 s
[2015-09-30T17:10Z] INFO  18:10:45,610 ProgressMeter - Total runtime 19.89 secs, 0.33 min, 0.01 hours
[2015-09-30T17:10Z] INFO  18:10:45,613 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 329386 total reads (0.00%)
[2015-09-30T17:10Z] INFO  18:10:45,614 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:10Z] INFO  18:10:45,614 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:10Z] INFO  18:10:45,614 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:10Z] INFO  18:10:46,654 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:10Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam
[2015-09-30T17:10Z] GATK pre-alignment ('13', 63745563, 94765401) : syn3-tumor
[2015-09-30T17:10Z] INFO  18:10:51,105 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:51,107 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:10Z] INFO  18:10:51,108 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:10Z] INFO  18:10:51,108 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:10Z] INFO  18:10:51,111 HelpFormatter - Program Args: -T PrintReads -L 13:63745564-94765401 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpp12UTo/2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam
[2015-09-30T17:10Z] INFO  18:10:51,117 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:10Z] INFO  18:10:51,117 HelpFormatter - Date/Time: 2015/09/30 18:10:51
[2015-09-30T17:10Z] INFO  18:10:51,118 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:51,118 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:10Z] INFO  18:10:51,220 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:10Z] INFO  18:10:52,109 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:10Z] INFO  18:10:52,158 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:10Z] INFO  18:10:52,165 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:10Z] INFO  18:10:52,180 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:10Z] INFO  18:10:52,192 IntervalUtils - Processing 31019838 bp from intervals
[2015-09-30T17:10Z] INFO  18:10:52,247 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:10Z] INFO  18:10:52,426 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:10Z] INFO  18:10:52,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:10Z] INFO  18:10:52,427 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:10Z] INFO  18:10:52,427 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:10Z] INFO  18:10:52,438 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:10Z] INFO  18:10:52,615 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:10Z] INFO  18:10:58,583 ProgressMeter -    12:119944181   2.6761771E7    30.0 s       1.0 s       86.3%    34.0 s       4.0 s
[2015-09-30T17:10Z] INFO  18:10:59,082 ProgressMeter -     13:55015410    500006.0    60.0 s     120.0 s       76.6%    78.0 s      18.0 s
[2015-09-30T17:11Z] INFO  18:11:01,762 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:11Z] INFO  18:11:01,921 ProgressMeter -            done    591714.0    62.0 s     106.0 s      100.0%    62.0 s       0.0 s
[2015-09-30T17:11Z] INFO  18:11:01,922 ProgressMeter - Total runtime 62.84 secs, 1.05 min, 0.02 hours
[2015-09-30T17:11Z] INFO  18:11:01,922 MicroScheduler - 1775 reads were filtered out during the traversal out of approximately 593489 total reads (0.30%)
[2015-09-30T17:11Z] INFO  18:11:01,922 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:11Z] INFO  18:11:01,923 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:11Z] INFO  18:11:01,923 MicroScheduler -   -> 1775 reads (0.30% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:11Z] INFO  18:11:02,978 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:11Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam
[2015-09-30T17:11Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam 13:31036378-62334609
[2015-09-30T17:11Z] GATK: RealignerTargetCreator
[2015-09-30T17:11Z] INFO  18:11:06,507 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:06,509 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:11Z] INFO  18:11:06,509 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:11Z] INFO  18:11:06,509 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:11Z] INFO  18:11:06,513 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpOhmNDX/2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign-realign.intervals -l INFO -L 13:31036378-62334609 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:11Z] INFO  18:11:06,519 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:11Z] INFO  18:11:06,519 HelpFormatter - Date/Time: 2015/09/30 18:11:06
[2015-09-30T17:11Z] INFO  18:11:06,519 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:06,519 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:06,580 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:11Z] INFO  18:11:06,693 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:11Z] INFO  18:11:06,702 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:11Z] INFO  18:11:06,718 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:11Z] INFO  18:11:06,773 ProgressMeter -            done   3.1020377E7    38.0 s       1.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T17:11Z] INFO  18:11:06,774 ProgressMeter - Total runtime 38.19 secs, 0.64 min, 0.01 hours
[2015-09-30T17:11Z] INFO  18:11:06,777 MicroScheduler - 110283 reads were filtered out during the traversal out of approximately 1489617 total reads (7.40%)
[2015-09-30T17:11Z] INFO  18:11:06,777 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:11Z] INFO  18:11:06,778 MicroScheduler -   -> 16728 reads (1.12% of total) failing BadMateFilter
[2015-09-30T17:11Z] INFO  18:11:06,778 MicroScheduler -   -> 68040 reads (4.57% of total) failing DuplicateReadFilter
[2015-09-30T17:11Z] INFO  18:11:06,778 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:11Z] INFO  18:11:06,778 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:11Z] INFO  18:11:06,779 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:11Z] INFO  18:11:06,779 MicroScheduler -   -> 25515 reads (1.71% of total) failing MappingQualityZeroFilter
[2015-09-30T17:11Z] INFO  18:11:06,779 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:11Z] INFO  18:11:06,779 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:11Z] INFO  18:11:06,780 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:11Z] INFO  18:11:07,143 IntervalUtils - Processing 31298232 bp from intervals
[2015-09-30T17:11Z] WARN  18:11:07,147 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:11Z] INFO  18:11:07,207 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:11Z] INFO  18:11:07,354 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:11Z] INFO  18:11:07,355 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:11Z] INFO  18:11:07,355 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:11Z] INFO  18:11:07,356 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:11Z] INFO  18:11:07,860 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:11Z] GATK: realign ('12', 93169109, 124189486) : syn3-tumor
[2015-09-30T17:11Z] INFO  18:11:09,605 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:09,607 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:11Z] INFO  18:11:09,607 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:11Z] INFO  18:11:09,607 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:11Z] INFO  18:11:09,611 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep-prealign-realign.intervals -L 12:93169110-124189486 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/tx/tmpVVETz9/2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam
[2015-09-30T17:11Z] INFO  18:11:09,617 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:11Z] INFO  18:11:09,617 HelpFormatter - Date/Time: 2015/09/30 18:11:09
[2015-09-30T17:11Z] INFO  18:11:09,617 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:09,617 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:09,790 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:11Z] INFO  18:11:09,991 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:11Z] INFO  18:11:09,999 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:11Z] INFO  18:11:10,169 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17
[2015-09-30T17:11Z] INFO  18:11:10,761 IntervalUtils - Processing 31020377 bp from intervals
[2015-09-30T17:11Z] WARN  18:11:10,765 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:11Z] INFO  18:11:10,852 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:11Z] INFO  18:11:11,244 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:11Z] INFO  18:11:11,338 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:11Z] INFO  18:11:11,339 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:11Z] INFO  18:11:11,339 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:11Z] INFO  18:11:11,339 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:11Z] INFO  18:11:11,549 ProgressMeter -            done    157034.0    19.0 s       2.0 m      100.0%    19.0 s       0.0 s
[2015-09-30T17:11Z] INFO  18:11:11,549 ProgressMeter - Total runtime 19.12 secs, 0.32 min, 0.01 hours
[2015-09-30T17:11Z] INFO  18:11:11,550 MicroScheduler - 891 reads were filtered out during the traversal out of approximately 157925 total reads (0.56%)
[2015-09-30T17:11Z] INFO  18:11:11,550 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:11Z] INFO  18:11:11,550 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:11Z] INFO  18:11:11,550 MicroScheduler -   -> 891 reads (0.56% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:11Z] INFO  18:11:11,581 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:11Z] INFO  18:11:11,769 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:11Z] INFO  18:11:12,586 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:11Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam
[2015-09-30T17:11Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam 13:63745564-94765401
[2015-09-30T17:11Z] GATK: RealignerTargetCreator
[2015-09-30T17:11Z] INFO  18:11:15,722 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:15,725 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:11Z] INFO  18:11:15,725 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:11Z] INFO  18:11:15,725 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:11Z] INFO  18:11:15,729 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpNJtMID/2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign-realign.intervals -l INFO -L 13:63745564-94765401 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:11Z] INFO  18:11:15,734 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:11Z] INFO  18:11:15,734 HelpFormatter - Date/Time: 2015/09/30 18:11:15
[2015-09-30T17:11Z] INFO  18:11:15,735 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:15,735 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:15,802 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:11Z] INFO  18:11:16,054 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:11Z] INFO  18:11:16,062 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:11Z] INFO  18:11:16,077 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:11Z] INFO  18:11:16,319 IntervalUtils - Processing 31019838 bp from intervals
[2015-09-30T17:11Z] WARN  18:11:16,323 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:11Z] INFO  18:11:16,380 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:11Z] INFO  18:11:16,506 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:11Z] INFO  18:11:16,506 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:11Z] INFO  18:11:16,506 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:11Z] INFO  18:11:16,507 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:11Z] INFO  18:11:31,552 ProgressMeter -            done   3.1298232E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T17:11Z] INFO  18:11:31,553 ProgressMeter - Total runtime 24.20 secs, 0.40 min, 0.01 hours
[2015-09-30T17:11Z] INFO  18:11:31,556 MicroScheduler - 56625 reads were filtered out during the traversal out of approximately 595845 total reads (9.50%)
[2015-09-30T17:11Z] INFO  18:11:31,556 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:11Z] INFO  18:11:31,556 MicroScheduler -   -> 9214 reads (1.55% of total) failing BadMateFilter
[2015-09-30T17:11Z] INFO  18:11:31,557 MicroScheduler -   -> 23441 reads (3.93% of total) failing DuplicateReadFilter
[2015-09-30T17:11Z] INFO  18:11:31,557 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:11Z] INFO  18:11:31,557 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:11Z] INFO  18:11:31,557 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:11Z] INFO  18:11:31,558 MicroScheduler -   -> 23970 reads (4.02% of total) failing MappingQualityZeroFilter
[2015-09-30T17:11Z] INFO  18:11:31,558 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:11Z] INFO  18:11:31,558 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:11Z] INFO  18:11:31,558 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:11Z] INFO  18:11:32,528 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:11Z] GATK: realign ('13', 31036377, 62334609) : syn3-tumor
[2015-09-30T17:11Z] INFO  18:11:32,956 ProgressMeter -            done   3.1019838E7    16.0 s       0.0 s      100.0%    16.0 s       0.0 s
[2015-09-30T17:11Z] INFO  18:11:32,956 ProgressMeter - Total runtime 16.45 secs, 0.27 min, 0.00 hours
[2015-09-30T17:11Z] INFO  18:11:32,959 MicroScheduler - 15002 reads were filtered out during the traversal out of approximately 157992 total reads (9.50%)
[2015-09-30T17:11Z] INFO  18:11:32,960 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:11Z] INFO  18:11:32,960 MicroScheduler -   -> 5690 reads (3.60% of total) failing BadMateFilter
[2015-09-30T17:11Z] INFO  18:11:32,960 MicroScheduler -   -> 5910 reads (3.74% of total) failing DuplicateReadFilter
[2015-09-30T17:11Z] INFO  18:11:32,961 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:11Z] INFO  18:11:32,961 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:11Z] INFO  18:11:32,961 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:11Z] INFO  18:11:32,961 MicroScheduler -   -> 3402 reads (2.15% of total) failing MappingQualityZeroFilter
[2015-09-30T17:11Z] INFO  18:11:32,961 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:11Z] INFO  18:11:32,962 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:11Z] INFO  18:11:32,962 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:11Z] INFO  18:11:33,925 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:11Z] GATK: realign ('13', 63745563, 94765401) : syn3-tumor
[2015-09-30T17:11Z] INFO  18:11:34,472 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:34,474 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:11Z] INFO  18:11:34,474 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:11Z] INFO  18:11:34,475 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:11Z] INFO  18:11:34,478 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep-prealign-realign.intervals -L 13:31036378-62334609 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpQzCwPx/2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam
[2015-09-30T17:11Z] INFO  18:11:34,484 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:11Z] INFO  18:11:34,484 HelpFormatter - Date/Time: 2015/09/30 18:11:34
[2015-09-30T17:11Z] INFO  18:11:34,484 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:34,484 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:34,617 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:11Z] INFO  18:11:34,714 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:11Z] INFO  18:11:34,722 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:11Z] INFO  18:11:34,738 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:11Z] INFO  18:11:34,978 IntervalUtils - Processing 31298232 bp from intervals
[2015-09-30T17:11Z] WARN  18:11:34,982 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:11Z] INFO  18:11:35,040 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:11Z] INFO  18:11:35,188 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:11Z] INFO  18:11:35,189 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:11Z] INFO  18:11:35,189 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:11Z] INFO  18:11:35,189 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:11Z] INFO  18:11:35,336 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:11Z] INFO  18:11:35,530 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:11Z] INFO  18:11:35,695 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:35,697 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:11Z] INFO  18:11:35,697 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:11Z] INFO  18:11:35,698 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:11Z] INFO  18:11:35,701 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep-prealign-realign.intervals -L 13:63745564-94765401 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpaHoF7q/2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam
[2015-09-30T17:11Z] INFO  18:11:35,707 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:11Z] INFO  18:11:35,707 HelpFormatter - Date/Time: 2015/09/30 18:11:35
[2015-09-30T17:11Z] INFO  18:11:35,707 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:35,707 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:35,833 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:11Z] INFO  18:11:35,895 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:11Z] INFO  18:11:35,903 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:11Z] INFO  18:11:35,919 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:11Z] INFO  18:11:36,353 IntervalUtils - Processing 31019838 bp from intervals
[2015-09-30T17:11Z] WARN  18:11:36,357 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:11Z] INFO  18:11:36,411 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:11Z] INFO  18:11:36,536 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:11Z] INFO  18:11:36,537 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:11Z] INFO  18:11:36,537 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:11Z] INFO  18:11:36,538 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:11Z] INFO  18:11:36,692 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:11Z] INFO  18:11:36,870 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:11Z] INFO  18:11:41,472 ProgressMeter -    12:109523529    500005.0    30.0 s      60.0 s       52.7%    56.0 s      26.0 s
[2015-09-30T17:11Z] INFO  18:11:47,009 ProgressMeter -            done    157034.0    10.0 s      66.0 s      100.0%    10.0 s       0.0 s
[2015-09-30T17:11Z] INFO  18:11:47,010 ProgressMeter - Total runtime 10.47 secs, 0.17 min, 0.00 hours
[2015-09-30T17:11Z] INFO  18:11:47,013 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 157034 total reads (0.00%)
[2015-09-30T17:11Z] INFO  18:11:47,013 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:11Z] INFO  18:11:47,013 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:11Z] INFO  18:11:47,013 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:11Z] INFO  18:11:48,056 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:11Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam
[2015-09-30T17:11Z] GATK pre-alignment ('13', 94938309, 115169878) : syn3-tumor
[2015-09-30T17:11Z] INFO  18:11:57,855 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:57,857 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:11Z] INFO  18:11:57,857 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:11Z] INFO  18:11:57,858 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:11Z] INFO  18:11:57,861 HelpFormatter - Program Args: -T PrintReads -L 13:94938310-115169878 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpFRd8c9/2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam
[2015-09-30T17:11Z] INFO  18:11:57,867 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:11Z] INFO  18:11:57,867 HelpFormatter - Date/Time: 2015/09/30 18:11:57
[2015-09-30T17:11Z] INFO  18:11:57,868 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:57,868 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:11Z] INFO  18:11:57,975 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:11Z] INFO  18:11:58,756 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:11Z] INFO  18:11:58,806 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:11Z] INFO  18:11:58,814 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:11Z] INFO  18:11:58,829 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:11Z] INFO  18:11:58,842 IntervalUtils - Processing 20231569 bp from intervals
[2015-09-30T17:11Z] INFO  18:11:58,898 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:11Z] INFO  18:11:59,082 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:11Z] INFO  18:11:59,082 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:11Z] INFO  18:11:59,083 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:11Z] INFO  18:11:59,083 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:11Z] INFO  18:11:59,094 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:11Z] INFO  18:11:59,231 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:12Z] INFO  18:12:04,382 ProgressMeter -            done    591714.0    29.0 s      49.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T17:12Z] INFO  18:12:04,382 ProgressMeter - Total runtime 29.19 secs, 0.49 min, 0.01 hours
[2015-09-30T17:12Z] INFO  18:12:04,385 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 591714 total reads (0.00%)
[2015-09-30T17:12Z] INFO  18:12:04,385 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:12Z] INFO  18:12:04,386 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:12Z] INFO  18:12:04,386 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:12Z] INFO  18:12:05,537 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:12Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam
[2015-09-30T17:12Z] GATK pre-alignment ('14', 0, 31050569) : syn3-tumor
[2015-09-30T17:12Z] INFO  18:12:09,648 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:12Z] INFO  18:12:09,650 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:12Z] INFO  18:12:09,651 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:12Z] INFO  18:12:09,651 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:12Z] INFO  18:12:09,654 HelpFormatter - Program Args: -T PrintReads -L 14:1-31050569 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmpAooLS4/2_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam
[2015-09-30T17:12Z] INFO  18:12:09,660 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:12Z] INFO  18:12:09,660 HelpFormatter - Date/Time: 2015/09/30 18:12:09
[2015-09-30T17:12Z] INFO  18:12:09,661 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:12Z] INFO  18:12:09,661 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:12Z] INFO  18:12:09,774 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:12Z] INFO  18:12:10,808 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:12Z] INFO  18:12:10,859 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:12Z] INFO  18:12:10,867 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:12Z] INFO  18:12:10,882 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:12Z] INFO  18:12:10,895 IntervalUtils - Processing 31050569 bp from intervals
[2015-09-30T17:12Z] INFO  18:12:10,952 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:12Z] INFO  18:12:11,184 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:12Z] INFO  18:12:11,184 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:12Z] INFO  18:12:11,185 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:12Z] INFO  18:12:11,185 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:12Z] INFO  18:12:11,197 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:12Z] INFO  18:12:11,269 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:12Z] INFO  18:12:11,922 ProgressMeter -    12:122246381   1200016.0    60.0 s      50.0 s       93.7%    64.0 s       4.0 s
[2015-09-30T17:12Z] INFO  18:12:19,845 ProgressMeter -            done   1481462.0    68.0 s      46.0 s      100.0%    68.0 s       0.0 s
[2015-09-30T17:12Z] INFO  18:12:19,846 ProgressMeter - Total runtime 68.51 secs, 1.14 min, 0.02 hours
[2015-09-30T17:12Z] INFO  18:12:19,849 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1481462 total reads (0.00%)
[2015-09-30T17:12Z] INFO  18:12:19,849 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:12Z] INFO  18:12:19,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:12Z] INFO  18:12:19,850 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:12Z] INFO  18:12:20,912 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:12Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam
[2015-09-30T17:12Z] GATK pre-alignment ('14', 31055710, 62162825) : syn3-tumor
[2015-09-30T17:12Z] INFO  18:12:26,880 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:12Z] INFO  18:12:26,882 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:12Z] INFO  18:12:26,882 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:12Z] INFO  18:12:26,882 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:12Z] INFO  18:12:26,886 HelpFormatter - Program Args: -T PrintReads -L 14:31055711-62162825 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmp5fUeHc/2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam
[2015-09-30T17:12Z] INFO  18:12:26,891 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:12Z] INFO  18:12:26,891 HelpFormatter - Date/Time: 2015/09/30 18:12:26
[2015-09-30T17:12Z] INFO  18:12:26,892 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:12Z] INFO  18:12:26,892 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:12Z] INFO  18:12:26,997 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:12Z] INFO  18:12:28,141 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:12Z] INFO  18:12:28,191 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:12Z] INFO  18:12:28,199 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:12Z] INFO  18:12:28,213 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:12Z] INFO  18:12:28,226 IntervalUtils - Processing 31107115 bp from intervals
[2015-09-30T17:12Z] INFO  18:12:28,284 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:12Z] INFO  18:12:28,474 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:12Z] INFO  18:12:28,474 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:12Z] INFO  18:12:28,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:12Z] INFO  18:12:28,475 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:12Z] INFO  18:12:28,486 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:12Z] INFO  18:12:28,680 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:12Z] INFO  18:12:29,096 ProgressMeter -    13:110804354    200002.0    30.0 s       2.5 m       78.4%    38.0 s       8.0 s
[2015-09-30T17:12Z] INFO  18:12:41,187 ProgressMeter -     14:23017088    200003.0    30.0 s       2.5 m       74.1%    40.0 s      10.0 s
[2015-09-30T17:12Z] INFO  18:12:55,790 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:12Z] INFO  18:12:55,943 ProgressMeter -            done    543785.0    56.0 s     104.0 s       99.6%    56.0 s       0.0 s
[2015-09-30T17:12Z] INFO  18:12:55,943 ProgressMeter - Total runtime 56.86 secs, 0.95 min, 0.02 hours
[2015-09-30T17:12Z] INFO  18:12:55,944 MicroScheduler - 1142 reads were filtered out during the traversal out of approximately 544927 total reads (0.21%)
[2015-09-30T17:12Z] INFO  18:12:55,944 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:12Z] INFO  18:12:55,944 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:12Z] INFO  18:12:55,944 MicroScheduler -   -> 1142 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:12Z] INFO  18:12:56,919 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:12Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam
[2015-09-30T17:12Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam 13:94938310-115169878
[2015-09-30T17:12Z] GATK: RealignerTargetCreator
[2015-09-30T17:12Z] INFO  18:12:58,477 ProgressMeter -     14:50218817    200002.0    30.0 s       2.5 m       61.6%    48.0 s      18.0 s
[2015-09-30T17:13Z] INFO  18:13:00,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:00,363 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:13Z] INFO  18:13:00,363 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:13Z] INFO  18:13:00,364 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:13Z] INFO  18:13:00,367 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpljcp9a/2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign-realign.intervals -l INFO -L 13:94938310-115169878 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:13Z] INFO  18:13:00,373 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:13Z] INFO  18:13:00,373 HelpFormatter - Date/Time: 2015/09/30 18:13:00
[2015-09-30T17:13Z] INFO  18:13:00,373 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:00,373 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:00,429 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:13Z] INFO  18:13:00,542 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:13Z] INFO  18:13:00,550 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:13Z] INFO  18:13:00,565 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:13Z] INFO  18:13:00,825 IntervalUtils - Processing 20231569 bp from intervals
[2015-09-30T17:13Z] WARN  18:13:00,828 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:13Z] INFO  18:13:00,884 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:13Z] INFO  18:13:00,990 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:13Z] INFO  18:13:00,990 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:13Z] INFO  18:13:00,991 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:13Z] INFO  18:13:00,991 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:13Z] INFO  18:13:11,188 ProgressMeter -     14:30102187    500007.0    60.0 s     120.0 s       96.9%    61.0 s       1.0 s
[2015-09-30T17:13Z] INFO  18:13:11,541 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:13Z] INFO  18:13:11,669 ProgressMeter -            done    567706.0    60.0 s     106.0 s      100.0%    60.0 s       0.0 s
[2015-09-30T17:13Z] INFO  18:13:11,669 ProgressMeter - Total runtime 60.48 secs, 1.01 min, 0.02 hours
[2015-09-30T17:13Z] INFO  18:13:11,669 MicroScheduler - 915 reads were filtered out during the traversal out of approximately 568621 total reads (0.16%)
[2015-09-30T17:13Z] INFO  18:13:11,670 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:13Z] INFO  18:13:11,670 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:13Z] INFO  18:13:11,670 MicroScheduler -   -> 915 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:13Z] INFO  18:13:12,655 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:13Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam
[2015-09-30T17:13Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam 14:1-31050569
[2015-09-30T17:13Z] GATK: RealignerTargetCreator
[2015-09-30T17:13Z] INFO  18:13:16,656 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:16,658 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:13Z] INFO  18:13:16,658 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:13Z] INFO  18:13:16,658 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:13Z] INFO  18:13:16,662 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmp8QAuYn/2_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign-realign.intervals -l INFO -L 14:1-31050569 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:13Z] INFO  18:13:16,667 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:13Z] INFO  18:13:16,668 HelpFormatter - Date/Time: 2015/09/30 18:13:16
[2015-09-30T17:13Z] INFO  18:13:16,668 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:16,668 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:16,725 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:13Z] INFO  18:13:17,128 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:13Z] INFO  18:13:17,136 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:13Z] INFO  18:13:17,151 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:13Z] INFO  18:13:17,408 IntervalUtils - Processing 31050569 bp from intervals
[2015-09-30T17:13Z] WARN  18:13:17,412 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:13Z] INFO  18:13:17,468 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:13Z] INFO  18:13:17,662 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:13Z] INFO  18:13:17,663 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:13Z] INFO  18:13:17,663 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:13Z] INFO  18:13:17,664 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:13Z] INFO  18:13:19,892 ProgressMeter -            done   2.0231569E7    18.0 s       0.0 s      100.0%    18.0 s       0.0 s
[2015-09-30T17:13Z] INFO  18:13:19,892 ProgressMeter - Total runtime 18.90 secs, 0.32 min, 0.01 hours
[2015-09-30T17:13Z] INFO  18:13:19,895 MicroScheduler - 42010 reads were filtered out during the traversal out of approximately 547112 total reads (7.68%)
[2015-09-30T17:13Z] INFO  18:13:19,896 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:13Z] INFO  18:13:19,896 MicroScheduler -   -> 6699 reads (1.22% of total) failing BadMateFilter
[2015-09-30T17:13Z] INFO  18:13:19,896 MicroScheduler -   -> 25728 reads (4.70% of total) failing DuplicateReadFilter
[2015-09-30T17:13Z] INFO  18:13:19,897 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:13Z] INFO  18:13:19,897 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:13Z] INFO  18:13:19,897 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:13Z] INFO  18:13:19,897 MicroScheduler -   -> 9583 reads (1.75% of total) failing MappingQualityZeroFilter
[2015-09-30T17:13Z] INFO  18:13:19,898 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:13Z] INFO  18:13:19,898 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:13Z] INFO  18:13:19,898 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:13Z] INFO  18:13:20,828 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:13Z] GATK: realign ('13', 94938309, 115169878) : syn3-tumor
[2015-09-30T17:13Z] INFO  18:13:22,559 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:22,561 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:13Z] INFO  18:13:22,561 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:13Z] INFO  18:13:22,562 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:13Z] INFO  18:13:22,565 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep-prealign-realign.intervals -L 13:94938310-115169878 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/tx/tmpGHsyJU/2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam
[2015-09-30T17:13Z] INFO  18:13:22,570 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:13Z] INFO  18:13:22,571 HelpFormatter - Date/Time: 2015/09/30 18:13:22
[2015-09-30T17:13Z] INFO  18:13:22,571 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:22,571 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:22,674 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:13Z] INFO  18:13:22,739 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:13Z] INFO  18:13:22,747 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:13Z] INFO  18:13:22,762 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:13Z] INFO  18:13:22,972 IntervalUtils - Processing 20231569 bp from intervals
[2015-09-30T17:13Z] WARN  18:13:22,975 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:13Z] INFO  18:13:23,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:13Z] INFO  18:13:23,953 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:13Z] INFO  18:13:23,953 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:13Z] INFO  18:13:23,954 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:13Z] INFO  18:13:23,954 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:13Z] INFO  18:13:24,097 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:13Z] INFO  18:13:24,236 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:13Z] INFO  18:13:28,478 ProgressMeter -     14:60193553    500006.0    60.0 s     120.0 s       93.7%    64.0 s       4.0 s
[2015-09-30T17:13Z] INFO  18:13:32,645 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:13Z] INFO  18:13:32,821 ProgressMeter -            done    616593.0    64.0 s     104.0 s      100.0%    64.0 s       0.0 s
[2015-09-30T17:13Z] INFO  18:13:32,821 ProgressMeter - Total runtime 64.35 secs, 1.07 min, 0.02 hours
[2015-09-30T17:13Z] INFO  18:13:32,822 MicroScheduler - 2035 reads were filtered out during the traversal out of approximately 618628 total reads (0.33%)
[2015-09-30T17:13Z] INFO  18:13:32,822 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:13Z] INFO  18:13:32,822 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:13Z] INFO  18:13:32,822 MicroScheduler -   -> 2035 reads (0.33% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:13Z] INFO  18:13:33,888 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:13Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam
[2015-09-30T17:13Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam 14:31055711-62162825
[2015-09-30T17:13Z] GATK: RealignerTargetCreator
[2015-09-30T17:13Z] INFO  18:13:37,562 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:37,564 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:13Z] INFO  18:13:37,565 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:13Z] INFO  18:13:37,565 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:13Z] INFO  18:13:37,568 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmp5fSjhA/2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign-realign.intervals -l INFO -L 14:31055711-62162825 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:13Z] INFO  18:13:37,575 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:13Z] INFO  18:13:37,575 HelpFormatter - Date/Time: 2015/09/30 18:13:37
[2015-09-30T17:13Z] INFO  18:13:37,575 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:37,576 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:37,781 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:13Z] INFO  18:13:37,950 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:13Z] INFO  18:13:37,958 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:13Z] INFO  18:13:38,056 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2015-09-30T17:13Z] INFO  18:13:38,513 ProgressMeter -            done   3.1050569E7    20.0 s       0.0 s      100.0%    20.0 s       0.0 s
[2015-09-30T17:13Z] INFO  18:13:38,513 ProgressMeter - Total runtime 20.85 secs, 0.35 min, 0.01 hours
[2015-09-30T17:13Z] INFO  18:13:38,516 MicroScheduler - 59838 reads were filtered out during the traversal out of approximately 570844 total reads (10.48%)
[2015-09-30T17:13Z] INFO  18:13:38,517 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:13Z] INFO  18:13:38,517 MicroScheduler -   -> 5589 reads (0.98% of total) failing BadMateFilter
[2015-09-30T17:13Z] INFO  18:13:38,517 MicroScheduler -   -> 26923 reads (4.72% of total) failing DuplicateReadFilter
[2015-09-30T17:13Z] INFO  18:13:38,518 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:13Z] INFO  18:13:38,518 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:13Z] INFO  18:13:38,518 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:13Z] INFO  18:13:38,518 MicroScheduler -   -> 27326 reads (4.79% of total) failing MappingQualityZeroFilter
[2015-09-30T17:13Z] INFO  18:13:38,519 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:13Z] INFO  18:13:38,519 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:13Z] INFO  18:13:38,519 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:13Z] INFO  18:13:38,695 IntervalUtils - Processing 31107115 bp from intervals
[2015-09-30T17:13Z] WARN  18:13:38,699 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:13Z] INFO  18:13:38,891 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:13Z] INFO  18:13:39,416 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:13Z] INFO  18:13:39,416 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:13Z] INFO  18:13:39,417 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:13Z] INFO  18:13:39,417 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:13Z] INFO  18:13:39,480 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:13Z] GATK: realign ('14', 0, 31050569) : syn3-tumor
[2015-09-30T17:13Z] INFO  18:13:41,537 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:41,539 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:13Z] INFO  18:13:41,540 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:13Z] INFO  18:13:41,540 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:13Z] INFO  18:13:41,543 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_0_31050569-prep-prealign-realign.intervals -L 14:1-31050569 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmpkbTe_w/2_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam
[2015-09-30T17:13Z] INFO  18:13:41,548 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:13Z] INFO  18:13:41,549 HelpFormatter - Date/Time: 2015/09/30 18:13:41
[2015-09-30T17:13Z] INFO  18:13:41,549 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:41,549 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:41,665 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:13Z] INFO  18:13:41,725 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:13Z] INFO  18:13:41,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:13Z] INFO  18:13:41,749 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:13Z] INFO  18:13:41,971 IntervalUtils - Processing 31050569 bp from intervals
[2015-09-30T17:13Z] WARN  18:13:41,975 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:13Z] INFO  18:13:42,029 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:13Z] INFO  18:13:42,191 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:13Z] INFO  18:13:42,191 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:13Z] INFO  18:13:42,192 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:13Z] INFO  18:13:42,192 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:13Z] INFO  18:13:42,295 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:13Z] INFO  18:13:42,364 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:13Z] INFO  18:13:51,497 ProgressMeter -            done    543785.0    27.0 s      50.0 s       99.6%    27.0 s       0.0 s
[2015-09-30T17:13Z] INFO  18:13:51,497 ProgressMeter - Total runtime 27.54 secs, 0.46 min, 0.01 hours
[2015-09-30T17:13Z] INFO  18:13:51,500 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 543785 total reads (0.00%)
[2015-09-30T17:13Z] INFO  18:13:51,501 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:13Z] INFO  18:13:51,501 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:13Z] INFO  18:13:51,501 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:13Z] INFO  18:13:52,675 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:13Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam
[2015-09-30T17:13Z] GATK pre-alignment ('14', 62186823, 93262365) : syn3-tumor
[2015-09-30T17:13Z] INFO  18:13:56,191 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:56,193 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:13Z] INFO  18:13:56,194 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:13Z] INFO  18:13:56,194 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:13Z] INFO  18:13:56,197 HelpFormatter - Program Args: -T PrintReads -L 14:62186824-93262365 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmpz5UzoA/2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam
[2015-09-30T17:13Z] INFO  18:13:56,203 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:13Z] INFO  18:13:56,203 HelpFormatter - Date/Time: 2015/09/30 18:13:56
[2015-09-30T17:13Z] INFO  18:13:56,203 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:56,203 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:13Z] INFO  18:13:56,302 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:13Z] INFO  18:13:57,364 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:13Z] INFO  18:13:57,412 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:13Z] INFO  18:13:57,419 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:13Z] INFO  18:13:57,434 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:13Z] INFO  18:13:57,447 IntervalUtils - Processing 31075542 bp from intervals
[2015-09-30T17:13Z] INFO  18:13:57,503 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:13Z] INFO  18:13:57,703 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:13Z] INFO  18:13:57,703 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:13Z] INFO  18:13:57,703 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:13Z] INFO  18:13:57,704 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:13Z] INFO  18:13:57,715 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:13Z] INFO  18:13:57,907 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:14Z] INFO  18:14:04,635 ProgressMeter -            done   3.1107115E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T17:14Z] INFO  18:14:04,635 ProgressMeter - Total runtime 25.22 secs, 0.42 min, 0.01 hours
[2015-09-30T17:14Z] INFO  18:14:04,638 MicroScheduler - 46571 reads were filtered out during the traversal out of approximately 620020 total reads (7.51%)
[2015-09-30T17:14Z] INFO  18:14:04,639 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:14Z] INFO  18:14:04,639 MicroScheduler -   -> 9990 reads (1.61% of total) failing BadMateFilter
[2015-09-30T17:14Z] INFO  18:14:04,639 MicroScheduler -   -> 24884 reads (4.01% of total) failing DuplicateReadFilter
[2015-09-30T17:14Z] INFO  18:14:04,639 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:14Z] INFO  18:14:04,640 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:14Z] INFO  18:14:04,640 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:14Z] INFO  18:14:04,640 MicroScheduler -   -> 11697 reads (1.89% of total) failing MappingQualityZeroFilter
[2015-09-30T17:14Z] INFO  18:14:04,640 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:14Z] INFO  18:14:04,641 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:14Z] INFO  18:14:04,641 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:14Z] INFO  18:14:05,716 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:14Z] GATK: realign ('14', 31055710, 62162825) : syn3-tumor
[2015-09-30T17:14Z] INFO  18:14:07,534 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:14Z] INFO  18:14:07,536 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:14Z] INFO  18:14:07,536 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:14Z] INFO  18:14:07,537 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:14Z] INFO  18:14:07,540 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep-prealign-realign.intervals -L 14:31055711-62162825 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmpNts3og/2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam
[2015-09-30T17:14Z] INFO  18:14:07,546 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:14Z] INFO  18:14:07,547 HelpFormatter - Date/Time: 2015/09/30 18:14:07
[2015-09-30T17:14Z] INFO  18:14:07,547 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:14Z] INFO  18:14:07,547 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:14Z] INFO  18:14:08,023 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:14Z] INFO  18:14:08,161 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:14Z] INFO  18:14:08,169 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:14Z] INFO  18:14:08,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
[2015-09-30T17:14Z] INFO  18:14:08,732 IntervalUtils - Processing 31107115 bp from intervals
[2015-09-30T17:14Z] WARN  18:14:08,737 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:14Z] INFO  18:14:08,839 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:14Z] INFO  18:14:10,171 ProgressMeter -            done    567706.0    27.0 s      49.0 s      100.0%    27.0 s       0.0 s
[2015-09-30T17:14Z] INFO  18:14:10,171 ProgressMeter - Total runtime 27.98 secs, 0.47 min, 0.01 hours
[2015-09-30T17:14Z] INFO  18:14:10,174 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 567706 total reads (0.00%)
[2015-09-30T17:14Z] INFO  18:14:10,175 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:14Z] INFO  18:14:10,175 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:14Z] INFO  18:14:10,175 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:14Z] INFO  18:14:10,268 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:14Z] INFO  18:14:10,268 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:14Z] INFO  18:14:10,269 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:14Z] INFO  18:14:10,269 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:14Z] INFO  18:14:10,537 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:14Z] INFO  18:14:10,733 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:14Z] INFO  18:14:11,671 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:14Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam
[2015-09-30T17:14Z] GATK pre-alignment ('14', 93263525, 107349540) : syn3-tumor
[2015-09-30T17:14Z] INFO  18:14:18,787 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:14Z] INFO  18:14:18,790 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:14Z] INFO  18:14:18,790 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:14Z] INFO  18:14:18,790 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:14Z] INFO  18:14:18,794 HelpFormatter - Program Args: -T PrintReads -L 14:93263526-107349540 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmpNZo0b2/2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam
[2015-09-30T17:14Z] INFO  18:14:18,800 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:14Z] INFO  18:14:18,800 HelpFormatter - Date/Time: 2015/09/30 18:14:18
[2015-09-30T17:14Z] INFO  18:14:18,800 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:14Z] INFO  18:14:18,800 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:14Z] INFO  18:14:18,909 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:14Z] INFO  18:14:19,601 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:14Z] INFO  18:14:19,652 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:14Z] INFO  18:14:19,660 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:14Z] INFO  18:14:19,681 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:14Z] INFO  18:14:19,695 IntervalUtils - Processing 14086015 bp from intervals
[2015-09-30T17:14Z] INFO  18:14:20,394 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:14Z] INFO  18:14:20,562 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:14Z] INFO  18:14:20,563 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:14Z] INFO  18:14:20,563 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:14Z] INFO  18:14:20,563 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:14Z] INFO  18:14:20,575 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:14Z] INFO  18:14:20,670 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:14Z] INFO  18:14:27,737 ProgressMeter -     14:68268292    200003.0    30.0 s       2.5 m       19.6%     2.6 m       2.1 m
[2015-09-30T17:14Z] INFO  18:14:41,365 ProgressMeter -     14:51288085    300004.0    31.0 s     103.0 s       65.0%    47.0 s      16.0 s
[2015-09-30T17:14Z] INFO  18:14:51,074 ProgressMeter -    14:101301528    200004.0    30.0 s       2.5 m       57.1%    52.0 s      22.0 s
[2015-09-30T17:14Z] INFO  18:14:51,954 ProgressMeter -            done    616593.0    41.0 s      67.0 s      100.0%    41.0 s       0.0 s
[2015-09-30T17:14Z] INFO  18:14:51,954 ProgressMeter - Total runtime 41.69 secs, 0.69 min, 0.01 hours
[2015-09-30T17:14Z] INFO  18:14:51,957 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 616593 total reads (0.00%)
[2015-09-30T17:14Z] INFO  18:14:51,958 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:14Z] INFO  18:14:51,958 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:14Z] INFO  18:14:51,958 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:14Z] INFO  18:14:53,031 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:14Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam
[2015-09-30T17:14Z] GATK pre-alignment ('15', 0, 31041107) : syn3-tumor
[2015-09-30T17:14Z] INFO  18:14:57,737 ProgressMeter -     14:75352379    500006.0    60.0 s     120.0 s       42.4%     2.4 m      81.0 s
[2015-09-30T17:14Z] INFO  18:14:58,298 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:14Z] INFO  18:14:58,300 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:14Z] INFO  18:14:58,300 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:14Z] INFO  18:14:58,301 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:14Z] INFO  18:14:58,304 HelpFormatter - Program Args: -T PrintReads -L 15:1-31041107 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmpDBQzPr/2_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam
[2015-09-30T17:14Z] INFO  18:14:58,310 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:14Z] INFO  18:14:58,310 HelpFormatter - Date/Time: 2015/09/30 18:14:58
[2015-09-30T17:14Z] INFO  18:14:58,310 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:14Z] INFO  18:14:58,310 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:14Z] INFO  18:14:58,415 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:14Z] INFO  18:14:59,610 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:14Z] INFO  18:14:59,658 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:14Z] INFO  18:14:59,666 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:14Z] INFO  18:14:59,680 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:14Z] INFO  18:14:59,693 IntervalUtils - Processing 31041107 bp from intervals
[2015-09-30T17:14Z] INFO  18:14:59,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:14Z] INFO  18:14:59,979 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:14Z] INFO  18:14:59,980 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:14Z] INFO  18:14:59,980 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:14Z] INFO  18:14:59,980 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:14Z] INFO  18:14:59,991 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:15Z] INFO  18:15:00,055 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:15Z] INFO  18:15:21,101 ProgressMeter -    14:105929985    600009.0    60.0 s     100.0 s       89.9%    66.0 s       6.0 s
[2015-09-30T17:15Z] INFO  18:15:26,331 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6dbf2c98
[2015-09-30T17:15Z] INFO  18:15:27,663 ProgressMeter -            done    739194.0    67.0 s      90.0 s       99.5%    67.0 s       0.0 s
[2015-09-30T17:15Z] INFO  18:15:27,664 ProgressMeter - Total runtime 67.10 secs, 1.12 min, 0.02 hours
[2015-09-30T17:15Z] INFO  18:15:27,664 MicroScheduler - 1701 reads were filtered out during the traversal out of approximately 740895 total reads (0.23%)
[2015-09-30T17:15Z] INFO  18:15:27,665 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:15Z] INFO  18:15:27,665 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:15Z] INFO  18:15:27,665 MicroScheduler -   -> 1701 reads (0.23% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:15Z] INFO  18:15:27,738 ProgressMeter -     14:90651542    800009.0    90.0 s     112.0 s       91.6%    98.0 s       8.0 s
[2015-09-30T17:15Z] INFO  18:15:28,765 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:15Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam
[2015-09-30T17:15Z] INFO  18:15:29,983 ProgressMeter -     15:25615742    200003.0    30.0 s       2.5 m       82.5%    36.0 s       6.0 s
[2015-09-30T17:15Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam 14:93263526-107349540
[2015-09-30T17:15Z] GATK: RealignerTargetCreator
[2015-09-30T17:15Z] INFO  18:15:34,186 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:15Z] INFO  18:15:34,188 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:15Z] INFO  18:15:34,189 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:15Z] INFO  18:15:34,189 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:15Z] INFO  18:15:34,192 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmpe6Yjqh/2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign-realign.intervals -l INFO -L 14:93263526-107349540 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:15Z] INFO  18:15:34,199 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:15Z] INFO  18:15:34,199 HelpFormatter - Date/Time: 2015/09/30 18:15:34
[2015-09-30T17:15Z] INFO  18:15:34,199 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:15Z] INFO  18:15:34,199 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:15Z] INFO  18:15:34,259 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:15Z] INFO  18:15:34,370 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:15Z] INFO  18:15:34,378 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:15Z] INFO  18:15:34,394 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:15Z] INFO  18:15:34,651 IntervalUtils - Processing 14086015 bp from intervals
[2015-09-30T17:15Z] WARN  18:15:34,655 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:15Z] INFO  18:15:34,713 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:15Z] INFO  18:15:34,804 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:15Z] INFO  18:15:34,804 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:15Z] INFO  18:15:34,805 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:15Z] INFO  18:15:34,805 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:15Z] INFO  18:15:40,212 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:15Z] INFO  18:15:40,438 ProgressMeter -            done   1006391.0   102.0 s     102.0 s      100.0%   102.0 s       0.0 s
[2015-09-30T17:15Z] INFO  18:15:40,439 ProgressMeter - Total runtime 102.74 secs, 1.71 min, 0.03 hours
[2015-09-30T17:15Z] INFO  18:15:40,439 MicroScheduler - 2507 reads were filtered out during the traversal out of approximately 1008898 total reads (0.25%)
[2015-09-30T17:15Z] INFO  18:15:40,439 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:15Z] INFO  18:15:40,440 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:15Z] INFO  18:15:40,440 MicroScheduler -   -> 2507 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:15Z] INFO  18:15:41,507 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:15Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam
[2015-09-30T17:15Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam 14:62186824-93262365
[2015-09-30T17:15Z] GATK: RealignerTargetCreator
[2015-09-30T17:15Z] INFO  18:15:45,782 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:15Z] INFO  18:15:45,784 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:15Z] INFO  18:15:45,784 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:15Z] INFO  18:15:45,784 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:15Z] INFO  18:15:45,788 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmpFqKcT7/2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign-realign.intervals -l INFO -L 14:62186824-93262365 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:15Z] INFO  18:15:45,795 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:15Z] INFO  18:15:45,795 HelpFormatter - Date/Time: 2015/09/30 18:15:45
[2015-09-30T17:15Z] INFO  18:15:45,795 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:15Z] INFO  18:15:45,795 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:15Z] INFO  18:15:45,853 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:15Z] INFO  18:15:50,142 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:15Z] INFO  18:15:50,150 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:15Z] INFO  18:15:50,167 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:15Z] INFO  18:15:50,809 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:15Z] INFO  18:15:50,887 ProgressMeter -            done    475139.0    50.0 s     107.0 s      100.0%    50.0 s       0.0 s
[2015-09-30T17:15Z] INFO  18:15:50,887 ProgressMeter - Total runtime 50.91 secs, 0.85 min, 0.01 hours
[2015-09-30T17:15Z] INFO  18:15:50,888 MicroScheduler - 796 reads were filtered out during the traversal out of approximately 475935 total reads (0.17%)
[2015-09-30T17:15Z] INFO  18:15:50,888 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:15Z] INFO  18:15:50,888 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:15Z] INFO  18:15:50,888 MicroScheduler -   -> 796 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:15Z] INFO  18:15:53,482 IntervalUtils - Processing 31075542 bp from intervals
[2015-09-30T17:15Z] WARN  18:15:53,486 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:15Z] INFO  18:15:53,781 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:15Z] INFO  18:15:53,851 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:15Z] INFO  18:15:53,926 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:15Z] INFO  18:15:53,927 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:15Z] INFO  18:15:53,927 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:15Z] INFO  18:15:53,928 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:15Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam
[2015-09-30T17:15Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam 15:1-31041107
[2015-09-30T17:15Z] GATK: RealignerTargetCreator
[2015-09-30T17:15Z] INFO  18:15:57,063 ProgressMeter -            done   1.4086015E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T17:15Z] INFO  18:15:57,064 ProgressMeter - Total runtime 22.26 secs, 0.37 min, 0.01 hours
[2015-09-30T17:15Z] INFO  18:15:57,067 MicroScheduler - 62079 reads were filtered out during the traversal out of approximately 744154 total reads (8.34%)
[2015-09-30T17:15Z] INFO  18:15:57,067 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:15Z] INFO  18:15:57,067 MicroScheduler -   -> 7404 reads (0.99% of total) failing BadMateFilter
[2015-09-30T17:15Z] INFO  18:15:57,068 MicroScheduler -   -> 37869 reads (5.09% of total) failing DuplicateReadFilter
[2015-09-30T17:15Z] INFO  18:15:57,068 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:15Z] INFO  18:15:57,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:15Z] INFO  18:15:57,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:15Z] INFO  18:15:57,069 MicroScheduler -   -> 16806 reads (2.26% of total) failing MappingQualityZeroFilter
[2015-09-30T17:15Z] INFO  18:15:57,069 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:15Z] INFO  18:15:57,069 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:15Z] INFO  18:15:57,069 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:15Z] INFO  18:15:57,204 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:15Z] INFO  18:15:57,206 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:15Z] INFO  18:15:57,206 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:15Z] INFO  18:15:57,206 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:15Z] INFO  18:15:57,209 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmpxlLzYX/2_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign-realign.intervals -l INFO -L 15:1-31041107 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:15Z] INFO  18:15:57,215 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:15Z] INFO  18:15:57,215 HelpFormatter - Date/Time: 2015/09/30 18:15:57
[2015-09-30T17:15Z] INFO  18:15:57,215 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:15Z] INFO  18:15:57,215 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:15Z] INFO  18:15:57,270 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:15Z] INFO  18:15:57,375 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:15Z] INFO  18:15:57,383 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:15Z] INFO  18:15:57,398 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:15Z] INFO  18:15:57,646 IntervalUtils - Processing 31041107 bp from intervals
[2015-09-30T17:15Z] WARN  18:15:57,650 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:15Z] INFO  18:15:57,704 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:15Z] INFO  18:15:57,864 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:15Z] INFO  18:15:57,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:15Z] INFO  18:15:57,865 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:15Z] INFO  18:15:57,866 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:15Z] INFO  18:15:58,038 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:15Z] GATK: realign ('14', 93263525, 107349540) : syn3-tumor
[2015-09-30T17:16Z] INFO  18:16:00,966 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:00,968 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:16Z] INFO  18:16:00,968 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:16Z] INFO  18:16:00,968 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:16Z] INFO  18:16:00,972 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep-prealign-realign.intervals -L 14:93263526-107349540 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmpRCjSPb/2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam
[2015-09-30T17:16Z] INFO  18:16:00,978 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:16Z] INFO  18:16:00,978 HelpFormatter - Date/Time: 2015/09/30 18:16:00
[2015-09-30T17:16Z] INFO  18:16:00,978 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:00,978 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:01,107 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:16Z] INFO  18:16:01,177 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:16Z] INFO  18:16:01,185 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:16Z] INFO  18:16:01,201 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:16Z] INFO  18:16:01,426 IntervalUtils - Processing 14086015 bp from intervals
[2015-09-30T17:16Z] WARN  18:16:01,430 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:16Z] INFO  18:16:01,488 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:16Z] INFO  18:16:01,579 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:16Z] INFO  18:16:01,580 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:16Z] INFO  18:16:01,580 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:16Z] INFO  18:16:01,580 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:16Z] INFO  18:16:01,712 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:01,816 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:17,095 ProgressMeter -            done   3.1041107E7    19.0 s       0.0 s      100.0%    19.0 s       0.0 s
[2015-09-30T17:16Z] INFO  18:16:17,095 ProgressMeter - Total runtime 19.23 secs, 0.32 min, 0.01 hours
[2015-09-30T17:16Z] INFO  18:16:17,098 MicroScheduler - 178702 reads were filtered out during the traversal out of approximately 478164 total reads (37.37%)
[2015-09-30T17:16Z] INFO  18:16:17,098 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:16Z] INFO  18:16:17,099 MicroScheduler -   -> 3456 reads (0.72% of total) failing BadMateFilter
[2015-09-30T17:16Z] INFO  18:16:17,099 MicroScheduler -   -> 15495 reads (3.24% of total) failing DuplicateReadFilter
[2015-09-30T17:16Z] INFO  18:16:17,099 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:16Z] INFO  18:16:17,099 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:16Z] INFO  18:16:17,100 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:16Z] INFO  18:16:17,100 MicroScheduler -   -> 159751 reads (33.41% of total) failing MappingQualityZeroFilter
[2015-09-30T17:16Z] INFO  18:16:17,100 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:16Z] INFO  18:16:17,100 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:16Z] INFO  18:16:17,101 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:16Z] INFO  18:16:18,061 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:16Z] GATK: realign ('15', 0, 31041107) : syn3-tumor
[2015-09-30T17:16Z] INFO  18:16:19,882 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:19,884 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:16Z] INFO  18:16:19,885 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:16Z] INFO  18:16:19,885 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:16Z] INFO  18:16:19,888 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_0_31041107-prep-prealign-realign.intervals -L 15:1-31041107 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmpnO8JDa/2_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam
[2015-09-30T17:16Z] INFO  18:16:19,893 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:16Z] INFO  18:16:19,894 HelpFormatter - Date/Time: 2015/09/30 18:16:19
[2015-09-30T17:16Z] INFO  18:16:19,894 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:19,894 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:20,016 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:16Z] INFO  18:16:20,081 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:16Z] INFO  18:16:20,089 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:16Z] INFO  18:16:20,105 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:16Z] INFO  18:16:21,216 IntervalUtils - Processing 31041107 bp from intervals
[2015-09-30T17:16Z] WARN  18:16:21,220 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:16Z] INFO  18:16:21,273 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:16Z] INFO  18:16:21,444 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:16Z] INFO  18:16:21,445 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:16Z] INFO  18:16:21,445 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:16Z] INFO  18:16:21,446 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:16Z] INFO  18:16:21,538 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:21,600 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:24,219 ProgressMeter -     14:93107489   3.0907065E7    30.0 s       0.0 s       99.5%    30.0 s       0.0 s
[2015-09-30T17:16Z] INFO  18:16:24,688 ProgressMeter -            done   3.1075542E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T17:16Z] INFO  18:16:24,688 ProgressMeter - Total runtime 30.76 secs, 0.51 min, 0.01 hours
[2015-09-30T17:16Z] INFO  18:16:24,691 MicroScheduler - 75895 reads were filtered out during the traversal out of approximately 1012538 total reads (7.50%)
[2015-09-30T17:16Z] INFO  18:16:24,692 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:16Z] INFO  18:16:24,692 MicroScheduler -   -> 12136 reads (1.20% of total) failing BadMateFilter
[2015-09-30T17:16Z] INFO  18:16:24,692 MicroScheduler -   -> 45610 reads (4.50% of total) failing DuplicateReadFilter
[2015-09-30T17:16Z] INFO  18:16:24,693 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:16Z] INFO  18:16:24,693 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:16Z] INFO  18:16:24,693 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:16Z] INFO  18:16:24,693 MicroScheduler -   -> 18149 reads (1.79% of total) failing MappingQualityZeroFilter
[2015-09-30T17:16Z] INFO  18:16:24,694 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:16Z] INFO  18:16:24,694 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:16Z] INFO  18:16:24,694 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:16Z] INFO  18:16:25,825 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:16Z] GATK: realign ('14', 62186823, 93262365) : syn3-tumor
[2015-09-30T17:16Z] INFO  18:16:28,332 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:28,334 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:16Z] INFO  18:16:28,334 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:16Z] INFO  18:16:28,334 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:16Z] INFO  18:16:28,337 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep-prealign-realign.intervals -L 14:62186824-93262365 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/tx/tmpO3lcAM/2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam
[2015-09-30T17:16Z] INFO  18:16:28,343 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:16Z] INFO  18:16:28,343 HelpFormatter - Date/Time: 2015/09/30 18:16:28
[2015-09-30T17:16Z] INFO  18:16:28,344 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:28,344 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:28,826 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:16Z] INFO  18:16:28,891 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:16Z] INFO  18:16:28,899 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:16Z] INFO  18:16:28,914 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:16Z] INFO  18:16:29,132 IntervalUtils - Processing 31075542 bp from intervals
[2015-09-30T17:16Z] WARN  18:16:29,136 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:16Z] INFO  18:16:29,190 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:16Z] INFO  18:16:29,332 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:16Z] INFO  18:16:29,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:16Z] INFO  18:16:29,333 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:16Z] INFO  18:16:29,333 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:16Z] INFO  18:16:29,482 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:29,659 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:32,769 ProgressMeter -    14:104379204    400007.0    31.0 s      77.0 s       78.9%    39.0 s       8.0 s
[2015-09-30T17:16Z] INFO  18:16:40,258 ProgressMeter -            done    739194.0    38.0 s      52.0 s       99.5%    38.0 s       0.0 s
[2015-09-30T17:16Z] INFO  18:16:40,258 ProgressMeter - Total runtime 38.68 secs, 0.64 min, 0.01 hours
[2015-09-30T17:16Z] INFO  18:16:40,262 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 739194 total reads (0.00%)
[2015-09-30T17:16Z] INFO  18:16:40,262 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:16Z] INFO  18:16:40,262 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:16Z] INFO  18:16:40,263 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:16Z] INFO  18:16:41,484 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:16Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam
[2015-09-30T17:16Z] GATK pre-alignment ('15', 31042312, 62147370) : syn3-tumor
[2015-09-30T17:16Z] INFO  18:16:45,343 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:45,345 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:16Z] INFO  18:16:45,345 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:16Z] INFO  18:16:45,345 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:16Z] INFO  18:16:45,349 HelpFormatter - Program Args: -T PrintReads -L 15:31042313-62147370 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmpJ70hxU/2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam
[2015-09-30T17:16Z] INFO  18:16:45,355 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:16Z] INFO  18:16:45,355 HelpFormatter - Date/Time: 2015/09/30 18:16:45
[2015-09-30T17:16Z] INFO  18:16:45,355 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:45,355 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:45,472 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:16Z] INFO  18:16:46,282 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:16Z] INFO  18:16:46,335 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:16Z] INFO  18:16:46,343 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:16Z] INFO  18:16:46,359 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:16Z] INFO  18:16:46,373 IntervalUtils - Processing 31105058 bp from intervals
[2015-09-30T17:16Z] INFO  18:16:46,433 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:16Z] INFO  18:16:46,628 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:16Z] INFO  18:16:46,629 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:16Z] INFO  18:16:46,629 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:16Z] INFO  18:16:46,629 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:16Z] INFO  18:16:46,641 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:46,834 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:47,347 ProgressMeter -            done    475139.0    25.0 s      54.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T17:16Z] INFO  18:16:47,347 ProgressMeter - Total runtime 25.90 secs, 0.43 min, 0.01 hours
[2015-09-30T17:16Z] INFO  18:16:47,350 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 475139 total reads (0.00%)
[2015-09-30T17:16Z] INFO  18:16:47,351 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:16Z] INFO  18:16:47,351 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:16Z] INFO  18:16:47,351 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:16Z] INFO  18:16:48,493 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:16Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam
[2015-09-30T17:16Z] GATK pre-alignment ('15', 62148224, 93170844) : syn3-tumor
[2015-09-30T17:16Z] INFO  18:16:51,751 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:51,754 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:16Z] INFO  18:16:51,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:16Z] INFO  18:16:51,754 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:16Z] INFO  18:16:51,758 HelpFormatter - Program Args: -T PrintReads -L 15:62148225-93170844 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmprfHaB6/2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam
[2015-09-30T17:16Z] INFO  18:16:51,764 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:16Z] INFO  18:16:51,764 HelpFormatter - Date/Time: 2015/09/30 18:16:51
[2015-09-30T17:16Z] INFO  18:16:51,764 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:51,764 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:16Z] INFO  18:16:51,875 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:16Z] INFO  18:16:52,792 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:16Z] INFO  18:16:52,843 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:16Z] INFO  18:16:52,851 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:16Z] INFO  18:16:52,866 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:16Z] INFO  18:16:52,880 IntervalUtils - Processing 31022620 bp from intervals
[2015-09-30T17:16Z] INFO  18:16:52,940 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:16Z] INFO  18:16:53,144 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:16Z] INFO  18:16:53,144 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:16Z] INFO  18:16:53,144 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:16Z] INFO  18:16:53,145 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:16Z] INFO  18:16:53,156 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:53,354 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:16Z] INFO  18:16:59,340 ProgressMeter -     14:75747904    500006.0    30.0 s      60.0 s       43.6%    68.0 s      38.0 s
[2015-09-30T17:17Z] INFO  18:17:14,756 ProgressMeter -            done   1006391.0    45.0 s      45.0 s      100.0%    45.0 s       0.0 s
[2015-09-30T17:17Z] INFO  18:17:14,757 ProgressMeter - Total runtime 45.42 secs, 0.76 min, 0.01 hours
[2015-09-30T17:17Z] INFO  18:17:14,760 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1006391 total reads (0.00%)
[2015-09-30T17:17Z] INFO  18:17:14,760 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:17Z] INFO  18:17:14,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:17Z] INFO  18:17:14,761 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:17Z] INFO  18:17:15,800 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:17Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam
[2015-09-30T17:17Z] INFO  18:17:16,631 ProgressMeter -     15:38796046    200002.0    30.0 s       2.5 m       24.9%   120.0 s      90.0 s
[2015-09-30T17:17Z] GATK pre-alignment ('15', 93173163, 102531392) : syn3-tumor
[2015-09-30T17:17Z] INFO  18:17:20,101 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:17Z] INFO  18:17:20,103 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:17Z] INFO  18:17:20,103 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:17Z] INFO  18:17:20,103 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:17Z] INFO  18:17:20,106 HelpFormatter - Program Args: -T PrintReads -L 15:93173164-102531392 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmpL5dYUk/2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam
[2015-09-30T17:17Z] INFO  18:17:20,112 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:17Z] INFO  18:17:20,112 HelpFormatter - Date/Time: 2015/09/30 18:17:20
[2015-09-30T17:17Z] INFO  18:17:20,112 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:17Z] INFO  18:17:20,112 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:17Z] INFO  18:17:20,617 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:17Z] INFO  18:17:21,287 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:17Z] INFO  18:17:21,335 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:17Z] INFO  18:17:21,343 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:17Z] INFO  18:17:21,356 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:17Z] INFO  18:17:21,368 IntervalUtils - Processing 9358229 bp from intervals
[2015-09-30T17:17Z] INFO  18:17:21,423 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:17Z] INFO  18:17:21,571 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:17Z] INFO  18:17:21,571 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:17Z] INFO  18:17:21,571 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:17Z] INFO  18:17:21,572 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:17Z] INFO  18:17:21,582 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:17Z] INFO  18:17:21,646 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:17Z] INFO  18:17:23,147 ProgressMeter -     15:65688947    200002.0    30.0 s       2.5 m       11.4%     4.4 m       3.9 m
[2015-09-30T17:17Z] INFO  18:17:45,246 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:17Z] INFO  18:17:45,816 ProgressMeter -            done    213355.0    24.0 s     113.0 s       99.8%    24.0 s       0.0 s
[2015-09-30T17:17Z] INFO  18:17:45,816 ProgressMeter - Total runtime 24.25 secs, 0.40 min, 0.01 hours
[2015-09-30T17:17Z] INFO  18:17:45,816 MicroScheduler - 512 reads were filtered out during the traversal out of approximately 213867 total reads (0.24%)
[2015-09-30T17:17Z] INFO  18:17:45,817 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:17Z] INFO  18:17:45,817 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:17Z] INFO  18:17:45,817 MicroScheduler -   -> 512 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:17Z] INFO  18:17:46,841 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:17Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam
[2015-09-30T17:17Z] INFO  18:17:47,226 ProgressMeter -     15:42459968    500005.0    60.0 s       2.0 m       36.7%     2.7 m     103.0 s
[2015-09-30T17:17Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam 15:93173164-102531392
[2015-09-30T17:17Z] GATK: RealignerTargetCreator
[2015-09-30T17:17Z] INFO  18:17:49,012 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:17Z] INFO  18:17:49,014 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:17Z] INFO  18:17:49,014 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:17Z] INFO  18:17:49,014 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:17Z] INFO  18:17:49,018 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmppCvof4/2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign-realign.intervals -l INFO -L 15:93173164-102531392 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:17Z] INFO  18:17:49,023 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:17Z] INFO  18:17:49,023 HelpFormatter - Date/Time: 2015/09/30 18:17:49
[2015-09-30T17:17Z] INFO  18:17:49,023 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:17Z] INFO  18:17:49,023 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:17Z] INFO  18:17:49,081 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:17Z] INFO  18:17:49,190 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:17Z] INFO  18:17:49,198 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:17Z] INFO  18:17:49,213 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:17Z] INFO  18:17:50,115 IntervalUtils - Processing 9358229 bp from intervals
[2015-09-30T17:17Z] WARN  18:17:50,119 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:17Z] INFO  18:17:50,176 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:17Z] INFO  18:17:50,238 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:17Z] INFO  18:17:50,238 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:17Z] INFO  18:17:50,239 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:17Z] INFO  18:17:50,239 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:17Z] INFO  18:17:53,158 ProgressMeter -     15:72950020    500005.0    60.0 s     120.0 s       34.8%     2.9 m     112.0 s
[2015-09-30T17:17Z] INFO  18:17:59,116 ProgressMeter -            done   9358229.0     8.0 s       0.0 s      100.0%     8.0 s       0.0 s
[2015-09-30T17:17Z] INFO  18:17:59,116 ProgressMeter - Total runtime 8.88 secs, 0.15 min, 0.00 hours
[2015-09-30T17:17Z] INFO  18:17:59,119 MicroScheduler - 26816 reads were filtered out during the traversal out of approximately 214745 total reads (12.49%)
[2015-09-30T17:17Z] INFO  18:17:59,119 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:17Z] INFO  18:17:59,119 MicroScheduler -   -> 2773 reads (1.29% of total) failing BadMateFilter
[2015-09-30T17:17Z] INFO  18:17:59,120 MicroScheduler -   -> 9663 reads (4.50% of total) failing DuplicateReadFilter
[2015-09-30T17:17Z] INFO  18:17:59,120 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:17Z] INFO  18:17:59,120 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:17Z] INFO  18:17:59,120 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:17Z] INFO  18:17:59,121 MicroScheduler -   -> 14380 reads (6.70% of total) failing MappingQualityZeroFilter
[2015-09-30T17:17Z] INFO  18:17:59,121 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:17Z] INFO  18:17:59,121 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:17Z] INFO  18:17:59,121 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:18Z] INFO  18:18:00,113 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:18Z] GATK: realign ('15', 93173163, 102531392) : syn3-tumor
[2015-09-30T17:18Z] INFO  18:18:02,580 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:18Z] INFO  18:18:02,582 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:18Z] INFO  18:18:02,582 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:18Z] INFO  18:18:02,582 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:18Z] INFO  18:18:02,585 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep-prealign-realign.intervals -L 15:93173164-102531392 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmpzJio5c/2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam
[2015-09-30T17:18Z] INFO  18:18:02,591 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:18Z] INFO  18:18:02,591 HelpFormatter - Date/Time: 2015/09/30 18:18:02
[2015-09-30T17:18Z] INFO  18:18:02,591 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:18Z] INFO  18:18:02,592 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:18Z] INFO  18:18:02,719 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:18Z] INFO  18:18:02,783 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:18Z] INFO  18:18:02,791 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:18Z] INFO  18:18:02,806 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:18Z] INFO  18:18:03,044 IntervalUtils - Processing 9358229 bp from intervals
[2015-09-30T17:18Z] WARN  18:18:03,048 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:18Z] INFO  18:18:03,102 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:18Z] INFO  18:18:03,384 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:18Z] INFO  18:18:03,385 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:18Z] INFO  18:18:03,385 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:18Z] INFO  18:18:03,386 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:18Z] INFO  18:18:03,486 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:18Z] INFO  18:18:03,556 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:18Z] INFO  18:18:17,114 ProgressMeter -            done    213355.0    13.0 s      64.0 s       99.8%    13.0 s       0.0 s
[2015-09-30T17:18Z] INFO  18:18:17,115 ProgressMeter - Total runtime 13.73 secs, 0.23 min, 0.00 hours
[2015-09-30T17:18Z] INFO  18:18:17,118 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 213355 total reads (0.00%)
[2015-09-30T17:18Z] INFO  18:18:17,118 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:18Z] INFO  18:18:17,118 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:18Z] INFO  18:18:17,118 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:18Z] INFO  18:18:17,288 ProgressMeter -     15:45428031    800009.0    90.0 s     113.0 s       46.2%     3.2 m     104.0 s
[2015-09-30T17:18Z] INFO  18:18:18,151 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:18Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam
[2015-09-30T17:18Z] GATK pre-alignment ('16', 0, 31021934) : syn3-tumor
[2015-09-30T17:18Z] INFO  18:18:20,428 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:18Z] INFO  18:18:20,430 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:18Z] INFO  18:18:20,431 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:18Z] INFO  18:18:20,431 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:18Z] INFO  18:18:20,434 HelpFormatter - Program Args: -T PrintReads -L 16:1-31021934 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/tx/tmpBw68K_/2_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam
[2015-09-30T17:18Z] INFO  18:18:20,440 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:18Z] INFO  18:18:20,440 HelpFormatter - Date/Time: 2015/09/30 18:18:20
[2015-09-30T17:18Z] INFO  18:18:20,440 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:18Z] INFO  18:18:20,440 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:18Z] INFO  18:18:21,044 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:18Z] INFO  18:18:21,820 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:18Z] INFO  18:18:21,871 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:18Z] INFO  18:18:21,878 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:18Z] INFO  18:18:21,893 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:18Z] INFO  18:18:21,906 IntervalUtils - Processing 31021934 bp from intervals
[2015-09-30T17:18Z] INFO  18:18:21,963 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:18Z] INFO  18:18:22,178 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:18Z] INFO  18:18:22,178 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:18Z] INFO  18:18:22,178 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:18Z] INFO  18:18:22,179 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:18Z] INFO  18:18:22,190 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:18Z] INFO  18:18:22,393 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:18Z] INFO  18:18:23,158 ProgressMeter -     15:76866899    800008.0    90.0 s     112.0 s       47.4%     3.2 m      99.0 s
[2015-09-30T17:18Z] INFO  18:18:47,289 ProgressMeter -     15:56207978   1200014.0   120.0 s     100.0 s       80.9%     2.5 m      28.0 s
[2015-09-30T17:18Z] INFO  18:18:52,181 ProgressMeter -      16:1395212    200002.0    30.0 s       2.5 m        4.5%    11.1 m      10.6 m
[2015-09-30T17:18Z] INFO  18:18:53,159 ProgressMeter -     15:83208875   1100011.0   120.0 s     109.0 s       67.9%     2.9 m      56.0 s
[2015-09-30T17:18Z] INFO  18:18:58,838 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:18Z] INFO  18:18:59,203 ProgressMeter -            done   1347322.0     2.2 m      98.0 s      100.0%     2.2 m       0.0 s
[2015-09-30T17:18Z] INFO  18:18:59,203 ProgressMeter - Total runtime 132.57 secs, 2.21 min, 0.04 hours
[2015-09-30T17:18Z] INFO  18:18:59,203 MicroScheduler - 2890 reads were filtered out during the traversal out of approximately 1350212 total reads (0.21%)
[2015-09-30T17:18Z] INFO  18:18:59,204 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:18Z] INFO  18:18:59,204 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:18Z] INFO  18:18:59,204 MicroScheduler -   -> 2890 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:19Z] INFO  18:19:00,258 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:19Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam
[2015-09-30T17:19Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam 15:31042313-62147370
[2015-09-30T17:19Z] GATK: RealignerTargetCreator
[2015-09-30T17:19Z] INFO  18:19:06,943 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:19Z] INFO  18:19:06,945 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:19Z] INFO  18:19:06,945 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:19Z] INFO  18:19:06,945 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:19Z] INFO  18:19:06,949 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmpFLVTHW/2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign-realign.intervals -l INFO -L 15:31042313-62147370 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:19Z] INFO  18:19:06,955 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:19Z] INFO  18:19:06,955 HelpFormatter - Date/Time: 2015/09/30 18:19:06
[2015-09-30T17:19Z] INFO  18:19:06,955 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:19Z] INFO  18:19:06,955 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:19Z] INFO  18:19:07,020 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:19Z] INFO  18:19:07,173 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:19Z] INFO  18:19:07,181 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:19Z] INFO  18:19:07,196 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:19Z] INFO  18:19:07,434 IntervalUtils - Processing 31105058 bp from intervals
[2015-09-30T17:19Z] WARN  18:19:07,438 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:19Z] INFO  18:19:07,493 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:19Z] INFO  18:19:07,630 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:19Z] INFO  18:19:07,631 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:19Z] INFO  18:19:07,631 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:19Z] INFO  18:19:07,631 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:19Z] INFO  18:19:22,182 ProgressMeter -      16:2375738    500005.0    60.0 s     120.0 s        7.7%    13.1 m      12.1 m
[2015-09-30T17:19Z] INFO  18:19:23,160 ProgressMeter -     15:90176095   1400014.0     2.5 m     107.0 s       90.3%     2.8 m      16.0 s
[2015-09-30T17:19Z] INFO  18:19:37,634 ProgressMeter -     15:56742093   2.569548E7    30.0 s       1.0 s       82.6%    36.0 s       6.0 s
[2015-09-30T17:19Z] INFO  18:19:37,814 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:19Z] INFO  18:19:38,021 ProgressMeter -            done   1634892.0     2.7 m     100.0 s      100.0%     2.7 m       0.0 s
[2015-09-30T17:19Z] INFO  18:19:38,021 ProgressMeter - Total runtime 164.88 secs, 2.75 min, 0.05 hours
[2015-09-30T17:19Z] INFO  18:19:38,021 MicroScheduler - 2813 reads were filtered out during the traversal out of approximately 1637705 total reads (0.17%)
[2015-09-30T17:19Z] INFO  18:19:38,022 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:19Z] INFO  18:19:38,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:19Z] INFO  18:19:38,022 MicroScheduler -   -> 2813 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:19Z] INFO  18:19:39,103 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:19Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam
[2015-09-30T17:19Z] INFO  18:19:42,446 ProgressMeter -            done   3.1105058E7    34.0 s       1.0 s      100.0%    34.0 s       0.0 s
[2015-09-30T17:19Z] INFO  18:19:42,446 ProgressMeter - Total runtime 34.82 secs, 0.58 min, 0.01 hours
[2015-09-30T17:19Z] INFO  18:19:42,450 MicroScheduler - 158795 reads were filtered out during the traversal out of approximately 1354948 total reads (11.72%)
[2015-09-30T17:19Z] INFO  18:19:42,450 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:19Z] INFO  18:19:42,450 MicroScheduler -   -> 14066 reads (1.04% of total) failing BadMateFilter
[2015-09-30T17:19Z] INFO  18:19:42,451 MicroScheduler -   -> 57400 reads (4.24% of total) failing DuplicateReadFilter
[2015-09-30T17:19Z] INFO  18:19:42,451 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:19Z] INFO  18:19:42,451 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:19Z] INFO  18:19:42,451 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:19Z] INFO  18:19:42,451 MicroScheduler -   -> 87329 reads (6.45% of total) failing MappingQualityZeroFilter
[2015-09-30T17:19Z] INFO  18:19:42,452 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:19Z] INFO  18:19:42,452 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:19Z] INFO  18:19:42,452 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:19Z] INFO  18:19:43,558 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:19Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam 15:62148225-93170844
[2015-09-30T17:19Z] GATK: RealignerTargetCreator
[2015-09-30T17:19Z] GATK: realign ('15', 31042312, 62147370) : syn3-tumor
[2015-09-30T17:19Z] INFO  18:19:45,734 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:19Z] INFO  18:19:45,736 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:19Z] INFO  18:19:45,736 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:19Z] INFO  18:19:45,736 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:19Z] INFO  18:19:45,740 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmptYIaz0/2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign-realign.intervals -l INFO -L 15:62148225-93170844 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:19Z] INFO  18:19:45,745 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:19Z] INFO  18:19:45,746 HelpFormatter - Date/Time: 2015/09/30 18:19:45
[2015-09-30T17:19Z] INFO  18:19:45,746 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:19Z] INFO  18:19:45,746 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:19Z] INFO  18:19:45,801 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:19Z] INFO  18:19:45,902 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:19Z] INFO  18:19:45,910 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:19Z] INFO  18:19:45,926 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:19Z] INFO  18:19:46,586 IntervalUtils - Processing 31022620 bp from intervals
[2015-09-30T17:19Z] WARN  18:19:46,590 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:19Z] INFO  18:19:46,647 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:19Z] INFO  18:19:46,791 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:19Z] INFO  18:19:46,791 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:19Z] INFO  18:19:46,792 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:19Z] INFO  18:19:46,792 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:19Z] INFO  18:19:46,824 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:19Z] INFO  18:19:46,826 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:19Z] INFO  18:19:46,827 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:19Z] INFO  18:19:46,827 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:19Z] INFO  18:19:46,830 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep-prealign-realign.intervals -L 15:31042313-62147370 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmpd8ytoG/2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam
[2015-09-30T17:19Z] INFO  18:19:46,836 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:19Z] INFO  18:19:46,836 HelpFormatter - Date/Time: 2015/09/30 18:19:46
[2015-09-30T17:19Z] INFO  18:19:46,836 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:19Z] INFO  18:19:46,836 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:19Z] INFO  18:19:46,957 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:19Z] INFO  18:19:47,021 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:19Z] INFO  18:19:47,029 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:19Z] INFO  18:19:47,045 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:19Z] INFO  18:19:47,267 IntervalUtils - Processing 31105058 bp from intervals
[2015-09-30T17:19Z] WARN  18:19:47,271 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:19Z] INFO  18:19:47,326 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:19Z] INFO  18:19:47,477 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:19Z] INFO  18:19:47,478 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:19Z] INFO  18:19:47,478 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:19Z] INFO  18:19:47,479 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:19Z] INFO  18:19:47,628 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:19Z] INFO  18:19:47,824 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:19Z] INFO  18:19:52,183 ProgressMeter -      16:4638073    800010.0    90.0 s     112.0 s       15.0%    10.0 m       8.5 m
[2015-09-30T17:20Z] INFO  18:20:16,795 ProgressMeter -     15:86283645   2.412992E7    30.0 s       1.0 s       77.8%    38.0 s       8.0 s
[2015-09-30T17:20Z] INFO  18:20:18,614 ProgressMeter -     15:42821843    600007.0    31.0 s      51.0 s       37.9%    81.0 s      50.0 s
[2015-09-30T17:20Z] INFO  18:20:22,183 ProgressMeter -     16:14927342   1100013.0   120.0 s     109.0 s       48.1%     4.2 m       2.2 m
[2015-09-30T17:20Z] INFO  18:20:24,030 ProgressMeter -            done   3.102262E7    37.0 s       1.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T17:20Z] INFO  18:20:24,030 ProgressMeter - Total runtime 37.24 secs, 0.62 min, 0.01 hours
[2015-09-30T17:20Z] INFO  18:20:24,033 MicroScheduler - 225216 reads were filtered out during the traversal out of approximately 1645467 total reads (13.69%)
[2015-09-30T17:20Z] INFO  18:20:24,034 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:20Z] INFO  18:20:24,034 MicroScheduler -   -> 15075 reads (0.92% of total) failing BadMateFilter
[2015-09-30T17:20Z] INFO  18:20:24,034 MicroScheduler -   -> 74378 reads (4.52% of total) failing DuplicateReadFilter
[2015-09-30T17:20Z] INFO  18:20:24,035 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:20Z] INFO  18:20:24,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:20Z] INFO  18:20:24,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:20Z] INFO  18:20:24,035 MicroScheduler -   -> 135763 reads (8.25% of total) failing MappingQualityZeroFilter
[2015-09-30T17:20Z] INFO  18:20:24,035 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:20Z] INFO  18:20:24,036 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:20Z] INFO  18:20:24,036 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:20Z] INFO  18:20:25,090 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:20Z] GATK: realign ('15', 62148224, 93170844) : syn3-tumor
[2015-09-30T17:20Z] INFO  18:20:26,809 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:20Z] INFO  18:20:26,811 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:20Z] INFO  18:20:26,811 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:20Z] INFO  18:20:26,811 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:20Z] INFO  18:20:26,814 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep-prealign-realign.intervals -L 15:62148225-93170844 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/tx/tmpx8_wOk/2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam
[2015-09-30T17:20Z] INFO  18:20:26,820 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:20Z] INFO  18:20:26,820 HelpFormatter - Date/Time: 2015/09/30 18:20:26
[2015-09-30T17:20Z] INFO  18:20:26,820 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:20Z] INFO  18:20:26,821 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:20Z] INFO  18:20:27,188 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:20Z] INFO  18:20:27,536 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:20Z] INFO  18:20:27,544 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:20Z] INFO  18:20:27,696 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
[2015-09-30T17:20Z] INFO  18:20:28,604 IntervalUtils - Processing 31022620 bp from intervals
[2015-09-30T17:20Z] WARN  18:20:28,608 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:20Z] INFO  18:20:28,708 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:20Z] INFO  18:20:29,159 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:20Z] INFO  18:20:29,159 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:20Z] INFO  18:20:29,160 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:20Z] INFO  18:20:29,160 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:20Z] INFO  18:20:29,429 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:20Z] INFO  18:20:29,631 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:20Z] INFO  18:20:48,470 ProgressMeter -            done   1347322.0    60.0 s      45.0 s      100.0%    60.0 s       0.0 s
[2015-09-30T17:20Z] INFO  18:20:48,470 ProgressMeter - Total runtime 60.99 secs, 1.02 min, 0.02 hours
[2015-09-30T17:20Z] INFO  18:20:48,473 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1347322 total reads (0.00%)
[2015-09-30T17:20Z] INFO  18:20:48,474 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:20Z] INFO  18:20:48,474 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:20Z] INFO  18:20:48,474 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:20Z] INFO  18:20:49,535 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:20Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam
[2015-09-30T17:20Z] INFO  18:20:52,184 ProgressMeter -     16:18842017   1400016.0     2.5 m     107.0 s       60.7%     4.1 m      96.0 s
[2015-09-30T17:20Z] GATK pre-alignment ('16', 31044089, 62860191) : syn3-tumor
[2015-09-30T17:20Z] INFO  18:20:55,350 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:20Z] INFO  18:20:55,352 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:20Z] INFO  18:20:55,352 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:20Z] INFO  18:20:55,352 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:20Z] INFO  18:20:55,355 HelpFormatter - Program Args: -T PrintReads -L 16:31044090-62860191 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/tx/tmpAFT6CE/2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam
[2015-09-30T17:20Z] INFO  18:20:55,360 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:20Z] INFO  18:20:55,360 HelpFormatter - Date/Time: 2015/09/30 18:20:55
[2015-09-30T17:20Z] INFO  18:20:55,360 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:20Z] INFO  18:20:55,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:20Z] INFO  18:20:55,459 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:20Z] INFO  18:20:56,137 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:20Z] INFO  18:20:56,185 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:20Z] INFO  18:20:56,192 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:20Z] INFO  18:20:56,207 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:20Z] INFO  18:20:56,219 IntervalUtils - Processing 31816102 bp from intervals
[2015-09-30T17:20Z] INFO  18:20:56,273 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:20Z] INFO  18:20:56,462 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:20Z] INFO  18:20:56,462 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:20Z] INFO  18:20:56,463 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:20Z] INFO  18:20:56,463 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:20Z] INFO  18:20:56,474 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:20Z] INFO  18:20:56,654 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:20Z] INFO  18:20:59,831 ProgressMeter -     15:73621733    500005.0    30.0 s      61.0 s       37.0%    81.0 s      51.0 s
[2015-09-30T17:21Z] INFO  18:21:22,196 ProgressMeter -     16:22587482   1700019.0     3.0 m     105.0 s       72.8%     4.1 m      67.0 s
[2015-09-30T17:21Z] INFO  18:21:26,520 ProgressMeter -     16:46654986    200002.0    30.0 s       2.5 m       49.1%    61.0 s      31.0 s
[2015-09-30T17:21Z] INFO  18:21:31,343 ProgressMeter -     15:85449162   1300013.0    62.0 s      47.0 s       75.1%    82.0 s      20.0 s
[2015-09-30T17:21Z] INFO  18:21:43,231 ProgressMeter -            done   1634892.0    74.0 s      45.0 s      100.0%    74.0 s       0.0 s
[2015-09-30T17:21Z] INFO  18:21:43,232 ProgressMeter - Total runtime 74.07 secs, 1.23 min, 0.02 hours
[2015-09-30T17:21Z] INFO  18:21:43,235 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1634892 total reads (0.00%)
[2015-09-30T17:21Z] INFO  18:21:43,235 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:21Z] INFO  18:21:43,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:21Z] INFO  18:21:43,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:21Z] INFO  18:21:44,350 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:21Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam
[2015-09-30T17:21Z] GATK pre-alignment ('16', 64294277, 90354753) : syn3-tumor
[2015-09-30T17:21Z] INFO  18:21:51,216 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:21Z] INFO  18:21:51,218 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:21Z] INFO  18:21:51,218 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:21Z] INFO  18:21:51,218 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:21Z] INFO  18:21:51,222 HelpFormatter - Program Args: -T PrintReads -L 16:64294278-90354753 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/tx/tmpgxmxTH/2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam
[2015-09-30T17:21Z] INFO  18:21:51,228 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:21Z] INFO  18:21:51,228 HelpFormatter - Date/Time: 2015/09/30 18:21:51
[2015-09-30T17:21Z] INFO  18:21:51,228 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:21Z] INFO  18:21:51,228 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:21Z] INFO  18:21:51,333 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:21Z] INFO  18:21:52,197 ProgressMeter -     16:28949300   2000022.0     3.5 m     105.0 s       93.3%     3.8 m      15.0 s
[2015-09-30T17:21Z] INFO  18:21:52,490 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:21Z] INFO  18:21:52,541 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:21Z] INFO  18:21:52,549 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:21Z] INFO  18:21:52,565 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:21Z] INFO  18:21:52,579 IntervalUtils - Processing 26060476 bp from intervals
[2015-09-30T17:21Z] INFO  18:21:52,640 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:21Z] INFO  18:21:52,841 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:21Z] INFO  18:21:52,842 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:21Z] INFO  18:21:52,842 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:21Z] INFO  18:21:52,842 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:21Z] INFO  18:21:52,855 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:21Z] INFO  18:21:53,021 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:21Z] INFO  18:21:56,521 ProgressMeter -     16:56388710    500009.0    60.0 s     120.0 s       79.7%    75.0 s      15.0 s
[2015-09-30T17:22Z] INFO  18:22:20,322 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:22Z] INFO  18:22:20,495 ProgressMeter -            done   2393202.0     4.0 m      99.0 s      100.0%     4.0 m       0.0 s
[2015-09-30T17:22Z] INFO  18:22:20,496 ProgressMeter - Total runtime 238.32 secs, 3.97 min, 0.07 hours
[2015-09-30T17:22Z] INFO  18:22:20,496 MicroScheduler - 3741 reads were filtered out during the traversal out of approximately 2396943 total reads (0.16%)
[2015-09-30T17:22Z] INFO  18:22:20,496 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:22Z] INFO  18:22:20,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:22Z] INFO  18:22:20,497 MicroScheduler -   -> 3741 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:22Z] INFO  18:22:21,618 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:22Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam
[2015-09-30T17:22Z] INFO  18:22:22,866 ProgressMeter -     16:67995740    200002.0    30.0 s       2.5 m       14.2%     3.5 m       3.0 m
[2015-09-30T17:22Z] INFO  18:22:23,518 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:22Z] INFO  18:22:23,676 ProgressMeter -            done    808494.0    87.0 s     107.0 s      100.0%    87.0 s       0.0 s
[2015-09-30T17:22Z] INFO  18:22:23,676 ProgressMeter - Total runtime 87.21 secs, 1.45 min, 0.02 hours
[2015-09-30T17:22Z] INFO  18:22:23,676 MicroScheduler - 1700 reads were filtered out during the traversal out of approximately 810194 total reads (0.21%)
[2015-09-30T17:22Z] INFO  18:22:23,677 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:22Z] INFO  18:22:23,677 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:22Z] INFO  18:22:23,677 MicroScheduler -   -> 1700 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:22Z] INFO  18:22:24,716 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:22Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam
[2015-09-30T17:22Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam 16:31044090-62860191
[2015-09-30T17:22Z] GATK: RealignerTargetCreator
[2015-09-30T17:22Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam 16:1-31021934
[2015-09-30T17:22Z] GATK: RealignerTargetCreator
[2015-09-30T17:22Z] INFO  18:22:29,409 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:22Z] INFO  18:22:29,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:22Z] INFO  18:22:29,411 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:22Z] INFO  18:22:29,412 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:22Z] INFO  18:22:29,415 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/tx/tmpWhVR95/2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign-realign.intervals -l INFO -L 16:31044090-62860191 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:22Z] INFO  18:22:29,451 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:22Z] INFO  18:22:29,451 HelpFormatter - Date/Time: 2015/09/30 18:22:29
[2015-09-30T17:22Z] INFO  18:22:29,452 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:22Z] INFO  18:22:29,452 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:22Z] INFO  18:22:29,495 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:22Z] INFO  18:22:29,497 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:22Z] INFO  18:22:29,498 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:22Z] INFO  18:22:29,498 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:22Z] INFO  18:22:29,501 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/tx/tmpjDrMn0/2_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign-realign.intervals -l INFO -L 16:1-31021934 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:22Z] INFO  18:22:29,508 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:22Z] INFO  18:22:29,508 HelpFormatter - Date/Time: 2015/09/30 18:22:29
[2015-09-30T17:22Z] INFO  18:22:29,508 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:22Z] INFO  18:22:29,508 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:22Z] INFO  18:22:29,748 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:22Z] INFO  18:22:29,772 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:22Z] INFO  18:22:30,025 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:22Z] INFO  18:22:30,034 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:22Z] INFO  18:22:30,039 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:22Z] INFO  18:22:30,047 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:22Z] INFO  18:22:30,175 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2015-09-30T17:22Z] INFO  18:22:30,186 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
[2015-09-30T17:22Z] INFO  18:22:30,618 IntervalUtils - Processing 31021934 bp from intervals
[2015-09-30T17:22Z] WARN  18:22:30,621 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:22Z] INFO  18:22:30,679 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:22Z] INFO  18:22:31,210 IntervalUtils - Processing 31816102 bp from intervals
[2015-09-30T17:22Z] WARN  18:22:31,215 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:22Z] INFO  18:22:31,433 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:22Z] INFO  18:22:31,690 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:22Z] INFO  18:22:31,690 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:22Z] INFO  18:22:31,691 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:22Z] INFO  18:22:31,691 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:22Z] INFO  18:22:32,757 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:22Z] INFO  18:22:32,757 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:22Z] INFO  18:22:32,758 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:22Z] INFO  18:22:32,758 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:22Z] INFO  18:22:52,983 ProgressMeter -     16:71061903    500005.0    60.0 s     120.0 s       26.0%     3.9 m       2.9 m
[2015-09-30T17:22Z] INFO  18:22:58,147 ProgressMeter -            done   3.1816102E7    25.0 s       0.0 s      100.0%    25.0 s       0.0 s
[2015-09-30T17:22Z] INFO  18:22:58,147 ProgressMeter - Total runtime 25.39 secs, 0.42 min, 0.01 hours
[2015-09-30T17:22Z] INFO  18:22:58,150 MicroScheduler - 109735 reads were filtered out during the traversal out of approximately 813840 total reads (13.48%)
[2015-09-30T17:22Z] INFO  18:22:58,151 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:22Z] INFO  18:22:58,151 MicroScheduler -   -> 9626 reads (1.18% of total) failing BadMateFilter
[2015-09-30T17:22Z] INFO  18:22:58,151 MicroScheduler -   -> 37630 reads (4.62% of total) failing DuplicateReadFilter
[2015-09-30T17:22Z] INFO  18:22:58,151 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:22Z] INFO  18:22:58,151 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:22Z] INFO  18:22:58,152 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:22Z] INFO  18:22:58,152 MicroScheduler -   -> 62479 reads (7.68% of total) failing MappingQualityZeroFilter
[2015-09-30T17:22Z] INFO  18:22:58,152 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:22Z] INFO  18:22:58,152 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:22Z] INFO  18:22:58,153 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:22Z] INFO  18:22:59,125 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:22Z] GATK: realign ('16', 31044089, 62860191) : syn3-tumor
[2015-09-30T17:23Z] INFO  18:23:01,693 ProgressMeter -     16:18810133   1.8808832E7    30.0 s       1.0 s       60.6%    49.0 s      19.0 s
[2015-09-30T17:23Z] INFO  18:23:02,422 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:23Z] INFO  18:23:02,424 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:23Z] INFO  18:23:02,425 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:23Z] INFO  18:23:02,425 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:23Z] INFO  18:23:02,428 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep-prealign-realign.intervals -L 16:31044090-62860191 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/tx/tmpBkM__3/2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam
[2015-09-30T17:23Z] INFO  18:23:02,434 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:23Z] INFO  18:23:02,434 HelpFormatter - Date/Time: 2015/09/30 18:23:02
[2015-09-30T17:23Z] INFO  18:23:02,434 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:23Z] INFO  18:23:02,434 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:23Z] INFO  18:23:02,871 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:23Z] INFO  18:23:02,933 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:23Z] INFO  18:23:02,941 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:23Z] INFO  18:23:02,956 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:23Z] INFO  18:23:03,180 IntervalUtils - Processing 31816102 bp from intervals
[2015-09-30T17:23Z] WARN  18:23:03,184 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:23Z] INFO  18:23:03,237 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:23Z] INFO  18:23:03,353 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:23Z] INFO  18:23:03,353 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:23Z] INFO  18:23:03,354 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:23Z] INFO  18:23:03,354 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:23Z] INFO  18:23:03,477 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:23Z] INFO  18:23:03,659 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:23Z] INFO  18:23:20,102 ProgressMeter -            done   3.1021934E7    48.0 s       1.0 s      100.0%    48.0 s       0.0 s
[2015-09-30T17:23Z] INFO  18:23:20,102 ProgressMeter - Total runtime 48.41 secs, 0.81 min, 0.01 hours
[2015-09-30T17:23Z] INFO  18:23:20,105 MicroScheduler - 440959 reads were filtered out during the traversal out of approximately 2406635 total reads (18.32%)
[2015-09-30T17:23Z] INFO  18:23:20,106 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:23Z] INFO  18:23:20,106 MicroScheduler -   -> 19018 reads (0.79% of total) failing BadMateFilter
[2015-09-30T17:23Z] INFO  18:23:20,106 MicroScheduler -   -> 110145 reads (4.58% of total) failing DuplicateReadFilter
[2015-09-30T17:23Z] INFO  18:23:20,106 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:23Z] INFO  18:23:20,107 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:23Z] INFO  18:23:20,107 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:23Z] INFO  18:23:20,107 MicroScheduler -   -> 311796 reads (12.96% of total) failing MappingQualityZeroFilter
[2015-09-30T17:23Z] INFO  18:23:20,107 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:23Z] INFO  18:23:20,107 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:23Z] INFO  18:23:20,108 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:23Z] INFO  18:23:21,068 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:23Z] GATK: realign ('16', 0, 31021934) : syn3-tumor
[2015-09-30T17:23Z] INFO  18:23:22,983 ProgressMeter -     16:81236238    800011.0    90.0 s     112.0 s       65.0%     2.3 m      48.0 s
[2015-09-30T17:23Z] INFO  18:23:23,164 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:23Z] INFO  18:23:23,166 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:23Z] INFO  18:23:23,166 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:23Z] INFO  18:23:23,166 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:23Z] INFO  18:23:23,170 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_0_31021934-prep-prealign-realign.intervals -L 16:1-31021934 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/tx/tmpKtu7iE/2_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam
[2015-09-30T17:23Z] INFO  18:23:23,175 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:23Z] INFO  18:23:23,176 HelpFormatter - Date/Time: 2015/09/30 18:23:23
[2015-09-30T17:23Z] INFO  18:23:23,176 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:23Z] INFO  18:23:23,176 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:23Z] INFO  18:23:23,301 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:23Z] INFO  18:23:23,363 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:23Z] INFO  18:23:23,371 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:23Z] INFO  18:23:23,386 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:23Z] INFO  18:23:24,036 IntervalUtils - Processing 31021934 bp from intervals
[2015-09-30T17:23Z] WARN  18:23:24,040 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:23Z] INFO  18:23:24,095 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:23Z] INFO  18:23:24,241 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:23Z] INFO  18:23:24,242 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:23Z] INFO  18:23:24,242 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:23Z] INFO  18:23:24,242 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:23Z] INFO  18:23:24,383 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:23Z] INFO  18:23:24,569 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:23Z] INFO  18:23:35,133 ProgressMeter -     16:56642376    500009.0    31.0 s      63.0 s       80.5%    38.0 s       7.0 s
[2015-09-30T17:23Z] INFO  18:23:44,551 ProgressMeter -            done    808494.0    41.0 s      50.0 s      100.0%    41.0 s       0.0 s
[2015-09-30T17:23Z] INFO  18:23:44,551 ProgressMeter - Total runtime 41.20 secs, 0.69 min, 0.01 hours
[2015-09-30T17:23Z] INFO  18:23:44,554 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 808494 total reads (0.00%)
[2015-09-30T17:23Z] INFO  18:23:44,555 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:23Z] INFO  18:23:44,555 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:23Z] INFO  18:23:44,555 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:23Z] INFO  18:23:45,614 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:23Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam
[2015-09-30T17:23Z] GATK pre-alignment ('17', 0, 31039439) : syn3-tumor
[2015-09-30T17:23Z] INFO  18:23:50,621 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:23Z] INFO  18:23:50,623 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:23Z] INFO  18:23:50,623 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:23Z] INFO  18:23:50,623 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:23Z] INFO  18:23:50,626 HelpFormatter - Program Args: -T PrintReads -L 17:1-31039439 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/tx/tmpZ4eGYr/2_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam
[2015-09-30T17:23Z] INFO  18:23:50,632 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:23Z] INFO  18:23:50,632 HelpFormatter - Date/Time: 2015/09/30 18:23:50
[2015-09-30T17:23Z] INFO  18:23:50,632 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:23Z] INFO  18:23:50,632 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:23Z] INFO  18:23:50,747 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:23Z] INFO  18:23:51,425 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:23Z] INFO  18:23:51,474 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:23Z] INFO  18:23:51,481 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:23Z] INFO  18:23:51,495 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:23Z] INFO  18:23:51,508 IntervalUtils - Processing 31039439 bp from intervals
[2015-09-30T17:23Z] INFO  18:23:51,562 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:23Z] INFO  18:23:51,757 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:23Z] INFO  18:23:51,758 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:23Z] INFO  18:23:51,758 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:23Z] INFO  18:23:51,758 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:23Z] INFO  18:23:51,769 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:23Z] INFO  18:23:51,976 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:23Z] INFO  18:23:52,984 ProgressMeter -     16:88773918   1100015.0   120.0 s     109.0 s       93.9%     2.1 m       7.0 s
[2015-09-30T17:23Z] INFO  18:23:55,864 ProgressMeter -      16:2349471    500005.0    31.0 s      63.0 s        7.6%     6.8 m       6.3 m
[2015-09-30T17:24Z] INFO  18:24:12,744 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:24Z] INFO  18:24:12,906 ProgressMeter -            done   1418713.0     2.3 m      98.0 s       99.6%     2.3 m       0.0 s
[2015-09-30T17:24Z] INFO  18:24:12,906 ProgressMeter - Total runtime 140.06 secs, 2.33 min, 0.04 hours
[2015-09-30T17:24Z] INFO  18:24:12,906 MicroScheduler - 2446 reads were filtered out during the traversal out of approximately 1421159 total reads (0.17%)
[2015-09-30T17:24Z] INFO  18:24:12,907 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:24Z] INFO  18:24:12,907 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:24Z] INFO  18:24:12,907 MicroScheduler -   -> 2446 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:24Z] INFO  18:24:13,919 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:24Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam
[2015-09-30T17:24Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam 16:64294278-90354753
[2015-09-30T17:24Z] GATK: RealignerTargetCreator
[2015-09-30T17:24Z] INFO  18:24:19,126 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:24Z] INFO  18:24:19,128 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:24Z] INFO  18:24:19,128 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:24Z] INFO  18:24:19,129 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:24Z] INFO  18:24:19,132 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/tx/tmpmEVtw8/2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign-realign.intervals -l INFO -L 16:64294278-90354753 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:24Z] INFO  18:24:19,138 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:24Z] INFO  18:24:19,139 HelpFormatter - Date/Time: 2015/09/30 18:24:19
[2015-09-30T17:24Z] INFO  18:24:19,139 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:24Z] INFO  18:24:19,139 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:24Z] INFO  18:24:19,197 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:24Z] INFO  18:24:19,309 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:24Z] INFO  18:24:19,317 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:24Z] INFO  18:24:19,333 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:24Z] INFO  18:24:20,056 IntervalUtils - Processing 26060476 bp from intervals
[2015-09-30T17:24Z] WARN  18:24:20,060 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:24Z] INFO  18:24:20,118 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:24Z] INFO  18:24:20,246 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:24Z] INFO  18:24:20,247 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:24Z] INFO  18:24:20,247 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:24Z] INFO  18:24:20,248 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:24Z] INFO  18:24:21,761 ProgressMeter -      17:3058350    200002.0    30.0 s       2.5 m        9.9%     5.1 m       4.6 m
[2015-09-30T17:24Z] INFO  18:24:27,959 ProgressMeter -     16:16269557   1200014.0    63.0 s      53.0 s       52.4%   120.0 s      57.0 s
[2015-09-30T17:24Z] INFO  18:24:50,250 ProgressMeter -     16:88907985   2.4605307E7    30.0 s       1.0 s       94.4%    31.0 s       1.0 s
[2015-09-30T17:24Z] INFO  18:24:51,762 ProgressMeter -      17:5329762    500006.0    60.0 s     120.0 s       17.2%     5.8 m       4.8 m
[2015-09-30T17:24Z] INFO  18:24:53,643 ProgressMeter -            done   2.6060476E7    33.0 s       1.0 s      100.0%    33.0 s       0.0 s
[2015-09-30T17:24Z] INFO  18:24:53,643 ProgressMeter - Total runtime 33.40 secs, 0.56 min, 0.01 hours
[2015-09-30T17:24Z] INFO  18:24:53,646 MicroScheduler - 136283 reads were filtered out during the traversal out of approximately 1428166 total reads (9.54%)
[2015-09-30T17:24Z] INFO  18:24:53,647 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:24Z] INFO  18:24:53,647 MicroScheduler -   -> 14376 reads (1.01% of total) failing BadMateFilter
[2015-09-30T17:24Z] INFO  18:24:53,647 MicroScheduler -   -> 70830 reads (4.96% of total) failing DuplicateReadFilter
[2015-09-30T17:24Z] INFO  18:24:53,648 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:24Z] INFO  18:24:53,648 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:24Z] INFO  18:24:53,648 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:24Z] INFO  18:24:53,648 MicroScheduler -   -> 51077 reads (3.58% of total) failing MappingQualityZeroFilter
[2015-09-30T17:24Z] INFO  18:24:53,648 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:24Z] INFO  18:24:53,649 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:24Z] INFO  18:24:53,649 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:24Z] INFO  18:24:54,623 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:24Z] GATK: realign ('16', 64294277, 90354753) : syn3-tumor
[2015-09-30T17:24Z] INFO  18:24:56,485 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:24Z] INFO  18:24:56,487 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:24Z] INFO  18:24:56,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:24Z] INFO  18:24:56,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:24Z] INFO  18:24:56,490 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep-prealign-realign.intervals -L 16:64294278-90354753 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/tx/tmp1yBK7B/2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam
[2015-09-30T17:24Z] INFO  18:24:56,496 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:24Z] INFO  18:24:56,496 HelpFormatter - Date/Time: 2015/09/30 18:24:56
[2015-09-30T17:24Z] INFO  18:24:56,497 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:24Z] INFO  18:24:56,497 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:24Z] INFO  18:24:56,967 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:24Z] INFO  18:24:57,037 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:24Z] INFO  18:24:57,044 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:24Z] INFO  18:24:57,060 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:24Z] INFO  18:24:57,291 IntervalUtils - Processing 26060476 bp from intervals
[2015-09-30T17:24Z] WARN  18:24:57,295 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:24Z] INFO  18:24:57,350 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:24Z] INFO  18:24:57,502 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:24Z] INFO  18:24:57,502 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:24Z] INFO  18:24:57,503 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:24Z] INFO  18:24:57,503 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:24Z] INFO  18:24:57,649 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:24Z] INFO  18:24:57,809 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:24Z] INFO  18:24:59,045 ProgressMeter -     16:28510033   2000022.0    94.0 s      47.0 s       91.9%   102.0 s       8.0 s
[2015-09-30T17:25Z] INFO  18:25:11,524 ProgressMeter -            done   2393202.0   107.0 s      44.0 s      100.0%   107.0 s       0.0 s
[2015-09-30T17:25Z] INFO  18:25:11,525 ProgressMeter - Total runtime 107.28 secs, 1.79 min, 0.03 hours
[2015-09-30T17:25Z] INFO  18:25:11,528 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2393202 total reads (0.00%)
[2015-09-30T17:25Z] INFO  18:25:11,528 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:25Z] INFO  18:25:11,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:25Z] INFO  18:25:11,529 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:25Z] INFO  18:25:12,590 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:25Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam
[2015-09-30T17:25Z] GATK pre-alignment ('17', 31047756, 62076645) : syn3-tumor
[2015-09-30T17:25Z] INFO  18:25:20,968 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:25Z] INFO  18:25:20,970 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:25Z] INFO  18:25:20,971 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:25Z] INFO  18:25:20,971 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:25Z] INFO  18:25:20,974 HelpFormatter - Program Args: -T PrintReads -L 17:31047757-62076645 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/tx/tmp0dQ35E/2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam
[2015-09-30T17:25Z] INFO  18:25:20,980 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:25Z] INFO  18:25:20,980 HelpFormatter - Date/Time: 2015/09/30 18:25:20
[2015-09-30T17:25Z] INFO  18:25:20,981 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:25Z] INFO  18:25:20,981 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:25Z] INFO  18:25:21,093 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:25Z] INFO  18:25:21,762 ProgressMeter -      17:7910762    800011.0    90.0 s     112.0 s       25.5%     5.9 m       4.4 m
[2015-09-30T17:25Z] INFO  18:25:22,865 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:25Z] INFO  18:25:22,919 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:25Z] INFO  18:25:22,927 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:25Z] INFO  18:25:23,053 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2015-09-30T17:25Z] INFO  18:25:23,126 IntervalUtils - Processing 31028889 bp from intervals
[2015-09-30T17:25Z] INFO  18:25:23,230 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:25Z] INFO  18:25:23,659 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:25Z] INFO  18:25:23,660 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:25Z] INFO  18:25:23,660 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:25Z] INFO  18:25:23,660 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:25Z] INFO  18:25:23,672 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:25Z] INFO  18:25:23,894 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:25Z] INFO  18:25:28,407 ProgressMeter -     16:70815852    500005.0    30.0 s      61.0 s       25.0%   119.0 s      89.0 s
[2015-09-30T17:25Z] INFO  18:25:51,763 ProgressMeter -     17:15134122   1100015.0   120.0 s     109.0 s       48.8%     4.1 m       2.1 m
[2015-09-30T17:25Z] INFO  18:25:53,663 ProgressMeter -     17:35599331    200002.0    30.0 s       2.5 m       14.7%     3.4 m       2.9 m
[2015-09-30T17:25Z] INFO  18:25:58,684 ProgressMeter -     16:89219853   1200017.0    61.0 s      50.0 s       95.6%    63.0 s       2.0 s
[2015-09-30T17:26Z] INFO  18:26:04,600 ProgressMeter -            done   1418713.0    67.0 s      47.0 s       99.6%    67.0 s       0.0 s
[2015-09-30T17:26Z] INFO  18:26:04,600 ProgressMeter - Total runtime 67.10 secs, 1.12 min, 0.02 hours
[2015-09-30T17:26Z] INFO  18:26:04,604 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1418713 total reads (0.00%)
[2015-09-30T17:26Z] INFO  18:26:04,604 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:26Z] INFO  18:26:04,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:26Z] INFO  18:26:04,604 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:26Z] INFO  18:26:05,706 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:26Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam
[2015-09-30T17:26Z] GATK pre-alignment ('17', 62078196, 81195210) : syn3-tumor
[2015-09-30T17:26Z] INFO  18:26:13,009 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:26Z] INFO  18:26:13,011 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:26Z] INFO  18:26:13,011 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:26Z] INFO  18:26:13,011 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:26Z] INFO  18:26:13,014 HelpFormatter - Program Args: -T PrintReads -L 17:62078197-81195210 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/tx/tmpx48JQU/2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam
[2015-09-30T17:26Z] INFO  18:26:13,020 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:26Z] INFO  18:26:13,020 HelpFormatter - Date/Time: 2015/09/30 18:26:13
[2015-09-30T17:26Z] INFO  18:26:13,020 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:26Z] INFO  18:26:13,021 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:26Z] INFO  18:26:13,129 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:26Z] INFO  18:26:14,373 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:26Z] INFO  18:26:14,423 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:26Z] INFO  18:26:14,430 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:26Z] INFO  18:26:14,445 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:26Z] INFO  18:26:14,457 IntervalUtils - Processing 19117014 bp from intervals
[2015-09-30T17:26Z] INFO  18:26:14,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:26Z] INFO  18:26:14,687 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:26Z] INFO  18:26:14,687 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:26Z] INFO  18:26:14,688 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:26Z] INFO  18:26:14,688 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:26Z] INFO  18:26:14,699 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:26Z] INFO  18:26:14,828 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:26Z] INFO  18:26:21,764 ProgressMeter -     17:18404311   1400019.0     2.5 m     107.0 s       59.3%     4.2 m     102.0 s
[2015-09-30T17:26Z] INFO  18:26:23,664 ProgressMeter -     17:38341133    500005.0    60.0 s     120.0 s       23.5%     4.3 m       3.3 m
[2015-09-30T17:26Z] INFO  18:26:44,690 ProgressMeter -     17:66979542    200003.0    30.0 s       2.5 m       25.6%   117.0 s      87.0 s
[2015-09-30T17:26Z] INFO  18:26:52,100 ProgressMeter -     17:26699014   1800024.0     3.0 m     100.0 s       86.0%     3.5 m      29.0 s
[2015-09-30T17:26Z] INFO  18:26:53,664 ProgressMeter -     17:40484118    800008.0    90.0 s     112.0 s       30.4%     4.9 m       3.4 m
[2015-09-30T17:27Z] INFO  18:27:14,691 ProgressMeter -     17:73612067    500007.0    60.0 s     120.0 s       60.3%    99.0 s      39.0 s
[2015-09-30T17:27Z] INFO  18:27:22,101 ProgressMeter -     17:30510279   2100028.0     3.5 m     100.0 s       98.3%     3.6 m       3.0 s
[2015-09-30T17:27Z] INFO  18:27:23,665 ProgressMeter -     17:42855225   1100013.0   120.0 s     109.0 s       38.1%     5.3 m       3.3 m
[2015-09-30T17:27Z] INFO  18:27:24,619 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:27Z] INFO  18:27:25,517 ProgressMeter -            done   2179660.0     3.6 m      98.0 s      100.0%     3.6 m       0.0 s
[2015-09-30T17:27Z] INFO  18:27:25,518 ProgressMeter - Total runtime 213.76 secs, 3.56 min, 0.06 hours
[2015-09-30T17:27Z] INFO  18:27:25,518 MicroScheduler - 3511 reads were filtered out during the traversal out of approximately 2183171 total reads (0.16%)
[2015-09-30T17:27Z] INFO  18:27:25,518 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:27Z] INFO  18:27:25,519 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:27Z] INFO  18:27:25,519 MicroScheduler -   -> 3511 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:27Z] INFO  18:27:26,744 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:27Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam
[2015-09-30T17:27Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam 17:1-31039439
[2015-09-30T17:27Z] GATK: RealignerTargetCreator
[2015-09-30T17:27Z] INFO  18:27:33,937 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:27Z] INFO  18:27:33,939 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:27Z] INFO  18:27:33,939 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:27Z] INFO  18:27:33,939 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:27Z] INFO  18:27:33,943 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/tx/tmpl1F9fO/2_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign-realign.intervals -l INFO -L 17:1-31039439 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:27Z] INFO  18:27:33,949 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:27Z] INFO  18:27:33,950 HelpFormatter - Date/Time: 2015/09/30 18:27:33
[2015-09-30T17:27Z] INFO  18:27:33,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:27Z] INFO  18:27:33,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:27Z] INFO  18:27:34,005 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:27Z] INFO  18:27:34,113 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:27Z] INFO  18:27:34,121 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:27Z] INFO  18:27:34,136 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:27Z] INFO  18:27:34,384 IntervalUtils - Processing 31039439 bp from intervals
[2015-09-30T17:27Z] WARN  18:27:34,388 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:27Z] INFO  18:27:34,443 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:27Z] INFO  18:27:34,588 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:27Z] INFO  18:27:34,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:27Z] INFO  18:27:34,589 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:27Z] INFO  18:27:34,590 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:27Z] INFO  18:27:44,692 ProgressMeter -     17:76448967    800011.0    90.0 s     112.0 s       75.2%   119.0 s      29.0 s
[2015-09-30T17:27Z] INFO  18:27:53,666 ProgressMeter -     17:46266377   1400017.0     2.5 m     107.0 s       49.0%     5.1 m       2.6 m
[2015-09-30T17:28Z] INFO  18:28:04,592 ProgressMeter -     17:18670577   1.8661376E7    30.0 s       1.0 s       60.2%    49.0 s      19.0 s
[2015-09-30T17:28Z] INFO  18:28:18,045 ProgressMeter -            done   3.1039439E7    43.0 s       1.0 s      100.0%    43.0 s       0.0 s
[2015-09-30T17:28Z] INFO  18:28:18,045 ProgressMeter - Total runtime 43.46 secs, 0.72 min, 0.01 hours
[2015-09-30T17:28Z] INFO  18:28:18,048 MicroScheduler - 220459 reads were filtered out during the traversal out of approximately 2193088 total reads (10.05%)
[2015-09-30T17:28Z] INFO  18:28:18,049 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:28Z] INFO  18:28:18,049 MicroScheduler -   -> 19697 reads (0.90% of total) failing BadMateFilter
[2015-09-30T17:28Z] INFO  18:28:18,049 MicroScheduler -   -> 106445 reads (4.85% of total) failing DuplicateReadFilter
[2015-09-30T17:28Z] INFO  18:28:18,050 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:28Z] INFO  18:28:18,050 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:28Z] INFO  18:28:18,050 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:28Z] INFO  18:28:18,050 MicroScheduler -   -> 94317 reads (4.30% of total) failing MappingQualityZeroFilter
[2015-09-30T17:28Z] INFO  18:28:18,050 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:28Z] INFO  18:28:18,051 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:28Z] INFO  18:28:18,051 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:28Z] INFO  18:28:19,105 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:28Z] GATK: realign ('17', 0, 31039439) : syn3-tumor
[2015-09-30T17:28Z] INFO  18:28:20,909 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:28Z] INFO  18:28:20,911 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:28Z] INFO  18:28:20,911 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:28Z] INFO  18:28:20,911 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:28Z] INFO  18:28:20,915 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_0_31039439-prep-prealign-realign.intervals -L 17:1-31039439 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/tx/tmp1DoH8a/2_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam
[2015-09-30T17:28Z] INFO  18:28:20,920 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:28Z] INFO  18:28:20,920 HelpFormatter - Date/Time: 2015/09/30 18:28:20
[2015-09-30T17:28Z] INFO  18:28:20,921 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:28Z] INFO  18:28:20,921 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:28Z] INFO  18:28:21,037 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:28Z] INFO  18:28:21,097 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:28Z] INFO  18:28:21,105 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:28Z] INFO  18:28:21,120 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:28Z] INFO  18:28:21,342 IntervalUtils - Processing 31039439 bp from intervals
[2015-09-30T17:28Z] WARN  18:28:21,345 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:28Z] INFO  18:28:21,397 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:28Z] INFO  18:28:21,529 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:28Z] INFO  18:28:21,530 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:28Z] INFO  18:28:21,530 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:28Z] INFO  18:28:21,530 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:28Z] INFO  18:28:21,672 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:28Z] INFO  18:28:21,847 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:28Z] INFO  18:28:24,693 ProgressMeter -     17:80015198   1200020.0     2.2 m     108.0 s       93.8%     2.3 m       8.0 s
[2015-09-30T17:28Z] INFO  18:28:33,667 ProgressMeter -     17:56400703   1800022.0     3.2 m     105.0 s       81.7%     3.9 m      42.0 s
[2015-09-30T17:28Z] INFO  18:28:36,161 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:28Z] INFO  18:28:36,307 ProgressMeter -            done   1410234.0     2.4 m     100.0 s      100.0%     2.4 m       0.0 s
[2015-09-30T17:28Z] INFO  18:28:36,307 ProgressMeter - Total runtime 141.62 secs, 2.36 min, 0.04 hours
[2015-09-30T17:28Z] INFO  18:28:36,308 MicroScheduler - 2289 reads were filtered out during the traversal out of approximately 1412523 total reads (0.16%)
[2015-09-30T17:28Z] INFO  18:28:36,308 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:28Z] INFO  18:28:36,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:28Z] INFO  18:28:36,308 MicroScheduler -   -> 2289 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:28Z] INFO  18:28:37,275 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:28Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam
[2015-09-30T17:28Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam 17:62078197-81195210
[2015-09-30T17:28Z] GATK: RealignerTargetCreator
[2015-09-30T17:28Z] INFO  18:28:42,581 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:28Z] INFO  18:28:42,583 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:28Z] INFO  18:28:42,583 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:28Z] INFO  18:28:42,583 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:28Z] INFO  18:28:42,587 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/tx/tmpru9lZI/2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign-realign.intervals -l INFO -L 17:62078197-81195210 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:28Z] INFO  18:28:42,592 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:28Z] INFO  18:28:42,592 HelpFormatter - Date/Time: 2015/09/30 18:28:42
[2015-09-30T17:28Z] INFO  18:28:42,592 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:28Z] INFO  18:28:42,593 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:28Z] INFO  18:28:42,648 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:28Z] INFO  18:28:42,750 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:28Z] INFO  18:28:42,758 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:28Z] INFO  18:28:42,773 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:28Z] INFO  18:28:43,392 IntervalUtils - Processing 19117014 bp from intervals
[2015-09-30T17:28Z] WARN  18:28:43,396 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:28Z] INFO  18:28:43,452 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:28Z] INFO  18:28:43,570 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:28Z] INFO  18:28:43,571 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:28Z] INFO  18:28:43,571 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:28Z] INFO  18:28:43,571 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:28Z] INFO  18:28:51,977 ProgressMeter -      17:5994152    500006.0    30.0 s      60.0 s       19.3%     2.6 m       2.1 m
[2015-09-30T17:29Z] INFO  18:29:03,667 ProgressMeter -     17:61699661   2100025.0     3.7 m     104.0 s       98.8%     3.7 m       2.0 s
[2015-09-30T17:29Z] INFO  18:29:09,473 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:29Z] INFO  18:29:09,594 ProgressMeter -            done   2224733.0     3.8 m     101.0 s      100.0%     3.8 m       0.0 s
[2015-09-30T17:29Z] INFO  18:29:09,595 ProgressMeter - Total runtime 225.94 secs, 3.77 min, 0.06 hours
[2015-09-30T17:29Z] INFO  18:29:09,595 MicroScheduler - 3534 reads were filtered out during the traversal out of approximately 2228267 total reads (0.16%)
[2015-09-30T17:29Z] INFO  18:29:09,595 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:29Z] INFO  18:29:09,596 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:29Z] INFO  18:29:09,596 MicroScheduler -   -> 3534 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:29Z] INFO  18:29:10,741 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:29Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam
[2015-09-30T17:29Z] INFO  18:29:13,303 ProgressMeter -            done   1.9117014E7    29.0 s       1.0 s      100.0%    29.0 s       0.0 s
[2015-09-30T17:29Z] INFO  18:29:13,303 ProgressMeter - Total runtime 29.73 secs, 0.50 min, 0.01 hours
[2015-09-30T17:29Z] INFO  18:29:13,306 MicroScheduler - 114750 reads were filtered out during the traversal out of approximately 1417998 total reads (8.09%)
[2015-09-30T17:29Z] INFO  18:29:13,307 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:29Z] INFO  18:29:13,307 MicroScheduler -   -> 12723 reads (0.90% of total) failing BadMateFilter
[2015-09-30T17:29Z] INFO  18:29:13,307 MicroScheduler -   -> 73381 reads (5.17% of total) failing DuplicateReadFilter
[2015-09-30T17:29Z] INFO  18:29:13,308 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:29Z] INFO  18:29:13,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:29Z] INFO  18:29:13,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:29Z] INFO  18:29:13,308 MicroScheduler -   -> 28646 reads (2.02% of total) failing MappingQualityZeroFilter
[2015-09-30T17:29Z] INFO  18:29:13,308 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:29Z] INFO  18:29:13,309 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:29Z] INFO  18:29:13,309 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:29Z] INFO  18:29:14,300 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:29Z] GATK: realign ('17', 62078196, 81195210) : syn3-tumor
[2015-09-30T17:29Z] INFO  18:29:16,632 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:29Z] INFO  18:29:16,634 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:29Z] INFO  18:29:16,634 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:29Z] INFO  18:29:16,634 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:29Z] INFO  18:29:16,638 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep-prealign-realign.intervals -L 17:62078197-81195210 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/tx/tmpoibRp0/2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam
[2015-09-30T17:29Z] INFO  18:29:16,643 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:29Z] INFO  18:29:16,643 HelpFormatter - Date/Time: 2015/09/30 18:29:16
[2015-09-30T17:29Z] INFO  18:29:16,643 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:29Z] INFO  18:29:16,644 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:29Z] INFO  18:29:17,051 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:29Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam 17:31047757-62076645
[2015-09-30T17:29Z] GATK: RealignerTargetCreator
[2015-09-30T17:29Z] INFO  18:29:17,659 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:29Z] INFO  18:29:17,666 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:29Z] INFO  18:29:17,683 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:29Z] INFO  18:29:17,929 IntervalUtils - Processing 19117014 bp from intervals
[2015-09-30T17:29Z] WARN  18:29:17,933 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:29Z] INFO  18:29:17,992 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:29Z] INFO  18:29:18,106 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:29Z] INFO  18:29:18,107 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:29Z] INFO  18:29:18,107 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:29Z] INFO  18:29:18,107 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:29Z] INFO  18:29:18,251 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:29Z] INFO  18:29:18,392 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:29Z] INFO  18:29:19,166 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:29Z] INFO  18:29:19,168 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:29Z] INFO  18:29:19,169 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:29Z] INFO  18:29:19,169 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:29Z] INFO  18:29:19,172 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/tx/tmpMF4XwR/2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign-realign.intervals -l INFO -L 17:31047757-62076645 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:29Z] INFO  18:29:19,177 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:29Z] INFO  18:29:19,178 HelpFormatter - Date/Time: 2015/09/30 18:29:19
[2015-09-30T17:29Z] INFO  18:29:19,178 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:29Z] INFO  18:29:19,178 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:29Z] INFO  18:29:19,235 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:29Z] INFO  18:29:19,339 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:29Z] INFO  18:29:19,347 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:29Z] INFO  18:29:19,363 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:29Z] INFO  18:29:19,981 IntervalUtils - Processing 31028889 bp from intervals
[2015-09-30T17:29Z] WARN  18:29:19,985 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:29Z] INFO  18:29:20,043 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:29Z] INFO  18:29:20,189 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:29Z] INFO  18:29:20,189 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:29Z] INFO  18:29:20,190 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:29Z] INFO  18:29:20,190 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:29Z] INFO  18:29:21,978 ProgressMeter -     17:16876007   1200016.0    60.0 s      50.0 s       54.4%   110.0 s      50.0 s
[2015-09-30T17:29Z] INFO  18:29:49,097 ProgressMeter -     17:73627052    500007.0    30.0 s      61.0 s       60.4%    49.0 s      19.0 s
[2015-09-30T17:29Z] INFO  18:29:50,192 ProgressMeter -     17:46669033   1.5613876E7    30.0 s       1.0 s       50.3%    59.0 s      29.0 s
[2015-09-30T17:29Z] INFO  18:29:52,487 ProgressMeter -     17:27999278   1900026.0    90.0 s      47.0 s       90.2%    99.0 s       9.0 s
[2015-09-30T17:29Z] INFO  18:29:58,612 ProgressMeter -            done   2179660.0    97.0 s      44.0 s      100.0%    97.0 s       0.0 s
[2015-09-30T17:29Z] INFO  18:29:58,612 ProgressMeter - Total runtime 97.08 secs, 1.62 min, 0.03 hours
[2015-09-30T17:29Z] INFO  18:29:58,615 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2179660 total reads (0.00%)
[2015-09-30T17:29Z] INFO  18:29:58,616 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:29Z] INFO  18:29:58,616 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:29Z] INFO  18:29:58,616 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:29Z] INFO  18:29:59,830 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:30Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam
[2015-09-30T17:30Z] GATK pre-alignment ('18', 0, 31142016) : syn3-tumor
[2015-09-30T17:30Z] INFO  18:30:09,129 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:30Z] INFO  18:30:09,131 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:30Z] INFO  18:30:09,131 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:30Z] INFO  18:30:09,131 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:30Z] INFO  18:30:09,135 HelpFormatter - Program Args: -T PrintReads -L 18:1-31142016 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/tx/tmp9Z92ni/2_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam
[2015-09-30T17:30Z] INFO  18:30:09,141 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:30Z] INFO  18:30:09,142 HelpFormatter - Date/Time: 2015/09/30 18:30:09
[2015-09-30T17:30Z] INFO  18:30:09,142 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:30Z] INFO  18:30:09,142 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:30Z] INFO  18:30:09,246 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:30Z] INFO  18:30:09,938 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:30Z] INFO  18:30:09,988 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:30Z] INFO  18:30:09,996 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:30Z] INFO  18:30:10,078 ProgressMeter -            done   3.1028889E7    49.0 s       1.0 s      100.0%    49.0 s       0.0 s
[2015-09-30T17:30Z] INFO  18:30:10,079 ProgressMeter - Total runtime 49.89 secs, 0.83 min, 0.01 hours
[2015-09-30T17:30Z] INFO  18:30:10,079 MicroScheduler - 245812 reads were filtered out during the traversal out of approximately 2238779 total reads (10.98%)
[2015-09-30T17:30Z] INFO  18:30:10,079 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:30Z] INFO  18:30:10,080 MicroScheduler -   -> 20377 reads (0.91% of total) failing BadMateFilter
[2015-09-30T17:30Z] INFO  18:30:10,080 MicroScheduler -   -> 105456 reads (4.71% of total) failing DuplicateReadFilter
[2015-09-30T17:30Z] INFO  18:30:10,080 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:30Z] INFO  18:30:10,080 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:30Z] INFO  18:30:10,080 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:30Z] INFO  18:30:10,081 MicroScheduler -   -> 119979 reads (5.36% of total) failing MappingQualityZeroFilter
[2015-09-30T17:30Z] INFO  18:30:10,081 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:30Z] INFO  18:30:10,081 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:30Z] INFO  18:30:10,081 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:30Z] INFO  18:30:10,086 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2015-09-30T17:30Z] INFO  18:30:10,100 IntervalUtils - Processing 31142016 bp from intervals
[2015-09-30T17:30Z] INFO  18:30:10,160 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:30Z] INFO  18:30:10,818 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:30Z] INFO  18:30:10,819 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:30Z] INFO  18:30:10,819 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:30Z] INFO  18:30:10,819 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:30Z] INFO  18:30:10,830 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:30Z] INFO  18:30:11,018 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:30Z] INFO  18:30:11,029 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:30Z] GATK: realign ('17', 31047756, 62076645) : syn3-tumor
[2015-09-30T17:30Z] INFO  18:30:13,906 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:30Z] INFO  18:30:13,908 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:30Z] INFO  18:30:13,908 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:30Z] INFO  18:30:13,909 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:30Z] INFO  18:30:13,912 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep-prealign-realign.intervals -L 17:31047757-62076645 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/tx/tmpKudHY0/2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam
[2015-09-30T17:30Z] INFO  18:30:13,918 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:30Z] INFO  18:30:13,918 HelpFormatter - Date/Time: 2015/09/30 18:30:13
[2015-09-30T17:30Z] INFO  18:30:13,918 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:30Z] INFO  18:30:13,918 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:30Z] INFO  18:30:14,015 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:30Z] INFO  18:30:14,082 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:30Z] INFO  18:30:14,089 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:30Z] INFO  18:30:14,105 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:30Z] INFO  18:30:14,338 IntervalUtils - Processing 31028889 bp from intervals
[2015-09-30T17:30Z] WARN  18:30:14,342 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:30Z] INFO  18:30:14,397 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:30Z] INFO  18:30:14,547 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:30Z] INFO  18:30:14,547 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:30Z] INFO  18:30:14,548 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:30Z] INFO  18:30:14,548 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:30Z] INFO  18:30:14,691 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:30Z] INFO  18:30:14,880 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:30Z] INFO  18:30:20,970 ProgressMeter -     17:79651018   1100019.0    62.0 s      57.0 s       91.9%    67.0 s       5.0 s
[2015-09-30T17:30Z] INFO  18:30:30,271 ProgressMeter -            done   1410234.0    72.0 s      51.0 s      100.0%    72.0 s       0.0 s
[2015-09-30T17:30Z] INFO  18:30:30,272 ProgressMeter - Total runtime 72.17 secs, 1.20 min, 0.02 hours
[2015-09-30T17:30Z] INFO  18:30:30,275 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1410234 total reads (0.00%)
[2015-09-30T17:30Z] INFO  18:30:30,275 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:30Z] INFO  18:30:30,276 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:30Z] INFO  18:30:30,276 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:30Z] INFO  18:30:31,674 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:30Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam
[2015-09-30T17:30Z] GATK pre-alignment ('18', 31158315, 63430522) : syn3-tumor
[2015-09-30T17:30Z] INFO  18:30:37,524 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:30Z] INFO  18:30:37,526 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:30Z] INFO  18:30:37,526 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:30Z] INFO  18:30:37,526 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:30Z] INFO  18:30:37,530 HelpFormatter - Program Args: -T PrintReads -L 18:31158316-63430522 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/tx/tmpPu2OiC/2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam
[2015-09-30T17:30Z] INFO  18:30:37,535 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:30Z] INFO  18:30:37,535 HelpFormatter - Date/Time: 2015/09/30 18:30:37
[2015-09-30T17:30Z] INFO  18:30:37,535 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:30Z] INFO  18:30:37,536 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:30Z] INFO  18:30:37,642 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:30Z] INFO  18:30:38,833 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:30Z] INFO  18:30:38,883 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:30Z] INFO  18:30:38,890 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:30Z] INFO  18:30:38,904 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:30Z] INFO  18:30:38,917 IntervalUtils - Processing 32272207 bp from intervals
[2015-09-30T17:30Z] INFO  18:30:38,973 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:30Z] INFO  18:30:39,164 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:30Z] INFO  18:30:39,165 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:30Z] INFO  18:30:39,165 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:30Z] INFO  18:30:39,165 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:30Z] INFO  18:30:39,176 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:30Z] INFO  18:30:39,368 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:30Z] INFO  18:30:40,839 ProgressMeter -     18:10752837    200002.0    30.0 s       2.5 m       34.5%    86.0 s      56.0 s
[2015-09-30T17:30Z] INFO  18:30:44,550 ProgressMeter -     17:38245774    500005.0    30.0 s      60.0 s       23.2%     2.2 m      99.0 s
[2015-09-30T17:31Z] INFO  18:31:09,167 ProgressMeter -     18:44555210    200003.0    30.0 s       2.5 m       41.5%    72.0 s      42.0 s
[2015-09-30T17:31Z] INFO  18:31:10,839 ProgressMeter -     18:24128343    500007.0    60.0 s     120.0 s       77.5%    77.0 s      17.0 s
[2015-09-30T17:31Z] INFO  18:31:15,601 ProgressMeter -     17:43316400   1100013.0    61.0 s      55.0 s       39.5%     2.6 m      93.0 s
[2015-09-30T17:31Z] INFO  18:31:18,408 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:31Z] INFO  18:31:18,689 ProgressMeter -            done    643841.0    67.0 s     105.0 s      100.0%    67.0 s       0.0 s
[2015-09-30T17:31Z] INFO  18:31:18,689 ProgressMeter - Total runtime 67.87 secs, 1.13 min, 0.02 hours
[2015-09-30T17:31Z] INFO  18:31:18,690 MicroScheduler - 1736 reads were filtered out during the traversal out of approximately 645577 total reads (0.27%)
[2015-09-30T17:31Z] INFO  18:31:18,690 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:31Z] INFO  18:31:18,690 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:31Z] INFO  18:31:18,690 MicroScheduler -   -> 1736 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:31Z] INFO  18:31:19,863 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:31Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam
[2015-09-30T17:31Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam 18:1-31142016
[2015-09-30T17:31Z] GATK: RealignerTargetCreator
[2015-09-30T17:31Z] INFO  18:31:23,338 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:31Z] INFO  18:31:23,340 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:31Z] INFO  18:31:23,340 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:31Z] INFO  18:31:23,340 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:31Z] INFO  18:31:23,344 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/tx/tmp4QHift/2_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign-realign.intervals -l INFO -L 18:1-31142016 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:31Z] INFO  18:31:23,349 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:31Z] INFO  18:31:23,349 HelpFormatter - Date/Time: 2015/09/30 18:31:23
[2015-09-30T17:31Z] INFO  18:31:23,349 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:31Z] INFO  18:31:23,350 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:31Z] INFO  18:31:23,406 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:31Z] INFO  18:31:24,044 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:31Z] INFO  18:31:24,051 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:31Z] INFO  18:31:24,394 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.34
[2015-09-30T17:31Z] INFO  18:31:24,850 IntervalUtils - Processing 31142016 bp from intervals
[2015-09-30T17:31Z] WARN  18:31:24,854 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:31Z] INFO  18:31:24,909 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:31Z] INFO  18:31:25,267 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:31Z] INFO  18:31:25,267 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:31Z] INFO  18:31:25,267 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:31Z] INFO  18:31:25,268 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:31Z] INFO  18:31:39,199 ProgressMeter -     18:61077436    500006.0    60.0 s     120.0 s       92.7%    64.0 s       4.0 s
[2015-09-30T17:31Z] INFO  18:31:42,118 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:31Z] INFO  18:31:42,414 ProgressMeter -            done    593972.0    63.0 s     106.0 s      100.0%    63.0 s       0.0 s
[2015-09-30T17:31Z] INFO  18:31:42,414 ProgressMeter - Total runtime 63.25 secs, 1.05 min, 0.02 hours
[2015-09-30T17:31Z] INFO  18:31:42,414 MicroScheduler - 1662 reads were filtered out during the traversal out of approximately 595634 total reads (0.28%)
[2015-09-30T17:31Z] INFO  18:31:42,415 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:31Z] INFO  18:31:42,415 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:31Z] INFO  18:31:42,415 MicroScheduler -   -> 1662 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:31Z] INFO  18:31:43,407 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:31Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam
[2015-09-30T17:31Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam 18:31158316-63430522
[2015-09-30T17:31Z] GATK: RealignerTargetCreator
[2015-09-30T17:31Z] INFO  18:31:45,602 ProgressMeter -     17:57776433   1900023.0    91.0 s      47.0 s       86.1%   105.0 s      14.0 s
[2015-09-30T17:31Z] INFO  18:31:47,013 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:31Z] INFO  18:31:47,015 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:31Z] INFO  18:31:47,015 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:31Z] INFO  18:31:47,015 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:31Z] INFO  18:31:47,019 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/tx/tmp2LR_Tj/2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign-realign.intervals -l INFO -L 18:31158316-63430522 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:31Z] INFO  18:31:47,025 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:31Z] INFO  18:31:47,026 HelpFormatter - Date/Time: 2015/09/30 18:31:47
[2015-09-30T17:31Z] INFO  18:31:47,026 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:31Z] INFO  18:31:47,026 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:31Z] INFO  18:31:47,084 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:31Z] INFO  18:31:47,682 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:31Z] INFO  18:31:47,690 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:31Z] INFO  18:31:47,706 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:31Z] INFO  18:31:47,948 IntervalUtils - Processing 32272207 bp from intervals
[2015-09-30T17:31Z] WARN  18:31:47,952 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:31Z] INFO  18:31:48,009 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:31Z] INFO  18:31:48,152 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:31Z] INFO  18:31:48,153 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:31Z] INFO  18:31:48,153 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:31Z] INFO  18:31:48,153 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:31Z] INFO  18:31:49,264 ProgressMeter -            done   3.1142016E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T17:31Z] INFO  18:31:49,265 ProgressMeter - Total runtime 24.00 secs, 0.40 min, 0.01 hours
[2015-09-30T17:31Z] INFO  18:31:49,268 MicroScheduler - 52776 reads were filtered out during the traversal out of approximately 647057 total reads (8.16%)
[2015-09-30T17:31Z] INFO  18:31:49,268 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:31Z] INFO  18:31:49,268 MicroScheduler -   -> 9928 reads (1.53% of total) failing BadMateFilter
[2015-09-30T17:31Z] INFO  18:31:49,269 MicroScheduler -   -> 26709 reads (4.13% of total) failing DuplicateReadFilter
[2015-09-30T17:31Z] INFO  18:31:49,269 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:31Z] INFO  18:31:49,269 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:31Z] INFO  18:31:49,269 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:31Z] INFO  18:31:49,270 MicroScheduler -   -> 16139 reads (2.49% of total) failing MappingQualityZeroFilter
[2015-09-30T17:31Z] INFO  18:31:49,270 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:31Z] INFO  18:31:49,270 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:31Z] INFO  18:31:49,270 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:31Z] INFO  18:31:50,233 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:31Z] GATK: realign ('18', 0, 31142016) : syn3-tumor
[2015-09-30T17:31Z] INFO  18:31:52,037 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:31Z] INFO  18:31:52,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:31Z] INFO  18:31:52,040 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:31Z] INFO  18:31:52,040 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:31Z] INFO  18:31:52,043 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_0_31142016-prep-prealign-realign.intervals -L 18:1-31142016 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/tx/tmpeXYPgb/2_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam
[2015-09-30T17:31Z] INFO  18:31:52,049 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:31Z] INFO  18:31:52,049 HelpFormatter - Date/Time: 2015/09/30 18:31:52
[2015-09-30T17:31Z] INFO  18:31:52,049 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:31Z] INFO  18:31:52,049 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:31Z] INFO  18:31:52,174 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:31Z] INFO  18:31:52,237 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:31Z] INFO  18:31:52,245 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:31Z] INFO  18:31:52,260 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:31Z] INFO  18:31:52,995 IntervalUtils - Processing 31142016 bp from intervals
[2015-09-30T17:31Z] WARN  18:31:52,999 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:31Z] INFO  18:31:53,055 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:31Z] INFO  18:31:53,187 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:31Z] INFO  18:31:53,188 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:31Z] INFO  18:31:53,188 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:31Z] INFO  18:31:53,188 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:31Z] INFO  18:31:53,326 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:31Z] INFO  18:31:53,507 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:31Z] INFO  18:31:55,632 ProgressMeter -            done   2224733.0   101.0 s      45.0 s      100.0%   101.0 s       0.0 s
[2015-09-30T17:31Z] INFO  18:31:55,632 ProgressMeter - Total runtime 101.09 secs, 1.68 min, 0.03 hours
[2015-09-30T17:31Z] INFO  18:31:55,636 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2224733 total reads (0.00%)
[2015-09-30T17:31Z] INFO  18:31:55,636 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:31Z] INFO  18:31:55,636 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:31Z] INFO  18:31:55,636 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:31Z] INFO  18:31:57,258 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:31Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam
[2015-09-30T17:32Z] GATK pre-alignment ('18', 63476668, 78077248) : syn3-tumor
[2015-09-30T17:32Z] INFO  18:32:06,040 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:06,042 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:32Z] INFO  18:32:06,042 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:32Z] INFO  18:32:06,043 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:32Z] INFO  18:32:06,046 HelpFormatter - Program Args: -T PrintReads -L 18:63476669-78077248 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/tx/tmpAgwWZc/2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam
[2015-09-30T17:32Z] INFO  18:32:06,052 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:32Z] INFO  18:32:06,053 HelpFormatter - Date/Time: 2015/09/30 18:32:06
[2015-09-30T17:32Z] INFO  18:32:06,053 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:06,053 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:06,760 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:32Z] INFO  18:32:07,861 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:32Z] INFO  18:32:07,911 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:32Z] INFO  18:32:07,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:32Z] INFO  18:32:07,934 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:32Z] INFO  18:32:07,948 IntervalUtils - Processing 14600580 bp from intervals
[2015-09-30T17:32Z] INFO  18:32:08,006 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:32Z] INFO  18:32:08,153 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:32Z] INFO  18:32:08,153 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:32Z] INFO  18:32:08,153 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:32Z] INFO  18:32:08,154 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:32Z] INFO  18:32:08,165 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:32Z] INFO  18:32:08,267 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:32Z] INFO  18:32:12,946 ProgressMeter -            done   3.2272207E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T17:32Z] INFO  18:32:12,946 ProgressMeter - Total runtime 24.79 secs, 0.41 min, 0.01 hours
[2015-09-30T17:32Z] INFO  18:32:12,949 MicroScheduler - 66733 reads were filtered out during the traversal out of approximately 597755 total reads (11.16%)
[2015-09-30T17:32Z] INFO  18:32:12,950 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:32Z] INFO  18:32:12,950 MicroScheduler -   -> 9512 reads (1.59% of total) failing BadMateFilter
[2015-09-30T17:32Z] INFO  18:32:12,950 MicroScheduler -   -> 24803 reads (4.15% of total) failing DuplicateReadFilter
[2015-09-30T17:32Z] INFO  18:32:12,951 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:32Z] INFO  18:32:12,951 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:32Z] INFO  18:32:12,951 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:32Z] INFO  18:32:12,951 MicroScheduler -   -> 32418 reads (5.42% of total) failing MappingQualityZeroFilter
[2015-09-30T17:32Z] INFO  18:32:12,951 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:32Z] INFO  18:32:12,952 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:32Z] INFO  18:32:12,952 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:32Z] INFO  18:32:13,971 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:32Z] GATK: realign ('18', 31158315, 63430522) : syn3-tumor
[2015-09-30T17:32Z] INFO  18:32:15,971 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:15,974 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:32Z] INFO  18:32:15,974 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:32Z] INFO  18:32:15,974 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:32Z] INFO  18:32:15,978 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep-prealign-realign.intervals -L 18:31158316-63430522 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/tx/tmpm2sl_b/2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam
[2015-09-30T17:32Z] INFO  18:32:15,985 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:32Z] INFO  18:32:15,985 HelpFormatter - Date/Time: 2015/09/30 18:32:15
[2015-09-30T17:32Z] INFO  18:32:15,985 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:15,986 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:16,118 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:32Z] INFO  18:32:16,315 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:32Z] INFO  18:32:16,323 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:32Z] INFO  18:32:16,339 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:32Z] INFO  18:32:16,569 IntervalUtils - Processing 32272207 bp from intervals
[2015-09-30T17:32Z] WARN  18:32:16,573 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:32Z] INFO  18:32:16,629 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:32Z] INFO  18:32:16,774 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:32Z] INFO  18:32:16,774 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:32Z] INFO  18:32:16,775 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:32Z] INFO  18:32:16,775 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:32Z] INFO  18:32:16,916 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:32Z] INFO  18:32:17,110 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:32Z] INFO  18:32:24,137 ProgressMeter -     18:21489315    400006.0    30.0 s      77.0 s       69.0%    43.0 s      13.0 s
[2015-09-30T17:32Z] INFO  18:32:26,147 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:32Z] INFO  18:32:26,258 ProgressMeter -            done    169093.0    18.0 s     107.0 s       99.5%    18.0 s       0.0 s
[2015-09-30T17:32Z] INFO  18:32:26,258 ProgressMeter - Total runtime 18.11 secs, 0.30 min, 0.01 hours
[2015-09-30T17:32Z] INFO  18:32:26,259 MicroScheduler - 458 reads were filtered out during the traversal out of approximately 169551 total reads (0.27%)
[2015-09-30T17:32Z] INFO  18:32:26,259 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:32Z] INFO  18:32:26,259 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:32Z] INFO  18:32:26,259 MicroScheduler -   -> 458 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:32Z] INFO  18:32:27,288 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:32Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam
[2015-09-30T17:32Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam 18:63476669-78077248
[2015-09-30T17:32Z] GATK: RealignerTargetCreator
[2015-09-30T17:32Z] INFO  18:32:28,923 ProgressMeter -            done    643841.0    35.0 s      55.0 s      100.0%    35.0 s       0.0 s
[2015-09-30T17:32Z] INFO  18:32:28,923 ProgressMeter - Total runtime 35.74 secs, 0.60 min, 0.01 hours
[2015-09-30T17:32Z] INFO  18:32:28,926 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 643841 total reads (0.00%)
[2015-09-30T17:32Z] INFO  18:32:28,926 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:32Z] INFO  18:32:28,927 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:32Z] INFO  18:32:28,927 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:32Z] INFO  18:32:29,903 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:29,905 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:32Z] INFO  18:32:29,905 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:32Z] INFO  18:32:29,905 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:32Z] INFO  18:32:29,908 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/tx/tmp08sfn2/2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign-realign.intervals -l INFO -L 18:63476669-78077248 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:32Z] INFO  18:32:29,914 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:32Z] INFO  18:32:29,914 HelpFormatter - Date/Time: 2015/09/30 18:32:29
[2015-09-30T17:32Z] INFO  18:32:29,914 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:29,914 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:29,966 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:32Z] INFO  18:32:29,971 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:32Z] INFO  18:32:30,076 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:32Z] INFO  18:32:30,084 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:32Z] INFO  18:32:30,100 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:32Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam
[2015-09-30T17:32Z] INFO  18:32:30,933 IntervalUtils - Processing 14600580 bp from intervals
[2015-09-30T17:32Z] WARN  18:32:30,937 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:32Z] INFO  18:32:31,037 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:32Z] INFO  18:32:31,121 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:32Z] INFO  18:32:31,121 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:32Z] INFO  18:32:31,121 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:32Z] INFO  18:32:31,122 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:32Z] GATK pre-alignment ('19', 0, 31026185) : syn3-tumor
[2015-09-30T17:32Z] INFO  18:32:34,392 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:34,394 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:32Z] INFO  18:32:34,394 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:32Z] INFO  18:32:34,394 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:32Z] INFO  18:32:34,398 HelpFormatter - Program Args: -T PrintReads -L 19:1-31026185 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/tx/tmpcDYnZS/2_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam
[2015-09-30T17:32Z] INFO  18:32:34,403 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:32Z] INFO  18:32:34,404 HelpFormatter - Date/Time: 2015/09/30 18:32:34
[2015-09-30T17:32Z] INFO  18:32:34,404 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:34,404 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:35,200 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:32Z] INFO  18:32:36,900 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:32Z] INFO  18:32:36,951 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:32Z] INFO  18:32:36,959 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:32Z] INFO  18:32:36,974 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:32Z] INFO  18:32:36,987 IntervalUtils - Processing 31026185 bp from intervals
[2015-09-30T17:32Z] INFO  18:32:37,417 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:32Z] INFO  18:32:37,645 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:32Z] INFO  18:32:37,645 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:32Z] INFO  18:32:37,645 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:32Z] INFO  18:32:37,646 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:32Z] INFO  18:32:37,657 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:32Z] INFO  18:32:37,874 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:32Z] INFO  18:32:41,887 ProgressMeter -            done   1.460058E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2015-09-30T17:32Z] INFO  18:32:41,887 ProgressMeter - Total runtime 10.77 secs, 0.18 min, 0.00 hours
[2015-09-30T17:32Z] INFO  18:32:41,890 MicroScheduler - 14431 reads were filtered out during the traversal out of approximately 169927 total reads (8.49%)
[2015-09-30T17:32Z] INFO  18:32:41,891 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:32Z] INFO  18:32:41,891 MicroScheduler -   -> 3328 reads (1.96% of total) failing BadMateFilter
[2015-09-30T17:32Z] INFO  18:32:41,891 MicroScheduler -   -> 7768 reads (4.57% of total) failing DuplicateReadFilter
[2015-09-30T17:32Z] INFO  18:32:41,891 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:32Z] INFO  18:32:41,892 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:32Z] INFO  18:32:41,892 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:32Z] INFO  18:32:41,892 MicroScheduler -   -> 3335 reads (1.96% of total) failing MappingQualityZeroFilter
[2015-09-30T17:32Z] INFO  18:32:41,892 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:32Z] INFO  18:32:41,893 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:32Z] INFO  18:32:41,893 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:32Z] INFO  18:32:42,946 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:32Z] GATK: realign ('18', 63476668, 78077248) : syn3-tumor
[2015-09-30T17:32Z] INFO  18:32:46,679 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:46,681 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:32Z] INFO  18:32:46,681 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:32Z] INFO  18:32:46,682 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:32Z] INFO  18:32:46,685 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep-prealign-realign.intervals -L 18:63476669-78077248 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/tx/tmpi8Kxy5/2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam
[2015-09-30T17:32Z] INFO  18:32:46,691 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:32Z] INFO  18:32:46,691 HelpFormatter - Date/Time: 2015/09/30 18:32:46
[2015-09-30T17:32Z] INFO  18:32:46,691 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:46,691 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:46,815 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:32Z] INFO  18:32:46,880 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:32Z] INFO  18:32:46,887 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:32Z] INFO  18:32:46,903 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:32Z] INFO  18:32:46,925 ProgressMeter -     18:60207577    500006.0    30.0 s      60.0 s       90.0%    33.0 s       3.0 s
[2015-09-30T17:32Z] INFO  18:32:47,515 IntervalUtils - Processing 14600580 bp from intervals
[2015-09-30T17:32Z] WARN  18:32:47,519 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:32Z] INFO  18:32:47,815 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:32Z] INFO  18:32:48,088 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:32Z] INFO  18:32:48,088 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:32Z] INFO  18:32:48,089 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:32Z] INFO  18:32:48,089 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:32Z] INFO  18:32:48,203 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:32Z] INFO  18:32:48,309 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:32Z] INFO  18:32:49,263 ProgressMeter -            done    593972.0    32.0 s      54.0 s      100.0%    32.0 s       0.0 s
[2015-09-30T17:32Z] INFO  18:32:49,263 ProgressMeter - Total runtime 32.49 secs, 0.54 min, 0.01 hours
[2015-09-30T17:32Z] INFO  18:32:49,266 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 593972 total reads (0.00%)
[2015-09-30T17:32Z] INFO  18:32:49,267 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:32Z] INFO  18:32:49,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:32Z] INFO  18:32:49,267 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:32Z] INFO  18:32:50,424 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:32Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam
[2015-09-30T17:32Z] GATK pre-alignment ('19', 31038548, 59128983) : syn3-tumor
[2015-09-30T17:32Z] INFO  18:32:55,713 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:55,715 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:32Z] INFO  18:32:55,715 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:32Z] INFO  18:32:55,715 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:32Z] INFO  18:32:55,719 HelpFormatter - Program Args: -T PrintReads -L 19:31038549-59128983 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/tx/tmpkchXPw/2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam
[2015-09-30T17:32Z] INFO  18:32:55,725 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:32Z] INFO  18:32:55,725 HelpFormatter - Date/Time: 2015/09/30 18:32:55
[2015-09-30T17:32Z] INFO  18:32:55,725 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:55,725 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:32Z] INFO  18:32:55,831 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:32Z] INFO  18:32:56,858 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:32Z] INFO  18:32:56,908 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:32Z] INFO  18:32:56,916 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:32Z] INFO  18:32:56,931 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:32Z] INFO  18:32:56,945 IntervalUtils - Processing 28090435 bp from intervals
[2015-09-30T17:32Z] INFO  18:32:57,006 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:32Z] INFO  18:32:57,255 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:32Z] INFO  18:32:57,255 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:32Z] INFO  18:32:57,255 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:32Z] INFO  18:32:57,256 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:32Z] INFO  18:32:57,267 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:32Z] INFO  18:32:57,469 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:33Z] INFO  18:33:02,823 ProgressMeter -            done    169093.0    14.0 s      87.0 s       99.5%    14.0 s       0.0 s
[2015-09-30T17:33Z] INFO  18:33:02,824 ProgressMeter - Total runtime 14.74 secs, 0.25 min, 0.00 hours
[2015-09-30T17:33Z] INFO  18:33:02,827 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 169093 total reads (0.00%)
[2015-09-30T17:33Z] INFO  18:33:02,827 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:33Z] INFO  18:33:02,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:33Z] INFO  18:33:02,827 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:33Z] INFO  18:33:03,871 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:33Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam
[2015-09-30T17:33Z] GATK pre-alignment ('20', 0, 31018105) : syn3-tumor
[2015-09-30T17:33Z] INFO  18:33:06,346 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:33Z] INFO  18:33:06,348 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:33Z] INFO  18:33:06,348 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:33Z] INFO  18:33:06,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:33Z] INFO  18:33:06,352 HelpFormatter - Program Args: -T PrintReads -L 20:1-31018105 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/tx/tmpN0Nh4W/2_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam
[2015-09-30T17:33Z] INFO  18:33:06,357 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:33Z] INFO  18:33:06,358 HelpFormatter - Date/Time: 2015/09/30 18:33:06
[2015-09-30T17:33Z] INFO  18:33:06,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:33Z] INFO  18:33:06,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:33Z] INFO  18:33:06,475 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:33Z] INFO  18:33:07,635 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:33Z] INFO  18:33:07,687 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:33Z] INFO  18:33:07,695 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:33Z] INFO  18:33:07,709 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:33Z] INFO  18:33:07,722 IntervalUtils - Processing 31018105 bp from intervals
[2015-09-30T17:33Z] INFO  18:33:07,749 ProgressMeter -      19:1819265    200002.0    30.0 s       2.5 m        5.9%     8.5 m       8.0 m
[2015-09-30T17:33Z] INFO  18:33:07,779 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:33Z] INFO  18:33:07,977 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:33Z] INFO  18:33:07,978 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:33Z] INFO  18:33:07,978 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:33Z] INFO  18:33:07,978 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:33Z] INFO  18:33:07,989 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:33Z] INFO  18:33:08,196 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:33Z] INFO  18:33:27,681 ProgressMeter -     19:36003144    200002.0    30.0 s       2.5 m       17.7%     2.8 m       2.3 m
[2015-09-30T17:33Z] INFO  18:33:37,750 ProgressMeter -      19:4360084    600007.0    60.0 s     100.0 s       14.1%     7.1 m       6.1 m
[2015-09-30T17:33Z] INFO  18:33:37,980 ProgressMeter -      20:3674674    200002.0    30.0 s       2.5 m       11.8%     4.2 m       3.7 m
[2015-09-30T17:33Z] INFO  18:33:57,841 ProgressMeter -     19:38979411    500007.0    60.0 s       2.0 m       28.3%     3.5 m       2.5 m
[2015-09-30T17:34Z] INFO  18:34:07,774 ProgressMeter -      19:7569449   1000027.0    90.0 s      90.0 s       24.4%     6.1 m       4.6 m
[2015-09-30T17:34Z] INFO  18:34:07,981 ProgressMeter -     20:18450177    500006.0    60.0 s     120.0 s       59.5%   100.0 s      40.0 s
[2015-09-30T17:34Z] INFO  18:34:27,871 ProgressMeter -     19:41112204    800010.0    90.0 s     113.0 s       35.9%     4.2 m       2.7 m
[2015-09-30T17:34Z] INFO  18:34:37,775 ProgressMeter -     19:10416090   1300031.0   120.0 s      92.0 s       33.6%     6.0 m       4.0 m
[2015-09-30T17:34Z] INFO  18:34:37,982 ProgressMeter -     20:30459011    800012.0    90.0 s     112.0 s       98.2%    91.0 s       1.0 s
[2015-09-30T17:34Z] INFO  18:34:43,451 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:34Z] INFO  18:34:44,181 ProgressMeter -            done    912072.0    96.0 s     105.0 s      100.0%    96.0 s       0.0 s
[2015-09-30T17:34Z] INFO  18:34:44,181 ProgressMeter - Total runtime 96.20 secs, 1.60 min, 0.03 hours
[2015-09-30T17:34Z] INFO  18:34:44,182 MicroScheduler - 2073 reads were filtered out during the traversal out of approximately 914145 total reads (0.23%)
[2015-09-30T17:34Z] INFO  18:34:44,182 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:34Z] INFO  18:34:44,182 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:34Z] INFO  18:34:44,182 MicroScheduler -   -> 2073 reads (0.23% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:34Z] INFO  18:34:45,494 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:34Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam
[2015-09-30T17:34Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam 20:1-31018105
[2015-09-30T17:34Z] GATK: RealignerTargetCreator
[2015-09-30T17:34Z] INFO  18:34:52,058 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:34Z] INFO  18:34:52,060 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:34Z] INFO  18:34:52,060 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:34Z] INFO  18:34:52,060 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:34Z] INFO  18:34:52,064 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/tx/tmpFn9EId/2_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign-realign.intervals -l INFO -L 20:1-31018105 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:34Z] INFO  18:34:52,069 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:34Z] INFO  18:34:52,070 HelpFormatter - Date/Time: 2015/09/30 18:34:52
[2015-09-30T17:34Z] INFO  18:34:52,070 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:34Z] INFO  18:34:52,070 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:34Z] INFO  18:34:52,126 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:34Z] INFO  18:34:52,580 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:34Z] INFO  18:34:52,588 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:34Z] INFO  18:34:52,604 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:34Z] INFO  18:34:52,848 IntervalUtils - Processing 31018105 bp from intervals
[2015-09-30T17:34Z] WARN  18:34:52,852 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:34Z] INFO  18:34:52,909 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:34Z] INFO  18:34:53,064 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:34Z] INFO  18:34:53,064 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:34Z] INFO  18:34:53,065 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:34Z] INFO  18:34:53,065 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:34Z] INFO  18:34:57,872 ProgressMeter -     19:43763617   1100014.0   120.0 s     109.0 s       45.3%     4.4 m       2.4 m
[2015-09-30T17:35Z] INFO  18:35:07,776 ProgressMeter -     19:13041557   1700038.0     2.5 m      88.0 s       42.0%     5.9 m       3.4 m
[2015-09-30T17:35Z] INFO  18:35:21,406 ProgressMeter -            done   3.1018105E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2015-09-30T17:35Z] INFO  18:35:21,406 ProgressMeter - Total runtime 28.34 secs, 0.47 min, 0.01 hours
[2015-09-30T17:35Z] INFO  18:35:21,409 MicroScheduler - 76236 reads were filtered out during the traversal out of approximately 917214 total reads (8.31%)
[2015-09-30T17:35Z] INFO  18:35:21,410 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:35Z] INFO  18:35:21,410 MicroScheduler -   -> 11283 reads (1.23% of total) failing BadMateFilter
[2015-09-30T17:35Z] INFO  18:35:21,410 MicroScheduler -   -> 42783 reads (4.66% of total) failing DuplicateReadFilter
[2015-09-30T17:35Z] INFO  18:35:21,411 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:35Z] INFO  18:35:21,411 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:35Z] INFO  18:35:21,411 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:35Z] INFO  18:35:21,411 MicroScheduler -   -> 22170 reads (2.42% of total) failing MappingQualityZeroFilter
[2015-09-30T17:35Z] INFO  18:35:21,411 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:35Z] INFO  18:35:21,412 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:35Z] INFO  18:35:21,412 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:35Z] INFO  18:35:22,442 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:35Z] GATK: realign ('20', 0, 31018105) : syn3-tumor
[2015-09-30T17:35Z] INFO  18:35:24,143 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:35Z] INFO  18:35:24,145 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:35Z] INFO  18:35:24,145 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:35Z] INFO  18:35:24,145 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:35Z] INFO  18:35:24,149 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_0_31018105-prep-prealign-realign.intervals -L 20:1-31018105 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/tx/tmpL4CVfn/2_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam
[2015-09-30T17:35Z] INFO  18:35:24,155 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:35Z] INFO  18:35:24,155 HelpFormatter - Date/Time: 2015/09/30 18:35:24
[2015-09-30T17:35Z] INFO  18:35:24,155 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:35Z] INFO  18:35:24,155 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:35Z] INFO  18:35:24,279 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:35Z] INFO  18:35:24,345 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:35Z] INFO  18:35:24,352 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:35Z] INFO  18:35:24,368 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:35Z] INFO  18:35:24,596 IntervalUtils - Processing 31018105 bp from intervals
[2015-09-30T17:35Z] WARN  18:35:24,600 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:35Z] INFO  18:35:24,654 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:35Z] INFO  18:35:24,785 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:35Z] INFO  18:35:24,786 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:35Z] INFO  18:35:24,786 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:35Z] INFO  18:35:24,786 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:35Z] INFO  18:35:24,921 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:35Z] INFO  18:35:25,100 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:35Z] INFO  18:35:27,873 ProgressMeter -     19:46287532   1400022.0     2.5 m     107.0 s       54.3%     4.6 m       2.1 m
[2015-09-30T17:35Z] INFO  18:35:38,067 ProgressMeter -     19:16536122   2100043.0     3.0 m      85.0 s       53.3%     5.6 m       2.6 m
[2015-09-30T17:35Z] INFO  18:35:55,127 ProgressMeter -     20:20051367    500006.0    30.0 s      60.0 s       64.6%    46.0 s      16.0 s
[2015-09-30T17:35Z] INFO  18:35:57,874 ProgressMeter -     19:49173417   1700026.0     3.0 m     106.0 s       64.6%     4.6 m      98.0 s
[2015-09-30T17:36Z] INFO  18:36:08,068 ProgressMeter -     19:19104358   2500047.0     3.5 m      84.0 s       61.6%     5.7 m       2.2 m
[2015-09-30T17:36Z] INFO  18:36:11,396 ProgressMeter -            done    912072.0    46.0 s      51.0 s      100.0%    46.0 s       0.0 s
[2015-09-30T17:36Z] INFO  18:36:11,397 ProgressMeter - Total runtime 46.61 secs, 0.78 min, 0.01 hours
[2015-09-30T17:36Z] INFO  18:36:11,399 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 912072 total reads (0.00%)
[2015-09-30T17:36Z] INFO  18:36:11,400 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:36Z] INFO  18:36:11,400 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:36Z] INFO  18:36:11,400 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:36Z] INFO  18:36:12,570 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:36Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam
[2015-09-30T17:36Z] GATK pre-alignment ('20', 31018873, 62038916) : syn3-tumor
[2015-09-30T17:36Z] INFO  18:36:20,746 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:36Z] INFO  18:36:20,748 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:36Z] INFO  18:36:20,748 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:36Z] INFO  18:36:20,749 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:36Z] INFO  18:36:20,752 HelpFormatter - Program Args: -T PrintReads -L 20:31018874-62038916 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/tx/tmpcKUjb9/2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam
[2015-09-30T17:36Z] INFO  18:36:20,757 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:36Z] INFO  18:36:20,758 HelpFormatter - Date/Time: 2015/09/30 18:36:20
[2015-09-30T17:36Z] INFO  18:36:20,758 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:36Z] INFO  18:36:20,758 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:36Z] INFO  18:36:21,264 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:36Z] INFO  18:36:22,342 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:36Z] INFO  18:36:22,390 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:36Z] INFO  18:36:22,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:36Z] INFO  18:36:22,412 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:36Z] INFO  18:36:22,425 IntervalUtils - Processing 31020043 bp from intervals
[2015-09-30T17:36Z] INFO  18:36:22,480 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:36Z] INFO  18:36:22,670 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:36Z] INFO  18:36:22,671 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:36Z] INFO  18:36:22,671 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:36Z] INFO  18:36:22,671 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:36Z] INFO  18:36:22,682 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:36Z] INFO  18:36:23,219 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:36Z] INFO  18:36:24,880 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:36Z] INFO  18:36:24,991 ProgressMeter -            done   2750224.0     3.8 m      82.0 s      100.0%     3.8 m       0.0 s
[2015-09-30T17:36Z] INFO  18:36:24,991 ProgressMeter - Total runtime 227.35 secs, 3.79 min, 0.06 hours
[2015-09-30T17:36Z] INFO  18:36:24,991 MicroScheduler - 4153 reads were filtered out during the traversal out of approximately 2754377 total reads (0.15%)
[2015-09-30T17:36Z] INFO  18:36:24,992 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:36Z] INFO  18:36:24,992 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:36Z] INFO  18:36:24,992 MicroScheduler -   -> 4153 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:36Z] INFO  18:36:26,293 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:36Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam
[2015-09-30T17:36Z] INFO  18:36:27,875 ProgressMeter -     19:50812925   2000029.0     3.5 m     105.0 s       70.4%     5.0 m      88.0 s
[2015-09-30T17:36Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam 19:1-31026185
[2015-09-30T17:36Z] GATK: RealignerTargetCreator
[2015-09-30T17:36Z] INFO  18:36:35,275 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:36Z] INFO  18:36:35,277 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:36Z] INFO  18:36:35,277 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:36Z] INFO  18:36:35,277 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:36Z] INFO  18:36:35,281 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/tx/tmpL3kJcs/2_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign-realign.intervals -l INFO -L 19:1-31026185 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:36Z] INFO  18:36:35,286 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:36Z] INFO  18:36:35,287 HelpFormatter - Date/Time: 2015/09/30 18:36:35
[2015-09-30T17:36Z] INFO  18:36:35,287 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:36Z] INFO  18:36:35,287 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:36Z] INFO  18:36:35,344 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:36Z] INFO  18:36:35,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:36Z] INFO  18:36:35,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:36Z] INFO  18:36:35,480 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:36Z] INFO  18:36:35,945 IntervalUtils - Processing 31026185 bp from intervals
[2015-09-30T17:36Z] WARN  18:36:35,949 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:36Z] INFO  18:36:36,008 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:36Z] INFO  18:36:36,152 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:36Z] INFO  18:36:36,152 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:36Z] INFO  18:36:36,152 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:36Z] INFO  18:36:36,153 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:36Z] INFO  18:36:52,673 ProgressMeter -     20:33918522    200002.0    30.0 s       2.5 m        9.3%     5.3 m       4.8 m
[2015-09-30T17:36Z] INFO  18:36:57,876 ProgressMeter -     19:53794136   2300034.0     4.0 m     104.0 s       81.0%     4.9 m      56.0 s
[2015-09-30T17:37Z] INFO  18:37:06,155 ProgressMeter -     19:11661225   1.1649024E7    30.0 s       2.0 s       37.6%    79.0 s      49.0 s
[2015-09-30T17:37Z] INFO  18:37:22,674 ProgressMeter -     20:40738990    600006.0    60.0 s     100.0 s       31.3%     3.2 m       2.2 m
[2015-09-30T17:37Z] INFO  18:37:29,195 ProgressMeter -     19:56001839   2700041.0     4.5 m     100.0 s       88.9%     5.1 m      33.0 s
[2015-09-30T17:37Z] INFO  18:37:31,904 ProgressMeter -            done   3.1026185E7    55.0 s       1.0 s      100.0%    55.0 s       0.0 s
[2015-09-30T17:37Z] INFO  18:37:31,904 ProgressMeter - Total runtime 55.75 secs, 0.93 min, 0.02 hours
[2015-09-30T17:37Z] INFO  18:37:31,905 MicroScheduler - 239687 reads were filtered out during the traversal out of approximately 2766060 total reads (8.67%)
[2015-09-30T17:37Z] INFO  18:37:31,905 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:37Z] INFO  18:37:31,905 MicroScheduler -   -> 24721 reads (0.89% of total) failing BadMateFilter
[2015-09-30T17:37Z] INFO  18:37:31,906 MicroScheduler -   -> 145773 reads (5.27% of total) failing DuplicateReadFilter
[2015-09-30T17:37Z] INFO  18:37:31,906 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:37Z] INFO  18:37:31,906 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:37Z] INFO  18:37:31,906 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:37Z] INFO  18:37:31,906 MicroScheduler -   -> 69193 reads (2.50% of total) failing MappingQualityZeroFilter
[2015-09-30T17:37Z] INFO  18:37:31,907 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:37Z] INFO  18:37:31,907 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:37Z] INFO  18:37:31,907 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:37Z] INFO  18:37:32,915 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:37Z] GATK: realign ('19', 0, 31026185) : syn3-tumor
[2015-09-30T17:37Z] INFO  18:37:34,731 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:37Z] INFO  18:37:34,733 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:37Z] INFO  18:37:34,734 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:37Z] INFO  18:37:34,734 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:37Z] INFO  18:37:34,737 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_0_31026185-prep-prealign-realign.intervals -L 19:1-31026185 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/tx/tmpN9FSkA/2_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam
[2015-09-30T17:37Z] INFO  18:37:34,744 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:37Z] INFO  18:37:34,745 HelpFormatter - Date/Time: 2015/09/30 18:37:34
[2015-09-30T17:37Z] INFO  18:37:34,745 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:37Z] INFO  18:37:34,745 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:37Z] INFO  18:37:34,853 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:37Z] INFO  18:37:34,927 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:37Z] INFO  18:37:34,935 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:37Z] INFO  18:37:34,951 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:37Z] INFO  18:37:35,375 IntervalUtils - Processing 31026185 bp from intervals
[2015-09-30T17:37Z] WARN  18:37:35,379 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:37Z] INFO  18:37:35,436 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:37Z] INFO  18:37:35,581 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:37Z] INFO  18:37:35,582 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:37Z] INFO  18:37:35,582 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:37Z] INFO  18:37:35,583 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:37Z] INFO  18:37:35,737 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:37Z] INFO  18:37:35,925 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:37Z] INFO  18:37:52,801 ProgressMeter -     20:47591032   1000011.0    90.0 s      90.0 s       53.4%     2.8 m      78.0 s
[2015-09-30T17:37Z] INFO  18:37:57,212 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:37Z] INFO  18:37:57,418 ProgressMeter -            done   3027184.0     5.0 m      99.0 s       99.9%     5.0 m       0.0 s
[2015-09-30T17:37Z] INFO  18:37:57,418 ProgressMeter - Total runtime 300.16 secs, 5.00 min, 0.08 hours
[2015-09-30T17:37Z] INFO  18:37:57,419 MicroScheduler - 4609 reads were filtered out during the traversal out of approximately 3031793 total reads (0.15%)
[2015-09-30T17:37Z] INFO  18:37:57,419 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:37Z] INFO  18:37:57,419 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:37Z] INFO  18:37:57,420 MicroScheduler -   -> 4609 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:37Z] INFO  18:37:58,421 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:37Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam
[2015-09-30T17:38Z] INFO  18:38:05,585 ProgressMeter -      19:3201935    400005.0    30.0 s      75.0 s       10.3%     4.8 m       4.3 m
[2015-09-30T17:38Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam 19:31038549-59128983
[2015-09-30T17:38Z] GATK: RealignerTargetCreator
[2015-09-30T17:38Z] INFO  18:38:07,640 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:38Z] INFO  18:38:07,642 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:38Z] INFO  18:38:07,642 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:38Z] INFO  18:38:07,642 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:38Z] INFO  18:38:07,646 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/tx/tmphT_mT8/2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign-realign.intervals -l INFO -L 19:31038549-59128983 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:38Z] INFO  18:38:07,651 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:38Z] INFO  18:38:07,651 HelpFormatter - Date/Time: 2015/09/30 18:38:07
[2015-09-30T17:38Z] INFO  18:38:07,652 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:38Z] INFO  18:38:07,652 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:38Z] INFO  18:38:07,705 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:38Z] INFO  18:38:07,813 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:38Z] INFO  18:38:07,820 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:38Z] INFO  18:38:07,836 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:38Z] INFO  18:38:08,552 IntervalUtils - Processing 28090435 bp from intervals
[2015-09-30T17:38Z] WARN  18:38:08,556 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:38Z] INFO  18:38:08,612 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:38Z] INFO  18:38:08,758 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:38Z] INFO  18:38:08,759 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:38Z] INFO  18:38:08,759 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:38Z] INFO  18:38:08,760 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:38Z] INFO  18:38:23,131 ProgressMeter -     20:60505053   1400017.0   120.0 s      86.0 s       95.1%     2.1 m       6.0 s
[2015-09-30T17:38Z] INFO  18:38:36,179 ProgressMeter -      19:7978348   1000027.0    60.0 s      60.0 s       25.7%     3.9 m       2.9 m
[2015-09-30T17:38Z] INFO  18:38:36,851 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:38Z] INFO  18:38:36,965 ProgressMeter -            done   1631555.0     2.2 m      82.0 s      100.0%     2.2 m       0.0 s
[2015-09-30T17:38Z] INFO  18:38:36,965 ProgressMeter - Total runtime 134.29 secs, 2.24 min, 0.04 hours
[2015-09-30T17:38Z] INFO  18:38:36,966 MicroScheduler - 2882 reads were filtered out during the traversal out of approximately 1634437 total reads (0.18%)
[2015-09-30T17:38Z] INFO  18:38:36,966 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:38Z] INFO  18:38:36,966 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:38Z] INFO  18:38:36,966 MicroScheduler -   -> 2882 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:38Z] INFO  18:38:38,000 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:38Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam
[2015-09-30T17:38Z] INFO  18:38:38,762 ProgressMeter -     19:46967645   1.5917996E7    30.0 s       1.0 s       56.7%    52.0 s      22.0 s
[2015-09-30T17:38Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam 20:31018874-62038916
[2015-09-30T17:38Z] GATK: RealignerTargetCreator
[2015-09-30T17:38Z] INFO  18:38:43,851 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:38Z] INFO  18:38:43,853 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:38Z] INFO  18:38:43,853 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:38Z] INFO  18:38:43,853 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:38Z] INFO  18:38:43,856 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/tx/tmpfW42yS/2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign-realign.intervals -l INFO -L 20:31018874-62038916 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:38Z] INFO  18:38:43,861 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:38Z] INFO  18:38:43,862 HelpFormatter - Date/Time: 2015/09/30 18:38:43
[2015-09-30T17:38Z] INFO  18:38:43,862 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:38Z] INFO  18:38:43,862 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:38Z] INFO  18:38:43,918 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:38Z] INFO  18:38:44,022 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:38Z] INFO  18:38:44,029 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:38Z] INFO  18:38:44,045 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:38Z] INFO  18:38:44,663 IntervalUtils - Processing 31020043 bp from intervals
[2015-09-30T17:38Z] WARN  18:38:44,667 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:38Z] INFO  18:38:44,721 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:38Z] INFO  18:38:44,909 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:38Z] INFO  18:38:44,910 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:38Z] INFO  18:38:44,910 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:38Z] INFO  18:38:44,911 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:39Z] INFO  18:39:05,291 ProgressMeter -            done   2.8090435E7    56.0 s       2.0 s      100.0%    56.0 s       0.0 s
[2015-09-30T17:39Z] INFO  18:39:05,291 ProgressMeter - Total runtime 56.53 secs, 0.94 min, 0.02 hours
[2015-09-30T17:39Z] INFO  18:39:05,294 MicroScheduler - 261830 reads were filtered out during the traversal out of approximately 3044318 total reads (8.60%)
[2015-09-30T17:39Z] INFO  18:39:05,295 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:39Z] INFO  18:39:05,295 MicroScheduler -   -> 25894 reads (0.85% of total) failing BadMateFilter
[2015-09-30T17:39Z] INFO  18:39:05,295 MicroScheduler -   -> 152973 reads (5.02% of total) failing DuplicateReadFilter
[2015-09-30T17:39Z] INFO  18:39:05,295 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:39Z] INFO  18:39:05,296 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:39Z] INFO  18:39:05,296 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:39Z] INFO  18:39:05,296 MicroScheduler -   -> 82963 reads (2.73% of total) failing MappingQualityZeroFilter
[2015-09-30T17:39Z] INFO  18:39:05,296 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:39Z] INFO  18:39:05,296 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:39Z] INFO  18:39:05,297 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:39Z] INFO  18:39:06,265 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:39Z] GATK: realign ('19', 31038548, 59128983) : syn3-tumor
[2015-09-30T17:39Z] INFO  18:39:07,763 ProgressMeter -     19:14153551   1800039.0    92.0 s      51.0 s       45.6%     3.4 m     109.0 s
[2015-09-30T17:39Z] INFO  18:39:08,144 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:39Z] INFO  18:39:08,146 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:39Z] INFO  18:39:08,146 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:39Z] INFO  18:39:08,146 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:39Z] INFO  18:39:08,150 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep-prealign-realign.intervals -L 19:31038549-59128983 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/tx/tmp9h7B_F/2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam
[2015-09-30T17:39Z] INFO  18:39:08,155 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:39Z] INFO  18:39:08,155 HelpFormatter - Date/Time: 2015/09/30 18:39:08
[2015-09-30T17:39Z] INFO  18:39:08,156 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:39Z] INFO  18:39:08,156 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:39Z] INFO  18:39:08,278 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:39Z] INFO  18:39:08,345 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:39Z] INFO  18:39:08,352 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:39Z] INFO  18:39:08,368 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:39Z] INFO  18:39:08,970 IntervalUtils - Processing 28090435 bp from intervals
[2015-09-30T17:39Z] WARN  18:39:08,974 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:39Z] INFO  18:39:09,026 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:39Z] INFO  18:39:09,180 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:39Z] INFO  18:39:09,180 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:39Z] INFO  18:39:09,181 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:39Z] INFO  18:39:09,181 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:39Z] INFO  18:39:09,327 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:39Z] INFO  18:39:09,499 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:39Z] INFO  18:39:14,913 ProgressMeter -     20:55092809   2.4064135E7    30.0 s       1.0 s       77.6%    38.0 s       8.0 s
[2015-09-30T17:39Z] INFO  18:39:23,144 ProgressMeter -            done   3.1020043E7    38.0 s       1.0 s      100.0%    38.0 s       0.0 s
[2015-09-30T17:39Z] INFO  18:39:23,145 ProgressMeter - Total runtime 38.24 secs, 0.64 min, 0.01 hours
[2015-09-30T17:39Z] INFO  18:39:23,148 MicroScheduler - 124998 reads were filtered out during the traversal out of approximately 1641655 total reads (7.61%)
[2015-09-30T17:39Z] INFO  18:39:23,148 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:39Z] INFO  18:39:23,149 MicroScheduler -   -> 16361 reads (1.00% of total) failing BadMateFilter
[2015-09-30T17:39Z] INFO  18:39:23,149 MicroScheduler -   -> 81033 reads (4.94% of total) failing DuplicateReadFilter
[2015-09-30T17:39Z] INFO  18:39:23,149 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:39Z] INFO  18:39:23,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:39Z] INFO  18:39:23,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:39Z] INFO  18:39:23,150 MicroScheduler -   -> 27604 reads (1.68% of total) failing MappingQualityZeroFilter
[2015-09-30T17:39Z] INFO  18:39:23,150 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:39Z] INFO  18:39:23,150 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:39Z] INFO  18:39:23,150 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:39Z] INFO  18:39:24,173 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:39Z] GATK: realign ('20', 31018873, 62038916) : syn3-tumor
[2015-09-30T17:39Z] INFO  18:39:26,063 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:39Z] INFO  18:39:26,065 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:39Z] INFO  18:39:26,065 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:39Z] INFO  18:39:26,065 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:39Z] INFO  18:39:26,068 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep-prealign-realign.intervals -L 20:31018874-62038916 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/tx/tmpr37Tvo/2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam
[2015-09-30T17:39Z] INFO  18:39:26,074 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:39Z] INFO  18:39:26,074 HelpFormatter - Date/Time: 2015/09/30 18:39:26
[2015-09-30T17:39Z] INFO  18:39:26,074 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:39Z] INFO  18:39:26,074 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:39Z] INFO  18:39:26,200 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:39Z] INFO  18:39:26,262 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:39Z] INFO  18:39:26,270 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:39Z] INFO  18:39:26,285 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:39Z] INFO  18:39:26,805 IntervalUtils - Processing 31020043 bp from intervals
[2015-09-30T17:39Z] WARN  18:39:26,809 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:39Z] INFO  18:39:26,864 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:39Z] INFO  18:39:27,008 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:39Z] INFO  18:39:27,009 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:39Z] INFO  18:39:27,009 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:39Z] INFO  18:39:27,009 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:39Z] INFO  18:39:27,151 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:39Z] INFO  18:39:27,335 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:39Z] INFO  18:39:37,866 ProgressMeter -     19:19298392   2500047.0     2.0 m      48.0 s       62.2%     3.3 m      74.0 s
[2015-09-30T17:39Z] INFO  18:39:39,183 ProgressMeter -     19:38885214    500007.0    30.0 s      60.0 s       27.9%   107.0 s      77.0 s
[2015-09-30T17:39Z] INFO  18:39:45,373 ProgressMeter -            done   2750224.0     2.2 m      47.0 s      100.0%     2.2 m       0.0 s
[2015-09-30T17:39Z] INFO  18:39:45,373 ProgressMeter - Total runtime 129.79 secs, 2.16 min, 0.04 hours
[2015-09-30T17:39Z] INFO  18:39:45,376 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2750224 total reads (0.00%)
[2015-09-30T17:39Z] INFO  18:39:45,377 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:39Z] INFO  18:39:45,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:39Z] INFO  18:39:45,377 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:39Z] INFO  18:39:46,507 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:39Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam
[2015-09-30T17:39Z] GATK pre-alignment ('20', 62039427, 63025520) : syn3-tumor
[2015-09-30T17:39Z] INFO  18:39:55,205 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:39Z] INFO  18:39:55,207 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:39Z] INFO  18:39:55,207 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:39Z] INFO  18:39:55,207 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:39Z] INFO  18:39:55,211 HelpFormatter - Program Args: -T PrintReads -L 20:62039428-63025520 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/tx/tmpD1PikF/2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam
[2015-09-30T17:39Z] INFO  18:39:55,217 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:39Z] INFO  18:39:55,217 HelpFormatter - Date/Time: 2015/09/30 18:39:55
[2015-09-30T17:39Z] INFO  18:39:55,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:39Z] INFO  18:39:55,218 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:39Z] INFO  18:39:55,888 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:39Z] INFO  18:39:56,596 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:39Z] INFO  18:39:56,648 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:39Z] INFO  18:39:56,655 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:39Z] INFO  18:39:56,670 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:39Z] INFO  18:39:56,684 IntervalUtils - Processing 986093 bp from intervals
[2015-09-30T17:39Z] INFO  18:39:56,741 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:39Z] INFO  18:39:56,847 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:39Z] INFO  18:39:56,847 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:39Z] INFO  18:39:56,847 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:39Z] INFO  18:39:56,848 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:39Z] INFO  18:39:56,859 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:39Z] INFO  18:39:56,868 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:39Z] INFO  18:39:57,012 ProgressMeter -     20:36770926    500005.0    30.0 s      60.0 s       18.5%     2.7 m       2.2 m
[2015-09-30T17:40Z] INFO  18:40:09,583 ProgressMeter -     19:44156278   1200017.0    60.0 s      50.0 s       46.7%     2.1 m      68.0 s
[2015-09-30T17:40Z] INFO  18:40:14,879 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:40Z] INFO  18:40:15,003 ProgressMeter -            done    156221.0    18.0 s     116.0 s       93.3%    19.0 s       1.0 s
[2015-09-30T17:40Z] INFO  18:40:15,003 ProgressMeter - Total runtime 18.16 secs, 0.30 min, 0.01 hours
[2015-09-30T17:40Z] INFO  18:40:15,004 MicroScheduler - 196 reads were filtered out during the traversal out of approximately 156417 total reads (0.13%)
[2015-09-30T17:40Z] INFO  18:40:15,004 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:40Z] INFO  18:40:15,004 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:40Z] INFO  18:40:15,004 MicroScheduler -   -> 196 reads (0.13% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:40Z] INFO  18:40:15,972 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:40Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam
[2015-09-30T17:40Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam 20:62039428-63025520
[2015-09-30T17:40Z] GATK: RealignerTargetCreator
[2015-09-30T17:40Z] INFO  18:40:18,195 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:18,197 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:40Z] INFO  18:40:18,197 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:40Z] INFO  18:40:18,197 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:40Z] INFO  18:40:18,201 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/tx/tmpixLhKI/2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign-realign.intervals -l INFO -L 20:62039428-63025520 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:40Z] INFO  18:40:18,206 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:40Z] INFO  18:40:18,207 HelpFormatter - Date/Time: 2015/09/30 18:40:18
[2015-09-30T17:40Z] INFO  18:40:18,207 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:18,207 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:18,265 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:40Z] INFO  18:40:18,374 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:40Z] INFO  18:40:18,382 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:40Z] INFO  18:40:18,398 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:40Z] INFO  18:40:18,651 IntervalUtils - Processing 986093 bp from intervals
[2015-09-30T17:40Z] WARN  18:40:18,654 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:40Z] INFO  18:40:18,712 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:40Z] INFO  18:40:18,740 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:40Z] INFO  18:40:18,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:40Z] INFO  18:40:18,741 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:40Z] INFO  18:40:18,741 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:40Z] INFO  18:40:23,305 ProgressMeter -            done    986093.0     4.0 s       4.0 s      100.0%     4.0 s       0.0 s
[2015-09-30T17:40Z] INFO  18:40:23,306 ProgressMeter - Total runtime 4.57 secs, 0.08 min, 0.00 hours
[2015-09-30T17:40Z] INFO  18:40:23,308 MicroScheduler - 13598 reads were filtered out during the traversal out of approximately 157066 total reads (8.66%)
[2015-09-30T17:40Z] INFO  18:40:23,309 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:40Z] INFO  18:40:23,309 MicroScheduler -   -> 1136 reads (0.72% of total) failing BadMateFilter
[2015-09-30T17:40Z] INFO  18:40:23,309 MicroScheduler -   -> 8820 reads (5.62% of total) failing DuplicateReadFilter
[2015-09-30T17:40Z] INFO  18:40:23,310 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:40Z] INFO  18:40:23,310 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:40Z] INFO  18:40:23,310 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:40Z] INFO  18:40:23,310 MicroScheduler -   -> 3642 reads (2.32% of total) failing MappingQualityZeroFilter
[2015-09-30T17:40Z] INFO  18:40:23,311 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:40Z] INFO  18:40:23,311 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:40Z] INFO  18:40:23,311 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:40Z] INFO  18:40:24,432 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:40Z] GATK: realign ('20', 62039427, 63025520) : syn3-tumor
[2015-09-30T17:40Z] INFO  18:40:26,454 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:26,456 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:40Z] INFO  18:40:26,457 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:40Z] INFO  18:40:26,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:40Z] INFO  18:40:26,460 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep-prealign-realign.intervals -L 20:62039428-63025520 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/tx/tmp9YDPE1/2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam
[2015-09-30T17:40Z] INFO  18:40:26,466 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:40Z] INFO  18:40:26,466 HelpFormatter - Date/Time: 2015/09/30 18:40:26
[2015-09-30T17:40Z] INFO  18:40:26,466 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:26,467 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:26,597 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:40Z] INFO  18:40:26,661 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:40Z] INFO  18:40:26,669 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:40Z] INFO  18:40:26,685 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:40Z] INFO  18:40:26,918 IntervalUtils - Processing 986093 bp from intervals
[2015-09-30T17:40Z] WARN  18:40:26,922 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:40Z] INFO  18:40:26,976 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:40Z] INFO  18:40:27,009 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:40Z] INFO  18:40:27,009 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:40Z] INFO  18:40:27,010 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:40Z] INFO  18:40:27,010 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:40Z] INFO  18:40:27,012 ProgressMeter -     20:52583977   1200014.0    60.0 s      50.0 s       69.5%    86.0 s      26.0 s
[2015-09-30T17:40Z] INFO  18:40:27,047 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:40Z] INFO  18:40:27,056 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:40Z] INFO  18:40:38,397 ProgressMeter -            done    156221.0    11.0 s      72.0 s       93.3%    11.0 s       0.0 s
[2015-09-30T17:40Z] INFO  18:40:38,397 ProgressMeter - Total runtime 11.39 secs, 0.19 min, 0.00 hours
[2015-09-30T17:40Z] INFO  18:40:38,400 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 156221 total reads (0.00%)
[2015-09-30T17:40Z] INFO  18:40:38,400 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:40Z] INFO  18:40:38,401 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:40Z] INFO  18:40:38,401 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:40Z] INFO  18:40:39,475 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:40Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam
[2015-09-30T17:40Z] GATK pre-alignment ('21', 0, 31023863) : syn3-tumor
[2015-09-30T17:40Z] INFO  18:40:41,249 ProgressMeter -     19:50100736   1900028.0    92.0 s      48.0 s       67.9%     2.3 m      43.0 s
[2015-09-30T17:40Z] INFO  18:40:41,646 ProgressMeter -            done   1631555.0    74.0 s      45.0 s      100.0%    74.0 s       0.0 s
[2015-09-30T17:40Z] INFO  18:40:41,647 ProgressMeter - Total runtime 74.64 secs, 1.24 min, 0.02 hours
[2015-09-30T17:40Z] INFO  18:40:41,650 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1631555 total reads (0.00%)
[2015-09-30T17:40Z] INFO  18:40:41,650 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:40Z] INFO  18:40:41,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:40Z] INFO  18:40:41,651 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:40Z] INFO  18:40:42,267 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:42,269 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:40Z] INFO  18:40:42,269 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:40Z] INFO  18:40:42,269 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:40Z] INFO  18:40:42,273 HelpFormatter - Program Args: -T PrintReads -L 21:1-31023863 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/tx/tmpbqpObx/2_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam
[2015-09-30T17:40Z] INFO  18:40:42,278 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:40Z] INFO  18:40:42,278 HelpFormatter - Date/Time: 2015/09/30 18:40:42
[2015-09-30T17:40Z] INFO  18:40:42,278 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:42,279 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:42,615 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:40Z] INFO  18:40:42,759 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:40Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam
[2015-09-30T17:40Z] INFO  18:40:43,319 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:40Z] INFO  18:40:43,370 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:40Z] INFO  18:40:43,378 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:40Z] INFO  18:40:43,393 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:40Z] INFO  18:40:43,406 IntervalUtils - Processing 31023863 bp from intervals
[2015-09-30T17:40Z] INFO  18:40:43,462 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:40Z] INFO  18:40:43,670 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:40Z] INFO  18:40:43,671 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:40Z] INFO  18:40:43,671 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:40Z] INFO  18:40:43,671 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:40Z] INFO  18:40:43,683 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:40Z] INFO  18:40:43,817 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:40Z] GATK pre-alignment ('21', 31026814, 48129895) : syn3-tumor
[2015-09-30T17:40Z] INFO  18:40:48,866 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:48,868 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:40Z] INFO  18:40:48,868 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:40Z] INFO  18:40:48,868 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:40Z] INFO  18:40:48,872 HelpFormatter - Program Args: -T PrintReads -L 21:31026815-48129895 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/tx/tmpoRAzQe/2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam
[2015-09-30T17:40Z] INFO  18:40:48,877 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:40Z] INFO  18:40:48,878 HelpFormatter - Date/Time: 2015/09/30 18:40:48
[2015-09-30T17:40Z] INFO  18:40:48,878 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:48,878 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:40Z] INFO  18:40:48,988 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:40Z] INFO  18:40:50,310 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:40Z] INFO  18:40:50,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:40Z] INFO  18:40:50,367 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:40Z] INFO  18:40:50,381 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:40Z] INFO  18:40:50,394 IntervalUtils - Processing 17103081 bp from intervals
[2015-09-30T17:40Z] INFO  18:40:50,450 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:40Z] INFO  18:40:50,611 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:40Z] INFO  18:40:50,612 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:40Z] INFO  18:40:50,612 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:40Z] INFO  18:40:50,612 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:40Z] INFO  18:40:50,623 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:40Z] INFO  18:40:50,739 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:41Z] INFO  18:41:08,287 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:41Z] INFO  18:41:08,453 ProgressMeter -            done    203408.0    24.0 s       2.0 m      100.0%    24.0 s       0.0 s
[2015-09-30T17:41Z] INFO  18:41:08,453 ProgressMeter - Total runtime 24.78 secs, 0.41 min, 0.01 hours
[2015-09-30T17:41Z] INFO  18:41:08,453 MicroScheduler - 1115 reads were filtered out during the traversal out of approximately 204523 total reads (0.55%)
[2015-09-30T17:41Z] INFO  18:41:08,454 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:41Z] INFO  18:41:08,454 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:41Z] INFO  18:41:08,454 MicroScheduler -   -> 1115 reads (0.55% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:41Z] INFO  18:41:09,527 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:41Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam
[2015-09-30T17:41Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam 21:1-31023863
[2015-09-30T17:41Z] GATK: RealignerTargetCreator
[2015-09-30T17:41Z] INFO  18:41:11,761 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:11,763 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:41Z] INFO  18:41:11,763 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:41Z] INFO  18:41:11,764 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:41Z] INFO  18:41:11,767 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/tx/tmpUyPt2P/2_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign-realign.intervals -l INFO -L 21:1-31023863 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:41Z] INFO  18:41:11,773 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:41Z] INFO  18:41:11,773 HelpFormatter - Date/Time: 2015/09/30 18:41:11
[2015-09-30T17:41Z] INFO  18:41:11,773 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:11,773 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:11,810 ProgressMeter -     19:55777932   2600038.0     2.0 m      47.0 s       88.1%     2.3 m      16.0 s
[2015-09-30T17:41Z] INFO  18:41:11,829 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:41Z] INFO  18:41:12,272 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:41Z] INFO  18:41:12,279 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:41Z] INFO  18:41:12,294 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:41Z] INFO  18:41:12,531 IntervalUtils - Processing 31023863 bp from intervals
[2015-09-30T17:41Z] WARN  18:41:12,534 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:41Z] INFO  18:41:12,589 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:41Z] INFO  18:41:12,725 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:41Z] INFO  18:41:12,726 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:41Z] INFO  18:41:12,726 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:41Z] INFO  18:41:12,727 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:41Z] INFO  18:41:20,614 ProgressMeter -     21:37602942    200003.0    30.0 s       2.5 m       38.4%    78.0 s      48.0 s
[2015-09-30T17:41Z] INFO  18:41:24,906 ProgressMeter -            done   3027184.0     2.3 m      44.0 s       99.9%     2.3 m       0.0 s
[2015-09-30T17:41Z] INFO  18:41:24,906 ProgressMeter - Total runtime 135.73 secs, 2.26 min, 0.04 hours
[2015-09-30T17:41Z] INFO  18:41:24,909 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3027184 total reads (0.00%)
[2015-09-30T17:41Z] INFO  18:41:24,910 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:41Z] INFO  18:41:24,910 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:41Z] INFO  18:41:24,910 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:41Z] INFO  18:41:26,027 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:41Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam
[2015-09-30T17:41Z] INFO  18:41:28,317 ProgressMeter -            done   3.1023863E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2015-09-30T17:41Z] INFO  18:41:28,318 ProgressMeter - Total runtime 15.59 secs, 0.26 min, 0.00 hours
[2015-09-30T17:41Z] INFO  18:41:28,318 MicroScheduler - 27916 reads were filtered out during the traversal out of approximately 204526 total reads (13.65%)
[2015-09-30T17:41Z] INFO  18:41:28,318 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:41Z] INFO  18:41:28,319 MicroScheduler -   -> 5101 reads (2.49% of total) failing BadMateFilter
[2015-09-30T17:41Z] INFO  18:41:28,319 MicroScheduler -   -> 8769 reads (4.29% of total) failing DuplicateReadFilter
[2015-09-30T17:41Z] INFO  18:41:28,319 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:41Z] INFO  18:41:28,320 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:41Z] INFO  18:41:28,320 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:41Z] INFO  18:41:28,320 MicroScheduler -   -> 14046 reads (6.87% of total) failing MappingQualityZeroFilter
[2015-09-30T17:41Z] INFO  18:41:28,320 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:41Z] INFO  18:41:28,320 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:41Z] INFO  18:41:28,321 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:41Z] INFO  18:41:29,255 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:41Z] GATK: realign ('21', 0, 31023863) : syn3-tumor
[2015-09-30T17:41Z] INFO  18:41:31,688 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:31,690 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:41Z] INFO  18:41:31,690 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:41Z] INFO  18:41:31,691 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:41Z] INFO  18:41:31,694 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_0_31023863-prep-prealign-realign.intervals -L 21:1-31023863 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/tx/tmp3JqN29/2_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam
[2015-09-30T17:41Z] INFO  18:41:31,700 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:41Z] INFO  18:41:31,700 HelpFormatter - Date/Time: 2015/09/30 18:41:31
[2015-09-30T17:41Z] INFO  18:41:31,700 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:31,700 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:32,226 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:41Z] INFO  18:41:32,421 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:41Z] INFO  18:41:32,428 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:41Z] INFO  18:41:32,830 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.40
[2015-09-30T17:41Z] INFO  18:41:33,936 IntervalUtils - Processing 31023863 bp from intervals
[2015-09-30T17:41Z] WARN  18:41:33,940 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:41Z] INFO  18:41:34,036 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:41Z] GATK pre-alignment ('22', 0, 31019358) : syn3-tumor
[2015-09-30T17:41Z] INFO  18:41:35,114 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:41Z] INFO  18:41:35,114 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:41Z] INFO  18:41:35,115 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:41Z] INFO  18:41:35,115 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:41Z] INFO  18:41:35,234 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:41Z] INFO  18:41:35,357 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:41Z] INFO  18:41:36,630 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:36,632 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:41Z] INFO  18:41:36,632 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:41Z] INFO  18:41:36,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:41Z] INFO  18:41:36,636 HelpFormatter - Program Args: -T PrintReads -L 22:1-31019358 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/tx/tmp5Gy6iI/2_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam
[2015-09-30T17:41Z] INFO  18:41:36,641 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:41Z] INFO  18:41:36,641 HelpFormatter - Date/Time: 2015/09/30 18:41:36
[2015-09-30T17:41Z] INFO  18:41:36,641 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:36,641 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:37,097 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:41Z] INFO  18:41:38,269 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:41Z] INFO  18:41:38,320 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:41Z] INFO  18:41:38,328 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:41Z] INFO  18:41:38,343 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:41Z] INFO  18:41:38,357 IntervalUtils - Processing 31019358 bp from intervals
[2015-09-30T17:41Z] INFO  18:41:38,416 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:41Z] INFO  18:41:39,136 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:41Z] INFO  18:41:39,137 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:41Z] INFO  18:41:39,137 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:41Z] INFO  18:41:39,137 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:41Z] INFO  18:41:39,148 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:41Z] INFO  18:41:39,248 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:41Z] INFO  18:41:49,501 ProgressMeter -            done    203408.0    14.0 s      70.0 s      100.0%    14.0 s       0.0 s
[2015-09-30T17:41Z] INFO  18:41:49,501 ProgressMeter - Total runtime 14.39 secs, 0.24 min, 0.00 hours
[2015-09-30T17:41Z] INFO  18:41:49,504 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 203408 total reads (0.00%)
[2015-09-30T17:41Z] INFO  18:41:49,504 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:41Z] INFO  18:41:49,505 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:41Z] INFO  18:41:49,505 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:41Z] INFO  18:41:50,615 ProgressMeter -     21:44164205    500006.0    60.0 s     120.0 s       76.8%    78.0 s      18.0 s
[2015-09-30T17:41Z] INFO  18:41:50,638 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:41Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam
[2015-09-30T17:41Z] GATK pre-alignment ('22', 31022170, 51304566) : syn3-tumor
[2015-09-30T17:41Z] INFO  18:41:53,196 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:53,198 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:41Z] INFO  18:41:53,198 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:41Z] INFO  18:41:53,198 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:41Z] INFO  18:41:53,202 HelpFormatter - Program Args: -T PrintReads -L 22:31022171-51304566 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/tx/tmp13XwGF/2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam
[2015-09-30T17:41Z] INFO  18:41:53,208 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:41Z] INFO  18:41:53,208 HelpFormatter - Date/Time: 2015/09/30 18:41:53
[2015-09-30T17:41Z] INFO  18:41:53,208 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:53,208 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:41Z] INFO  18:41:53,325 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:41Z] INFO  18:41:54,499 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:41Z] INFO  18:41:54,548 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:41Z] INFO  18:41:54,555 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:41Z] INFO  18:41:54,570 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:41Z] INFO  18:41:54,582 IntervalUtils - Processing 20282396 bp from intervals
[2015-09-30T17:41Z] INFO  18:41:54,638 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:41Z] INFO  18:41:54,804 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:41Z] INFO  18:41:54,804 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:41Z] INFO  18:41:54,804 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:41Z] INFO  18:41:54,805 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:41Z] INFO  18:41:54,815 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:41Z] INFO  18:41:54,945 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:42Z] INFO  18:42:09,140 ProgressMeter -     22:19444291    200002.0    30.0 s       2.5 m       62.7%    47.0 s      17.0 s
[2015-09-30T17:42Z] INFO  18:42:20,616 ProgressMeter -     21:46936168    800009.0    90.0 s     112.0 s       93.0%    96.0 s       6.0 s
[2015-09-30T17:42Z] INFO  18:42:24,835 ProgressMeter -     22:36627357    200002.0    30.0 s       2.5 m       27.6%   108.0 s      78.0 s
[2015-09-30T17:42Z] INFO  18:42:32,381 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6edcce68
[2015-09-30T17:42Z] INFO  18:42:32,642 ProgressMeter -            done    964283.0   102.0 s     105.0 s       99.9%   102.0 s       0.0 s
[2015-09-30T17:42Z] INFO  18:42:32,643 ProgressMeter - Total runtime 102.03 secs, 1.70 min, 0.03 hours
[2015-09-30T17:42Z] INFO  18:42:32,643 MicroScheduler - 1707 reads were filtered out during the traversal out of approximately 965990 total reads (0.18%)
[2015-09-30T17:42Z] INFO  18:42:32,643 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:42Z] INFO  18:42:32,643 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:42Z] INFO  18:42:32,644 MicroScheduler -   -> 1707 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:42Z] INFO  18:42:33,865 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:42Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam
[2015-09-30T17:42Z] INFO  18:42:39,140 ProgressMeter -     22:21805058    500008.0    60.0 s     120.0 s       70.3%    85.0 s      25.0 s
[2015-09-30T17:42Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam 21:31026815-48129895
[2015-09-30T17:42Z] GATK: RealignerTargetCreator
[2015-09-30T17:42Z] INFO  18:42:40,830 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:42Z] INFO  18:42:40,832 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:42Z] INFO  18:42:40,832 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:42Z] INFO  18:42:40,832 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:42Z] INFO  18:42:40,835 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/tx/tmpevw8OM/2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign-realign.intervals -l INFO -L 21:31026815-48129895 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:42Z] INFO  18:42:40,842 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:42Z] INFO  18:42:40,842 HelpFormatter - Date/Time: 2015/09/30 18:42:40
[2015-09-30T17:42Z] INFO  18:42:40,842 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:42Z] INFO  18:42:40,842 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:42Z] INFO  18:42:40,907 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:42Z] INFO  18:42:41,037 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:42Z] INFO  18:42:41,045 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:42Z] INFO  18:42:41,060 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:42Z] INFO  18:42:41,309 IntervalUtils - Processing 17103081 bp from intervals
[2015-09-30T17:42Z] WARN  18:42:41,313 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:42Z] INFO  18:42:41,367 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:42Z] INFO  18:42:41,467 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:42Z] INFO  18:42:41,468 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:42Z] INFO  18:42:41,468 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:42Z] INFO  18:42:41,469 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:42Z] INFO  18:42:54,836 ProgressMeter -     22:39219214    500006.0    60.0 s     120.0 s       40.4%     2.5 m      88.0 s
[2015-09-30T17:43Z] INFO  18:43:05,171 ProgressMeter -            done   1.7103081E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T17:43Z] INFO  18:43:05,171 ProgressMeter - Total runtime 23.70 secs, 0.40 min, 0.01 hours
[2015-09-30T17:43Z] INFO  18:43:05,174 MicroScheduler - 74966 reads were filtered out during the traversal out of approximately 970223 total reads (7.73%)
[2015-09-30T17:43Z] INFO  18:43:05,175 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:43Z] INFO  18:43:05,175 MicroScheduler -   -> 9799 reads (1.01% of total) failing BadMateFilter
[2015-09-30T17:43Z] INFO  18:43:05,175 MicroScheduler -   -> 48075 reads (4.96% of total) failing DuplicateReadFilter
[2015-09-30T17:43Z] INFO  18:43:05,176 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:43Z] INFO  18:43:05,176 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:43Z] INFO  18:43:05,176 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:43Z] INFO  18:43:05,177 MicroScheduler -   -> 17092 reads (1.76% of total) failing MappingQualityZeroFilter
[2015-09-30T17:43Z] INFO  18:43:05,177 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:43Z] INFO  18:43:05,177 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:43Z] INFO  18:43:05,177 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:43Z] INFO  18:43:06,171 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:43Z] GATK: realign ('21', 31026814, 48129895) : syn3-tumor
[2015-09-30T17:43Z] INFO  18:43:07,884 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:43Z] INFO  18:43:07,887 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:43Z] INFO  18:43:07,887 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:43Z] INFO  18:43:07,887 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:43Z] INFO  18:43:07,890 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep-prealign-realign.intervals -L 21:31026815-48129895 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/tx/tmp79PWcW/2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam
[2015-09-30T17:43Z] INFO  18:43:07,896 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:43Z] INFO  18:43:07,896 HelpFormatter - Date/Time: 2015/09/30 18:43:07
[2015-09-30T17:43Z] INFO  18:43:07,897 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:43Z] INFO  18:43:07,897 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:43Z] INFO  18:43:08,023 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:43Z] INFO  18:43:08,090 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:43Z] INFO  18:43:08,098 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:43Z] INFO  18:43:08,114 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:43Z] INFO  18:43:08,644 IntervalUtils - Processing 17103081 bp from intervals
[2015-09-30T17:43Z] WARN  18:43:08,648 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:43Z] INFO  18:43:08,703 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:43Z] INFO  18:43:08,799 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:43Z] INFO  18:43:08,800 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:43Z] INFO  18:43:08,800 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:43Z] INFO  18:43:08,800 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:43Z] INFO  18:43:08,936 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:43Z] INFO  18:43:09,060 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:43Z] INFO  18:43:09,141 ProgressMeter -     22:24982929    800013.0    90.0 s     112.0 s       80.5%   111.0 s      21.0 s
[2015-09-30T17:43Z] INFO  18:43:24,836 ProgressMeter -     22:42537792    800009.0    90.0 s     112.0 s       56.8%     2.6 m      68.0 s
[2015-09-30T17:43Z] INFO  18:43:38,851 ProgressMeter -     21:44296941    500006.0    30.0 s      60.0 s       77.6%    38.0 s       8.0 s
[2015-09-30T17:43Z] INFO  18:43:39,142 ProgressMeter -     22:30734561   1100016.0   120.0 s     109.0 s       99.1%     2.0 m       1.0 s
[2015-09-30T17:43Z] INFO  18:43:43,539 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:43Z] INFO  18:43:43,733 ProgressMeter -            done   1241524.0     2.1 m     100.0 s      100.0%     2.1 m       0.0 s
[2015-09-30T17:43Z] INFO  18:43:43,734 ProgressMeter - Total runtime 124.60 secs, 2.08 min, 0.03 hours
[2015-09-30T17:43Z] INFO  18:43:43,734 MicroScheduler - 1739 reads were filtered out during the traversal out of approximately 1243263 total reads (0.14%)
[2015-09-30T17:43Z] INFO  18:43:43,734 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:43Z] INFO  18:43:43,734 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:43Z] INFO  18:43:43,735 MicroScheduler -   -> 1739 reads (0.14% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:43Z] INFO  18:43:44,780 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:43Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam
[2015-09-30T17:43Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam 22:1-31019358
[2015-09-30T17:43Z] GATK: RealignerTargetCreator
[2015-09-30T17:43Z] INFO  18:43:51,920 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:43Z] INFO  18:43:51,922 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:43Z] INFO  18:43:51,922 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:43Z] INFO  18:43:51,922 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:43Z] INFO  18:43:51,926 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/tx/tmpSEIBBi/2_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign-realign.intervals -l INFO -L 22:1-31019358 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:43Z] INFO  18:43:51,931 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:43Z] INFO  18:43:51,931 HelpFormatter - Date/Time: 2015/09/30 18:43:51
[2015-09-30T17:43Z] INFO  18:43:51,932 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:43Z] INFO  18:43:51,932 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:43Z] INFO  18:43:51,987 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:43Z] INFO  18:43:52,094 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:43Z] INFO  18:43:52,102 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:43Z] INFO  18:43:52,117 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:43Z] INFO  18:43:52,363 IntervalUtils - Processing 31019358 bp from intervals
[2015-09-30T17:43Z] WARN  18:43:52,367 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:43Z] INFO  18:43:52,420 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:43Z] INFO  18:43:52,588 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:43Z] INFO  18:43:52,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:43Z] INFO  18:43:52,589 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:43Z] INFO  18:43:52,589 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:43Z] INFO  18:43:55,567 ProgressMeter -     22:47071307   1200013.0   120.0 s     100.0 s       79.1%     2.5 m      31.0 s
[2015-09-30T17:43Z] INFO  18:43:56,555 ProgressMeter -            done    964283.0    47.0 s      49.0 s       99.9%    47.0 s       0.0 s
[2015-09-30T17:43Z] INFO  18:43:56,555 ProgressMeter - Total runtime 47.76 secs, 0.80 min, 0.01 hours
[2015-09-30T17:43Z] INFO  18:43:56,559 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 964283 total reads (0.00%)
[2015-09-30T17:43Z] INFO  18:43:56,559 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:43Z] INFO  18:43:56,559 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:43Z] INFO  18:43:56,559 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:43Z] INFO  18:43:57,701 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:43Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam
[2015-09-30T17:44Z] GATK pre-alignment ('X', 0, 31090302) : syn3-tumor
[2015-09-30T17:44Z] INFO  18:44:02,014 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:44Z] INFO  18:44:02,016 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:44Z] INFO  18:44:02,016 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:44Z] INFO  18:44:02,016 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:44Z] INFO  18:44:02,020 HelpFormatter - Program Args: -T PrintReads -L X:1-31090302 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpgaolTI/2_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam
[2015-09-30T17:44Z] INFO  18:44:02,026 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:44Z] INFO  18:44:02,026 HelpFormatter - Date/Time: 2015/09/30 18:44:02
[2015-09-30T17:44Z] INFO  18:44:02,027 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:44Z] INFO  18:44:02,027 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:44Z] INFO  18:44:02,137 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:44Z] INFO  18:44:03,697 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:44Z] INFO  18:44:03,784 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:44Z] INFO  18:44:03,797 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:44Z] INFO  18:44:03,887 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2015-09-30T17:44Z] INFO  18:44:03,947 IntervalUtils - Processing 31090302 bp from intervals
[2015-09-30T17:44Z] INFO  18:44:04,004 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:44Z] INFO  18:44:04,600 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:44Z] INFO  18:44:04,600 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:44Z] INFO  18:44:04,601 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:44Z] INFO  18:44:04,601 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:44Z] INFO  18:44:04,612 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:44Z] INFO  18:44:04,809 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:44Z] INFO  18:44:16,556 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:44Z] INFO  18:44:17,029 ProgressMeter -            done   1454822.0     2.4 m      97.0 s       99.7%     2.4 m       0.0 s
[2015-09-30T17:44Z] INFO  18:44:17,029 ProgressMeter - Total runtime 142.23 secs, 2.37 min, 0.04 hours
[2015-09-30T17:44Z] INFO  18:44:17,029 MicroScheduler - 2125 reads were filtered out during the traversal out of approximately 1456947 total reads (0.15%)
[2015-09-30T17:44Z] INFO  18:44:17,030 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:44Z] INFO  18:44:17,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:44Z] INFO  18:44:17,030 MicroScheduler -   -> 2125 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:44Z] INFO  18:44:18,091 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:44Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam
[2015-09-30T17:44Z] INFO  18:44:22,592 ProgressMeter -     22:30795637   3.0785536E7    30.0 s       0.0 s       99.3%    30.0 s       0.0 s
[2015-09-30T17:44Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam 22:31022171-51304566
[2015-09-30T17:44Z] GATK: RealignerTargetCreator
[2015-09-30T17:44Z] INFO  18:44:23,444 ProgressMeter -            done   3.1019358E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2015-09-30T17:44Z] INFO  18:44:23,444 ProgressMeter - Total runtime 30.86 secs, 0.51 min, 0.01 hours
[2015-09-30T17:44Z] INFO  18:44:23,447 MicroScheduler - 213816 reads were filtered out during the traversal out of approximately 1249337 total reads (17.11%)
[2015-09-30T17:44Z] INFO  18:44:23,448 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:44Z] INFO  18:44:23,448 MicroScheduler -   -> 9313 reads (0.75% of total) failing BadMateFilter
[2015-09-30T17:44Z] INFO  18:44:23,448 MicroScheduler -   -> 58467 reads (4.68% of total) failing DuplicateReadFilter
[2015-09-30T17:44Z] INFO  18:44:23,448 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:44Z] INFO  18:44:23,449 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:44Z] INFO  18:44:23,449 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:44Z] INFO  18:44:23,449 MicroScheduler -   -> 146036 reads (11.69% of total) failing MappingQualityZeroFilter
[2015-09-30T17:44Z] INFO  18:44:23,449 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:44Z] INFO  18:44:23,449 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:44Z] INFO  18:44:23,449 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:44Z] INFO  18:44:24,418 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:44Z] GATK: realign ('22', 0, 31019358) : syn3-tumor
[2015-09-30T17:44Z] INFO  18:44:24,496 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:44Z] INFO  18:44:24,498 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:44Z] INFO  18:44:24,498 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:44Z] INFO  18:44:24,498 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:44Z] INFO  18:44:24,502 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/tx/tmpp4ki_4/2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign-realign.intervals -l INFO -L 22:31022171-51304566 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:44Z] INFO  18:44:24,507 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:44Z] INFO  18:44:24,507 HelpFormatter - Date/Time: 2015/09/30 18:44:24
[2015-09-30T17:44Z] INFO  18:44:24,508 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:44Z] INFO  18:44:24,508 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:44Z] INFO  18:44:24,592 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:44Z] INFO  18:44:24,702 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:44Z] INFO  18:44:24,710 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:44Z] INFO  18:44:24,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:44Z] INFO  18:44:25,583 IntervalUtils - Processing 20282396 bp from intervals
[2015-09-30T17:44Z] WARN  18:44:25,587 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:44Z] INFO  18:44:25,646 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:44Z] INFO  18:44:25,774 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:44Z] INFO  18:44:25,774 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:44Z] INFO  18:44:25,775 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:44Z] INFO  18:44:25,775 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:44Z] INFO  18:44:26,339 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:44Z] INFO  18:44:26,341 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:44Z] INFO  18:44:26,341 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:44Z] INFO  18:44:26,341 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:44Z] INFO  18:44:26,345 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_0_31019358-prep-prealign-realign.intervals -L 22:1-31019358 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/tx/tmpjYpCJV/2_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam
[2015-09-30T17:44Z] INFO  18:44:26,350 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:44Z] INFO  18:44:26,351 HelpFormatter - Date/Time: 2015/09/30 18:44:26
[2015-09-30T17:44Z] INFO  18:44:26,351 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:44Z] INFO  18:44:26,351 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:44Z] INFO  18:44:26,456 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:44Z] INFO  18:44:26,524 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:44Z] INFO  18:44:26,531 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:44Z] INFO  18:44:26,548 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:44Z] INFO  18:44:26,783 IntervalUtils - Processing 31019358 bp from intervals
[2015-09-30T17:44Z] WARN  18:44:26,787 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:44Z] INFO  18:44:26,844 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:44Z] INFO  18:44:27,037 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:44Z] INFO  18:44:27,038 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:44Z] INFO  18:44:27,038 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:44Z] INFO  18:44:27,039 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:44Z] INFO  18:44:27,152 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:44Z] INFO  18:44:27,244 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:44Z] INFO  18:44:34,603 ProgressMeter -      X:13062427    200004.0    30.0 s       2.5 m       42.0%    71.0 s      41.0 s
[2015-09-30T17:44Z] INFO  18:44:55,777 ProgressMeter -     22:50961641   1.993207E7    30.0 s       1.0 s       98.3%    30.0 s       0.0 s
[2015-09-30T17:44Z] INFO  18:44:56,829 ProgressMeter -            done   2.0282396E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T17:44Z] INFO  18:44:56,830 ProgressMeter - Total runtime 31.06 secs, 0.52 min, 0.01 hours
[2015-09-30T17:44Z] INFO  18:44:56,833 MicroScheduler - 123056 reads were filtered out during the traversal out of approximately 1463219 total reads (8.41%)
[2015-09-30T17:44Z] INFO  18:44:56,833 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:44Z] INFO  18:44:56,834 MicroScheduler -   -> 13530 reads (0.92% of total) failing BadMateFilter
[2015-09-30T17:44Z] INFO  18:44:56,834 MicroScheduler -   -> 75964 reads (5.19% of total) failing DuplicateReadFilter
[2015-09-30T17:44Z] INFO  18:44:56,834 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:44Z] INFO  18:44:56,834 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:44Z] INFO  18:44:56,834 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:44Z] INFO  18:44:56,835 MicroScheduler -   -> 33562 reads (2.29% of total) failing MappingQualityZeroFilter
[2015-09-30T17:44Z] INFO  18:44:56,835 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:44Z] INFO  18:44:56,835 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:44Z] INFO  18:44:56,835 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:44Z] INFO  18:44:57,366 ProgressMeter -     22:21676432    500008.0    30.0 s      60.0 s       69.9%    42.0 s      12.0 s
[2015-09-30T17:44Z] INFO  18:44:57,915 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:44Z] GATK: realign ('22', 31022170, 51304566) : syn3-tumor
[2015-09-30T17:45Z] INFO  18:45:00,040 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:00,042 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:45Z] INFO  18:45:00,042 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:45Z] INFO  18:45:00,042 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:45Z] INFO  18:45:00,046 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep-prealign-realign.intervals -L 22:31022171-51304566 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/tx/tmpp1tsIn/2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam
[2015-09-30T17:45Z] INFO  18:45:00,052 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:45Z] INFO  18:45:00,052 HelpFormatter - Date/Time: 2015/09/30 18:45:00
[2015-09-30T17:45Z] INFO  18:45:00,052 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:00,053 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:00,151 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:45Z] INFO  18:45:00,220 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:45Z] INFO  18:45:00,228 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:45Z] INFO  18:45:00,245 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:45Z] INFO  18:45:00,738 IntervalUtils - Processing 20282396 bp from intervals
[2015-09-30T17:45Z] WARN  18:45:00,742 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:45Z] INFO  18:45:00,798 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:45Z] INFO  18:45:00,914 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:45Z] INFO  18:45:00,914 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:45Z] INFO  18:45:00,914 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:45Z] INFO  18:45:00,915 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:45Z] INFO  18:45:01,057 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:45Z] INFO  18:45:01,203 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:45Z] INFO  18:45:04,616 ProgressMeter -      X:24381992    500009.0    60.0 s     120.0 s       78.4%    76.0 s      16.0 s
[2015-09-30T17:45Z] INFO  18:45:10,257 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:45Z] INFO  18:45:10,420 ProgressMeter -            done    614124.0    65.0 s     107.0 s      100.0%    65.0 s       0.0 s
[2015-09-30T17:45Z] INFO  18:45:10,421 ProgressMeter - Total runtime 65.82 secs, 1.10 min, 0.02 hours
[2015-09-30T17:45Z] INFO  18:45:10,421 MicroScheduler - 2072 reads were filtered out during the traversal out of approximately 616196 total reads (0.34%)
[2015-09-30T17:45Z] INFO  18:45:10,421 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:45Z] INFO  18:45:10,421 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:45Z] INFO  18:45:10,422 MicroScheduler -   -> 2072 reads (0.34% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:45Z] INFO  18:45:11,481 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:45Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam
[2015-09-30T17:45Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam X:1-31090302
[2015-09-30T17:45Z] GATK: RealignerTargetCreator
[2015-09-30T17:45Z] INFO  18:45:15,252 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:15,254 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:45Z] INFO  18:45:15,254 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:45Z] INFO  18:45:15,255 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:45Z] INFO  18:45:15,258 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpdpWmJU/2_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign-realign.intervals -l INFO -L X:1-31090302 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:45Z] INFO  18:45:15,264 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:45Z] INFO  18:45:15,264 HelpFormatter - Date/Time: 2015/09/30 18:45:15
[2015-09-30T17:45Z] INFO  18:45:15,265 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:15,265 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:15,325 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:45Z] INFO  18:45:15,435 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:45Z] INFO  18:45:15,443 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:45Z] INFO  18:45:15,459 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:45Z] INFO  18:45:15,708 IntervalUtils - Processing 31090302 bp from intervals
[2015-09-30T17:45Z] WARN  18:45:15,712 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:45Z] INFO  18:45:15,765 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:45Z] INFO  18:45:15,889 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:45Z] INFO  18:45:15,889 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:45Z] INFO  18:45:15,890 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:45Z] INFO  18:45:15,890 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:45Z] INFO  18:45:25,043 ProgressMeter -            done   1241524.0    58.0 s      46.0 s      100.0%    58.0 s       0.0 s
[2015-09-30T17:45Z] INFO  18:45:25,043 ProgressMeter - Total runtime 58.01 secs, 0.97 min, 0.02 hours
[2015-09-30T17:45Z] INFO  18:45:25,046 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1241524 total reads (0.00%)
[2015-09-30T17:45Z] INFO  18:45:25,046 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:45Z] INFO  18:45:25,046 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:45Z] INFO  18:45:25,047 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:45Z] INFO  18:45:26,165 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:45Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam
[2015-09-30T17:45Z] GATK pre-alignment ('X', 31132529, 62519711) : syn3-tumor
[2015-09-30T17:45Z] INFO  18:45:31,091 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:31,093 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:45Z] INFO  18:45:31,093 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:45Z] INFO  18:45:31,093 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:45Z] INFO  18:45:31,096 HelpFormatter - Program Args: -T PrintReads -L X:31132530-62519711 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmptZb4Lx/2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam
[2015-09-30T17:45Z] INFO  18:45:31,102 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:45Z] INFO  18:45:31,102 HelpFormatter - Date/Time: 2015/09/30 18:45:31
[2015-09-30T17:45Z] INFO  18:45:31,102 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:31,102 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:31,383 ProgressMeter -     22:39267418    500006.0    30.0 s      60.0 s       40.7%    73.0 s      43.0 s
[2015-09-30T17:45Z] INFO  18:45:31,405 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:45Z] INFO  18:45:32,054 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:45Z] INFO  18:45:32,100 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:45Z] INFO  18:45:32,107 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:45Z] INFO  18:45:32,121 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:45Z] INFO  18:45:32,133 IntervalUtils - Processing 31387182 bp from intervals
[2015-09-30T17:45Z] INFO  18:45:32,185 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:45Z] INFO  18:45:32,369 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:45Z] INFO  18:45:32,370 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:45Z] INFO  18:45:32,370 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:45Z] INFO  18:45:32,370 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:45Z] INFO  18:45:32,381 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:45Z] INFO  18:45:32,570 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:45Z] INFO  18:45:39,727 ProgressMeter -            done   3.1090302E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T17:45Z] INFO  18:45:39,727 ProgressMeter - Total runtime 23.84 secs, 0.40 min, 0.01 hours
[2015-09-30T17:45Z] INFO  18:45:39,730 MicroScheduler - 52865 reads were filtered out during the traversal out of approximately 618308 total reads (8.55%)
[2015-09-30T17:45Z] INFO  18:45:39,730 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:45Z] INFO  18:45:39,731 MicroScheduler -   -> 9831 reads (1.59% of total) failing BadMateFilter
[2015-09-30T17:45Z] INFO  18:45:39,731 MicroScheduler -   -> 26928 reads (4.36% of total) failing DuplicateReadFilter
[2015-09-30T17:45Z] INFO  18:45:39,731 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:45Z] INFO  18:45:39,731 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:45Z] INFO  18:45:39,731 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:45Z] INFO  18:45:39,732 MicroScheduler -   -> 16106 reads (2.60% of total) failing MappingQualityZeroFilter
[2015-09-30T17:45Z] INFO  18:45:39,732 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:45Z] INFO  18:45:39,732 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:45Z] INFO  18:45:39,732 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:45Z] INFO  18:45:40,743 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:45Z] GATK: realign ('X', 0, 31090302) : syn3-tumor
[2015-09-30T17:45Z] INFO  18:45:42,892 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:42,894 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:45Z] INFO  18:45:42,894 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:45Z] INFO  18:45:42,894 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:45Z] INFO  18:45:42,897 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_0_31090302-prep-prealign-realign.intervals -L X:1-31090302 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpHziyVf/2_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam
[2015-09-30T17:45Z] INFO  18:45:42,903 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:45Z] INFO  18:45:42,903 HelpFormatter - Date/Time: 2015/09/30 18:45:42
[2015-09-30T17:45Z] INFO  18:45:42,903 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:42,904 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:45Z] INFO  18:45:43,032 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:45Z] INFO  18:45:43,102 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:45Z] INFO  18:45:43,110 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:45Z] INFO  18:45:43,127 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:45Z] INFO  18:45:43,864 IntervalUtils - Processing 31090302 bp from intervals
[2015-09-30T17:45Z] WARN  18:45:43,868 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:45Z] INFO  18:45:43,921 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:45Z] INFO  18:45:44,048 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:45Z] INFO  18:45:44,048 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:45Z] INFO  18:45:44,049 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:45Z] INFO  18:45:44,049 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:45Z] INFO  18:45:44,159 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:45Z] INFO  18:45:44,343 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:46Z] INFO  18:46:01,384 ProgressMeter -     22:50355620   1200013.0    60.0 s      50.0 s       95.3%    62.0 s       2.0 s
[2015-09-30T17:46Z] INFO  18:46:02,375 ProgressMeter -      X:46952299    200003.0    30.0 s       2.5 m       50.4%    59.0 s      29.0 s
[2015-09-30T17:46Z] INFO  18:46:08,507 ProgressMeter -            done   1454822.0    67.0 s      46.0 s       99.7%    67.0 s       0.0 s
[2015-09-30T17:46Z] INFO  18:46:08,507 ProgressMeter - Total runtime 67.59 secs, 1.13 min, 0.02 hours
[2015-09-30T17:46Z] INFO  18:46:08,510 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1454822 total reads (0.00%)
[2015-09-30T17:46Z] INFO  18:46:08,511 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:46Z] INFO  18:46:08,511 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:46Z] INFO  18:46:08,511 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:46Z] INFO  18:46:09,656 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:46Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam
[2015-09-30T17:46Z] GATK pre-alignment ('X', 62568928, 94148729) : syn3-tumor
[2015-09-30T17:46Z] INFO  18:46:14,406 ProgressMeter -      X:24753560    500009.0    30.0 s      60.0 s       79.6%    37.0 s       7.0 s
[2015-09-30T17:46Z] INFO  18:46:15,935 ProgressMeter -            done    614124.0    31.0 s      51.0 s      100.0%    31.0 s       0.0 s
[2015-09-30T17:46Z] INFO  18:46:15,936 ProgressMeter - Total runtime 31.89 secs, 0.53 min, 0.01 hours
[2015-09-30T17:46Z] INFO  18:46:15,936 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:46Z] INFO  18:46:15,939 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 614124 total reads (0.00%)
[2015-09-30T17:46Z] INFO  18:46:15,938 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:46Z] INFO  18:46:15,939 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:46Z] INFO  18:46:15,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:46Z] INFO  18:46:15,938 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:46Z] INFO  18:46:15,940 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:46Z] INFO  18:46:15,939 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:46Z] INFO  18:46:15,942 HelpFormatter - Program Args: -T PrintReads -L X:62568929-94148729 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpNkf7mL/2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam
[2015-09-30T17:46Z] INFO  18:46:15,949 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:46Z] INFO  18:46:15,949 HelpFormatter - Date/Time: 2015/09/30 18:46:15
[2015-09-30T17:46Z] INFO  18:46:15,949 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:46Z] INFO  18:46:15,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:46Z] INFO  18:46:16,737 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:46Z] INFO  18:46:16,974 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:46Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam
[2015-09-30T17:46Z] INFO  18:46:17,468 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:46Z] INFO  18:46:17,518 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:46Z] INFO  18:46:17,525 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:46Z] INFO  18:46:17,545 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:46Z] INFO  18:46:17,558 IntervalUtils - Processing 31579801 bp from intervals
[2015-09-30T17:46Z] INFO  18:46:17,616 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:46Z] INFO  18:46:17,841 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:46Z] INFO  18:46:17,842 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:46Z] INFO  18:46:17,842 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:46Z] INFO  18:46:17,842 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:46Z] INFO  18:46:17,853 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:46Z] INFO  18:46:18,053 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:46Z] GATK pre-alignment ('X', 94317773, 125687021) : syn3-tumor
[2015-09-30T17:46Z] INFO  18:46:20,559 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:46Z] INFO  18:46:20,561 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:46Z] INFO  18:46:20,561 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:46Z] INFO  18:46:20,561 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:46Z] INFO  18:46:20,565 HelpFormatter - Program Args: -T PrintReads -L X:94317774-125687021 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmp0MwBG2/2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam
[2015-09-30T17:46Z] INFO  18:46:20,571 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:46Z] INFO  18:46:20,571 HelpFormatter - Date/Time: 2015/09/30 18:46:20
[2015-09-30T17:46Z] INFO  18:46:20,571 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:46Z] INFO  18:46:20,571 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:46Z] INFO  18:46:21,606 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:46Z] INFO  18:46:23,726 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:46Z] INFO  18:46:23,779 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:46Z] INFO  18:46:23,786 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:46Z] INFO  18:46:23,801 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:46Z] INFO  18:46:23,813 IntervalUtils - Processing 31369248 bp from intervals
[2015-09-30T17:46Z] INFO  18:46:23,869 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:46Z] INFO  18:46:24,075 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:46Z] INFO  18:46:24,076 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:46Z] INFO  18:46:24,076 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:46Z] INFO  18:46:24,076 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:46Z] INFO  18:46:24,088 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:46Z] INFO  18:46:24,293 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:46Z] INFO  18:46:32,602 ProgressMeter -      X:49857902    500008.0    60.0 s     120.0 s       59.7%   100.0 s      40.0 s
[2015-09-30T17:46Z] INFO  18:46:47,844 ProgressMeter -      X:70824820    200002.0    30.0 s       2.5 m       26.1%   114.0 s      84.0 s
[2015-09-30T17:46Z] INFO  18:46:54,094 ProgressMeter -     X:107261444    200002.0    30.0 s       2.5 m       41.3%    72.0 s      42.0 s
[2015-09-30T17:46Z] INFO  18:46:59,179 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:46Z] INFO  18:46:59,348 ProgressMeter -            done    810577.0    86.0 s     107.0 s      100.0%    86.0 s       0.0 s
[2015-09-30T17:46Z] INFO  18:46:59,348 ProgressMeter - Total runtime 86.98 secs, 1.45 min, 0.02 hours
[2015-09-30T17:46Z] INFO  18:46:59,349 MicroScheduler - 1807 reads were filtered out during the traversal out of approximately 812384 total reads (0.22%)
[2015-09-30T17:46Z] INFO  18:46:59,349 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:46Z] INFO  18:46:59,349 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:46Z] INFO  18:46:59,349 MicroScheduler -   -> 1807 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:47Z] INFO  18:47:00,390 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:47Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam
[2015-09-30T17:47Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam X:31132530-62519711
[2015-09-30T17:47Z] GATK: RealignerTargetCreator
[2015-09-30T17:47Z] INFO  18:47:04,731 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:04,733 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:47Z] INFO  18:47:04,733 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:47Z] INFO  18:47:04,733 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:47Z] INFO  18:47:04,737 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpysmJxl/2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign-realign.intervals -l INFO -L X:31132530-62519711 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:47Z] INFO  18:47:04,742 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:47Z] INFO  18:47:04,743 HelpFormatter - Date/Time: 2015/09/30 18:47:04
[2015-09-30T17:47Z] INFO  18:47:04,743 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:04,743 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:04,800 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:47Z] INFO  18:47:04,909 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:47Z] INFO  18:47:04,916 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:47Z] INFO  18:47:04,932 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:47Z] INFO  18:47:05,183 IntervalUtils - Processing 31387182 bp from intervals
[2015-09-30T17:47Z] WARN  18:47:05,187 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:47Z] INFO  18:47:05,244 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:47Z] INFO  18:47:05,373 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:47Z] INFO  18:47:05,373 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:47Z] INFO  18:47:05,374 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:47Z] INFO  18:47:05,374 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:47Z] INFO  18:47:08,449 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:47Z] INFO  18:47:08,551 ProgressMeter -            done    467967.0    50.0 s     108.0 s      100.0%    50.0 s       0.0 s
[2015-09-30T17:47Z] INFO  18:47:08,551 ProgressMeter - Total runtime 50.71 secs, 0.85 min, 0.01 hours
[2015-09-30T17:47Z] INFO  18:47:08,551 MicroScheduler - 1297 reads were filtered out during the traversal out of approximately 469264 total reads (0.28%)
[2015-09-30T17:47Z] INFO  18:47:08,551 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:47Z] INFO  18:47:08,552 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:47Z] INFO  18:47:08,552 MicroScheduler -   -> 1297 reads (0.28% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:47Z] INFO  18:47:09,724 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:47Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam
[2015-09-30T17:47Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam X:62568929-94148729
[2015-09-30T17:47Z] GATK: RealignerTargetCreator
[2015-09-30T17:47Z] INFO  18:47:13,979 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:13,981 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:47Z] INFO  18:47:13,981 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:47Z] INFO  18:47:13,982 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:47Z] INFO  18:47:13,985 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpZCF1OY/2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign-realign.intervals -l INFO -L X:62568929-94148729 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:47Z] INFO  18:47:13,992 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:47Z] INFO  18:47:13,992 HelpFormatter - Date/Time: 2015/09/30 18:47:13
[2015-09-30T17:47Z] INFO  18:47:13,992 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:13,992 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:14,061 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:47Z] INFO  18:47:14,178 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:47Z] INFO  18:47:14,186 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:47Z] INFO  18:47:14,201 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:47Z] INFO  18:47:14,437 IntervalUtils - Processing 31579801 bp from intervals
[2015-09-30T17:47Z] WARN  18:47:14,441 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:47Z] INFO  18:47:14,496 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:47Z] INFO  18:47:14,627 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:47Z] INFO  18:47:14,627 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:47Z] INFO  18:47:14,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:47Z] INFO  18:47:14,628 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:47Z] INFO  18:47:23,583 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5025536c
[2015-09-30T17:47Z] INFO  18:47:23,785 ProgressMeter -            done    639083.0    59.0 s      93.0 s      100.0%    59.0 s       0.0 s
[2015-09-30T17:47Z] INFO  18:47:23,785 ProgressMeter - Total runtime 59.71 secs, 1.00 min, 0.02 hours
[2015-09-30T17:47Z] INFO  18:47:23,786 MicroScheduler - 1722 reads were filtered out during the traversal out of approximately 640805 total reads (0.27%)
[2015-09-30T17:47Z] INFO  18:47:23,786 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:47Z] INFO  18:47:23,786 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:47Z] INFO  18:47:23,786 MicroScheduler -   -> 1722 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:47Z] INFO  18:47:24,851 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:47Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam
[2015-09-30T17:47Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam X:94317774-125687021
[2015-09-30T17:47Z] GATK: RealignerTargetCreator
[2015-09-30T17:47Z] INFO  18:47:30,133 ProgressMeter -            done   3.1387182E7    24.0 s       0.0 s      100.0%    24.0 s       0.0 s
[2015-09-30T17:47Z] INFO  18:47:30,133 ProgressMeter - Total runtime 24.76 secs, 0.41 min, 0.01 hours
[2015-09-30T17:47Z] INFO  18:47:30,136 MicroScheduler - 138575 reads were filtered out during the traversal out of approximately 815450 total reads (16.99%)
[2015-09-30T17:47Z] INFO  18:47:30,136 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:47Z] INFO  18:47:30,136 MicroScheduler -   -> 9577 reads (1.17% of total) failing BadMateFilter
[2015-09-30T17:47Z] INFO  18:47:30,137 MicroScheduler -   -> 33230 reads (4.08% of total) failing DuplicateReadFilter
[2015-09-30T17:47Z] INFO  18:47:30,137 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:47Z] INFO  18:47:30,137 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:47Z] INFO  18:47:30,137 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:47Z] INFO  18:47:30,137 MicroScheduler -   -> 95768 reads (11.74% of total) failing MappingQualityZeroFilter
[2015-09-30T17:47Z] INFO  18:47:30,138 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:47Z] INFO  18:47:30,138 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:47Z] INFO  18:47:30,138 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:47Z] INFO  18:47:30,951 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:30,953 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:47Z] INFO  18:47:30,953 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:47Z] INFO  18:47:30,954 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:47Z] INFO  18:47:30,957 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpOorEzP/2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign-realign.intervals -l INFO -L X:94317774-125687021 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:47Z] INFO  18:47:30,962 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:47Z] INFO  18:47:30,963 HelpFormatter - Date/Time: 2015/09/30 18:47:30
[2015-09-30T17:47Z] INFO  18:47:30,963 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:30,963 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:31,017 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:47Z] INFO  18:47:31,117 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:47Z] INFO  18:47:31,123 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:47Z] INFO  18:47:31,131 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:47Z] INFO  18:47:31,147 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:47Z] GATK: realign ('X', 31132529, 62519711) : syn3-tumor
[2015-09-30T17:47Z] INFO  18:47:32,153 IntervalUtils - Processing 31369248 bp from intervals
[2015-09-30T17:47Z] WARN  18:47:32,157 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:47Z] INFO  18:47:32,212 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:47Z] INFO  18:47:32,351 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:47Z] INFO  18:47:32,351 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:47Z] INFO  18:47:32,352 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:47Z] INFO  18:47:32,352 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:47Z] INFO  18:47:33,058 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:33,060 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:47Z] INFO  18:47:33,060 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:47Z] INFO  18:47:33,061 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:47Z] INFO  18:47:33,064 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep-prealign-realign.intervals -L X:31132530-62519711 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpAnWcso/2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam
[2015-09-30T17:47Z] INFO  18:47:33,069 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:47Z] INFO  18:47:33,070 HelpFormatter - Date/Time: 2015/09/30 18:47:33
[2015-09-30T17:47Z] INFO  18:47:33,070 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:33,070 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:33,201 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:47Z] INFO  18:47:33,266 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:47Z] INFO  18:47:33,274 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:47Z] INFO  18:47:33,290 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:47Z] INFO  18:47:33,523 IntervalUtils - Processing 31387182 bp from intervals
[2015-09-30T17:47Z] WARN  18:47:33,528 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:47Z] INFO  18:47:33,586 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:47Z] INFO  18:47:33,716 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:47Z] INFO  18:47:33,716 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:47Z] INFO  18:47:33,717 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:47Z] INFO  18:47:33,717 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:47Z] INFO  18:47:33,806 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:47Z] INFO  18:47:33,992 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:47Z] INFO  18:47:35,165 ProgressMeter -            done   3.1579801E7    20.0 s       0.0 s      100.0%    20.0 s       0.0 s
[2015-09-30T17:47Z] INFO  18:47:35,166 ProgressMeter - Total runtime 20.54 secs, 0.34 min, 0.01 hours
[2015-09-30T17:47Z] INFO  18:47:35,169 MicroScheduler - 51418 reads were filtered out during the traversal out of approximately 470525 total reads (10.93%)
[2015-09-30T17:47Z] INFO  18:47:35,169 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:47Z] INFO  18:47:35,169 MicroScheduler -   -> 7669 reads (1.63% of total) failing BadMateFilter
[2015-09-30T17:47Z] INFO  18:47:35,170 MicroScheduler -   -> 19175 reads (4.08% of total) failing DuplicateReadFilter
[2015-09-30T17:47Z] INFO  18:47:35,170 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:47Z] INFO  18:47:35,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:47Z] INFO  18:47:35,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:47Z] INFO  18:47:35,170 MicroScheduler -   -> 24574 reads (5.22% of total) failing MappingQualityZeroFilter
[2015-09-30T17:47Z] INFO  18:47:35,171 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:47Z] INFO  18:47:35,171 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:47Z] INFO  18:47:35,171 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:47Z] INFO  18:47:36,149 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:47Z] GATK: realign ('X', 62568928, 94148729) : syn3-tumor
[2015-09-30T17:47Z] INFO  18:47:39,119 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:39,121 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:47Z] INFO  18:47:39,121 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:47Z] INFO  18:47:39,121 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:47Z] INFO  18:47:39,125 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep-prealign-realign.intervals -L X:62568929-94148729 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpHYXW6i/2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam
[2015-09-30T17:47Z] INFO  18:47:39,130 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:47Z] INFO  18:47:39,131 HelpFormatter - Date/Time: 2015/09/30 18:47:39
[2015-09-30T17:47Z] INFO  18:47:39,131 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:39,131 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:39,693 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:47Z] INFO  18:47:39,817 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:47Z] INFO  18:47:39,824 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:47Z] INFO  18:47:39,840 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:47Z] INFO  18:47:40,449 IntervalUtils - Processing 31579801 bp from intervals
[2015-09-30T17:47Z] WARN  18:47:40,453 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:47Z] INFO  18:47:40,510 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:47Z] INFO  18:47:40,646 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:47Z] INFO  18:47:40,646 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:47Z] INFO  18:47:40,646 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:47Z] INFO  18:47:40,647 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:47Z] INFO  18:47:40,742 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:47Z] INFO  18:47:40,935 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:47Z] INFO  18:47:56,053 ProgressMeter -            done   3.1369248E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T17:47Z] INFO  18:47:56,053 ProgressMeter - Total runtime 23.70 secs, 0.40 min, 0.01 hours
[2015-09-30T17:47Z] INFO  18:47:56,056 MicroScheduler - 76593 reads were filtered out during the traversal out of approximately 643361 total reads (11.91%)
[2015-09-30T17:47Z] INFO  18:47:56,057 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:47Z] INFO  18:47:56,057 MicroScheduler -   -> 9032 reads (1.40% of total) failing BadMateFilter
[2015-09-30T17:47Z] INFO  18:47:56,057 MicroScheduler -   -> 25818 reads (4.01% of total) failing DuplicateReadFilter
[2015-09-30T17:47Z] INFO  18:47:56,057 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:47Z] INFO  18:47:56,058 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:47Z] INFO  18:47:56,058 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:47Z] INFO  18:47:56,058 MicroScheduler -   -> 41743 reads (6.49% of total) failing MappingQualityZeroFilter
[2015-09-30T17:47Z] INFO  18:47:56,058 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:47Z] INFO  18:47:56,058 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:47Z] INFO  18:47:56,059 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:47Z] INFO  18:47:57,051 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:47Z] GATK: realign ('X', 94317773, 125687021) : syn3-tumor
[2015-09-30T17:47Z] INFO  18:47:59,094 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:59,096 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:47Z] INFO  18:47:59,096 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:47Z] INFO  18:47:59,096 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:47Z] INFO  18:47:59,100 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep-prealign-realign.intervals -L X:94317774-125687021 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmptLoYju/2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam
[2015-09-30T17:47Z] INFO  18:47:59,105 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:47Z] INFO  18:47:59,106 HelpFormatter - Date/Time: 2015/09/30 18:47:59
[2015-09-30T17:47Z] INFO  18:47:59,106 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:59,106 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:47Z] INFO  18:47:59,231 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:47Z] INFO  18:47:59,293 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:47Z] INFO  18:47:59,300 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:47Z] INFO  18:47:59,316 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:47Z] INFO  18:47:59,842 IntervalUtils - Processing 31369248 bp from intervals
[2015-09-30T17:47Z] WARN  18:47:59,846 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:48Z] INFO  18:48:00,007 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:48Z] INFO  18:48:01,333 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:48Z] INFO  18:48:01,334 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:48Z] INFO  18:48:01,334 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:48Z] INFO  18:48:01,334 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:48Z] INFO  18:48:01,426 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:48Z] INFO  18:48:01,613 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:48Z] INFO  18:48:04,382 ProgressMeter -            done    467967.0    23.0 s      50.0 s      100.0%    23.0 s       0.0 s
[2015-09-30T17:48Z] INFO  18:48:04,382 ProgressMeter - Total runtime 23.74 secs, 0.40 min, 0.01 hours
[2015-09-30T17:48Z] INFO  18:48:04,385 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 467967 total reads (0.00%)
[2015-09-30T17:48Z] INFO  18:48:04,386 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:48Z] INFO  18:48:04,386 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:48Z] INFO  18:48:04,386 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:48Z] INFO  18:48:04,789 ProgressMeter -      X:49302251    400005.0    31.0 s      77.0 s       57.9%    53.0 s      22.0 s
[2015-09-30T17:48Z] INFO  18:48:05,428 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:48Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam
[2015-09-30T17:48Z] GATK pre-alignment ('X', 125953527, 155270560) : syn3-tumor
[2015-09-30T17:48Z] INFO  18:48:10,748 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:10,750 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:48Z] INFO  18:48:10,750 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:48Z] INFO  18:48:10,750 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:48Z] INFO  18:48:10,754 HelpFormatter - Program Args: -T PrintReads -L X:125953528-155270560 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpKbhqUO/2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam
[2015-09-30T17:48Z] INFO  18:48:10,760 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:48Z] INFO  18:48:10,760 HelpFormatter - Date/Time: 2015/09/30 18:48:10
[2015-09-30T17:48Z] INFO  18:48:10,760 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:10,760 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:10,865 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:48Z] INFO  18:48:11,556 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:48Z] INFO  18:48:11,606 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:48Z] INFO  18:48:11,614 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:48Z] INFO  18:48:11,629 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:48Z] INFO  18:48:11,642 IntervalUtils - Processing 29317033 bp from intervals
[2015-09-30T17:48Z] INFO  18:48:11,699 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:48Z] INFO  18:48:11,897 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:48Z] INFO  18:48:11,898 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:48Z] INFO  18:48:11,898 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:48Z] INFO  18:48:11,898 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:48Z] INFO  18:48:11,909 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:48Z] INFO  18:48:12,098 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:48Z] INFO  18:48:14,736 ProgressMeter -            done    810577.0    41.0 s      50.0 s      100.0%    41.0 s       0.0 s
[2015-09-30T17:48Z] INFO  18:48:14,737 ProgressMeter - Total runtime 41.02 secs, 0.68 min, 0.01 hours
[2015-09-30T17:48Z] INFO  18:48:14,740 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 810577 total reads (0.00%)
[2015-09-30T17:48Z] INFO  18:48:14,740 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:48Z] INFO  18:48:14,741 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:48Z] INFO  18:48:14,741 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:48Z] INFO  18:48:15,850 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:48Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam
[2015-09-30T17:48Z] GATK pre-alignment ('Y', 0, 28716339) : syn3-tumor
[2015-09-30T17:48Z] INFO  18:48:21,626 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:21,629 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:48Z] INFO  18:48:21,629 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:48Z] INFO  18:48:21,629 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:48Z] INFO  18:48:21,632 HelpFormatter - Program Args: -T PrintReads -L Y:1-28716339 -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.bam --downsample_to_coverage 10000 -BQSR /home/cancer-dream-syn3/work/align/syn3-tumor/2_2014-08-13_dream-syn3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/Y/tx/tmpYToDJw/2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam
[2015-09-30T17:48Z] INFO  18:48:21,638 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:48Z] INFO  18:48:21,638 HelpFormatter - Date/Time: 2015/09/30 18:48:21
[2015-09-30T17:48Z] INFO  18:48:21,638 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:21,638 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:22,382 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:48Z] INFO  18:48:23,820 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2015-09-30T17:48Z] INFO  18:48:23,872 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T17:48Z] INFO  18:48:23,879 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:48Z] INFO  18:48:23,895 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:48Z] INFO  18:48:23,909 IntervalUtils - Processing 28716339 bp from intervals
[2015-09-30T17:48Z] INFO  18:48:23,967 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:48Z] INFO  18:48:24,110 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:48Z] INFO  18:48:24,110 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:48Z] INFO  18:48:24,111 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:48Z] INFO  18:48:24,111 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:48Z] INFO  18:48:24,122 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:48Z] INFO  18:48:24,264 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:48Z] INFO  18:48:27,081 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:48Z] INFO  18:48:27,126 ProgressMeter -            done     16924.0     3.0 s       3.0 m       99.9%     3.0 s       0.0 s
[2015-09-30T17:48Z] INFO  18:48:27,127 ProgressMeter - Total runtime 3.02 secs, 0.05 min, 0.00 hours
[2015-09-30T17:48Z] INFO  18:48:27,127 MicroScheduler - 763 reads were filtered out during the traversal out of approximately 17687 total reads (4.31%)
[2015-09-30T17:48Z] INFO  18:48:27,128 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:48Z] INFO  18:48:27,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:48Z] INFO  18:48:27,128 MicroScheduler -   -> 763 reads (4.31% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:48Z] INFO  18:48:28,074 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:48Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam
[2015-09-30T17:48Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam Y:1-28716339
[2015-09-30T17:48Z] GATK: RealignerTargetCreator
[2015-09-30T17:48Z] INFO  18:48:30,227 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:30,229 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:48Z] INFO  18:48:30,229 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:48Z] INFO  18:48:30,230 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:48Z] INFO  18:48:30,233 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/Y/2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/Y/tx/tmp62YvSf/2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign-realign.intervals -l INFO -L Y:1-28716339 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:48Z] INFO  18:48:30,239 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:48Z] INFO  18:48:30,239 HelpFormatter - Date/Time: 2015/09/30 18:48:30
[2015-09-30T17:48Z] INFO  18:48:30,239 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:30,240 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:30,301 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:48Z] INFO  18:48:30,413 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:48Z] INFO  18:48:30,421 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:48Z] INFO  18:48:30,438 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:48Z] INFO  18:48:31,027 IntervalUtils - Processing 28716339 bp from intervals
[2015-09-30T17:48Z] WARN  18:48:31,031 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:48Z] INFO  18:48:31,091 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:48Z] INFO  18:48:31,194 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:48Z] INFO  18:48:31,194 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:48Z] INFO  18:48:31,195 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:48Z] INFO  18:48:31,195 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:48Z] INFO  18:48:31,661 ProgressMeter -     X:114869088    400004.0    30.0 s      75.0 s       65.5%    45.0 s      15.0 s
[2015-09-30T17:48Z] INFO  18:48:39,298 ProgressMeter -            done    639083.0    37.0 s      59.0 s      100.0%    37.0 s       0.0 s
[2015-09-30T17:48Z] INFO  18:48:39,299 ProgressMeter - Total runtime 37.97 secs, 0.63 min, 0.01 hours
[2015-09-30T17:48Z] INFO  18:48:39,302 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 639083 total reads (0.00%)
[2015-09-30T17:48Z] INFO  18:48:39,303 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:48Z] INFO  18:48:39,303 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:48Z] INFO  18:48:39,303 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:48Z] INFO  18:48:40,359 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:48Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam
[2015-09-30T17:48Z] INFO  18:48:41,900 ProgressMeter -     X:135570274    200003.0    30.0 s       2.5 m       32.8%    91.0 s      61.0 s
[2015-09-30T17:48Z] Select unmapped reads
[2015-09-30T17:48Z] INFO  18:48:42,207 ProgressMeter -            done   2.8716339E7    11.0 s       0.0 s      100.0%    11.0 s       0.0 s
[2015-09-30T17:48Z] INFO  18:48:42,207 ProgressMeter - Total runtime 11.01 secs, 0.18 min, 0.00 hours
[2015-09-30T17:48Z] INFO  18:48:42,210 MicroScheduler - 8499 reads were filtered out during the traversal out of approximately 16949 total reads (50.14%)
[2015-09-30T17:48Z] INFO  18:48:42,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:48Z] INFO  18:48:42,211 MicroScheduler -   -> 1943 reads (11.46% of total) failing BadMateFilter
[2015-09-30T17:48Z] INFO  18:48:42,211 MicroScheduler -   -> 659 reads (3.89% of total) failing DuplicateReadFilter
[2015-09-30T17:48Z] INFO  18:48:42,212 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:48Z] INFO  18:48:42,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:48Z] INFO  18:48:42,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:48Z] INFO  18:48:42,212 MicroScheduler -   -> 5897 reads (34.79% of total) failing MappingQualityZeroFilter
[2015-09-30T17:48Z] INFO  18:48:42,213 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:48Z] INFO  18:48:42,213 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:48Z] INFO  18:48:42,213 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:48Z] INFO  18:48:43,270 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:48Z] GATK: realign ('Y', 0, 28716339) : syn3-tumor
[2015-09-30T17:48Z] INFO  18:48:45,273 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:45,275 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:48Z] INFO  18:48:45,275 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:48Z] INFO  18:48:45,275 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:48Z] INFO  18:48:45,279 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/Y/2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/Y/2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep-prealign-realign.intervals -L Y:1-28716339 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/Y/tx/tmpD8mwFW/2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam
[2015-09-30T17:48Z] INFO  18:48:45,285 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:48Z] INFO  18:48:45,285 HelpFormatter - Date/Time: 2015/09/30 18:48:45
[2015-09-30T17:48Z] INFO  18:48:45,285 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:45,285 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:48Z] INFO  18:48:45,437 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:48Z] INFO  18:48:45,504 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:48Z] INFO  18:48:45,512 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:48Z] INFO  18:48:45,527 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:48Z] INFO  18:48:46,407 IntervalUtils - Processing 28716339 bp from intervals
[2015-09-30T17:48Z] WARN  18:48:46,412 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:48Z] INFO  18:48:46,466 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:48Z] INFO  18:48:47,139 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:48Z] INFO  18:48:47,140 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:48Z] INFO  18:48:47,140 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:48Z] INFO  18:48:47,140 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:48Z] INFO  18:48:47,172 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:48Z] INFO  18:48:47,343 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:48Z] INFO  18:48:49,593 ProgressMeter -            done     16924.0     2.0 s       2.4 m       99.9%     2.0 s       0.0 s
[2015-09-30T17:48Z] INFO  18:48:49,594 ProgressMeter - Total runtime 2.45 secs, 0.04 min, 0.00 hours
[2015-09-30T17:48Z] INFO  18:48:49,597 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 16924 total reads (0.00%)
[2015-09-30T17:48Z] INFO  18:48:49,597 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:48Z] INFO  18:48:49,597 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:48Z] INFO  18:48:49,598 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:48Z] INFO  18:48:50,533 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:48Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam
[2015-09-30T17:48Z] Select unanalyzed reads
[2015-09-30T17:48Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-noanalysis-prep.bam
[2015-09-30T17:49Z] INFO  18:49:12,623 ProgressMeter -     X:152968395    500008.0    60.0 s       2.0 m       92.1%    65.0 s       5.0 s
[2015-09-30T17:49Z] INFO  18:49:36,268 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@4288008f
[2015-09-30T17:49Z] INFO  18:49:36,426 ProgressMeter -            done    809710.0    84.0 s     104.0 s       99.9%    84.0 s       0.0 s
[2015-09-30T17:49Z] INFO  18:49:36,427 ProgressMeter - Total runtime 84.53 secs, 1.41 min, 0.02 hours
[2015-09-30T17:49Z] INFO  18:49:36,427 MicroScheduler - 1683 reads were filtered out during the traversal out of approximately 811393 total reads (0.21%)
[2015-09-30T17:49Z] INFO  18:49:36,427 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:49Z] INFO  18:49:36,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:49Z] INFO  18:49:36,428 MicroScheduler -   -> 1683 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:49Z] INFO  18:49:37,758 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:49Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam
[2015-09-30T17:49Z] GATK RealignerTargetCreator: 2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam X:125953528-155270560
[2015-09-30T17:49Z] GATK: RealignerTargetCreator
[2015-09-30T17:49Z] INFO  18:49:42,441 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:49Z] INFO  18:49:42,442 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:49Z] INFO  18:49:42,443 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:49Z] INFO  18:49:42,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:49Z] INFO  18:49:42,446 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmp2RNOZg/2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign-realign.intervals -l INFO -L X:125953528-155270560 --interval_set_rule INTERSECTION --known /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T17:49Z] INFO  18:49:42,451 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:49Z] INFO  18:49:42,452 HelpFormatter - Date/Time: 2015/09/30 18:49:42
[2015-09-30T17:49Z] INFO  18:49:42,452 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:49Z] INFO  18:49:42,452 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:49Z] INFO  18:49:42,505 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:49Z] INFO  18:49:43,045 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T17:49Z] INFO  18:49:43,052 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:49Z] INFO  18:49:43,067 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2015-09-30T17:49Z] INFO  18:49:43,294 IntervalUtils - Processing 29317033 bp from intervals
[2015-09-30T17:49Z] WARN  18:49:43,298 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:49Z] INFO  18:49:43,352 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:49Z] INFO  18:49:43,484 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:49Z] INFO  18:49:43,485 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:49Z] INFO  18:49:43,485 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:49Z] INFO  18:49:43,486 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T17:50Z] INFO  18:50:06,031 ProgressMeter -            done   2.9317033E7    22.0 s       0.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T17:50Z] INFO  18:50:06,031 ProgressMeter - Total runtime 22.55 secs, 0.38 min, 0.01 hours
[2015-09-30T17:50Z] INFO  18:50:06,034 MicroScheduler - 138254 reads were filtered out during the traversal out of approximately 814673 total reads (16.97%)
[2015-09-30T17:50Z] INFO  18:50:06,034 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:50Z] INFO  18:50:06,035 MicroScheduler -   -> 8727 reads (1.07% of total) failing BadMateFilter
[2015-09-30T17:50Z] INFO  18:50:06,035 MicroScheduler -   -> 35355 reads (4.34% of total) failing DuplicateReadFilter
[2015-09-30T17:50Z] INFO  18:50:06,035 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T17:50Z] INFO  18:50:06,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:50Z] INFO  18:50:06,036 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2015-09-30T17:50Z] INFO  18:50:06,036 MicroScheduler -   -> 94172 reads (11.56% of total) failing MappingQualityZeroFilter
[2015-09-30T17:50Z] INFO  18:50:06,036 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:50Z] INFO  18:50:06,036 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2015-09-30T17:50Z] INFO  18:50:06,036 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2015-09-30T17:50Z] INFO  18:50:06,986 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:50Z] GATK: realign ('X', 125953527, 155270560) : syn3-tumor
[2015-09-30T17:50Z] INFO  18:50:10,011 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:50Z] INFO  18:50:10,013 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T17:50Z] INFO  18:50:10,014 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T17:50Z] INFO  18:50:10,014 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T17:50Z] INFO  18:50:10,017 HelpFormatter - Program Args: -T IndelRealigner -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign.bam -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep-prealign-realign.intervals -L X:125953528-155270560 --knownAlleles /data/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/tx/tmpeaKqKp/2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam
[2015-09-30T17:50Z] INFO  18:50:10,023 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T17:50Z] INFO  18:50:10,023 HelpFormatter - Date/Time: 2015/09/30 18:50:10
[2015-09-30T17:50Z] INFO  18:50:10,023 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:50Z] INFO  18:50:10,024 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T17:50Z] INFO  18:50:10,384 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T17:50Z] INFO  18:50:10,447 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2015-09-30T17:50Z] INFO  18:50:10,454 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T17:50Z] INFO  18:50:10,469 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T17:50Z] INFO  18:50:11,066 IntervalUtils - Processing 29317033 bp from intervals
[2015-09-30T17:50Z] WARN  18:50:11,070 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T17:50Z] INFO  18:50:11,126 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2015-09-30T17:50Z] INFO  18:50:11,260 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T17:50Z] INFO  18:50:11,261 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T17:50Z] INFO  18:50:11,261 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T17:50Z] INFO  18:50:11,262 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2015-09-30T17:50Z] INFO  18:50:11,356 ReadShardBalancer$1 - Loading BAM index data
[2015-09-30T17:50Z] INFO  18:50:11,538 ReadShardBalancer$1 - Done loading BAM index data
[2015-09-30T17:50Z] INFO  18:50:42,216 ProgressMeter -     X:153171051    500008.0    30.0 s      61.0 s       92.8%    32.0 s       2.0 s
[2015-09-30T17:50Z] INFO  18:50:48,534 ProgressMeter -            done    809710.0    37.0 s      46.0 s       99.9%    37.0 s       0.0 s
[2015-09-30T17:50Z] INFO  18:50:48,535 ProgressMeter - Total runtime 37.27 secs, 0.62 min, 0.01 hours
[2015-09-30T17:50Z] INFO  18:50:48,537 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 809710 total reads (0.00%)
[2015-09-30T17:50Z] INFO  18:50:48,538 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T17:50Z] INFO  18:50:48,538 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T17:50Z] INFO  18:50:48,538 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T17:50Z] INFO  18:50:49,632 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T17:50Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam
[2015-09-30T17:51Z] Index BAM file: 2_2014-08-13_dream-syn3-sort-nochrom-prep.bam
[2015-09-30T17:51Z] Timing: variant calling
[2015-09-30T17:51Z] multiprocessing: variantcall_sample
[2015-09-30T17:51Z] Genotyping with VarDict: Inference
[2015-09-30T17:51Z] Genotyping with VarDict: Inference
[2015-09-30T17:51Z] Genotyping with VarDict: Inference
[2015-09-30T17:52Z] tabix index syn3-1_62231753_93258244-raw.vcf.gz
[2015-09-30T17:52Z] Annotate with dbSNP
[2015-09-30T17:53Z] tabix index syn3-1_31187762_62229084-raw.vcf.gz
[2015-09-30T17:53Z] Annotate with dbSNP
[2015-09-30T17:54Z] Genotyping with VarDict: Inference
[2015-09-30T17:55Z] tabix index syn3-1_0_31187470-raw.vcf.gz
[2015-09-30T17:55Z] Annotate with dbSNP
[2015-09-30T17:56Z] Genotyping with VarDict: Inference
[2015-09-30T17:56Z] tabix index syn3-1_93297335_142653959-raw.vcf.gz
[2015-09-30T17:56Z] Annotate with dbSNP
[2015-09-30T17:57Z] Genotyping with VarDict: Inference
[2015-09-30T17:58Z] Genotyping with VarDict: Inference
[2015-09-30T17:59Z] tabix index syn3-1_142666976_173685474-raw.vcf.gz
[2015-09-30T17:59Z] Annotate with dbSNP
[2015-09-30T17:59Z] tabix index syn3-1_173702591_204798081-raw.vcf.gz
[2015-09-30T17:59Z] Annotate with dbSNP
[2015-09-30T18:00Z] tabix index syn3-1_204839842_235860787-raw.vcf.gz
[2015-09-30T18:00Z] Annotate with dbSNP
[2015-09-30T18:01Z] Genotyping with VarDict: Inference
[2015-09-30T18:01Z] Genotyping with VarDict: Inference
[2015-09-30T18:02Z] tabix index syn3-1_235865791_249250621-raw.vcf.gz
[2015-09-30T18:02Z] Annotate with dbSNP
[2015-09-30T18:02Z] Genotyping with VarDict: Inference
[2015-09-30T18:03Z] tabix index syn3-2_0_31134137-raw.vcf.gz
[2015-09-30T18:03Z] Annotate with dbSNP
[2015-09-30T18:03Z] tabix index syn3-2_31134801_62196287-raw.vcf.gz
[2015-09-30T18:03Z] Annotate with dbSNP
[2015-09-30T18:04Z] Genotyping with VarDict: Inference
[2015-09-30T18:05Z] Genotyping with VarDict: Inference
[2015-09-30T18:06Z] Genotyping with VarDict: Inference
[2015-09-30T18:06Z] tabix index syn3-2_62227535_95457199-raw.vcf.gz
[2015-09-30T18:06Z] Annotate with dbSNP
[2015-09-30T18:07Z] tabix index syn3-2_127413596_158444156-raw.vcf.gz
[2015-09-30T18:07Z] Annotate with dbSNP
[2015-09-30T18:07Z] tabix index syn3-2_95457728_127315933-raw.vcf.gz
[2015-09-30T18:07Z] Annotate with dbSNP
[2015-09-30T18:08Z] Genotyping with VarDict: Inference
[2015-09-30T18:09Z] Genotyping with VarDict: Inference
[2015-09-30T18:09Z] Genotyping with VarDict: Inference
[2015-09-30T18:10Z] tabix index syn3-2_158484801_189599894-raw.vcf.gz
[2015-09-30T18:10Z] Annotate with dbSNP
[2015-09-30T18:11Z] tabix index syn3-2_189838937_221056966-raw.vcf.gz
[2015-09-30T18:11Z] Annotate with dbSNP
[2015-09-30T18:11Z] tabix index syn3-2_221341378_243199373-raw.vcf.gz
[2015-09-30T18:11Z] Annotate with dbSNP
[2015-09-30T18:12Z] Genotyping with VarDict: Inference
[2015-09-30T18:13Z] tabix index syn3-3_0_31203562-raw.vcf.gz
[2015-09-30T18:13Z] Annotate with dbSNP
[2015-09-30T18:13Z] Genotyping with VarDict: Inference
[2015-09-30T18:13Z] Genotyping with VarDict: Inference
[2015-09-30T18:14Z] tabix index syn3-3_62518267_93593495-raw.vcf.gz
[2015-09-30T18:14Z] Annotate with dbSNP
[2015-09-30T18:16Z] Genotyping with VarDict: Inference
[2015-09-30T18:16Z] Genotyping with VarDict: Inference
[2015-09-30T18:16Z] tabix index syn3-3_31494593_62516713-raw.vcf.gz
[2015-09-30T18:16Z] Annotate with dbSNP
[2015-09-30T18:17Z] tabix index syn3-3_93595554_124625281-raw.vcf.gz
[2015-09-30T18:17Z] Annotate with dbSNP
[2015-09-30T18:18Z] tabix index syn3-3_124626733_155649953-raw.vcf.gz
[2015-09-30T18:18Z] Annotate with dbSNP
[2015-09-30T18:18Z] Genotyping with VarDict: Inference
[2015-09-30T18:19Z] Genotyping with VarDict: Inference
[2015-09-30T18:20Z] tabix index syn3-3_155652401_186761310-raw.vcf.gz
[2015-09-30T18:20Z] Annotate with dbSNP
[2015-09-30T18:20Z] tabix index syn3-3_186768753_198022430-raw.vcf.gz
[2015-09-30T18:20Z] Annotate with dbSNP
[2015-09-30T18:20Z] Genotyping with VarDict: Inference
[2015-09-30T18:22Z] tabix index syn3-4_0_31018607-raw.vcf.gz
[2015-09-30T18:22Z] Annotate with dbSNP
[2015-09-30T18:22Z] Genotyping with VarDict: Inference
[2015-09-30T18:22Z] Genotyping with VarDict: Inference
[2015-09-30T18:23Z] tabix index syn3-4_31031389_62067173-raw.vcf.gz
[2015-09-30T18:23Z] Annotate with dbSNP
[2015-09-30T18:23Z] tabix index syn3-4_62292837_93511697-raw.vcf.gz
[2015-09-30T18:23Z] Annotate with dbSNP
[2015-09-30T18:24Z] Genotyping with VarDict: Inference
[2015-09-30T18:25Z] tabix index syn3-4_94005855_125588163-raw.vcf.gz
[2015-09-30T18:25Z] Annotate with dbSNP
[2015-09-30T18:25Z] Genotyping with VarDict: Inference
[2015-09-30T18:26Z] Genotyping with VarDict: Inference
[2015-09-30T18:26Z] tabix index syn3-4_125589908_156618518-raw.vcf.gz
[2015-09-30T18:26Z] Annotate with dbSNP
[2015-09-30T18:26Z] tabix index syn3-4_156624795_188926424-raw.vcf.gz
[2015-09-30T18:26Z] Annotate with dbSNP
[2015-09-30T18:27Z] Genotyping with VarDict: Inference
[2015-09-30T18:27Z] tabix index syn3-4_189012293_191154276-raw.vcf.gz
[2015-09-30T18:27Z] Annotate with dbSNP
[2015-09-30T18:28Z] Genotyping with VarDict: Inference
[2015-09-30T18:29Z] Genotyping with VarDict: Inference
[2015-09-30T18:29Z] tabix index syn3-5_0_31268043-raw.vcf.gz
[2015-09-30T18:29Z] Annotate with dbSNP
[2015-09-30T18:30Z] Genotyping with VarDict: Inference
[2015-09-30T18:30Z] tabix index syn3-5_31293868_62597714-raw.vcf.gz
[2015-09-30T18:30Z] Annotate with dbSNP
[2015-09-30T18:31Z] tabix index syn3-5_63256014_94276127-raw.vcf.gz
[2015-09-30T18:31Z] Annotate with dbSNP
[2015-09-30T18:31Z] Genotyping with VarDict: Inference
[2015-09-30T18:32Z] tabix index syn3-5_94277739_125696417-raw.vcf.gz
[2015-09-30T18:32Z] Annotate with dbSNP
[2015-09-30T18:32Z] Genotyping with VarDict: Inference
[2015-09-30T18:33Z] Genotyping with VarDict: Inference
[2015-09-30T18:34Z] Genotyping with VarDict: Inference
[2015-09-30T18:34Z] tabix index syn3-5_125759062_156781785-raw.vcf.gz
[2015-09-30T18:34Z] Annotate with dbSNP
[2015-09-30T18:34Z] tabix index syn3-5_156785743_180915260-raw.vcf.gz
[2015-09-30T18:34Z] Annotate with dbSNP
[2015-09-30T18:35Z] tabix index syn3-6_0_31080572-raw.vcf.gz
[2015-09-30T18:35Z] Annotate with dbSNP
[2015-09-30T18:36Z] Genotyping with VarDict: Inference
[2015-09-30T18:37Z] Genotyping with VarDict: Inference
[2015-09-30T18:37Z] tabix index syn3-6_62389878_93953543-raw.vcf.gz
[2015-09-30T18:37Z] Annotate with dbSNP
[2015-09-30T18:38Z] Genotyping with VarDict: Inference
[2015-09-30T18:39Z] tabix index syn3-6_93954776_124979769-raw.vcf.gz
[2015-09-30T18:39Z] Annotate with dbSNP
[2015-09-30T18:39Z] tabix index syn3-6_31082315_62284583-raw.vcf.gz
[2015-09-30T18:39Z] Annotate with dbSNP
[2015-09-30T18:40Z] Genotyping with VarDict: Inference
[2015-09-30T18:41Z] Genotyping with VarDict: Inference
[2015-09-30T18:41Z] tabix index syn3-6_125064552_156268261-raw.vcf.gz
[2015-09-30T18:41Z] Annotate with dbSNP
[2015-09-30T18:42Z] Genotyping with VarDict: Inference
[2015-09-30T18:42Z] tabix index syn3-6_156275378_171115067-raw.vcf.gz
[2015-09-30T18:42Z] Annotate with dbSNP
[2015-09-30T18:43Z] Genotyping with VarDict: Inference
[2015-09-30T18:43Z] tabix index syn3-7_0_31019109-raw.vcf.gz
[2015-09-30T18:43Z] Annotate with dbSNP
[2015-09-30T18:44Z] Genotyping with VarDict: Inference
[2015-09-30T18:44Z] tabix index syn3-7_31022897_62585293-raw.vcf.gz
[2015-09-30T18:44Z] Annotate with dbSNP
[2015-09-30T18:45Z] tabix index syn3-7_62708318_93925745-raw.vcf.gz
[2015-09-30T18:45Z] Annotate with dbSNP
[2015-09-30T18:45Z] Genotyping with VarDict: Inference
[2015-09-30T18:47Z] Genotyping with VarDict: Inference
[2015-09-30T18:48Z] tabix index syn3-7_94024041_125680568-raw.vcf.gz
[2015-09-30T18:48Z] Annotate with dbSNP
[2015-09-30T18:48Z] Genotyping with VarDict: Inference
[2015-09-30T18:48Z] tabix index syn3-7_157155595_159138663-raw.vcf.gz
[2015-09-30T18:48Z] Annotate with dbSNP
[2015-09-30T18:49Z] tabix index syn3-7_126078434_157151579-raw.vcf.gz
[2015-09-30T18:49Z] Annotate with dbSNP
[2015-09-30T18:50Z] Genotyping with VarDict: Inference
[2015-09-30T18:50Z] Genotyping with VarDict: Inference
[2015-09-30T18:51Z] Genotyping with VarDict: Inference
[2015-09-30T18:51Z] tabix index syn3-8_31030285_62213090-raw.vcf.gz
[2015-09-30T18:51Z] Annotate with dbSNP
[2015-09-30T18:52Z] tabix index syn3-8_0_31024990-raw.vcf.gz
[2015-09-30T18:52Z] Annotate with dbSNP
[2015-09-30T18:52Z] tabix index syn3-8_62288979_93648031-raw.vcf.gz
[2015-09-30T18:52Z] Annotate with dbSNP
[2015-09-30T18:53Z] Genotyping with VarDict: Inference
[2015-09-30T18:54Z] Genotyping with VarDict: Inference
[2015-09-30T18:54Z] Genotyping with VarDict: Inference
[2015-09-30T18:54Z] tabix index syn3-8_93896832_124968568-raw.vcf.gz
[2015-09-30T18:54Z] Annotate with dbSNP
[2015-09-30T18:55Z] tabix index syn3-9_0_32405837-raw.vcf.gz
[2015-09-30T18:55Z] Annotate with dbSNP
[2015-09-30T18:55Z] tabix index syn3-8_124975213_146364022-raw.vcf.gz
[2015-09-30T18:55Z] Annotate with dbSNP
[2015-09-30T18:56Z] Genotyping with VarDict: Inference
[2015-09-30T18:57Z] Genotyping with VarDict: Inference
[2015-09-30T18:57Z] Genotyping with VarDict: Inference
[2015-09-30T18:58Z] tabix index syn3-9_32406980_65488652-raw.vcf.gz
[2015-09-30T18:58Z] Annotate with dbSNP
[2015-09-30T18:59Z] tabix index syn3-9_65505265_96581951-raw.vcf.gz
[2015-09-30T18:59Z] Annotate with dbSNP
[2015-09-30T18:59Z] tabix index syn3-9_96714155_127734373-raw.vcf.gz
[2015-09-30T18:59Z] Annotate with dbSNP
[2015-09-30T19:00Z] Genotyping with VarDict: Inference
[2015-09-30T19:01Z] Genotyping with VarDict: Inference
[2015-09-30T19:01Z] Genotyping with VarDict: Inference
[2015-09-30T19:02Z] tabix index syn3-10_0_31134673-raw.vcf.gz
[2015-09-30T19:02Z] Annotate with dbSNP
[2015-09-30T19:02Z] tabix index syn3-9_127737328_141213431-raw.vcf.gz
[2015-09-30T19:02Z] Annotate with dbSNP
[2015-09-30T19:03Z] tabix index syn3-10_31137165_62208748-raw.vcf.gz
[2015-09-30T19:03Z] Annotate with dbSNP
[2015-09-30T19:05Z] Genotyping with VarDict: Inference
[2015-09-30T19:05Z] Genotyping with VarDict: Inference
[2015-09-30T19:05Z] Genotyping with VarDict: Inference
[2015-09-30T19:06Z] tabix index syn3-10_124438084_135534747-raw.vcf.gz
[2015-09-30T19:06Z] Annotate with dbSNP
[2015-09-30T19:06Z] tabix index syn3-10_62267938_93388847-raw.vcf.gz
[2015-09-30T19:06Z] Annotate with dbSNP
[2015-09-30T19:07Z] tabix index syn3-10_93389481_124436664-raw.vcf.gz
[2015-09-30T19:07Z] Annotate with dbSNP
[2015-09-30T19:08Z] Genotyping with VarDict: Inference
[2015-09-30T19:09Z] Genotyping with VarDict: Inference
[2015-09-30T19:09Z] Genotyping with VarDict: Inference
[2015-09-30T19:10Z] tabix index syn3-11_31085657_62105890-raw.vcf.gz
[2015-09-30T19:10Z] Annotate with dbSNP
[2015-09-30T19:11Z] tabix index syn3-11_0_31082819-raw.vcf.gz
[2015-09-30T19:11Z] Annotate with dbSNP
[2015-09-30T19:12Z] tabix index syn3-11_62123540_93141822-raw.vcf.gz
[2015-09-30T19:12Z] Annotate with dbSNP
[2015-09-30T19:12Z] Genotyping with VarDict: Inference
[2015-09-30T19:13Z] Genotyping with VarDict: Inference
[2015-09-30T19:13Z] tabix index syn3-11_124188917_135006516-raw.vcf.gz
[2015-09-30T19:13Z] Annotate with dbSNP
[2015-09-30T19:14Z] tabix index syn3-11_93147865_124180877-raw.vcf.gz
[2015-09-30T19:14Z] Annotate with dbSNP
[2015-09-30T19:14Z] Genotyping with VarDict: Inference
[2015-09-30T19:16Z] Genotyping with VarDict: Inference
[2015-09-30T19:16Z] tabix index syn3-12_0_31107241-raw.vcf.gz
[2015-09-30T19:16Z] Annotate with dbSNP
[2015-09-30T19:16Z] Genotyping with VarDict: Inference
[2015-09-30T19:17Z] tabix index syn3-12_62147092_93167456-raw.vcf.gz
[2015-09-30T19:17Z] Annotate with dbSNP
[2015-09-30T19:18Z] tabix index syn3-12_31116488_62142833-raw.vcf.gz
[2015-09-30T19:18Z] Annotate with dbSNP
[2015-09-30T19:19Z] Genotyping with VarDict: Inference
[2015-09-30T19:20Z] Genotyping with VarDict: Inference
[2015-09-30T19:20Z] tabix index syn3-12_124191013_133851895-raw.vcf.gz
[2015-09-30T19:20Z] Annotate with dbSNP
[2015-09-30T19:20Z] Genotyping with VarDict: Inference
[2015-09-30T19:21Z] tabix index syn3-13_0_31036104-raw.vcf.gz
[2015-09-30T19:21Z] Annotate with dbSNP
[2015-09-30T19:21Z] tabix index syn3-12_93169109_124189486-raw.vcf.gz
[2015-09-30T19:21Z] Annotate with dbSNP
[2015-09-30T19:23Z] Genotyping with VarDict: Inference
[2015-09-30T19:23Z] Genotyping with VarDict: Inference
[2015-09-30T19:23Z] Genotyping with VarDict: Inference
[2015-09-30T19:24Z] tabix index syn3-13_31036377_62334609-raw.vcf.gz
[2015-09-30T19:24Z] Annotate with dbSNP
[2015-09-30T19:24Z] tabix index syn3-13_63745563_94765401-raw.vcf.gz
[2015-09-30T19:24Z] Annotate with dbSNP
[2015-09-30T19:24Z] tabix index syn3-13_94938309_115169878-raw.vcf.gz
[2015-09-30T19:24Z] Annotate with dbSNP
[2015-09-30T19:26Z] Genotyping with VarDict: Inference
[2015-09-30T19:26Z] Genotyping with VarDict: Inference
[2015-09-30T19:27Z] Genotyping with VarDict: Inference
[2015-09-30T19:27Z] tabix index syn3-14_0_31050569-raw.vcf.gz
[2015-09-30T19:27Z] Annotate with dbSNP
[2015-09-30T19:27Z] tabix index syn3-14_31055710_62162825-raw.vcf.gz
[2015-09-30T19:27Z] Annotate with dbSNP
[2015-09-30T19:28Z] tabix index syn3-14_62186823_93262365-raw.vcf.gz
[2015-09-30T19:28Z] Annotate with dbSNP
[2015-09-30T19:29Z] Genotyping with VarDict: Inference
[2015-09-30T19:29Z] Genotyping with VarDict: Inference
[2015-09-30T19:30Z] tabix index syn3-15_0_31041107-raw.vcf.gz
[2015-09-30T19:30Z] Annotate with dbSNP
[2015-09-30T19:31Z] Genotyping with VarDict: Inference
[2015-09-30T19:31Z] tabix index syn3-14_93263525_107349540-raw.vcf.gz
[2015-09-30T19:31Z] Annotate with dbSNP
[2015-09-30T19:33Z] Genotyping with VarDict: Inference
[2015-09-30T19:33Z] tabix index syn3-15_31042312_62147370-raw.vcf.gz
[2015-09-30T19:33Z] Annotate with dbSNP
[2015-09-30T19:33Z] Genotyping with VarDict: Inference
[2015-09-30T19:33Z] tabix index syn3-15_93173163_102531392-raw.vcf.gz
[2015-09-30T19:33Z] Annotate with dbSNP
[2015-09-30T19:35Z] Genotyping with VarDict: Inference
[2015-09-30T19:35Z] tabix index syn3-15_62148224_93170844-raw.vcf.gz
[2015-09-30T19:35Z] Annotate with dbSNP
[2015-09-30T19:36Z] Genotyping with VarDict: Inference
[2015-09-30T19:37Z] tabix index syn3-16_31044089_62860191-raw.vcf.gz
[2015-09-30T19:37Z] Annotate with dbSNP
[2015-09-30T19:38Z] Genotyping with VarDict: Inference
[2015-09-30T19:39Z] tabix index syn3-16_0_31021934-raw.vcf.gz
[2015-09-30T19:39Z] Annotate with dbSNP
[2015-09-30T19:39Z] Genotyping with VarDict: Inference
[2015-09-30T19:40Z] tabix index syn3-16_64294277_90354753-raw.vcf.gz
[2015-09-30T19:40Z] Annotate with dbSNP
[2015-09-30T19:42Z] Genotyping with VarDict: Inference
[2015-09-30T19:42Z] Genotyping with VarDict: Inference
[2015-09-30T19:43Z] tabix index syn3-17_0_31039439-raw.vcf.gz
[2015-09-30T19:43Z] Annotate with dbSNP
[2015-09-30T19:45Z] tabix index syn3-17_62078196_81195210-raw.vcf.gz
[2015-09-30T19:45Z] Annotate with dbSNP
[2015-09-30T19:45Z] tabix index syn3-17_31047756_62076645-raw.vcf.gz
[2015-09-30T19:45Z] Annotate with dbSNP
[2015-09-30T19:45Z] Genotyping with VarDict: Inference
[2015-09-30T19:46Z] tabix index syn3-18_0_31142016-raw.vcf.gz
[2015-09-30T19:46Z] Annotate with dbSNP
[2015-09-30T19:47Z] Genotyping with VarDict: Inference
[2015-09-30T19:48Z] Genotyping with VarDict: Inference
[2015-09-30T19:48Z] tabix index syn3-18_63476668_78077248-raw.vcf.gz
[2015-09-30T19:48Z] Annotate with dbSNP
[2015-09-30T19:48Z] tabix index syn3-18_31158315_63430522-raw.vcf.gz
[2015-09-30T19:48Z] Annotate with dbSNP
[2015-09-30T19:49Z] Genotyping with VarDict: Inference
[2015-09-30T19:50Z] Genotyping with VarDict: Inference
[2015-09-30T19:51Z] Genotyping with VarDict: Inference
[2015-09-30T19:52Z] tabix index syn3-20_0_31018105-raw.vcf.gz
[2015-09-30T19:52Z] Annotate with dbSNP
[2015-09-30T19:54Z] tabix index syn3-19_0_31026185-raw.vcf.gz
[2015-09-30T19:54Z] Annotate with dbSNP
[2015-09-30T19:54Z] Genotyping with VarDict: Inference
[2015-09-30T19:55Z] tabix index syn3-19_31038548_59128983-raw.vcf.gz
[2015-09-30T19:55Z] Annotate with dbSNP
[2015-09-30T19:56Z] Genotyping with VarDict: Inference
[2015-09-30T19:56Z] tabix index syn3-20_62039427_63025520-raw.vcf.gz
[2015-09-30T19:56Z] Annotate with dbSNP
[2015-09-30T19:57Z] tabix index syn3-20_31018873_62038916-raw.vcf.gz
[2015-09-30T19:57Z] Annotate with dbSNP
[2015-09-30T19:58Z] Genotyping with VarDict: Inference
[2015-09-30T19:58Z] tabix index syn3-21_0_31023863-raw.vcf.gz
[2015-09-30T19:58Z] Annotate with dbSNP
[2015-09-30T19:59Z] Genotyping with VarDict: Inference
[2015-09-30T19:59Z] Genotyping with VarDict: Inference
[2015-09-30T20:00Z] tabix index syn3-21_31026814_48129895-raw.vcf.gz
[2015-09-30T20:00Z] Annotate with dbSNP
[2015-09-30T20:00Z] Genotyping with VarDict: Inference
[2015-09-30T20:01Z] tabix index syn3-22_0_31019358-raw.vcf.gz
[2015-09-30T20:01Z] Annotate with dbSNP
[2015-09-30T20:03Z] Genotyping with VarDict: Inference
[2015-09-30T20:03Z] tabix index syn3-22_31022170_51304566-raw.vcf.gz
[2015-09-30T20:03Z] Annotate with dbSNP
[2015-09-30T20:04Z] Genotyping with VarDict: Inference
[2015-09-30T20:04Z] tabix index syn3-X_0_31090302-raw.vcf.gz
[2015-09-30T20:04Z] Annotate with dbSNP
[2015-09-30T20:05Z] tabix index syn3-X_31132529_62519711-raw.vcf.gz
[2015-09-30T20:05Z] Annotate with dbSNP
[2015-09-30T20:05Z] Genotyping with VarDict: Inference
[2015-09-30T20:06Z] tabix index syn3-X_62568928_94148729-raw.vcf.gz
[2015-09-30T20:06Z] Annotate with dbSNP
[2015-09-30T20:06Z] Genotyping with VarDict: Inference
[2015-09-30T20:07Z] tabix index syn3-X_94317773_125687021-raw.vcf.gz
[2015-09-30T20:07Z] Annotate with dbSNP
[2015-09-30T20:07Z] Genotyping with VarDict: Inference
[2015-09-30T20:08Z] Genotyping with VarDict: Inference
[2015-09-30T20:08Z] tabix index syn3-Y_0_28716339-raw.vcf.gz
[2015-09-30T20:08Z] Annotate with dbSNP
[2015-09-30T20:09Z] tabix index syn3-X_125953527_155270560-raw.vcf.gz
[2015-09-30T20:09Z] Annotate with dbSNP
[2015-09-30T20:09Z] Genotyping with varscan: ('1', 0, 31187470) 1_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam
[2015-09-30T20:09Z] samtools mpileup
[2015-09-30T20:09Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:09Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:11Z] Genotyping with varscan: ('1', 31187762, 62229084) 1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam
[2015-09-30T20:11Z] samtools mpileup
[2015-09-30T20:11Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:11Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:11Z] Genotyping with varscan: ('1', 62231753, 93258244) 1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam
[2015-09-30T20:11Z] samtools mpileup
[2015-09-30T20:11Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:11Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:11Z] samtools mpileup
[2015-09-30T20:11Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:11Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:11Z] samtools mpileup
[2015-09-30T20:11Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:11Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:12Z] Varscan
[2015-09-30T20:12Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpqCjc2k/syn3-1_62231753_93258244-raw-normal.mpileup
[2015-09-30T20:12Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpqCjc2k/syn3-1_62231753_93258244-raw-tumor.mpileup
[2015-09-30T20:12Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:12Z] Min reads2:	2
[2015-09-30T20:12Z] Min strands2:	1
[2015-09-30T20:12Z] Min var freq:	0.1
[2015-09-30T20:12Z] Min freq for hom:	0.75
[2015-09-30T20:12Z] Normal purity:	1.0
[2015-09-30T20:12Z] Tumor purity:	1.0
[2015-09-30T20:12Z] Min avg qual:	15
[2015-09-30T20:12Z] P-value thresh:	0.98
[2015-09-30T20:12Z] Somatic p-value:	0.05
[2015-09-30T20:12Z] samtools mpileup
[2015-09-30T20:12Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:12Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:13Z] 1246195 positions in tumor
[2015-09-30T20:13Z] 1246177 positions shared in normal
[2015-09-30T20:13Z] 1189237 had sufficient coverage for comparison
[2015-09-30T20:13Z] 1187833 were called Reference
[2015-09-30T20:13Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:13Z] 89 were removed by the strand filter
[2015-09-30T20:13Z] 1356 were called Germline
[2015-09-30T20:13Z] 1 were called LOH
[2015-09-30T20:13Z] 33 were called Somatic
[2015-09-30T20:13Z] 14 were called Unknown
[2015-09-30T20:13Z] 0 were called Variant
[2015-09-30T20:13Z] Varscan paired fix
[2015-09-30T20:13Z] Varscan paired fix
[2015-09-30T20:13Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:13Z] bgzip syn3-1_62231753_93258244-raw.snp.vcf
[2015-09-30T20:13Z] tabix index syn3-1_62231753_93258244-raw.snp.vcf.gz
[2015-09-30T20:13Z] bgzip syn3-1_62231753_93258244-raw.indel.vcf
[2015-09-30T20:13Z] tabix index syn3-1_62231753_93258244-raw.indel.vcf.gz
[2015-09-30T20:13Z] Combine variant files
[2015-09-30T20:13Z] INFO  21:13:19,467 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:13Z] INFO  21:13:19,471 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:13Z] INFO  21:13:19,471 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:13Z] INFO  21:13:19,471 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:13Z] INFO  21:13:19,474 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpqCjc2k/tx/tmptqn8Rj/syn3-1_62231753_93258244-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/1/tx/tmpqCjc2k/syn3-1_62231753_93258244-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/1/tx/tmpqCjc2k/syn3-1_62231753_93258244-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_62231753_93258244-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:13Z] INFO  21:13:19,484 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:13Z] INFO  21:13:19,484 HelpFormatter - Date/Time: 2015/09/30 21:13:19
[2015-09-30T20:13Z] INFO  21:13:19,484 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:13Z] INFO  21:13:19,485 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:13Z] INFO  21:13:19,575 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:13Z] INFO  21:13:19,718 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:13Z] INFO  21:13:19,837 IntervalUtils - Processing 1257634 bp from intervals
[2015-09-30T20:13Z] WARN  21:13:19,838 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:13Z] WARN  21:13:19,838 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:13Z] INFO  21:13:19,924 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:13Z] INFO  21:13:19,927 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:13Z] INFO  21:13:19,927 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:13Z] INFO  21:13:19,928 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:13Z] INFO  21:13:19,928 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:13Z] INFO  21:13:21,376 ProgressMeter -            done      1520.0     1.0 s      15.9 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:13Z] INFO  21:13:21,377 ProgressMeter - Total runtime 1.45 secs, 0.02 min, 0.00 hours
[2015-09-30T20:13Z] bgzip syn3-1_62231753_93258244-raw.vcf
[2015-09-30T20:13Z] tabix index syn3-1_62231753_93258244-raw.vcf.gz
[2015-09-30T20:13Z] bgzip syn3-1_62231753_93258244-raw-rejectfix.vcf
[2015-09-30T20:13Z] tabix index syn3-1_62231753_93258244-raw-rejectfix.vcf.gz
[2015-09-30T20:13Z] GATK: VariantAnnotator
[2015-09-30T20:13Z] INFO  21:13:24,073 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:13Z] INFO  21:13:24,075 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:13Z] INFO  21:13:24,075 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:13Z] INFO  21:13:24,075 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:13Z] INFO  21:13:24,078 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/1/syn3-1_62231753_93258244-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpzFQkvN/syn3-1_62231753_93258244-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_62231753_93258244-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:13Z] INFO  21:13:24,084 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:13Z] INFO  21:13:24,084 HelpFormatter - Date/Time: 2015/09/30 21:13:24
[2015-09-30T20:13Z] INFO  21:13:24,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:13Z] INFO  21:13:24,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:13Z] INFO  21:13:24,172 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:13Z] INFO  21:13:24,247 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:13Z] INFO  21:13:24,254 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:13Z] INFO  21:13:24,276 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:13Z] INFO  21:13:24,666 IntervalUtils - Processing 1520 bp from intervals
[2015-09-30T20:13Z] WARN  21:13:24,671 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:13Z] WARN  21:13:24,671 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:13Z] INFO  21:13:24,726 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:13Z] INFO  21:13:24,839 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:13Z] INFO  21:13:24,839 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:13Z] INFO  21:13:24,840 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:13Z] INFO  21:13:24,840 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:13Z] INFO  21:13:25,110 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:13Z] INFO  21:13:31,253 VariantAnnotator - Processed 1305 loci.
[2015-09-30T20:13Z]
[2015-09-30T20:13Z] INFO  21:13:31,274 ProgressMeter -            done      4889.0     6.0 s      21.9 m       99.9%     6.0 s       0.0 s
[2015-09-30T20:13Z] INFO  21:13:31,275 ProgressMeter - Total runtime 6.44 secs, 0.11 min, 0.00 hours
[2015-09-30T20:13Z] INFO  21:13:31,275 MicroScheduler - 3518 reads were filtered out during the traversal out of approximately 86496 total reads (4.07%)
[2015-09-30T20:13Z] INFO  21:13:31,275 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:13Z] INFO  21:13:31,275 MicroScheduler -   -> 3497 reads (4.04% of total) failing DuplicateReadFilter
[2015-09-30T20:13Z] INFO  21:13:31,276 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:13Z] INFO  21:13:31,276 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:13Z] INFO  21:13:31,276 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:13Z] INFO  21:13:31,276 MicroScheduler -   -> 21 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:13Z] INFO  21:13:32,279 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:13Z] Genotyping with varscan: ('1', 93297335, 142653959) 1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam
[2015-09-30T20:13Z] samtools mpileup
[2015-09-30T20:13Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:13Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:13Z] Varscan
[2015-09-30T20:13Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmp77Ewg3/syn3-1_0_31187470-raw-normal.mpileup
[2015-09-30T20:13Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmp77Ewg3/syn3-1_0_31187470-raw-tumor.mpileup
[2015-09-30T20:13Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:13Z] Min reads2:	2
[2015-09-30T20:13Z] Min strands2:	1
[2015-09-30T20:13Z] Min var freq:	0.1
[2015-09-30T20:13Z] Min freq for hom:	0.75
[2015-09-30T20:13Z] Normal purity:	1.0
[2015-09-30T20:13Z] Tumor purity:	1.0
[2015-09-30T20:13Z] Min avg qual:	15
[2015-09-30T20:13Z] P-value thresh:	0.98
[2015-09-30T20:13Z] Somatic p-value:	0.05
[2015-09-30T20:14Z] Varscan
[2015-09-30T20:14Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpPVWG_j/syn3-1_31187762_62229084-raw-normal.mpileup
[2015-09-30T20:14Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpPVWG_j/syn3-1_31187762_62229084-raw-tumor.mpileup
[2015-09-30T20:14Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:14Z] Min reads2:	2
[2015-09-30T20:14Z] Min strands2:	1
[2015-09-30T20:14Z] Min var freq:	0.1
[2015-09-30T20:14Z] Min freq for hom:	0.75
[2015-09-30T20:14Z] Normal purity:	1.0
[2015-09-30T20:14Z] Tumor purity:	1.0
[2015-09-30T20:14Z] Min avg qual:	15
[2015-09-30T20:14Z] P-value thresh:	0.98
[2015-09-30T20:14Z] Somatic p-value:	0.05
[2015-09-30T20:14Z] samtools mpileup
[2015-09-30T20:14Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:14Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:15Z] Varscan
[2015-09-30T20:15Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpfSGrcL/syn3-1_93297335_142653959-raw-normal.mpileup
[2015-09-30T20:15Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpfSGrcL/syn3-1_93297335_142653959-raw-tumor.mpileup
[2015-09-30T20:15Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:15Z] Min reads2:	2
[2015-09-30T20:15Z] Min strands2:	1
[2015-09-30T20:15Z] Min var freq:	0.1
[2015-09-30T20:15Z] Min freq for hom:	0.75
[2015-09-30T20:15Z] Normal purity:	1.0
[2015-09-30T20:15Z] Tumor purity:	1.0
[2015-09-30T20:15Z] Min avg qual:	15
[2015-09-30T20:15Z] P-value thresh:	0.98
[2015-09-30T20:15Z] Somatic p-value:	0.05
[2015-09-30T20:15Z] 2348757 positions in tumor
[2015-09-30T20:15Z] 2348751 positions shared in normal
[2015-09-30T20:15Z] 2322981 had sufficient coverage for comparison
[2015-09-30T20:15Z] 2320806 were called Reference
[2015-09-30T20:15Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:15Z] 92 were removed by the strand filter
[2015-09-30T20:15Z] 2114 were called Germline
[2015-09-30T20:15Z] 8 were called LOH
[2015-09-30T20:15Z] 37 were called Somatic
[2015-09-30T20:15Z] 16 were called Unknown
[2015-09-30T20:15Z] 0 were called Variant
[2015-09-30T20:15Z] Varscan paired fix
[2015-09-30T20:15Z] Varscan paired fix
[2015-09-30T20:15Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:15Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:15Z] bgzip syn3-1_31187762_62229084-raw.snp.vcf
[2015-09-30T20:15Z] tabix index syn3-1_31187762_62229084-raw.snp.vcf.gz
[2015-09-30T20:15Z] bgzip syn3-1_31187762_62229084-raw.indel.vcf
[2015-09-30T20:15Z] tabix index syn3-1_31187762_62229084-raw.indel.vcf.gz
[2015-09-30T20:15Z] Combine variant files
[2015-09-30T20:16Z] INFO  21:16:00,181 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:00,183 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:16Z] INFO  21:16:00,183 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:16Z] INFO  21:16:00,183 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:16Z] INFO  21:16:00,187 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpPVWG_j/tx/tmpMHqiUP/syn3-1_31187762_62229084-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/1/tx/tmpPVWG_j/syn3-1_31187762_62229084-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/1/tx/tmpPVWG_j/syn3-1_31187762_62229084-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_31187762_62229084-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:16Z] INFO  21:16:00,192 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:16Z] INFO  21:16:00,193 HelpFormatter - Date/Time: 2015/09/30 21:16:00
[2015-09-30T20:16Z] INFO  21:16:00,193 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:00,193 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:00,267 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:16Z] INFO  21:16:00,613 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:16Z] INFO  21:16:00,755 IntervalUtils - Processing 2356624 bp from intervals
[2015-09-30T20:16Z] WARN  21:16:00,756 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] WARN  21:16:00,756 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] INFO  21:16:00,812 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:16Z] INFO  21:16:00,817 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:16Z] INFO  21:16:00,818 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:16Z] INFO  21:16:00,818 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:16Z] INFO  21:16:00,819 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:16Z] 3057121 positions in tumor
[2015-09-30T20:16Z] 3057114 positions shared in normal
[2015-09-30T20:16Z] 3035540 had sufficient coverage for comparison
[2015-09-30T20:16Z] 3030067 were called Reference
[2015-09-30T20:16Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:16Z] 539 were removed by the strand filter
[2015-09-30T20:16Z] 5331 were called Germline
[2015-09-30T20:16Z] 20 were called LOH
[2015-09-30T20:16Z] 92 were called Somatic
[2015-09-30T20:16Z] 30 were called Unknown
[2015-09-30T20:16Z] 0 were called Variant
[2015-09-30T20:16Z] Varscan paired fix
[2015-09-30T20:16Z] Varscan paired fix
[2015-09-30T20:16Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:16Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:16Z] bgzip syn3-1_0_31187470-raw.snp.vcf
[2015-09-30T20:16Z] tabix index syn3-1_0_31187470-raw.snp.vcf.gz
[2015-09-30T20:16Z] bgzip syn3-1_0_31187470-raw.indel.vcf
[2015-09-30T20:16Z] tabix index syn3-1_0_31187470-raw.indel.vcf.gz
[2015-09-30T20:16Z] Combine variant files
[2015-09-30T20:16Z] INFO  21:16:02,430 ProgressMeter -            done      2465.0     1.0 s      10.9 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:16Z] INFO  21:16:02,431 ProgressMeter - Total runtime 1.61 secs, 0.03 min, 0.00 hours
[2015-09-30T20:16Z] bgzip syn3-1_31187762_62229084-raw.vcf
[2015-09-30T20:16Z] tabix index syn3-1_31187762_62229084-raw.vcf.gz
[2015-09-30T20:16Z] bgzip syn3-1_31187762_62229084-raw-rejectfix.vcf
[2015-09-30T20:16Z] tabix index syn3-1_31187762_62229084-raw-rejectfix.vcf.gz
[2015-09-30T20:16Z] GATK: VariantAnnotator
[2015-09-30T20:16Z] INFO  21:16:03,981 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:03,983 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:16Z] INFO  21:16:03,983 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:16Z] INFO  21:16:03,983 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:16Z] INFO  21:16:03,986 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/1/tx/tmp77Ewg3/tx/tmpV4hZCd/syn3-1_0_31187470-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/1/tx/tmp77Ewg3/syn3-1_0_31187470-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/1/tx/tmp77Ewg3/syn3-1_0_31187470-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_0_31187470-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:16Z] INFO  21:16:03,992 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:16Z] INFO  21:16:03,992 HelpFormatter - Date/Time: 2015/09/30 21:16:03
[2015-09-30T20:16Z] INFO  21:16:03,992 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:03,992 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:04,071 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:16Z] INFO  21:16:04,648 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:16Z] INFO  21:16:04,794 IntervalUtils - Processing 3069806 bp from intervals
[2015-09-30T20:16Z] WARN  21:16:04,795 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] WARN  21:16:04,796 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] INFO  21:16:04,852 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:16Z] INFO  21:16:04,858 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:16Z] INFO  21:16:04,858 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:16Z] INFO  21:16:04,859 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:16Z] INFO  21:16:04,859 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:16Z] INFO  21:16:05,661 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:05,663 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:16Z] INFO  21:16:05,663 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:16Z] INFO  21:16:05,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:16Z] INFO  21:16:05,666 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/1/syn3-1_31187762_62229084-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/1/tx/tmp29Z8aR/syn3-1_31187762_62229084-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_31187762_62229084-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:16Z] INFO  21:16:05,672 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:16Z] INFO  21:16:05,672 HelpFormatter - Date/Time: 2015/09/30 21:16:05
[2015-09-30T20:16Z] INFO  21:16:05,673 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:05,673 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:05,763 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:16Z] INFO  21:16:06,105 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:16Z] INFO  21:16:06,112 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:16Z] INFO  21:16:06,135 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:16Z] INFO  21:16:06,549 IntervalUtils - Processing 2465 bp from intervals
[2015-09-30T20:16Z] WARN  21:16:06,553 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] WARN  21:16:06,553 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] INFO  21:16:06,609 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:16Z] INFO  21:16:06,815 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:16Z] INFO  21:16:06,816 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:16Z] INFO  21:16:06,816 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:16Z] INFO  21:16:06,816 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:16Z] INFO  21:16:06,849 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:16Z] INFO  21:16:07,295 ProgressMeter -            done      5649.0     2.0 s       7.2 m      100.0%     2.0 s       0.0 s
[2015-09-30T20:16Z] INFO  21:16:07,296 ProgressMeter - Total runtime 2.44 secs, 0.04 min, 0.00 hours
[2015-09-30T20:16Z] bgzip syn3-1_0_31187470-raw.vcf
[2015-09-30T20:16Z] tabix index syn3-1_0_31187470-raw.vcf.gz
[2015-09-30T20:16Z] bgzip syn3-1_0_31187470-raw-rejectfix.vcf
[2015-09-30T20:16Z] tabix index syn3-1_0_31187470-raw-rejectfix.vcf.gz
[2015-09-30T20:16Z] GATK: VariantAnnotator
[2015-09-30T20:16Z] INFO  21:16:10,577 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:10,579 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:16Z] INFO  21:16:10,580 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:16Z] INFO  21:16:10,580 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:16Z] INFO  21:16:10,583 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/1/syn3-1_0_31187470-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/1/tx/tmp9BUBev/syn3-1_0_31187470-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_0_31187470-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:16Z] INFO  21:16:10,589 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:16Z] INFO  21:16:10,589 HelpFormatter - Date/Time: 2015/09/30 21:16:10
[2015-09-30T20:16Z] INFO  21:16:10,589 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:10,590 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:10,680 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:16Z] INFO  21:16:10,757 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:16Z] INFO  21:16:10,765 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:16Z] INFO  21:16:10,796 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T20:16Z] INFO  21:16:11,357 IntervalUtils - Processing 5651 bp from intervals
[2015-09-30T20:16Z] WARN  21:16:11,362 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] WARN  21:16:11,362 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] INFO  21:16:11,416 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:16Z] INFO  21:16:11,575 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:16Z] INFO  21:16:11,576 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:16Z] INFO  21:16:11,576 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:16Z] INFO  21:16:11,577 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:16Z] INFO  21:16:11,606 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:16Z] INFO  21:16:18,564 VariantAnnotator - Processed 2071 loci.
[2015-09-30T20:16Z]
[2015-09-30T20:16Z] INFO  21:16:18,940 ProgressMeter -            done      9925.0    12.0 s      20.4 m      100.0%    12.0 s       0.0 s
[2015-09-30T20:16Z] INFO  21:16:18,941 ProgressMeter - Total runtime 12.13 secs, 0.20 min, 0.00 hours
[2015-09-30T20:16Z] INFO  21:16:18,941 MicroScheduler - 9924 reads were filtered out during the traversal out of approximately 196110 total reads (5.06%)
[2015-09-30T20:16Z] INFO  21:16:18,942 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:16Z] INFO  21:16:18,943 MicroScheduler -   -> 9869 reads (5.03% of total) failing DuplicateReadFilter
[2015-09-30T20:16Z] INFO  21:16:18,943 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:16Z] INFO  21:16:18,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:16Z] INFO  21:16:18,944 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:16Z] INFO  21:16:18,944 MicroScheduler -   -> 55 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:16Z] 1532503 positions in tumor
[2015-09-30T20:16Z] 1532493 positions shared in normal
[2015-09-30T20:16Z] 1493986 had sufficient coverage for comparison
[2015-09-30T20:16Z] 1492292 were called Reference
[2015-09-30T20:16Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:16Z] 93 were removed by the strand filter
[2015-09-30T20:16Z] 1652 were called Germline
[2015-09-30T20:16Z] 2 were called LOH
[2015-09-30T20:16Z] 25 were called Somatic
[2015-09-30T20:16Z] 15 were called Unknown
[2015-09-30T20:16Z] 0 were called Variant
[2015-09-30T20:16Z] Varscan paired fix
[2015-09-30T20:16Z] Varscan paired fix
[2015-09-30T20:16Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:16Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:16Z] bgzip syn3-1_93297335_142653959-raw.snp.vcf
[2015-09-30T20:16Z] tabix index syn3-1_93297335_142653959-raw.snp.vcf.gz
[2015-09-30T20:16Z] bgzip syn3-1_93297335_142653959-raw.indel.vcf
[2015-09-30T20:16Z] tabix index syn3-1_93297335_142653959-raw.indel.vcf.gz
[2015-09-30T20:16Z] Combine variant files
[2015-09-30T20:16Z] INFO  21:16:19,935 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:16Z] Genotyping with varscan: ('1', 142666976, 173685474) 1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam
[2015-09-30T20:16Z] samtools mpileup
[2015-09-30T20:16Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:16Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:16Z] INFO  21:16:21,313 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:21,315 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:16Z] INFO  21:16:21,315 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:16Z] INFO  21:16:21,315 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:16Z] INFO  21:16:21,318 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpfSGrcL/tx/tmpTCSAQ1/syn3-1_93297335_142653959-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/1/tx/tmpfSGrcL/syn3-1_93297335_142653959-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/1/tx/tmpfSGrcL/syn3-1_93297335_142653959-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_93297335_142653959-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:16Z] INFO  21:16:21,323 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:16Z] INFO  21:16:21,324 HelpFormatter - Date/Time: 2015/09/30 21:16:21
[2015-09-30T20:16Z] INFO  21:16:21,324 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:21,324 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:21,518 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:16Z] INFO  21:16:22,126 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:16Z] INFO  21:16:22,247 IntervalUtils - Processing 1539614 bp from intervals
[2015-09-30T20:16Z] WARN  21:16:22,248 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] WARN  21:16:22,248 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] INFO  21:16:22,301 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:16Z] INFO  21:16:22,304 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:16Z] INFO  21:16:22,304 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:16Z] INFO  21:16:22,305 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:16Z] INFO  21:16:22,305 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:16Z] INFO  21:16:23,734 ProgressMeter -            done      1907.0     1.0 s      12.5 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:16Z] INFO  21:16:23,735 ProgressMeter - Total runtime 1.43 secs, 0.02 min, 0.00 hours
[2015-09-30T20:16Z] bgzip syn3-1_93297335_142653959-raw.vcf
[2015-09-30T20:16Z] tabix index syn3-1_93297335_142653959-raw.vcf.gz
[2015-09-30T20:16Z] bgzip syn3-1_93297335_142653959-raw-rejectfix.vcf
[2015-09-30T20:16Z] tabix index syn3-1_93297335_142653959-raw-rejectfix.vcf.gz
[2015-09-30T20:16Z] GATK: VariantAnnotator
[2015-09-30T20:16Z] INFO  21:16:26,255 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:26,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:16Z] INFO  21:16:26,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:16Z] INFO  21:16:26,258 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:16Z] INFO  21:16:26,261 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/1/syn3-1_93297335_142653959-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/1/tx/tmphbfinM/syn3-1_93297335_142653959-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_93297335_142653959-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:16Z] INFO  21:16:26,267 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:16Z] INFO  21:16:26,267 HelpFormatter - Date/Time: 2015/09/30 21:16:26
[2015-09-30T20:16Z] INFO  21:16:26,267 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:26,267 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:16Z] INFO  21:16:26,361 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:16Z] INFO  21:16:26,438 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:16Z] INFO  21:16:26,445 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:16Z] INFO  21:16:26,467 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:16Z] INFO  21:16:26,864 IntervalUtils - Processing 1907 bp from intervals
[2015-09-30T20:16Z] WARN  21:16:26,868 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] WARN  21:16:26,868 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:16Z] INFO  21:16:26,924 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:16Z] INFO  21:16:27,123 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:16Z] INFO  21:16:27,123 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:16Z] INFO  21:16:27,124 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:16Z] INFO  21:16:27,124 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:16Z] INFO  21:16:27,157 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:16Z] INFO  21:16:35,999 VariantAnnotator - Processed 4913 loci.
[2015-09-30T20:16Z]
[2015-09-30T20:16Z] INFO  21:16:36,020 ProgressMeter -            done     49441.0    24.0 s       8.2 m      100.0%    24.0 s       0.0 s
[2015-09-30T20:16Z] INFO  21:16:36,020 ProgressMeter - Total runtime 24.44 secs, 0.41 min, 0.01 hours
[2015-09-30T20:16Z] INFO  21:16:36,020 MicroScheduler - 28053 reads were filtered out during the traversal out of approximately 511734 total reads (5.48%)
[2015-09-30T20:16Z] INFO  21:16:36,021 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:16Z] INFO  21:16:36,021 MicroScheduler -   -> 27918 reads (5.46% of total) failing DuplicateReadFilter
[2015-09-30T20:16Z] INFO  21:16:36,021 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:16Z] INFO  21:16:36,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:16Z] INFO  21:16:36,021 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:16Z] INFO  21:16:36,022 MicroScheduler -   -> 135 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:16Z] INFO  21:16:36,204 VariantAnnotator - Processed 1593 loci.
[2015-09-30T20:16Z]
[2015-09-30T20:16Z] INFO  21:16:36,227 ProgressMeter -            done      7366.0     9.0 s      20.6 m       99.9%     9.0 s       0.0 s
[2015-09-30T20:16Z] INFO  21:16:36,227 ProgressMeter - Total runtime 9.10 secs, 0.15 min, 0.00 hours
[2015-09-30T20:16Z] INFO  21:16:36,227 MicroScheduler - 6010 reads were filtered out during the traversal out of approximately 131615 total reads (4.57%)
[2015-09-30T20:16Z] INFO  21:16:36,228 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:16Z] INFO  21:16:36,228 MicroScheduler -   -> 5977 reads (4.54% of total) failing DuplicateReadFilter
[2015-09-30T20:16Z] INFO  21:16:36,228 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:16Z] INFO  21:16:36,228 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:16Z] INFO  21:16:36,228 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:16Z] INFO  21:16:36,229 MicroScheduler -   -> 33 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:16Z] INFO  21:16:36,975 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:16Z] Genotyping with varscan: ('1', 173702591, 204798081) 1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam
[2015-09-30T20:16Z] INFO  21:16:37,161 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:16Z] Genotyping with varscan: ('1', 204839842, 235860787) 1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam
[2015-09-30T20:16Z] samtools mpileup
[2015-09-30T20:16Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:16Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:16Z] samtools mpileup
[2015-09-30T20:16Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:16Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:17Z] samtools mpileup
[2015-09-30T20:17Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:17Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:17Z] samtools mpileup
[2015-09-30T20:17Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:17Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:18Z] samtools mpileup
[2015-09-30T20:18Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:18Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:18Z] Varscan
[2015-09-30T20:18Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpGhPVAR/syn3-1_173702591_204798081-raw-normal.mpileup
[2015-09-30T20:18Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpGhPVAR/syn3-1_173702591_204798081-raw-tumor.mpileup
[2015-09-30T20:18Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:18Z] Min reads2:	2
[2015-09-30T20:18Z] Min strands2:	1
[2015-09-30T20:18Z] Min var freq:	0.1
[2015-09-30T20:18Z] Min freq for hom:	0.75
[2015-09-30T20:18Z] Normal purity:	1.0
[2015-09-30T20:18Z] Tumor purity:	1.0
[2015-09-30T20:18Z] Min avg qual:	15
[2015-09-30T20:18Z] P-value thresh:	0.98
[2015-09-30T20:18Z] Somatic p-value:	0.05
[2015-09-30T20:18Z] Varscan
[2015-09-30T20:18Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpvtUUu_/syn3-1_204839842_235860787-raw-normal.mpileup
[2015-09-30T20:18Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpvtUUu_/syn3-1_204839842_235860787-raw-tumor.mpileup
[2015-09-30T20:18Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:18Z] Min reads2:	2
[2015-09-30T20:18Z] Min strands2:	1
[2015-09-30T20:18Z] Min var freq:	0.1
[2015-09-30T20:18Z] Min freq for hom:	0.75
[2015-09-30T20:18Z] Normal purity:	1.0
[2015-09-30T20:18Z] Tumor purity:	1.0
[2015-09-30T20:18Z] Min avg qual:	15
[2015-09-30T20:18Z] P-value thresh:	0.98
[2015-09-30T20:18Z] Somatic p-value:	0.05
[2015-09-30T20:19Z] 1697027 positions in tumor
[2015-09-30T20:19Z] 1697017 positions shared in normal
[2015-09-30T20:19Z] 1645805 had sufficient coverage for comparison
[2015-09-30T20:19Z] 1644011 were called Reference
[2015-09-30T20:19Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:19Z] 77 were removed by the strand filter
[2015-09-30T20:19Z] 1753 were called Germline
[2015-09-30T20:19Z] 6 were called LOH
[2015-09-30T20:19Z] 25 were called Somatic
[2015-09-30T20:19Z] 10 were called Unknown
[2015-09-30T20:19Z] 0 were called Variant
[2015-09-30T20:19Z] Varscan paired fix
[2015-09-30T20:19Z] Varscan paired fix
[2015-09-30T20:19Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:19Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:19Z] bgzip syn3-1_173702591_204798081-raw.snp.vcf
[2015-09-30T20:19Z] tabix index syn3-1_173702591_204798081-raw.snp.vcf.gz
[2015-09-30T20:19Z] bgzip syn3-1_173702591_204798081-raw.indel.vcf
[2015-09-30T20:19Z] tabix index syn3-1_173702591_204798081-raw.indel.vcf.gz
[2015-09-30T20:19Z] Combine variant files
[2015-09-30T20:19Z] INFO  21:19:45,083 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:19Z] INFO  21:19:45,085 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:19Z] INFO  21:19:45,085 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:19Z] INFO  21:19:45,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:19Z] INFO  21:19:45,089 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpGhPVAR/tx/tmpRvtapa/syn3-1_173702591_204798081-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/1/tx/tmpGhPVAR/syn3-1_173702591_204798081-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/1/tx/tmpGhPVAR/syn3-1_173702591_204798081-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_173702591_204798081-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:19Z] INFO  21:19:45,095 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:19Z] INFO  21:19:45,095 HelpFormatter - Date/Time: 2015/09/30 21:19:45
[2015-09-30T20:19Z] INFO  21:19:45,095 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:19Z] INFO  21:19:45,096 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:19Z] INFO  21:19:45,170 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:19Z] INFO  21:19:45,446 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:19Z] INFO  21:19:45,580 IntervalUtils - Processing 1710105 bp from intervals
[2015-09-30T20:19Z] WARN  21:19:45,581 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:19Z] WARN  21:19:45,581 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:19Z] INFO  21:19:45,638 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:19Z] INFO  21:19:45,642 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:19Z] INFO  21:19:45,643 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:19Z] INFO  21:19:45,643 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:19Z] INFO  21:19:45,643 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:19Z] INFO  21:19:47,267 ProgressMeter -            done      2082.0     1.0 s      13.0 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:19Z] INFO  21:19:47,268 ProgressMeter - Total runtime 1.63 secs, 0.03 min, 0.00 hours
[2015-09-30T20:19Z] bgzip syn3-1_173702591_204798081-raw.vcf
[2015-09-30T20:19Z] tabix index syn3-1_173702591_204798081-raw.vcf.gz
[2015-09-30T20:19Z] bgzip syn3-1_173702591_204798081-raw-rejectfix.vcf
[2015-09-30T20:19Z] tabix index syn3-1_173702591_204798081-raw-rejectfix.vcf.gz
[2015-09-30T20:19Z] GATK: VariantAnnotator
[2015-09-30T20:19Z] INFO  21:19:49,993 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:19Z] INFO  21:19:49,995 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:19Z] INFO  21:19:49,995 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:19Z] INFO  21:19:49,995 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:19Z] INFO  21:19:49,998 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/1/syn3-1_173702591_204798081-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpQsuyuc/syn3-1_173702591_204798081-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_173702591_204798081-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:19Z] INFO  21:19:50,004 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:19Z] INFO  21:19:50,004 HelpFormatter - Date/Time: 2015/09/30 21:19:49
[2015-09-30T20:19Z] INFO  21:19:50,004 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:19Z] INFO  21:19:50,004 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:19Z] INFO  21:19:50,066 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:19Z] INFO  21:19:50,137 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:19Z] INFO  21:19:50,144 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:19Z] INFO  21:19:50,165 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:19Z] INFO  21:19:50,508 IntervalUtils - Processing 2082 bp from intervals
[2015-09-30T20:19Z] WARN  21:19:50,512 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:19Z] WARN  21:19:50,512 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:19Z] INFO  21:19:50,565 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:19Z] INFO  21:19:52,512 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:19Z] INFO  21:19:52,512 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:19Z] INFO  21:19:52,512 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:19Z] INFO  21:19:52,513 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:19Z] INFO  21:19:52,545 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:19Z] 1753076 positions in tumor
[2015-09-30T20:19Z] 1753067 positions shared in normal
[2015-09-30T20:19Z] 1719140 had sufficient coverage for comparison
[2015-09-30T20:19Z] 1717080 were called Reference
[2015-09-30T20:19Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:19Z] 96 were removed by the strand filter
[2015-09-30T20:19Z] 1990 were called Germline
[2015-09-30T20:19Z] 5 were called LOH
[2015-09-30T20:19Z] 46 were called Somatic
[2015-09-30T20:19Z] 19 were called Unknown
[2015-09-30T20:19Z] 0 were called Variant
[2015-09-30T20:19Z] Varscan paired fix
[2015-09-30T20:19Z] Varscan paired fix
[2015-09-30T20:19Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:19Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:19Z] bgzip syn3-1_204839842_235860787-raw.snp.vcf
[2015-09-30T20:19Z] tabix index syn3-1_204839842_235860787-raw.snp.vcf.gz
[2015-09-30T20:19Z] bgzip syn3-1_204839842_235860787-raw.indel.vcf
[2015-09-30T20:19Z] tabix index syn3-1_204839842_235860787-raw.indel.vcf.gz
[2015-09-30T20:19Z] Combine variant files
[2015-09-30T20:20Z] INFO  21:20:01,010 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:20Z] INFO  21:20:01,012 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:20Z] INFO  21:20:01,012 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:20Z] INFO  21:20:01,012 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:20Z] INFO  21:20:01,016 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpvtUUu_/tx/tmpimfcL5/syn3-1_204839842_235860787-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/1/tx/tmpvtUUu_/syn3-1_204839842_235860787-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/1/tx/tmpvtUUu_/syn3-1_204839842_235860787-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_204839842_235860787-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:20Z] INFO  21:20:01,021 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:20Z] INFO  21:20:01,021 HelpFormatter - Date/Time: 2015/09/30 21:20:01
[2015-09-30T20:20Z] INFO  21:20:01,021 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:20Z] INFO  21:20:01,022 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:20Z] INFO  21:20:01,096 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:20Z] INFO  21:20:01,415 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:20Z] INFO  21:20:01,555 IntervalUtils - Processing 1760157 bp from intervals
[2015-09-30T20:20Z] WARN  21:20:01,556 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:20Z] WARN  21:20:01,556 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:20Z] INFO  21:20:01,616 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:20Z] INFO  21:20:01,620 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:20Z] INFO  21:20:01,620 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:20Z] INFO  21:20:01,621 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:20Z] INFO  21:20:01,621 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:20Z] INFO  21:20:01,874 VariantAnnotator - Processed 1710 loci.
[2015-09-30T20:20Z]
[2015-09-30T20:20Z] INFO  21:20:01,897 ProgressMeter -            done      9187.0     9.0 s      17.0 m      100.0%     9.0 s       0.0 s
[2015-09-30T20:20Z] INFO  21:20:01,898 ProgressMeter - Total runtime 9.39 secs, 0.16 min, 0.00 hours
[2015-09-30T20:20Z] INFO  21:20:01,898 MicroScheduler - 6791 reads were filtered out during the traversal out of approximately 142517 total reads (4.77%)
[2015-09-30T20:20Z] INFO  21:20:01,898 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:20Z] INFO  21:20:01,898 MicroScheduler -   -> 6765 reads (4.75% of total) failing DuplicateReadFilter
[2015-09-30T20:20Z] INFO  21:20:01,899 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:20Z] INFO  21:20:01,899 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:20Z] INFO  21:20:01,899 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:20Z] INFO  21:20:01,899 MicroScheduler -   -> 26 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:20Z] INFO  21:20:03,005 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:20Z] Genotyping with varscan: ('1', 235865791, 249250621) 1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam
[2015-09-30T20:20Z] INFO  21:20:03,181 ProgressMeter -            done      2275.0     1.0 s      11.4 m       99.6%     1.0 s       0.0 s
[2015-09-30T20:20Z] INFO  21:20:03,182 ProgressMeter - Total runtime 1.56 secs, 0.03 min, 0.00 hours
[2015-09-30T20:20Z] samtools mpileup
[2015-09-30T20:20Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:20Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:20Z] bgzip syn3-1_204839842_235860787-raw.vcf
[2015-09-30T20:20Z] tabix index syn3-1_204839842_235860787-raw.vcf.gz
[2015-09-30T20:20Z] bgzip syn3-1_204839842_235860787-raw-rejectfix.vcf
[2015-09-30T20:20Z] tabix index syn3-1_204839842_235860787-raw-rejectfix.vcf.gz
[2015-09-30T20:20Z] GATK: VariantAnnotator
[2015-09-30T20:20Z] INFO  21:20:06,109 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:20Z] INFO  21:20:06,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:20Z] INFO  21:20:06,111 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:20Z] INFO  21:20:06,111 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:20Z] INFO  21:20:06,115 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/1/syn3-1_204839842_235860787-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpE6GTja/syn3-1_204839842_235860787-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_204839842_235860787-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:20Z] INFO  21:20:06,120 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:20Z] INFO  21:20:06,121 HelpFormatter - Date/Time: 2015/09/30 21:20:06
[2015-09-30T20:20Z] INFO  21:20:06,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:20Z] INFO  21:20:06,121 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:20Z] INFO  21:20:06,194 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:20Z] INFO  21:20:06,267 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:20Z] INFO  21:20:06,275 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:20Z] INFO  21:20:06,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:20Z] INFO  21:20:06,633 IntervalUtils - Processing 2300 bp from intervals
[2015-09-30T20:20Z] WARN  21:20:06,637 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:20Z] WARN  21:20:06,637 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:20Z] INFO  21:20:06,762 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:20Z] INFO  21:20:06,921 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:20Z] INFO  21:20:06,922 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:20Z] INFO  21:20:06,922 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:20Z] INFO  21:20:06,922 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:20Z] INFO  21:20:06,955 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:20Z] INFO  21:20:17,292 VariantAnnotator - Processed 1951 loci.
[2015-09-30T20:20Z]
[2015-09-30T20:20Z] INFO  21:20:17,317 ProgressMeter -            done      8746.0    10.0 s      19.8 m      100.0%    10.0 s       0.0 s
[2015-09-30T20:20Z] INFO  21:20:17,317 ProgressMeter - Total runtime 10.40 secs, 0.17 min, 0.00 hours
[2015-09-30T20:20Z] INFO  21:20:17,317 MicroScheduler - 7506 reads were filtered out during the traversal out of approximately 161289 total reads (4.65%)
[2015-09-30T20:20Z] INFO  21:20:17,318 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:20Z] INFO  21:20:17,318 MicroScheduler -   -> 7478 reads (4.64% of total) failing DuplicateReadFilter
[2015-09-30T20:20Z] INFO  21:20:17,318 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:20Z] INFO  21:20:17,318 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:20Z] INFO  21:20:17,319 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:20Z] INFO  21:20:17,319 MicroScheduler -   -> 28 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:20Z] INFO  21:20:18,225 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:20Z] Genotyping with varscan: ('2', 0, 31134137) 1_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam
[2015-09-30T20:20Z] samtools mpileup
[2015-09-30T20:20Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:20Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:20Z] samtools mpileup
[2015-09-30T20:20Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:20Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:20Z] Varscan
[2015-09-30T20:20Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpAyMW3u/syn3-1_142666976_173685474-raw-normal.mpileup
[2015-09-30T20:20Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpAyMW3u/syn3-1_142666976_173685474-raw-tumor.mpileup
[2015-09-30T20:20Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:20Z] Min reads2:	2
[2015-09-30T20:20Z] Min strands2:	1
[2015-09-30T20:20Z] Min var freq:	0.1
[2015-09-30T20:20Z] Min freq for hom:	0.75
[2015-09-30T20:20Z] Normal purity:	1.0
[2015-09-30T20:20Z] Tumor purity:	1.0
[2015-09-30T20:20Z] Min avg qual:	15
[2015-09-30T20:20Z] P-value thresh:	0.98
[2015-09-30T20:20Z] Somatic p-value:	0.05
[2015-09-30T20:20Z] Varscan
[2015-09-30T20:20Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpBjUfSr/syn3-1_235865791_249250621-raw-normal.mpileup
[2015-09-30T20:20Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/1/tx/tmpBjUfSr/syn3-1_235865791_249250621-raw-tumor.mpileup
[2015-09-30T20:20Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:20Z] Min reads2:	2
[2015-09-30T20:20Z] Min strands2:	1
[2015-09-30T20:20Z] Min var freq:	0.1
[2015-09-30T20:20Z] Min freq for hom:	0.75
[2015-09-30T20:20Z] Normal purity:	1.0
[2015-09-30T20:20Z] Tumor purity:	1.0
[2015-09-30T20:20Z] Min avg qual:	15
[2015-09-30T20:20Z] P-value thresh:	0.98
[2015-09-30T20:20Z] Somatic p-value:	0.05
[2015-09-30T20:21Z] samtools mpileup
[2015-09-30T20:21Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:21Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:21Z] 667709 positions in tumor
[2015-09-30T20:21Z] 667704 positions shared in normal
[2015-09-30T20:21Z] 652265 had sufficient coverage for comparison
[2015-09-30T20:21Z] 651176 were called Reference
[2015-09-30T20:21Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:21Z] 54 were removed by the strand filter
[2015-09-30T20:21Z] 1065 were called Germline
[2015-09-30T20:21Z] 6 were called LOH
[2015-09-30T20:21Z] 12 were called Somatic
[2015-09-30T20:21Z] 6 were called Unknown
[2015-09-30T20:21Z] 0 were called Variant
[2015-09-30T20:21Z] Varscan paired fix
[2015-09-30T20:21Z] Varscan paired fix
[2015-09-30T20:21Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:21Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:21Z] bgzip syn3-1_235865791_249250621-raw.snp.vcf
[2015-09-30T20:21Z] tabix index syn3-1_235865791_249250621-raw.snp.vcf.gz
[2015-09-30T20:21Z] bgzip syn3-1_235865791_249250621-raw.indel.vcf
[2015-09-30T20:21Z] tabix index syn3-1_235865791_249250621-raw.indel.vcf.gz
[2015-09-30T20:21Z] Combine variant files
[2015-09-30T20:21Z] INFO  21:21:22,210 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:21Z] INFO  21:21:22,212 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:21Z] INFO  21:21:22,212 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:21Z] INFO  21:21:22,212 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:21Z] INFO  21:21:22,216 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpBjUfSr/tx/tmppS6Ua8/syn3-1_235865791_249250621-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/1/tx/tmpBjUfSr/syn3-1_235865791_249250621-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/1/tx/tmpBjUfSr/syn3-1_235865791_249250621-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_235865791_249250621-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:21Z] INFO  21:21:22,221 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:21Z] INFO  21:21:22,222 HelpFormatter - Date/Time: 2015/09/30 21:21:22
[2015-09-30T20:21Z] INFO  21:21:22,222 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:21Z] INFO  21:21:22,222 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:21Z] INFO  21:21:22,299 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:21Z] INFO  21:21:22,599 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:21Z] INFO  21:21:22,707 IntervalUtils - Processing 670628 bp from intervals
[2015-09-30T20:21Z] WARN  21:21:22,708 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:21Z] WARN  21:21:22,708 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:21Z] INFO  21:21:22,765 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:21Z] INFO  21:21:22,768 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:21Z] INFO  21:21:22,768 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:21Z] INFO  21:21:22,768 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:21Z] INFO  21:21:22,769 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:21Z] INFO  21:21:23,898 ProgressMeter -            done      1208.0     1.0 s      15.6 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:21Z] INFO  21:21:23,898 ProgressMeter - Total runtime 1.13 secs, 0.02 min, 0.00 hours
[2015-09-30T20:21Z] bgzip syn3-1_235865791_249250621-raw.vcf
[2015-09-30T20:21Z] tabix index syn3-1_235865791_249250621-raw.vcf.gz
[2015-09-30T20:21Z] bgzip syn3-1_235865791_249250621-raw-rejectfix.vcf
[2015-09-30T20:21Z] tabix index syn3-1_235865791_249250621-raw-rejectfix.vcf.gz
[2015-09-30T20:21Z] GATK: VariantAnnotator
[2015-09-30T20:21Z] INFO  21:21:26,328 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:21Z] INFO  21:21:26,330 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:21Z] INFO  21:21:26,331 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:21Z] INFO  21:21:26,331 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:21Z] INFO  21:21:26,334 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/1/syn3-1_235865791_249250621-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpNNPsfG/syn3-1_235865791_249250621-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_235865791_249250621-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:21Z] INFO  21:21:26,340 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:21Z] INFO  21:21:26,340 HelpFormatter - Date/Time: 2015/09/30 21:21:26
[2015-09-30T20:21Z] INFO  21:21:26,340 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:21Z] INFO  21:21:26,341 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:21Z] INFO  21:21:26,435 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:21Z] INFO  21:21:26,512 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:21Z] INFO  21:21:26,520 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:21Z] INFO  21:21:26,542 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:21Z] INFO  21:21:26,868 IntervalUtils - Processing 1212 bp from intervals
[2015-09-30T20:21Z] WARN  21:21:26,872 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:21Z] WARN  21:21:26,872 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:21Z] INFO  21:21:26,995 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:21Z] INFO  21:21:27,090 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:21Z] INFO  21:21:27,090 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:21Z] INFO  21:21:27,091 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:21Z] INFO  21:21:27,091 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:21Z] INFO  21:21:27,272 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:21Z] INFO  21:21:32,476 VariantAnnotator - Processed 1032 loci.
[2015-09-30T20:21Z]
[2015-09-30T20:21Z] INFO  21:21:32,512 ProgressMeter -            done      5129.0     5.0 s      17.6 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:21Z] INFO  21:21:32,512 ProgressMeter - Total runtime 5.42 secs, 0.09 min, 0.00 hours
[2015-09-30T20:21Z] INFO  21:21:32,513 MicroScheduler - 3129 reads were filtered out during the traversal out of approximately 68783 total reads (4.55%)
[2015-09-30T20:21Z] INFO  21:21:32,513 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:21Z] INFO  21:21:32,513 MicroScheduler -   -> 3112 reads (4.52% of total) failing DuplicateReadFilter
[2015-09-30T20:21Z] INFO  21:21:32,513 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:21Z] INFO  21:21:32,514 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:21Z] INFO  21:21:32,514 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:21Z] INFO  21:21:32,514 MicroScheduler -   -> 17 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:21Z] INFO  21:21:33,519 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:21Z] Genotyping with varscan: ('2', 31134801, 62196287) 1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam
[2015-09-30T20:21Z] samtools mpileup
[2015-09-30T20:21Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:21Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:21Z] Varscan
[2015-09-30T20:21Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpv57mJh/syn3-2_0_31134137-raw-normal.mpileup
[2015-09-30T20:21Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpv57mJh/syn3-2_0_31134137-raw-tumor.mpileup
[2015-09-30T20:21Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:21Z] Min reads2:	2
[2015-09-30T20:21Z] Min strands2:	1
[2015-09-30T20:21Z] Min var freq:	0.1
[2015-09-30T20:21Z] Min freq for hom:	0.75
[2015-09-30T20:21Z] Normal purity:	1.0
[2015-09-30T20:21Z] Tumor purity:	1.0
[2015-09-30T20:21Z] Min avg qual:	15
[2015-09-30T20:21Z] P-value thresh:	0.98
[2015-09-30T20:21Z] Somatic p-value:	0.05
[2015-09-30T20:22Z] samtools mpileup
[2015-09-30T20:22Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:22Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:22Z] 2887360 positions in tumor
[2015-09-30T20:22Z] 2887351 positions shared in normal
[2015-09-30T20:22Z] 2855629 had sufficient coverage for comparison
[2015-09-30T20:22Z] 2850461 were called Reference
[2015-09-30T20:22Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:22Z] 743 were removed by the strand filter
[2015-09-30T20:22Z] 4932 were called Germline
[2015-09-30T20:22Z] 40 were called LOH
[2015-09-30T20:22Z] 160 were called Somatic
[2015-09-30T20:22Z] 36 were called Unknown
[2015-09-30T20:22Z] 0 were called Variant
[2015-09-30T20:22Z] Varscan paired fix
[2015-09-30T20:22Z] Varscan paired fix
[2015-09-30T20:22Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:22Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:22Z] bgzip syn3-1_142666976_173685474-raw.snp.vcf
[2015-09-30T20:22Z] tabix index syn3-1_142666976_173685474-raw.snp.vcf.gz
[2015-09-30T20:22Z] bgzip syn3-1_142666976_173685474-raw.indel.vcf
[2015-09-30T20:22Z] tabix index syn3-1_142666976_173685474-raw.indel.vcf.gz
[2015-09-30T20:22Z] Combine variant files
[2015-09-30T20:22Z] INFO  21:22:51,173 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:22Z] INFO  21:22:51,175 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:22Z] INFO  21:22:51,175 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:22Z] INFO  21:22:51,175 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:22Z] INFO  21:22:51,179 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpAyMW3u/tx/tmp5zDHer/syn3-1_142666976_173685474-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/1/tx/tmpAyMW3u/syn3-1_142666976_173685474-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/1/tx/tmpAyMW3u/syn3-1_142666976_173685474-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_142666976_173685474-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:22Z] INFO  21:22:51,184 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:22Z] INFO  21:22:51,184 HelpFormatter - Date/Time: 2015/09/30 21:22:51
[2015-09-30T20:22Z] INFO  21:22:51,184 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:22Z] INFO  21:22:51,185 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:22Z] INFO  21:22:51,796 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:22Z] INFO  21:22:52,123 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:22Z] INFO  21:22:52,849 IntervalUtils - Processing 2894324 bp from intervals
[2015-09-30T20:22Z] WARN  21:22:52,851 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:22Z] WARN  21:22:52,851 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:22Z] INFO  21:22:52,943 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:22Z] INFO  21:22:52,950 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:22Z] INFO  21:22:52,952 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:22Z] INFO  21:22:52,953 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:22Z] INFO  21:22:52,953 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:22Z] INFO  21:22:56,799 ProgressMeter -            done      5002.0     3.0 s      12.8 m       99.7%     3.0 s       0.0 s
[2015-09-30T20:22Z] INFO  21:22:56,800 ProgressMeter - Total runtime 3.85 secs, 0.06 min, 0.00 hours
[2015-09-30T20:22Z] 1431622 positions in tumor
[2015-09-30T20:22Z] 1431617 positions shared in normal
[2015-09-30T20:22Z] 1410706 had sufficient coverage for comparison
[2015-09-30T20:22Z] 1408880 were called Reference
[2015-09-30T20:22Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:22Z] 77 were removed by the strand filter
[2015-09-30T20:22Z] 1775 were called Germline
[2015-09-30T20:22Z] 5 were called LOH
[2015-09-30T20:22Z] 37 were called Somatic
[2015-09-30T20:22Z] 9 were called Unknown
[2015-09-30T20:22Z] 0 were called Variant
[2015-09-30T20:22Z] Varscan paired fix
[2015-09-30T20:22Z] Varscan
[2015-09-30T20:22Z] Varscan paired fix
[2015-09-30T20:22Z] bgzip syn3-1_142666976_173685474-raw.vcf
[2015-09-30T20:22Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpiWYqEE/syn3-2_31134801_62196287-raw-normal.mpileup
[2015-09-30T20:22Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpiWYqEE/syn3-2_31134801_62196287-raw-tumor.mpileup
[2015-09-30T20:22Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:22Z] Min reads2:	2
[2015-09-30T20:22Z] Min strands2:	1
[2015-09-30T20:22Z] Min var freq:	0.1
[2015-09-30T20:22Z] Min freq for hom:	0.75
[2015-09-30T20:22Z] Normal purity:	1.0
[2015-09-30T20:22Z] Tumor purity:	1.0
[2015-09-30T20:22Z] Min avg qual:	15
[2015-09-30T20:22Z] P-value thresh:	0.98
[2015-09-30T20:22Z] Somatic p-value:	0.05
[2015-09-30T20:22Z] tabix index syn3-1_142666976_173685474-raw.vcf.gz
[2015-09-30T20:22Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:22Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:22Z] bgzip syn3-2_0_31134137-raw.snp.vcf
[2015-09-30T20:22Z] tabix index syn3-2_0_31134137-raw.snp.vcf.gz
[2015-09-30T20:22Z] bgzip syn3-2_0_31134137-raw.indel.vcf
[2015-09-30T20:22Z] tabix index syn3-2_0_31134137-raw.indel.vcf.gz
[2015-09-30T20:22Z] Combine variant files
[2015-09-30T20:22Z] bgzip syn3-1_142666976_173685474-raw-rejectfix.vcf
[2015-09-30T20:22Z] tabix index syn3-1_142666976_173685474-raw-rejectfix.vcf.gz
[2015-09-30T20:22Z] GATK: VariantAnnotator
[2015-09-30T20:23Z] INFO  21:23:01,424 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:01,426 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:23Z] INFO  21:23:01,426 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:23Z] INFO  21:23:01,426 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:23Z] INFO  21:23:01,430 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpv57mJh/tx/tmpTFLiw8/syn3-2_0_31134137-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/2/tx/tmpv57mJh/syn3-2_0_31134137-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/2/tx/tmpv57mJh/syn3-2_0_31134137-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_0_31134137-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:23Z] INFO  21:23:01,436 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:23Z] INFO  21:23:01,436 HelpFormatter - Date/Time: 2015/09/30 21:23:01
[2015-09-30T20:23Z] INFO  21:23:01,436 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:01,436 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:01,514 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:23Z] INFO  21:23:01,658 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:23Z] INFO  21:23:01,771 IntervalUtils - Processing 1436475 bp from intervals
[2015-09-30T20:23Z] WARN  21:23:01,772 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] WARN  21:23:01,772 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] INFO  21:23:01,831 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:23Z] INFO  21:23:01,835 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:23Z] INFO  21:23:01,836 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:23Z] INFO  21:23:01,836 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:23Z] INFO  21:23:01,836 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:23Z] INFO  21:23:01,923 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:01,925 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:23Z] INFO  21:23:01,926 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:23Z] INFO  21:23:01,926 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:23Z] INFO  21:23:01,929 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/1/syn3-1_142666976_173685474-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/1/tx/tmpXlTIgl/syn3-1_142666976_173685474-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/1/syn3-1_142666976_173685474-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:23Z] INFO  21:23:01,935 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:23Z] INFO  21:23:01,935 HelpFormatter - Date/Time: 2015/09/30 21:23:01
[2015-09-30T20:23Z] INFO  21:23:01,935 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:01,935 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:02,008 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:23Z] INFO  21:23:02,419 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:23Z] INFO  21:23:02,427 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:23Z] INFO  21:23:02,452 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:23Z] INFO  21:23:03,439 IntervalUtils - Processing 5002 bp from intervals
[2015-09-30T20:23Z] WARN  21:23:03,443 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] WARN  21:23:03,443 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] INFO  21:23:03,501 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:23Z] INFO  21:23:03,519 ProgressMeter -            done      2058.0     1.0 s      13.6 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:23Z] INFO  21:23:03,520 ProgressMeter - Total runtime 1.68 secs, 0.03 min, 0.00 hours
[2015-09-30T20:23Z] INFO  21:23:03,970 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:23Z] INFO  21:23:03,970 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:23Z] INFO  21:23:03,971 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:23Z] INFO  21:23:03,971 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:23Z] INFO  21:23:04,028 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:23Z] bgzip syn3-2_0_31134137-raw.vcf
[2015-09-30T20:23Z] tabix index syn3-2_0_31134137-raw.vcf.gz
[2015-09-30T20:23Z] bgzip syn3-2_0_31134137-raw-rejectfix.vcf
[2015-09-30T20:23Z] tabix index syn3-2_0_31134137-raw-rejectfix.vcf.gz
[2015-09-30T20:23Z] GATK: VariantAnnotator
[2015-09-30T20:23Z] INFO  21:23:07,593 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:07,595 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:23Z] INFO  21:23:07,595 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:23Z] INFO  21:23:07,595 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:23Z] INFO  21:23:07,599 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/2/syn3-2_0_31134137-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpsNgCMy/syn3-2_0_31134137-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_0_31134137-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:23Z] INFO  21:23:07,605 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:23Z] INFO  21:23:07,605 HelpFormatter - Date/Time: 2015/09/30 21:23:07
[2015-09-30T20:23Z] INFO  21:23:07,605 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:07,605 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:07,710 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:23Z] INFO  21:23:07,787 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:23Z] INFO  21:23:07,795 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:23Z] INFO  21:23:07,818 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:23Z] INFO  21:23:08,264 IntervalUtils - Processing 2075 bp from intervals
[2015-09-30T20:23Z] WARN  21:23:08,268 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] WARN  21:23:08,268 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] INFO  21:23:08,327 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:23Z] INFO  21:23:08,508 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:23Z] INFO  21:23:08,508 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:23Z] INFO  21:23:08,509 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:23Z] INFO  21:23:08,509 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:23Z] INFO  21:23:08,546 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:23Z] INFO  21:23:17,614 VariantAnnotator - Processed 1744 loci.
[2015-09-30T20:23Z]
[2015-09-30T20:23Z] INFO  21:23:17,637 ProgressMeter -            done      8998.0     9.0 s      16.9 m      100.0%     9.0 s       0.0 s
[2015-09-30T20:23Z] INFO  21:23:17,637 ProgressMeter - Total runtime 9.13 secs, 0.15 min, 0.00 hours
[2015-09-30T20:23Z] INFO  21:23:17,637 MicroScheduler - 7547 reads were filtered out during the traversal out of approximately 153986 total reads (4.90%)
[2015-09-30T20:23Z] INFO  21:23:17,638 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:23Z] INFO  21:23:17,638 MicroScheduler -   -> 7505 reads (4.87% of total) failing DuplicateReadFilter
[2015-09-30T20:23Z] INFO  21:23:17,638 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:23Z] INFO  21:23:17,638 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:23Z] INFO  21:23:17,639 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:23Z] INFO  21:23:17,639 MicroScheduler -   -> 42 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:23Z] INFO  21:23:18,633 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:23Z] Genotyping with varscan: ('2', 62227535, 95457199) 1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam
[2015-09-30T20:23Z] samtools mpileup
[2015-09-30T20:23Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:23Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:23Z] INFO  21:23:24,884 VariantAnnotator - Processed 4405 loci.
[2015-09-30T20:23Z]
[2015-09-30T20:23Z] INFO  21:23:24,908 ProgressMeter -            done     39940.0    20.0 s       8.7 m      100.0%    20.0 s       0.0 s
[2015-09-30T20:23Z] INFO  21:23:24,908 ProgressMeter - Total runtime 20.94 secs, 0.35 min, 0.01 hours
[2015-09-30T20:23Z] INFO  21:23:24,909 MicroScheduler - 20356 reads were filtered out during the traversal out of approximately 421081 total reads (4.83%)
[2015-09-30T20:23Z] INFO  21:23:24,909 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:23Z] INFO  21:23:24,909 MicroScheduler -   -> 20272 reads (4.81% of total) failing DuplicateReadFilter
[2015-09-30T20:23Z] INFO  21:23:24,909 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:23Z] INFO  21:23:24,909 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:23Z] INFO  21:23:24,910 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:23Z] INFO  21:23:24,910 MicroScheduler -   -> 84 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:23Z] INFO  21:23:25,916 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:23Z] Genotyping with varscan: ('2', 95457728, 127315933) 1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam
[2015-09-30T20:23Z] samtools mpileup
[2015-09-30T20:23Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:23Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:23Z] 1328875 positions in tumor
[2015-09-30T20:23Z] 1328869 positions shared in normal
[2015-09-30T20:23Z] 1289109 had sufficient coverage for comparison
[2015-09-30T20:23Z] 1287684 were called Reference
[2015-09-30T20:23Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:23Z] 67 were removed by the strand filter
[2015-09-30T20:23Z] 1366 were called Germline
[2015-09-30T20:23Z] 5 were called LOH
[2015-09-30T20:23Z] 40 were called Somatic
[2015-09-30T20:23Z] 14 were called Unknown
[2015-09-30T20:23Z] 0 were called Variant
[2015-09-30T20:23Z] Varscan paired fix
[2015-09-30T20:23Z] Varscan paired fix
[2015-09-30T20:23Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:23Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:23Z] bgzip syn3-2_31134801_62196287-raw.snp.vcf
[2015-09-30T20:23Z] tabix index syn3-2_31134801_62196287-raw.snp.vcf.gz
[2015-09-30T20:23Z] bgzip syn3-2_31134801_62196287-raw.indel.vcf
[2015-09-30T20:23Z] tabix index syn3-2_31134801_62196287-raw.indel.vcf.gz
[2015-09-30T20:23Z] Combine variant files
[2015-09-30T20:23Z] INFO  21:23:51,362 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:51,366 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:23Z] INFO  21:23:51,366 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:23Z] INFO  21:23:51,366 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:23Z] INFO  21:23:51,370 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpiWYqEE/tx/tmpF9cQ1S/syn3-2_31134801_62196287-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/2/tx/tmpiWYqEE/syn3-2_31134801_62196287-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/2/tx/tmpiWYqEE/syn3-2_31134801_62196287-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_31134801_62196287-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:23Z] INFO  21:23:51,378 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:23Z] INFO  21:23:51,379 HelpFormatter - Date/Time: 2015/09/30 21:23:51
[2015-09-30T20:23Z] INFO  21:23:51,380 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:51,380 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:51,611 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:23Z] INFO  21:23:51,753 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:23Z] INFO  21:23:51,886 IntervalUtils - Processing 1335510 bp from intervals
[2015-09-30T20:23Z] WARN  21:23:51,887 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] WARN  21:23:51,887 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] INFO  21:23:51,941 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:23Z] INFO  21:23:51,944 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:23Z] INFO  21:23:51,944 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:23Z] INFO  21:23:51,945 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:23Z] INFO  21:23:51,945 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:23Z] INFO  21:23:53,314 ProgressMeter -            done      1662.0     1.0 s      13.7 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:23Z] INFO  21:23:53,315 ProgressMeter - Total runtime 1.37 secs, 0.02 min, 0.00 hours
[2015-09-30T20:23Z] bgzip syn3-2_31134801_62196287-raw.vcf
[2015-09-30T20:23Z] tabix index syn3-2_31134801_62196287-raw.vcf.gz
[2015-09-30T20:23Z] bgzip syn3-2_31134801_62196287-raw-rejectfix.vcf
[2015-09-30T20:23Z] tabix index syn3-2_31134801_62196287-raw-rejectfix.vcf.gz
[2015-09-30T20:23Z] GATK: VariantAnnotator
[2015-09-30T20:23Z] INFO  21:23:55,795 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:55,797 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:23Z] INFO  21:23:55,797 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:23Z] INFO  21:23:55,797 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:23Z] INFO  21:23:55,801 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/2/syn3-2_31134801_62196287-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpW6_6ez/syn3-2_31134801_62196287-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_31134801_62196287-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:23Z] INFO  21:23:55,806 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:23Z] INFO  21:23:55,806 HelpFormatter - Date/Time: 2015/09/30 21:23:55
[2015-09-30T20:23Z] INFO  21:23:55,806 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:55,806 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:23Z] INFO  21:23:55,899 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:23Z] INFO  21:23:55,977 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:23Z] INFO  21:23:55,984 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:23Z] INFO  21:23:56,006 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:23Z] INFO  21:23:56,545 IntervalUtils - Processing 1662 bp from intervals
[2015-09-30T20:23Z] WARN  21:23:56,549 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] WARN  21:23:56,549 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:23Z] INFO  21:23:56,605 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:23Z] INFO  21:23:56,937 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:23Z] INFO  21:23:56,938 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:23Z] INFO  21:23:56,938 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:23Z] INFO  21:23:56,938 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:23Z] INFO  21:23:57,037 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:24Z] INFO  21:24:04,001 VariantAnnotator - Processed 1349 loci.
[2015-09-30T20:24Z]
[2015-09-30T20:24Z] INFO  21:24:04,033 ProgressMeter -            done      5374.0     7.0 s      22.0 m       99.9%     7.0 s       0.0 s
[2015-09-30T20:24Z] INFO  21:24:04,033 ProgressMeter - Total runtime 7.10 secs, 0.12 min, 0.00 hours
[2015-09-30T20:24Z] INFO  21:24:04,033 MicroScheduler - 4239 reads were filtered out during the traversal out of approximately 96644 total reads (4.39%)
[2015-09-30T20:24Z] INFO  21:24:04,034 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:24Z] INFO  21:24:04,034 MicroScheduler -   -> 4226 reads (4.37% of total) failing DuplicateReadFilter
[2015-09-30T20:24Z] INFO  21:24:04,034 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:24Z] INFO  21:24:04,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:24Z] INFO  21:24:04,035 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:24Z] INFO  21:24:04,035 MicroScheduler -   -> 13 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T20:24Z] INFO  21:24:04,981 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:24Z] Genotyping with varscan: ('2', 127413596, 158444156) 1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam
[2015-09-30T20:24Z] samtools mpileup
[2015-09-30T20:24Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:24Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:24Z] samtools mpileup
[2015-09-30T20:24Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:24Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:24Z] samtools mpileup
[2015-09-30T20:24Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:24Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:24Z] samtools mpileup
[2015-09-30T20:24Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:24Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:25Z] Varscan
[2015-09-30T20:25Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpZPYN9L/syn3-2_62227535_95457199-raw-normal.mpileup
[2015-09-30T20:25Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpZPYN9L/syn3-2_62227535_95457199-raw-tumor.mpileup
[2015-09-30T20:25Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:25Z] Min reads2:	2
[2015-09-30T20:25Z] Min strands2:	1
[2015-09-30T20:25Z] Min var freq:	0.1
[2015-09-30T20:25Z] Min freq for hom:	0.75
[2015-09-30T20:25Z] Normal purity:	1.0
[2015-09-30T20:25Z] Tumor purity:	1.0
[2015-09-30T20:25Z] Min avg qual:	15
[2015-09-30T20:25Z] P-value thresh:	0.98
[2015-09-30T20:25Z] Somatic p-value:	0.05
[2015-09-30T20:25Z] Varscan
[2015-09-30T20:25Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpO9fJa1/syn3-2_127413596_158444156-raw-normal.mpileup
[2015-09-30T20:25Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpO9fJa1/syn3-2_127413596_158444156-raw-tumor.mpileup
[2015-09-30T20:25Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:25Z] Min reads2:	2
[2015-09-30T20:25Z] Min strands2:	1
[2015-09-30T20:25Z] Min var freq:	0.1
[2015-09-30T20:25Z] Min freq for hom:	0.75
[2015-09-30T20:25Z] Normal purity:	1.0
[2015-09-30T20:25Z] Tumor purity:	1.0
[2015-09-30T20:25Z] Min avg qual:	15
[2015-09-30T20:25Z] P-value thresh:	0.98
[2015-09-30T20:25Z] Somatic p-value:	0.05
[2015-09-30T20:25Z] Varscan
[2015-09-30T20:25Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpvDiEF9/syn3-2_95457728_127315933-raw-normal.mpileup
[2015-09-30T20:25Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpvDiEF9/syn3-2_95457728_127315933-raw-tumor.mpileup
[2015-09-30T20:25Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:25Z] Min reads2:	2
[2015-09-30T20:25Z] Min strands2:	1
[2015-09-30T20:25Z] Min var freq:	0.1
[2015-09-30T20:25Z] Min freq for hom:	0.75
[2015-09-30T20:25Z] Normal purity:	1.0
[2015-09-30T20:25Z] Tumor purity:	1.0
[2015-09-30T20:25Z] Min avg qual:	15
[2015-09-30T20:25Z] P-value thresh:	0.98
[2015-09-30T20:25Z] Somatic p-value:	0.05
[2015-09-30T20:26Z] 1436382 positions in tumor
[2015-09-30T20:26Z] 1436377 positions shared in normal
[2015-09-30T20:26Z] 1413314 had sufficient coverage for comparison
[2015-09-30T20:26Z] 1411054 were called Reference
[2015-09-30T20:26Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:26Z] 360 were removed by the strand filter
[2015-09-30T20:26Z] 2158 were called Germline
[2015-09-30T20:26Z] 6 were called LOH
[2015-09-30T20:26Z] 76 were called Somatic
[2015-09-30T20:26Z] 20 were called Unknown
[2015-09-30T20:26Z] 0 were called Variant
[2015-09-30T20:26Z] Varscan paired fix
[2015-09-30T20:26Z] Varscan paired fix
[2015-09-30T20:26Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:26Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:26Z] bgzip syn3-2_62227535_95457199-raw.snp.vcf
[2015-09-30T20:26Z] tabix index syn3-2_62227535_95457199-raw.snp.vcf.gz
[2015-09-30T20:26Z] bgzip syn3-2_62227535_95457199-raw.indel.vcf
[2015-09-30T20:26Z] tabix index syn3-2_62227535_95457199-raw.indel.vcf.gz
[2015-09-30T20:26Z] Combine variant files
[2015-09-30T20:26Z] 1113239 positions in tumor
[2015-09-30T20:26Z] 1113227 positions shared in normal
[2015-09-30T20:26Z] 1084884 had sufficient coverage for comparison
[2015-09-30T20:26Z] 1083112 were called Reference
[2015-09-30T20:26Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:26Z] 176 were removed by the strand filter
[2015-09-30T20:26Z] 1713 were called Germline
[2015-09-30T20:26Z] 4 were called LOH
[2015-09-30T20:26Z] 45 were called Somatic
[2015-09-30T20:26Z] 10 were called Unknown
[2015-09-30T20:26Z] 0 were called Variant
[2015-09-30T20:26Z] Varscan paired fix
[2015-09-30T20:26Z] Varscan paired fix
[2015-09-30T20:26Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:26Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:26Z] bgzip syn3-2_127413596_158444156-raw.snp.vcf
[2015-09-30T20:26Z] tabix index syn3-2_127413596_158444156-raw.snp.vcf.gz
[2015-09-30T20:26Z] bgzip syn3-2_127413596_158444156-raw.indel.vcf
[2015-09-30T20:26Z] tabix index syn3-2_127413596_158444156-raw.indel.vcf.gz
[2015-09-30T20:26Z] Combine variant files
[2015-09-30T20:26Z] INFO  21:26:08,076 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:08,078 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:26Z] INFO  21:26:08,078 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:26Z] INFO  21:26:08,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:26Z] INFO  21:26:08,082 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpZPYN9L/tx/tmpbEHVTr/syn3-2_62227535_95457199-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/2/tx/tmpZPYN9L/syn3-2_62227535_95457199-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/2/tx/tmpZPYN9L/syn3-2_62227535_95457199-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_62227535_95457199-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:26Z] INFO  21:26:08,088 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:26Z] INFO  21:26:08,088 HelpFormatter - Date/Time: 2015/09/30 21:26:08
[2015-09-30T20:26Z] INFO  21:26:08,088 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:08,088 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:08,288 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:26Z] INFO  21:26:08,557 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:26Z] INFO  21:26:08,682 IntervalUtils - Processing 1441996 bp from intervals
[2015-09-30T20:26Z] WARN  21:26:08,683 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] WARN  21:26:08,683 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] INFO  21:26:08,741 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:26Z] INFO  21:26:08,745 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:26Z] INFO  21:26:08,745 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:26Z] INFO  21:26:08,746 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:26Z] INFO  21:26:08,746 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:26Z] INFO  21:26:08,824 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:08,826 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:26Z] INFO  21:26:08,826 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:26Z] INFO  21:26:08,826 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:26Z] INFO  21:26:08,830 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpO9fJa1/tx/tmp9tUi6K/syn3-2_127413596_158444156-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/2/tx/tmpO9fJa1/syn3-2_127413596_158444156-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/2/tx/tmpO9fJa1/syn3-2_127413596_158444156-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_127413596_158444156-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:26Z] INFO  21:26:08,835 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:26Z] INFO  21:26:08,835 HelpFormatter - Date/Time: 2015/09/30 21:26:08
[2015-09-30T20:26Z] INFO  21:26:08,836 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:08,836 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:08,913 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:26Z] INFO  21:26:09,113 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:26Z] INFO  21:26:09,231 IntervalUtils - Processing 1120292 bp from intervals
[2015-09-30T20:26Z] WARN  21:26:09,232 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] WARN  21:26:09,232 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] INFO  21:26:09,292 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:26Z] INFO  21:26:09,295 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:26Z] INFO  21:26:09,295 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:26Z] INFO  21:26:09,296 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:26Z] INFO  21:26:09,296 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:26Z] INFO  21:26:10,236 ProgressMeter -            done      2141.0     1.0 s      11.6 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:26Z] INFO  21:26:10,237 ProgressMeter - Total runtime 1.49 secs, 0.02 min, 0.00 hours
[2015-09-30T20:26Z] bgzip syn3-2_62227535_95457199-raw.vcf
[2015-09-30T20:26Z] tabix index syn3-2_62227535_95457199-raw.vcf.gz
[2015-09-30T20:26Z] bgzip syn3-2_62227535_95457199-raw-rejectfix.vcf
[2015-09-30T20:26Z] tabix index syn3-2_62227535_95457199-raw-rejectfix.vcf.gz
[2015-09-30T20:26Z] GATK: VariantAnnotator
[2015-09-30T20:26Z] INFO  21:26:11,462 ProgressMeter -            done      1780.0     2.0 s      20.3 m      100.0%     2.0 s       0.0 s
[2015-09-30T20:26Z] INFO  21:26:11,463 ProgressMeter - Total runtime 2.17 secs, 0.04 min, 0.00 hours
[2015-09-30T20:26Z] bgzip syn3-2_127413596_158444156-raw.vcf
[2015-09-30T20:26Z] tabix index syn3-2_127413596_158444156-raw.vcf.gz
[2015-09-30T20:26Z] bgzip syn3-2_127413596_158444156-raw-rejectfix.vcf
[2015-09-30T20:26Z] tabix index syn3-2_127413596_158444156-raw-rejectfix.vcf.gz
[2015-09-30T20:26Z] GATK: VariantAnnotator
[2015-09-30T20:26Z] INFO  21:26:12,865 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:12,867 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:26Z] INFO  21:26:12,867 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:26Z] INFO  21:26:12,867 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:26Z] INFO  21:26:12,871 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/2/syn3-2_62227535_95457199-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpbZow_D/syn3-2_62227535_95457199-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_62227535_95457199-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:26Z] INFO  21:26:12,877 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:26Z] INFO  21:26:12,877 HelpFormatter - Date/Time: 2015/09/30 21:26:12
[2015-09-30T20:26Z] INFO  21:26:12,877 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:12,878 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:12,980 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:26Z] INFO  21:26:13,058 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:26Z] INFO  21:26:13,066 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:26Z] INFO  21:26:13,092 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T20:26Z] INFO  21:26:13,516 IntervalUtils - Processing 2141 bp from intervals
[2015-09-30T20:26Z] WARN  21:26:13,521 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] WARN  21:26:13,521 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] INFO  21:26:13,579 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:26Z] INFO  21:26:13,772 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:26Z] INFO  21:26:13,772 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:26Z] INFO  21:26:13,773 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:26Z] INFO  21:26:13,773 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:26Z] INFO  21:26:13,806 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:26Z] INFO  21:26:13,905 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:13,907 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:26Z] INFO  21:26:13,907 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:26Z] INFO  21:26:13,908 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:26Z] INFO  21:26:13,911 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/2/syn3-2_127413596_158444156-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/2/tx/tmposBqSG/syn3-2_127413596_158444156-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_127413596_158444156-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:26Z] INFO  21:26:13,917 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:26Z] INFO  21:26:13,917 HelpFormatter - Date/Time: 2015/09/30 21:26:13
[2015-09-30T20:26Z] INFO  21:26:13,917 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:13,917 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:14,014 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:26Z] INFO  21:26:14,092 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:26Z] INFO  21:26:14,100 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:26Z] INFO  21:26:14,123 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:26Z] INFO  21:26:14,506 IntervalUtils - Processing 1780 bp from intervals
[2015-09-30T20:26Z] WARN  21:26:14,510 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] WARN  21:26:14,510 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] INFO  21:26:14,569 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:26Z] INFO  21:26:14,781 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:26Z] INFO  21:26:14,782 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:26Z] INFO  21:26:14,782 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:26Z] INFO  21:26:14,782 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:26Z] INFO  21:26:14,816 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:26Z] INFO  21:26:23,493 VariantAnnotator - Processed 1590 loci.
[2015-09-30T20:26Z]
[2015-09-30T20:26Z] INFO  21:26:23,515 ProgressMeter -            done     23733.0     8.0 s       6.1 m       99.9%     8.0 s       0.0 s
[2015-09-30T20:26Z] INFO  21:26:23,515 ProgressMeter - Total runtime 8.73 secs, 0.15 min, 0.00 hours
[2015-09-30T20:26Z] INFO  21:26:23,515 MicroScheduler - 6101 reads were filtered out during the traversal out of approximately 116637 total reads (5.23%)
[2015-09-30T20:26Z] INFO  21:26:23,515 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:26Z] INFO  21:26:23,516 MicroScheduler -   -> 6043 reads (5.18% of total) failing DuplicateReadFilter
[2015-09-30T20:26Z] INFO  21:26:23,516 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:26Z] INFO  21:26:23,516 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:26Z] INFO  21:26:23,516 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:26Z] INFO  21:26:23,517 MicroScheduler -   -> 58 reads (0.05% of total) failing UnmappedReadFilter
[2015-09-30T20:26Z] INFO  21:26:24,025 VariantAnnotator - Processed 1887 loci.
[2015-09-30T20:26Z]
[2015-09-30T20:26Z] INFO  21:26:24,088 ProgressMeter -            done     11563.0    10.0 s      14.9 m      100.0%    10.0 s       0.0 s
[2015-09-30T20:26Z] INFO  21:26:24,088 ProgressMeter - Total runtime 10.32 secs, 0.17 min, 0.00 hours
[2015-09-30T20:26Z] INFO  21:26:24,089 MicroScheduler - 9027 reads were filtered out during the traversal out of approximately 180109 total reads (5.01%)
[2015-09-30T20:26Z] INFO  21:26:24,089 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:26Z] INFO  21:26:24,089 MicroScheduler -   -> 8976 reads (4.98% of total) failing DuplicateReadFilter
[2015-09-30T20:26Z] INFO  21:26:24,090 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:26Z] INFO  21:26:24,090 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:26Z] INFO  21:26:24,090 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:26Z] INFO  21:26:24,090 MicroScheduler -   -> 51 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:26Z] INFO  21:26:24,452 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:26Z] Genotyping with varscan: ('2', 158484801, 189599894) 1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam
[2015-09-30T20:26Z] samtools mpileup
[2015-09-30T20:26Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:26Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:26Z] INFO  21:26:25,055 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:26Z] Genotyping with varscan: ('2', 189838937, 221056966) 1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam
[2015-09-30T20:26Z] samtools mpileup
[2015-09-30T20:26Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:26Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:26Z] 1621664 positions in tumor
[2015-09-30T20:26Z] 1621653 positions shared in normal
[2015-09-30T20:26Z] 1589383 had sufficient coverage for comparison
[2015-09-30T20:26Z] 1586434 were called Reference
[2015-09-30T20:26Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:26Z] 455 were removed by the strand filter
[2015-09-30T20:26Z] 2854 were called Germline
[2015-09-30T20:26Z] 9 were called LOH
[2015-09-30T20:26Z] 75 were called Somatic
[2015-09-30T20:26Z] 11 were called Unknown
[2015-09-30T20:26Z] 0 were called Variant
[2015-09-30T20:26Z] Varscan paired fix
[2015-09-30T20:26Z] Varscan paired fix
[2015-09-30T20:26Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:26Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:26Z] bgzip syn3-2_95457728_127315933-raw.snp.vcf
[2015-09-30T20:26Z] tabix index syn3-2_95457728_127315933-raw.snp.vcf.gz
[2015-09-30T20:26Z] bgzip syn3-2_95457728_127315933-raw.indel.vcf
[2015-09-30T20:26Z] tabix index syn3-2_95457728_127315933-raw.indel.vcf.gz
[2015-09-30T20:26Z] Combine variant files
[2015-09-30T20:26Z] INFO  21:26:34,547 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:34,549 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:26Z] INFO  21:26:34,549 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:26Z] INFO  21:26:34,549 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:26Z] INFO  21:26:34,553 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpvDiEF9/tx/tmpPPLe9T/syn3-2_95457728_127315933-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/2/tx/tmpvDiEF9/syn3-2_95457728_127315933-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/2/tx/tmpvDiEF9/syn3-2_95457728_127315933-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_95457728_127315933-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:26Z] INFO  21:26:34,558 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:26Z] INFO  21:26:34,558 HelpFormatter - Date/Time: 2015/09/30 21:26:34
[2015-09-30T20:26Z] INFO  21:26:34,558 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:34,558 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:34,630 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:26Z] INFO  21:26:34,773 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:26Z] INFO  21:26:34,903 IntervalUtils - Processing 1630830 bp from intervals
[2015-09-30T20:26Z] WARN  21:26:34,904 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] WARN  21:26:34,905 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] INFO  21:26:34,960 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:26Z] INFO  21:26:34,964 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:26Z] INFO  21:26:34,964 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:26Z] INFO  21:26:34,965 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:26Z] INFO  21:26:34,965 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:26Z] INFO  21:26:36,783 ProgressMeter -            done      2977.0     1.0 s      10.2 m       99.6%     1.0 s       0.0 s
[2015-09-30T20:26Z] INFO  21:26:36,783 ProgressMeter - Total runtime 1.82 secs, 0.03 min, 0.00 hours
[2015-09-30T20:26Z] bgzip syn3-2_95457728_127315933-raw.vcf
[2015-09-30T20:26Z] tabix index syn3-2_95457728_127315933-raw.vcf.gz
[2015-09-30T20:26Z] bgzip syn3-2_95457728_127315933-raw-rejectfix.vcf
[2015-09-30T20:26Z] tabix index syn3-2_95457728_127315933-raw-rejectfix.vcf.gz
[2015-09-30T20:26Z] GATK: VariantAnnotator
[2015-09-30T20:26Z] INFO  21:26:39,818 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:39,820 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:26Z] INFO  21:26:39,820 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:26Z] INFO  21:26:39,820 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:26Z] INFO  21:26:39,824 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/2/syn3-2_95457728_127315933-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpAwJFH7/syn3-2_95457728_127315933-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_95457728_127315933-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:26Z] INFO  21:26:39,829 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:26Z] INFO  21:26:39,829 HelpFormatter - Date/Time: 2015/09/30 21:26:39
[2015-09-30T20:26Z] INFO  21:26:39,829 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:39,830 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:26Z] INFO  21:26:39,921 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:26Z] INFO  21:26:39,994 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:26Z] INFO  21:26:40,002 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:26Z] INFO  21:26:40,026 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:26Z] INFO  21:26:40,444 IntervalUtils - Processing 2977 bp from intervals
[2015-09-30T20:26Z] WARN  21:26:40,448 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] WARN  21:26:40,448 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:26Z] INFO  21:26:40,503 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:26Z] INFO  21:26:40,704 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:26Z] INFO  21:26:40,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:26Z] INFO  21:26:40,705 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:26Z] INFO  21:26:40,705 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:26Z] INFO  21:26:40,737 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:26Z] INFO  21:26:51,347 VariantAnnotator - Processed 2487 loci.
[2015-09-30T20:26Z]
[2015-09-30T20:26Z] INFO  21:26:51,600 ProgressMeter -            done     31596.0    10.0 s       5.7 m      100.0%    10.0 s       0.0 s
[2015-09-30T20:26Z] INFO  21:26:51,601 ProgressMeter - Total runtime 10.90 secs, 0.18 min, 0.00 hours
[2015-09-30T20:26Z] INFO  21:26:51,601 MicroScheduler - 8121 reads were filtered out during the traversal out of approximately 181516 total reads (4.47%)
[2015-09-30T20:26Z] INFO  21:26:51,601 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:26Z] INFO  21:26:51,603 MicroScheduler -   -> 8068 reads (4.44% of total) failing DuplicateReadFilter
[2015-09-30T20:26Z] INFO  21:26:51,604 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:26Z] INFO  21:26:51,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:26Z] INFO  21:26:51,604 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:26Z] INFO  21:26:51,604 MicroScheduler -   -> 53 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:26Z] INFO  21:26:52,599 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:26Z] Genotyping with varscan: ('2', 221341378, 243199373) 1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam
[2015-09-30T20:26Z] samtools mpileup
[2015-09-30T20:26Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:26Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:27Z] samtools mpileup
[2015-09-30T20:27Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:27Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:27Z] samtools mpileup
[2015-09-30T20:27Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:27Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:27Z] samtools mpileup
[2015-09-30T20:27Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:27Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:28Z] Varscan
[2015-09-30T20:28Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpvoOcJ3/syn3-2_158484801_189599894-raw-normal.mpileup
[2015-09-30T20:28Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpvoOcJ3/syn3-2_158484801_189599894-raw-tumor.mpileup
[2015-09-30T20:28Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:28Z] Min reads2:	2
[2015-09-30T20:28Z] Min strands2:	1
[2015-09-30T20:28Z] Min var freq:	0.1
[2015-09-30T20:28Z] Min freq for hom:	0.75
[2015-09-30T20:28Z] Normal purity:	1.0
[2015-09-30T20:28Z] Tumor purity:	1.0
[2015-09-30T20:28Z] Min avg qual:	15
[2015-09-30T20:28Z] P-value thresh:	0.98
[2015-09-30T20:28Z] Somatic p-value:	0.05
[2015-09-30T20:28Z] Varscan
[2015-09-30T20:28Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpSJDTn0/syn3-2_189838937_221056966-raw-normal.mpileup
[2015-09-30T20:28Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmpSJDTn0/syn3-2_189838937_221056966-raw-tumor.mpileup
[2015-09-30T20:28Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:28Z] Min reads2:	2
[2015-09-30T20:28Z] Min strands2:	1
[2015-09-30T20:28Z] Min var freq:	0.1
[2015-09-30T20:28Z] Min freq for hom:	0.75
[2015-09-30T20:28Z] Normal purity:	1.0
[2015-09-30T20:28Z] Tumor purity:	1.0
[2015-09-30T20:28Z] Min avg qual:	15
[2015-09-30T20:28Z] P-value thresh:	0.98
[2015-09-30T20:28Z] Somatic p-value:	0.05
[2015-09-30T20:28Z] Varscan
[2015-09-30T20:28Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmplpVqbQ/syn3-2_221341378_243199373-raw-normal.mpileup
[2015-09-30T20:28Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/2/tx/tmplpVqbQ/syn3-2_221341378_243199373-raw-tumor.mpileup
[2015-09-30T20:28Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:28Z] Min reads2:	2
[2015-09-30T20:28Z] Min strands2:	1
[2015-09-30T20:28Z] Min var freq:	0.1
[2015-09-30T20:28Z] Min freq for hom:	0.75
[2015-09-30T20:28Z] Normal purity:	1.0
[2015-09-30T20:28Z] Tumor purity:	1.0
[2015-09-30T20:28Z] Min avg qual:	15
[2015-09-30T20:28Z] P-value thresh:	0.98
[2015-09-30T20:28Z] Somatic p-value:	0.05
[2015-09-30T20:29Z] 1642020 positions in tumor
[2015-09-30T20:29Z] 1642009 positions shared in normal
[2015-09-30T20:29Z] 1580452 had sufficient coverage for comparison
[2015-09-30T20:29Z] 1578776 were called Reference
[2015-09-30T20:29Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:29Z] 93 were removed by the strand filter
[2015-09-30T20:29Z] 1629 were called Germline
[2015-09-30T20:29Z] 5 were called LOH
[2015-09-30T20:29Z] 31 were called Somatic
[2015-09-30T20:29Z] 11 were called Unknown
[2015-09-30T20:29Z] 0 were called Variant
[2015-09-30T20:29Z] Varscan paired fix
[2015-09-30T20:29Z] Varscan paired fix
[2015-09-30T20:29Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:29Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:29Z] bgzip syn3-2_158484801_189599894-raw.snp.vcf
[2015-09-30T20:29Z] tabix index syn3-2_158484801_189599894-raw.snp.vcf.gz
[2015-09-30T20:29Z] bgzip syn3-2_158484801_189599894-raw.indel.vcf
[2015-09-30T20:29Z] tabix index syn3-2_158484801_189599894-raw.indel.vcf.gz
[2015-09-30T20:29Z] Combine variant files
[2015-09-30T20:29Z] INFO  21:29:04,749 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:04,751 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:29Z] INFO  21:29:04,751 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:29Z] INFO  21:29:04,751 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:29Z] INFO  21:29:04,754 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpvoOcJ3/tx/tmpuZDHsr/syn3-2_158484801_189599894-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/2/tx/tmpvoOcJ3/syn3-2_158484801_189599894-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/2/tx/tmpvoOcJ3/syn3-2_158484801_189599894-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_158484801_189599894-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:29Z] INFO  21:29:04,760 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:29Z] INFO  21:29:04,760 HelpFormatter - Date/Time: 2015/09/30 21:29:04
[2015-09-30T20:29Z] INFO  21:29:04,761 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:04,761 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:04,840 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:29Z] INFO  21:29:05,185 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:29Z] INFO  21:29:05,318 IntervalUtils - Processing 1652675 bp from intervals
[2015-09-30T20:29Z] WARN  21:29:05,319 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:29Z] WARN  21:29:05,319 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:29Z] INFO  21:29:05,379 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:29Z] INFO  21:29:05,383 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:29Z] INFO  21:29:05,383 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:29Z] INFO  21:29:05,384 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:29Z] INFO  21:29:05,384 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:29Z] INFO  21:29:06,983 ProgressMeter -            done      1913.0     1.0 s      13.9 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:29Z] INFO  21:29:06,984 ProgressMeter - Total runtime 1.60 secs, 0.03 min, 0.00 hours
[2015-09-30T20:29Z] bgzip syn3-2_158484801_189599894-raw.vcf
[2015-09-30T20:29Z] tabix index syn3-2_158484801_189599894-raw.vcf.gz
[2015-09-30T20:29Z] bgzip syn3-2_158484801_189599894-raw-rejectfix.vcf
[2015-09-30T20:29Z] tabix index syn3-2_158484801_189599894-raw-rejectfix.vcf.gz
[2015-09-30T20:29Z] GATK: VariantAnnotator
[2015-09-30T20:29Z] INFO  21:29:09,938 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:09,940 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:29Z] INFO  21:29:09,940 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:29Z] INFO  21:29:09,940 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:29Z] INFO  21:29:09,944 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/2/syn3-2_158484801_189599894-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpp4913a/syn3-2_158484801_189599894-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_158484801_189599894-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:29Z] INFO  21:29:09,949 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:29Z] INFO  21:29:09,949 HelpFormatter - Date/Time: 2015/09/30 21:29:09
[2015-09-30T20:29Z] INFO  21:29:09,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:09,950 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:10,018 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:29Z] INFO  21:29:10,095 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:29Z] INFO  21:29:10,103 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:29Z] INFO  21:29:10,125 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:29Z] INFO  21:29:10,524 IntervalUtils - Processing 1913 bp from intervals
[2015-09-30T20:29Z] WARN  21:29:10,528 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:29Z] WARN  21:29:10,528 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:29Z] INFO  21:29:10,585 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:29Z] INFO  21:29:10,794 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:29Z] INFO  21:29:10,795 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:29Z] INFO  21:29:10,795 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:29Z] INFO  21:29:10,796 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:29Z] INFO  21:29:10,829 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:29Z] INFO  21:29:19,112 VariantAnnotator - Processed 1578 loci.
[2015-09-30T20:29Z]
[2015-09-30T20:29Z] INFO  21:29:19,199 ProgressMeter -            done      6393.0     8.0 s      21.9 m       99.9%     8.0 s       0.0 s
[2015-09-30T20:29Z] INFO  21:29:19,199 ProgressMeter - Total runtime 8.40 secs, 0.14 min, 0.00 hours
[2015-09-30T20:29Z] INFO  21:29:19,200 MicroScheduler - 4419 reads were filtered out during the traversal out of approximately 108706 total reads (4.07%)
[2015-09-30T20:29Z] INFO  21:29:19,200 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:29Z] INFO  21:29:19,200 MicroScheduler -   -> 4389 reads (4.04% of total) failing DuplicateReadFilter
[2015-09-30T20:29Z] INFO  21:29:19,200 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:29Z] INFO  21:29:19,201 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:29Z] INFO  21:29:19,201 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:29Z] INFO  21:29:19,201 MicroScheduler -   -> 30 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:29Z] INFO  21:29:20,376 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:29Z] Genotyping with varscan: ('3', 0, 31203562) 1_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam
[2015-09-30T20:29Z] samtools mpileup
[2015-09-30T20:29Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:29Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:29Z] 1367351 positions in tumor
[2015-09-30T20:29Z] 1367343 positions shared in normal
[2015-09-30T20:29Z] 1348052 had sufficient coverage for comparison
[2015-09-30T20:29Z] 1346169 were called Reference
[2015-09-30T20:29Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:29Z] 89 were removed by the strand filter
[2015-09-30T20:29Z] 1840 were called Germline
[2015-09-30T20:29Z] 1 were called LOH
[2015-09-30T20:29Z] 32 were called Somatic
[2015-09-30T20:29Z] 10 were called Unknown
[2015-09-30T20:29Z] 0 were called Variant
[2015-09-30T20:29Z] Varscan paired fix
[2015-09-30T20:29Z] Varscan paired fix
[2015-09-30T20:29Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:29Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:29Z] bgzip syn3-2_221341378_243199373-raw.snp.vcf
[2015-09-30T20:29Z] tabix index syn3-2_221341378_243199373-raw.snp.vcf.gz
[2015-09-30T20:29Z] bgzip syn3-2_221341378_243199373-raw.indel.vcf
[2015-09-30T20:29Z] tabix index syn3-2_221341378_243199373-raw.indel.vcf.gz
[2015-09-30T20:29Z] Combine variant files
[2015-09-30T20:29Z] INFO  21:29:50,103 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:50,105 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:29Z] INFO  21:29:50,105 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:29Z] INFO  21:29:50,105 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:29Z] INFO  21:29:50,108 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/2/tx/tmplpVqbQ/tx/tmpEqPhqv/syn3-2_221341378_243199373-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/2/tx/tmplpVqbQ/syn3-2_221341378_243199373-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/2/tx/tmplpVqbQ/syn3-2_221341378_243199373-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_221341378_243199373-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:29Z] INFO  21:29:50,115 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:29Z] INFO  21:29:50,115 HelpFormatter - Date/Time: 2015/09/30 21:29:50
[2015-09-30T20:29Z] INFO  21:29:50,115 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:50,115 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:50,191 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:29Z] INFO  21:29:50,334 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:29Z] INFO  21:29:50,463 IntervalUtils - Processing 1372298 bp from intervals
[2015-09-30T20:29Z] WARN  21:29:50,464 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:29Z] WARN  21:29:50,464 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:29Z] INFO  21:29:50,521 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:29Z] INFO  21:29:50,525 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:29Z] INFO  21:29:50,525 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:29Z] INFO  21:29:50,526 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:29Z] INFO  21:29:50,526 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:29Z] 1918610 positions in tumor
[2015-09-30T20:29Z] 1918597 positions shared in normal
[2015-09-30T20:29Z] 1866668 had sufficient coverage for comparison
[2015-09-30T20:29Z] 1864640 were called Reference
[2015-09-30T20:29Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:29Z] 95 were removed by the strand filter
[2015-09-30T20:29Z] 1973 were called Germline
[2015-09-30T20:29Z] 4 were called LOH
[2015-09-30T20:29Z] 36 were called Somatic
[2015-09-30T20:29Z] 15 were called Unknown
[2015-09-30T20:29Z] 0 were called Variant
[2015-09-30T20:29Z] Varscan paired fix
[2015-09-30T20:29Z] Varscan paired fix
[2015-09-30T20:29Z] INFO  21:29:53,157 ProgressMeter -            done      2125.0     2.0 s      20.6 m      100.0%     2.0 s       0.0 s
[2015-09-30T20:29Z] INFO  21:29:53,157 ProgressMeter - Total runtime 2.63 secs, 0.04 min, 0.00 hours
[2015-09-30T20:29Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:29Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:29Z] bgzip syn3-2_189838937_221056966-raw.snp.vcf
[2015-09-30T20:29Z] tabix index syn3-2_189838937_221056966-raw.snp.vcf.gz
[2015-09-30T20:29Z] bgzip syn3-2_189838937_221056966-raw.indel.vcf
[2015-09-30T20:29Z] tabix index syn3-2_189838937_221056966-raw.indel.vcf.gz
[2015-09-30T20:29Z] bgzip syn3-2_221341378_243199373-raw.vcf
[2015-09-30T20:29Z] tabix index syn3-2_221341378_243199373-raw.vcf.gz
[2015-09-30T20:29Z] Combine variant files
[2015-09-30T20:29Z] bgzip syn3-2_221341378_243199373-raw-rejectfix.vcf
[2015-09-30T20:29Z] tabix index syn3-2_221341378_243199373-raw-rejectfix.vcf.gz
[2015-09-30T20:29Z] GATK: VariantAnnotator
[2015-09-30T20:29Z] INFO  21:29:58,778 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:58,780 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:29Z] INFO  21:29:58,780 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:29Z] INFO  21:29:58,781 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:29Z] INFO  21:29:58,784 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpSJDTn0/tx/tmpKuhMZP/syn3-2_189838937_221056966-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/2/tx/tmpSJDTn0/syn3-2_189838937_221056966-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/2/tx/tmpSJDTn0/syn3-2_189838937_221056966-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_189838937_221056966-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:29Z] INFO  21:29:58,789 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:29Z] INFO  21:29:58,789 HelpFormatter - Date/Time: 2015/09/30 21:29:58
[2015-09-30T20:29Z] INFO  21:29:58,790 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:58,790 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:58,866 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:29Z] INFO  21:29:59,011 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:29Z] INFO  21:29:59,152 IntervalUtils - Processing 1927521 bp from intervals
[2015-09-30T20:29Z] WARN  21:29:59,153 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:29Z] WARN  21:29:59,153 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:29Z] INFO  21:29:59,211 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:29Z] INFO  21:29:59,216 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:29Z] INFO  21:29:59,216 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:29Z] INFO  21:29:59,216 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:29Z] INFO  21:29:59,217 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:29Z] INFO  21:29:59,536 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:59,538 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:29Z] INFO  21:29:59,539 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:29Z] INFO  21:29:59,539 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:29Z] INFO  21:29:59,542 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/2/syn3-2_221341378_243199373-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpVLyfe7/syn3-2_221341378_243199373-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_221341378_243199373-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:29Z] INFO  21:29:59,548 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:29Z] INFO  21:29:59,548 HelpFormatter - Date/Time: 2015/09/30 21:29:59
[2015-09-30T20:29Z] INFO  21:29:59,548 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:59,548 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:29Z] INFO  21:29:59,920 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:29Z] INFO  21:29:59,997 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:30Z] INFO  21:30:00,005 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:30Z] INFO  21:30:00,027 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:30Z] INFO  21:30:00,358 IntervalUtils - Processing 2126 bp from intervals
[2015-09-30T20:30Z] WARN  21:30:00,362 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:30Z] WARN  21:30:00,362 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:30Z] INFO  21:30:00,419 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:30Z] INFO  21:30:00,661 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:30Z] INFO  21:30:00,662 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:30Z] INFO  21:30:00,662 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:30Z] INFO  21:30:00,663 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:30Z] INFO  21:30:00,696 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:30Z] INFO  21:30:01,475 ProgressMeter -            done      2305.0     2.0 s      16.3 m       99.9%     2.0 s       0.0 s
[2015-09-30T20:30Z] INFO  21:30:01,475 ProgressMeter - Total runtime 2.26 secs, 0.04 min, 0.00 hours
[2015-09-30T20:30Z] samtools mpileup
[2015-09-30T20:30Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:30Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:30Z] bgzip syn3-2_189838937_221056966-raw.vcf
[2015-09-30T20:30Z] tabix index syn3-2_189838937_221056966-raw.vcf.gz
[2015-09-30T20:30Z] bgzip syn3-2_189838937_221056966-raw-rejectfix.vcf
[2015-09-30T20:30Z] tabix index syn3-2_189838937_221056966-raw-rejectfix.vcf.gz
[2015-09-30T20:30Z] GATK: VariantAnnotator
[2015-09-30T20:30Z] INFO  21:30:04,968 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:30Z] INFO  21:30:04,970 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:30Z] INFO  21:30:04,970 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:30Z] INFO  21:30:04,971 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:30Z] INFO  21:30:04,974 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/2/syn3-2_189838937_221056966-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/2/tx/tmpZGKqM7/syn3-2_189838937_221056966-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/2/syn3-2_189838937_221056966-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:30Z] INFO  21:30:04,980 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:30Z] INFO  21:30:04,980 HelpFormatter - Date/Time: 2015/09/30 21:30:04
[2015-09-30T20:30Z] INFO  21:30:04,980 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:30Z] INFO  21:30:04,980 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:30Z] INFO  21:30:05,081 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:30Z] INFO  21:30:05,165 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:30Z] INFO  21:30:05,173 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:30Z] INFO  21:30:05,194 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:30Z] INFO  21:30:05,575 IntervalUtils - Processing 2305 bp from intervals
[2015-09-30T20:30Z] WARN  21:30:05,579 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:30Z] WARN  21:30:05,580 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:30Z] INFO  21:30:05,633 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:30Z] INFO  21:30:05,864 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:30Z] INFO  21:30:05,864 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:30Z] INFO  21:30:05,865 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:30Z] INFO  21:30:05,865 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:30Z] INFO  21:30:05,897 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:30Z] INFO  21:30:10,874 VariantAnnotator - Processed 1785 loci.
[2015-09-30T20:30Z]
[2015-09-30T20:30Z] INFO  21:30:10,912 ProgressMeter -            done      9733.0    10.0 s      17.6 m      100.0%    10.0 s       0.0 s
[2015-09-30T20:30Z] INFO  21:30:10,912 ProgressMeter - Total runtime 10.25 secs, 0.17 min, 0.00 hours
[2015-09-30T20:30Z] INFO  21:30:10,912 MicroScheduler - 8694 reads were filtered out during the traversal out of approximately 168108 total reads (5.17%)
[2015-09-30T20:30Z] INFO  21:30:10,912 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:30Z] INFO  21:30:10,913 MicroScheduler -   -> 8658 reads (5.15% of total) failing DuplicateReadFilter
[2015-09-30T20:30Z] INFO  21:30:10,913 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:30Z] INFO  21:30:10,913 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:30Z] INFO  21:30:10,913 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:30Z] INFO  21:30:10,914 MicroScheduler -   -> 36 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:30Z] INFO  21:30:11,817 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:30Z] Genotyping with varscan: ('3', 31494593, 62516713) 1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam
[2015-09-30T20:30Z] samtools mpileup
[2015-09-30T20:30Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:30Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:30Z] INFO  21:30:16,304 VariantAnnotator - Processed 1925 loci.
[2015-09-30T20:30Z]
[2015-09-30T20:30Z] INFO  21:30:16,330 ProgressMeter -            done      9309.0    10.0 s      18.7 m      100.0%    10.0 s       0.0 s
[2015-09-30T20:30Z] INFO  21:30:16,330 ProgressMeter - Total runtime 10.47 secs, 0.17 min, 0.00 hours
[2015-09-30T20:30Z] INFO  21:30:16,330 MicroScheduler - 7013 reads were filtered out during the traversal out of approximately 152524 total reads (4.60%)
[2015-09-30T20:30Z] INFO  21:30:16,331 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:30Z] INFO  21:30:16,331 MicroScheduler -   -> 6978 reads (4.58% of total) failing DuplicateReadFilter
[2015-09-30T20:30Z] INFO  21:30:16,331 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:30Z] INFO  21:30:16,331 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:30Z] INFO  21:30:16,332 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:30Z] INFO  21:30:16,332 MicroScheduler -   -> 35 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:30Z] INFO  21:30:17,267 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:30Z] Genotyping with varscan: ('3', 62518267, 93593495) 1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam
[2015-09-30T20:30Z] samtools mpileup
[2015-09-30T20:30Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:30Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:30Z] samtools mpileup
[2015-09-30T20:30Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:30Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:30Z] Varscan
[2015-09-30T20:30Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpisIqEe/syn3-3_0_31203562-raw-normal.mpileup
[2015-09-30T20:30Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpisIqEe/syn3-3_0_31203562-raw-tumor.mpileup
[2015-09-30T20:30Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:30Z] Min reads2:	2
[2015-09-30T20:30Z] Min strands2:	1
[2015-09-30T20:30Z] Min var freq:	0.1
[2015-09-30T20:30Z] Min freq for hom:	0.75
[2015-09-30T20:30Z] Normal purity:	1.0
[2015-09-30T20:30Z] Tumor purity:	1.0
[2015-09-30T20:30Z] Min avg qual:	15
[2015-09-30T20:30Z] P-value thresh:	0.98
[2015-09-30T20:30Z] Somatic p-value:	0.05
[2015-09-30T20:30Z] Varscan
[2015-09-30T20:30Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpnpoyBf/syn3-3_62518267_93593495-raw-normal.mpileup
[2015-09-30T20:30Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpnpoyBf/syn3-3_62518267_93593495-raw-tumor.mpileup
[2015-09-30T20:30Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:30Z] Min reads2:	2
[2015-09-30T20:30Z] Min strands2:	1
[2015-09-30T20:30Z] Min var freq:	0.1
[2015-09-30T20:30Z] Min freq for hom:	0.75
[2015-09-30T20:30Z] Normal purity:	1.0
[2015-09-30T20:30Z] Tumor purity:	1.0
[2015-09-30T20:30Z] Min avg qual:	15
[2015-09-30T20:30Z] P-value thresh:	0.98
[2015-09-30T20:30Z] Somatic p-value:	0.05
[2015-09-30T20:31Z] 501529 positions in tumor
[2015-09-30T20:31Z] 501528 positions shared in normal
[2015-09-30T20:31Z] 487267 had sufficient coverage for comparison
[2015-09-30T20:31Z] 486157 were called Reference
[2015-09-30T20:31Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:31Z] 86 were removed by the strand filter
[2015-09-30T20:31Z] 1092 were called Germline
[2015-09-30T20:31Z] 2 were called LOH
[2015-09-30T20:31Z] 12 were called Somatic
[2015-09-30T20:31Z] 4 were called Unknown
[2015-09-30T20:31Z] 0 were called Variant
[2015-09-30T20:31Z] Varscan paired fix
[2015-09-30T20:31Z] Varscan paired fix
[2015-09-30T20:31Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:31Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:31Z] bgzip syn3-3_62518267_93593495-raw.snp.vcf
[2015-09-30T20:31Z] tabix index syn3-3_62518267_93593495-raw.snp.vcf.gz
[2015-09-30T20:31Z] bgzip syn3-3_62518267_93593495-raw.indel.vcf
[2015-09-30T20:31Z] tabix index syn3-3_62518267_93593495-raw.indel.vcf.gz
[2015-09-30T20:31Z] Combine variant files
[2015-09-30T20:31Z] INFO  21:31:14,305 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:14,307 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:31Z] INFO  21:31:14,307 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:31Z] INFO  21:31:14,307 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:31Z] INFO  21:31:14,311 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/3/tx/tmpnpoyBf/tx/tmpCvrAlm/syn3-3_62518267_93593495-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/3/tx/tmpnpoyBf/syn3-3_62518267_93593495-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/3/tx/tmpnpoyBf/syn3-3_62518267_93593495-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_62518267_93593495-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:31Z] INFO  21:31:14,316 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:31Z] INFO  21:31:14,316 HelpFormatter - Date/Time: 2015/09/30 21:31:14
[2015-09-30T20:31Z] INFO  21:31:14,316 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:14,317 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:14,395 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:31Z] INFO  21:31:14,632 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:31Z] INFO  21:31:14,730 IntervalUtils - Processing 504096 bp from intervals
[2015-09-30T20:31Z] WARN  21:31:14,730 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:31Z] WARN  21:31:14,731 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:31Z] INFO  21:31:14,788 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:31Z] INFO  21:31:14,790 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:31Z] INFO  21:31:14,791 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:31Z] INFO  21:31:14,791 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:31Z] INFO  21:31:14,791 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:31Z] INFO  21:31:16,145 ProgressMeter -            done      1167.0     1.0 s      19.3 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:31Z] INFO  21:31:16,146 ProgressMeter - Total runtime 1.35 secs, 0.02 min, 0.00 hours
[2015-09-30T20:31Z] bgzip syn3-3_62518267_93593495-raw.vcf
[2015-09-30T20:31Z] tabix index syn3-3_62518267_93593495-raw.vcf.gz
[2015-09-30T20:31Z] bgzip syn3-3_62518267_93593495-raw-rejectfix.vcf
[2015-09-30T20:31Z] tabix index syn3-3_62518267_93593495-raw-rejectfix.vcf.gz
[2015-09-30T20:31Z] GATK: VariantAnnotator
[2015-09-30T20:31Z] INFO  21:31:18,727 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:18,729 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:31Z] INFO  21:31:18,729 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:31Z] INFO  21:31:18,729 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:31Z] INFO  21:31:18,733 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/3/syn3-3_62518267_93593495-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/3/tx/tmp2l3zE0/syn3-3_62518267_93593495-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_62518267_93593495-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:31Z] INFO  21:31:18,738 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:31Z] INFO  21:31:18,738 HelpFormatter - Date/Time: 2015/09/30 21:31:18
[2015-09-30T20:31Z] INFO  21:31:18,739 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:18,739 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:18,837 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:31Z] INFO  21:31:18,914 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:31Z] INFO  21:31:18,922 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:31Z] INFO  21:31:18,945 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:31Z] INFO  21:31:19,287 IntervalUtils - Processing 1167 bp from intervals
[2015-09-30T20:31Z] WARN  21:31:19,291 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:31Z] WARN  21:31:19,292 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:31Z] INFO  21:31:19,348 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:31Z] INFO  21:31:19,436 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:31Z] INFO  21:31:19,436 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:31Z] INFO  21:31:19,436 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:31Z] INFO  21:31:19,437 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:31Z] INFO  21:31:19,535 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:31Z] INFO  21:31:25,804 VariantAnnotator - Processed 1023 loci.
[2015-09-30T20:31Z]
[2015-09-30T20:31Z] INFO  21:31:25,832 ProgressMeter -            done     33756.0     6.0 s       3.2 m       99.9%     6.0 s       0.0 s
[2015-09-30T20:31Z] INFO  21:31:25,833 ProgressMeter - Total runtime 6.40 secs, 0.11 min, 0.00 hours
[2015-09-30T20:31Z] INFO  21:31:25,833 MicroScheduler - 7358 reads were filtered out during the traversal out of approximately 76516 total reads (9.62%)
[2015-09-30T20:31Z] INFO  21:31:25,833 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:31Z] INFO  21:31:25,834 MicroScheduler -   -> 7239 reads (9.46% of total) failing DuplicateReadFilter
[2015-09-30T20:31Z] INFO  21:31:25,834 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:31Z] INFO  21:31:25,834 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:31Z] INFO  21:31:25,834 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:31Z] INFO  21:31:25,835 MicroScheduler -   -> 119 reads (0.16% of total) failing UnmappedReadFilter
[2015-09-30T20:31Z] INFO  21:31:26,857 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:31Z] Genotyping with varscan: ('3', 93595554, 124625281) 1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam
[2015-09-30T20:31Z] samtools mpileup
[2015-09-30T20:31Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:31Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:31Z] 1182454 positions in tumor
[2015-09-30T20:31Z] 1182450 positions shared in normal
[2015-09-30T20:31Z] 1163873 had sufficient coverage for comparison
[2015-09-30T20:31Z] 1162388 were called Reference
[2015-09-30T20:31Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:31Z] 91 were removed by the strand filter
[2015-09-30T20:31Z] 1445 were called Germline
[2015-09-30T20:31Z] 12 were called LOH
[2015-09-30T20:31Z] 23 were called Somatic
[2015-09-30T20:31Z] 5 were called Unknown
[2015-09-30T20:31Z] 0 were called Variant
[2015-09-30T20:31Z] Varscan paired fix
[2015-09-30T20:31Z] Varscan paired fix
[2015-09-30T20:31Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:31Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:31Z] bgzip syn3-3_0_31203562-raw.snp.vcf
[2015-09-30T20:31Z] tabix index syn3-3_0_31203562-raw.snp.vcf.gz
[2015-09-30T20:31Z] bgzip syn3-3_0_31203562-raw.indel.vcf
[2015-09-30T20:31Z] tabix index syn3-3_0_31203562-raw.indel.vcf.gz
[2015-09-30T20:31Z] Combine variant files
[2015-09-30T20:31Z] INFO  21:31:31,812 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:31,814 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:31Z] INFO  21:31:31,814 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:31Z] INFO  21:31:31,814 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:31Z] INFO  21:31:31,817 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/3/tx/tmpisIqEe/tx/tmp9Vvl9c/syn3-3_0_31203562-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/3/tx/tmpisIqEe/syn3-3_0_31203562-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/3/tx/tmpisIqEe/syn3-3_0_31203562-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_0_31203562-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:31Z] INFO  21:31:31,823 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:31Z] INFO  21:31:31,823 HelpFormatter - Date/Time: 2015/09/30 21:31:31
[2015-09-30T20:31Z] INFO  21:31:31,823 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:31,823 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:31,894 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:31Z] INFO  21:31:32,217 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:31Z] INFO  21:31:32,318 IntervalUtils - Processing 1186072 bp from intervals
[2015-09-30T20:31Z] WARN  21:31:32,319 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:31Z] WARN  21:31:32,319 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:31Z] INFO  21:31:32,373 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:31Z] INFO  21:31:32,376 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:31Z] INFO  21:31:32,376 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:31Z] INFO  21:31:32,376 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:31Z] INFO  21:31:32,377 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:31Z] INFO  21:31:33,564 ProgressMeter -            done      1623.0     1.0 s      12.2 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:31Z] INFO  21:31:33,565 ProgressMeter - Total runtime 1.19 secs, 0.02 min, 0.00 hours
[2015-09-30T20:31Z] bgzip syn3-3_0_31203562-raw.vcf
[2015-09-30T20:31Z] tabix index syn3-3_0_31203562-raw.vcf.gz
[2015-09-30T20:31Z] bgzip syn3-3_0_31203562-raw-rejectfix.vcf
[2015-09-30T20:31Z] tabix index syn3-3_0_31203562-raw-rejectfix.vcf.gz
[2015-09-30T20:31Z] GATK: VariantAnnotator
[2015-09-30T20:31Z] INFO  21:31:35,922 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:35,924 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:31Z] INFO  21:31:35,924 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:31Z] INFO  21:31:35,924 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:31Z] INFO  21:31:35,928 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/3/syn3-3_0_31203562-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/3/tx/tmpesfNqR/syn3-3_0_31203562-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_0_31203562-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:31Z] INFO  21:31:35,933 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:31Z] INFO  21:31:35,933 HelpFormatter - Date/Time: 2015/09/30 21:31:35
[2015-09-30T20:31Z] INFO  21:31:35,933 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:35,933 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:31Z] INFO  21:31:36,025 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:31Z] INFO  21:31:36,098 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:31Z] INFO  21:31:36,106 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:31Z] INFO  21:31:36,128 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:31Z] INFO  21:31:36,495 IntervalUtils - Processing 1623 bp from intervals
[2015-09-30T20:31Z] WARN  21:31:36,499 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:31Z] WARN  21:31:36,499 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:31Z] INFO  21:31:36,553 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:31Z] INFO  21:31:36,656 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:31Z] INFO  21:31:36,656 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:31Z] INFO  21:31:36,656 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:31Z] INFO  21:31:36,657 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:31Z] INFO  21:31:36,755 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:31Z] INFO  21:31:44,516 VariantAnnotator - Processed 1391 loci.
[2015-09-30T20:31Z]
[2015-09-30T20:31Z] INFO  21:31:44,549 ProgressMeter -            done      6965.0     7.0 s      18.9 m       99.9%     7.0 s       0.0 s
[2015-09-30T20:31Z] INFO  21:31:44,549 ProgressMeter - Total runtime 7.89 secs, 0.13 min, 0.00 hours
[2015-09-30T20:31Z] INFO  21:31:44,549 MicroScheduler - 5630 reads were filtered out during the traversal out of approximately 117140 total reads (4.81%)
[2015-09-30T20:31Z] INFO  21:31:44,549 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:31Z] INFO  21:31:44,550 MicroScheduler -   -> 5610 reads (4.79% of total) failing DuplicateReadFilter
[2015-09-30T20:31Z] INFO  21:31:44,550 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:31Z] INFO  21:31:44,550 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:31Z] INFO  21:31:44,550 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:31Z] INFO  21:31:44,551 MicroScheduler -   -> 20 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:31Z] INFO  21:31:45,511 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:31Z] Genotyping with varscan: ('3', 124626733, 155649953) 1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam
[2015-09-30T20:31Z] samtools mpileup
[2015-09-30T20:31Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:31Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:32Z] samtools mpileup
[2015-09-30T20:32Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:32Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:32Z] samtools mpileup
[2015-09-30T20:32Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:32Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:32Z] samtools mpileup
[2015-09-30T20:32Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:32Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:32Z] Varscan
[2015-09-30T20:32Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpUQ2ZQx/syn3-3_93595554_124625281-raw-normal.mpileup
[2015-09-30T20:32Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpUQ2ZQx/syn3-3_93595554_124625281-raw-tumor.mpileup
[2015-09-30T20:32Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:32Z] Min reads2:	2
[2015-09-30T20:32Z] Min strands2:	1
[2015-09-30T20:32Z] Min var freq:	0.1
[2015-09-30T20:32Z] Min freq for hom:	0.75
[2015-09-30T20:32Z] Normal purity:	1.0
[2015-09-30T20:32Z] Tumor purity:	1.0
[2015-09-30T20:32Z] Min avg qual:	15
[2015-09-30T20:32Z] P-value thresh:	0.98
[2015-09-30T20:32Z] Somatic p-value:	0.05
[2015-09-30T20:33Z] Varscan
[2015-09-30T20:33Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpzo3kuL/syn3-3_124626733_155649953-raw-normal.mpileup
[2015-09-30T20:33Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpzo3kuL/syn3-3_124626733_155649953-raw-tumor.mpileup
[2015-09-30T20:33Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:33Z] Min reads2:	2
[2015-09-30T20:33Z] Min strands2:	1
[2015-09-30T20:33Z] Min var freq:	0.1
[2015-09-30T20:33Z] Min freq for hom:	0.75
[2015-09-30T20:33Z] Normal purity:	1.0
[2015-09-30T20:33Z] Tumor purity:	1.0
[2015-09-30T20:33Z] Min avg qual:	15
[2015-09-30T20:33Z] P-value thresh:	0.98
[2015-09-30T20:33Z] Somatic p-value:	0.05
[2015-09-30T20:33Z] 1328246 positions in tumor
[2015-09-30T20:33Z] 1328237 positions shared in normal
[2015-09-30T20:33Z] 1297450 had sufficient coverage for comparison
[2015-09-30T20:33Z] 1295832 were called Reference
[2015-09-30T20:33Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:33Z] 56 were removed by the strand filter
[2015-09-30T20:33Z] 1583 were called Germline
[2015-09-30T20:33Z] 3 were called LOH
[2015-09-30T20:33Z] 22 were called Somatic
[2015-09-30T20:33Z] 10 were called Unknown
[2015-09-30T20:33Z] 0 were called Variant
[2015-09-30T20:33Z] Varscan paired fix
[2015-09-30T20:33Z] Varscan paired fix
[2015-09-30T20:33Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:33Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:33Z] bgzip syn3-3_93595554_124625281-raw.snp.vcf
[2015-09-30T20:33Z] tabix index syn3-3_93595554_124625281-raw.snp.vcf.gz
[2015-09-30T20:33Z] bgzip syn3-3_93595554_124625281-raw.indel.vcf
[2015-09-30T20:33Z] tabix index syn3-3_93595554_124625281-raw.indel.vcf.gz
[2015-09-30T20:33Z] Combine variant files
[2015-09-30T20:33Z] INFO  21:33:51,327 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:33Z] INFO  21:33:51,329 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:33Z] INFO  21:33:51,329 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:33Z] INFO  21:33:51,329 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:33Z] INFO  21:33:51,332 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/3/tx/tmpUQ2ZQx/tx/tmp25IPBd/syn3-3_93595554_124625281-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/3/tx/tmpUQ2ZQx/syn3-3_93595554_124625281-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/3/tx/tmpUQ2ZQx/syn3-3_93595554_124625281-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_93595554_124625281-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:33Z] INFO  21:33:51,338 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:33Z] INFO  21:33:51,339 HelpFormatter - Date/Time: 2015/09/30 21:33:51
[2015-09-30T20:33Z] INFO  21:33:51,339 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:33Z] INFO  21:33:51,339 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:33Z] INFO  21:33:51,416 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:33Z] INFO  21:33:51,803 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:33Z] INFO  21:33:51,930 IntervalUtils - Processing 1334187 bp from intervals
[2015-09-30T20:33Z] WARN  21:33:51,931 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:33Z] WARN  21:33:51,931 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:33Z] INFO  21:33:51,987 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:33Z] INFO  21:33:51,991 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:33Z] INFO  21:33:51,991 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:33Z] INFO  21:33:51,991 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:33Z] INFO  21:33:51,992 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:33Z] INFO  21:33:54,035 ProgressMeter -            done      1874.0     2.0 s      18.2 m      100.0%     2.0 s       0.0 s
[2015-09-30T20:33Z] INFO  21:33:54,036 ProgressMeter - Total runtime 2.04 secs, 0.03 min, 0.00 hours
[2015-09-30T20:34Z] Varscan
[2015-09-30T20:34Z] bgzip syn3-3_93595554_124625281-raw.vcf
[2015-09-30T20:34Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpOII6hM/syn3-3_31494593_62516713-raw-normal.mpileup
[2015-09-30T20:34Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpOII6hM/syn3-3_31494593_62516713-raw-tumor.mpileup
[2015-09-30T20:34Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:34Z] Min reads2:	2
[2015-09-30T20:34Z] Min strands2:	1
[2015-09-30T20:34Z] Min var freq:	0.1
[2015-09-30T20:34Z] Min freq for hom:	0.75
[2015-09-30T20:34Z] Normal purity:	1.0
[2015-09-30T20:34Z] Tumor purity:	1.0
[2015-09-30T20:34Z] Min avg qual:	15
[2015-09-30T20:34Z] P-value thresh:	0.98
[2015-09-30T20:34Z] Somatic p-value:	0.05
[2015-09-30T20:34Z] tabix index syn3-3_93595554_124625281-raw.vcf.gz
[2015-09-30T20:34Z] bgzip syn3-3_93595554_124625281-raw-rejectfix.vcf
[2015-09-30T20:34Z] tabix index syn3-3_93595554_124625281-raw-rejectfix.vcf.gz
[2015-09-30T20:34Z] GATK: VariantAnnotator
[2015-09-30T20:34Z] INFO  21:34:04,579 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:34Z] INFO  21:34:04,581 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:34Z] INFO  21:34:04,581 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:34Z] INFO  21:34:04,582 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:34Z] INFO  21:34:04,585 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/3/syn3-3_93595554_124625281-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/3/tx/tmp2UuMWC/syn3-3_93595554_124625281-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_93595554_124625281-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:34Z] INFO  21:34:04,591 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:34Z] INFO  21:34:04,591 HelpFormatter - Date/Time: 2015/09/30 21:34:04
[2015-09-30T20:34Z] INFO  21:34:04,591 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:34Z] INFO  21:34:04,592 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:34Z] INFO  21:34:04,704 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:34Z] INFO  21:34:04,946 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:34Z] INFO  21:34:04,953 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:34Z] INFO  21:34:05,402 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.45
[2015-09-30T20:34Z] INFO  21:34:05,887 IntervalUtils - Processing 1874 bp from intervals
[2015-09-30T20:34Z] WARN  21:34:05,891 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:34Z] WARN  21:34:05,891 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:34Z] INFO  21:34:05,949 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:34Z] INFO  21:34:06,135 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:34Z] INFO  21:34:06,135 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:34Z] INFO  21:34:06,136 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:34Z] INFO  21:34:06,136 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:34Z] INFO  21:34:06,170 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:34Z] INFO  21:34:15,165 VariantAnnotator - Processed 1554 loci.
[2015-09-30T20:34Z]
[2015-09-30T20:34Z] INFO  21:34:15,187 ProgressMeter -            done      6466.0     9.0 s      23.3 m       99.9%     9.0 s       0.0 s
[2015-09-30T20:34Z] INFO  21:34:15,188 ProgressMeter - Total runtime 9.05 secs, 0.15 min, 0.00 hours
[2015-09-30T20:34Z] INFO  21:34:15,188 MicroScheduler - 5170 reads were filtered out during the traversal out of approximately 117572 total reads (4.40%)
[2015-09-30T20:34Z] INFO  21:34:15,188 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:34Z] INFO  21:34:15,189 MicroScheduler -   -> 5141 reads (4.37% of total) failing DuplicateReadFilter
[2015-09-30T20:34Z] INFO  21:34:15,189 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:34Z] INFO  21:34:15,189 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:34Z] INFO  21:34:15,189 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:34Z] INFO  21:34:15,189 MicroScheduler -   -> 29 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:34Z] INFO  21:34:16,122 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:34Z] Genotyping with varscan: ('3', 155652401, 186761310) 1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam
[2015-09-30T20:34Z] samtools mpileup
[2015-09-30T20:34Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:34Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:34Z] 1632085 positions in tumor
[2015-09-30T20:34Z] 1632076 positions shared in normal
[2015-09-30T20:34Z] 1593347 had sufficient coverage for comparison
[2015-09-30T20:34Z] 1591296 were called Reference
[2015-09-30T20:34Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:34Z] 90 were removed by the strand filter
[2015-09-30T20:34Z] 1997 were called Germline
[2015-09-30T20:34Z] 6 were called LOH
[2015-09-30T20:34Z] 33 were called Somatic
[2015-09-30T20:34Z] 15 were called Unknown
[2015-09-30T20:34Z] 0 were called Variant
[2015-09-30T20:34Z] Varscan paired fix
[2015-09-30T20:34Z] Varscan paired fix
[2015-09-30T20:34Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:34Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:34Z] bgzip syn3-3_124626733_155649953-raw.snp.vcf
[2015-09-30T20:34Z] tabix index syn3-3_124626733_155649953-raw.snp.vcf.gz
[2015-09-30T20:34Z] bgzip syn3-3_124626733_155649953-raw.indel.vcf
[2015-09-30T20:34Z] tabix index syn3-3_124626733_155649953-raw.indel.vcf.gz
[2015-09-30T20:34Z] Combine variant files
[2015-09-30T20:34Z] INFO  21:34:46,273 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:34Z] INFO  21:34:46,276 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:34Z] INFO  21:34:46,276 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:34Z] INFO  21:34:46,276 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:34Z] INFO  21:34:46,279 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/3/tx/tmpzo3kuL/tx/tmpzVTcXX/syn3-3_124626733_155649953-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/3/tx/tmpzo3kuL/syn3-3_124626733_155649953-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/3/tx/tmpzo3kuL/syn3-3_124626733_155649953-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_124626733_155649953-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:34Z] INFO  21:34:46,285 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:34Z] INFO  21:34:46,285 HelpFormatter - Date/Time: 2015/09/30 21:34:46
[2015-09-30T20:34Z] INFO  21:34:46,285 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:34Z] INFO  21:34:46,285 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:34Z] INFO  21:34:46,360 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:34Z] INFO  21:34:46,637 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:34Z] INFO  21:34:46,768 IntervalUtils - Processing 1640755 bp from intervals
[2015-09-30T20:34Z] WARN  21:34:46,769 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:34Z] WARN  21:34:46,769 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:34Z] INFO  21:34:46,826 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:34Z] INFO  21:34:46,830 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:34Z] INFO  21:34:46,830 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:34Z] INFO  21:34:46,831 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:34Z] INFO  21:34:46,831 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:34Z] INFO  21:34:48,506 ProgressMeter -            done      2250.0     1.0 s      12.4 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:34Z] INFO  21:34:48,507 ProgressMeter - Total runtime 1.68 secs, 0.03 min, 0.00 hours
[2015-09-30T20:34Z] bgzip syn3-3_124626733_155649953-raw.vcf
[2015-09-30T20:34Z] tabix index syn3-3_124626733_155649953-raw.vcf.gz
[2015-09-30T20:34Z] bgzip syn3-3_124626733_155649953-raw-rejectfix.vcf
[2015-09-30T20:34Z] tabix index syn3-3_124626733_155649953-raw-rejectfix.vcf.gz
[2015-09-30T20:34Z] GATK: VariantAnnotator
[2015-09-30T20:34Z] INFO  21:34:51,137 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:34Z] INFO  21:34:51,139 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:34Z] INFO  21:34:51,140 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:34Z] INFO  21:34:51,140 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:34Z] INFO  21:34:51,143 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/3/syn3-3_124626733_155649953-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/3/tx/tmp3A3LC1/syn3-3_124626733_155649953-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_124626733_155649953-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:34Z] INFO  21:34:51,149 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:34Z] INFO  21:34:51,149 HelpFormatter - Date/Time: 2015/09/30 21:34:51
[2015-09-30T20:34Z] INFO  21:34:51,149 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:34Z] INFO  21:34:51,150 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:34Z] INFO  21:34:51,244 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:34Z] INFO  21:34:51,480 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:34Z] INFO  21:34:51,488 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:34Z] INFO  21:34:51,509 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:34Z] INFO  21:34:51,901 IntervalUtils - Processing 2250 bp from intervals
[2015-09-30T20:34Z] WARN  21:34:51,905 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:34Z] WARN  21:34:51,905 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:34Z] INFO  21:34:51,958 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:34Z] INFO  21:34:52,157 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:34Z] INFO  21:34:52,157 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:34Z] INFO  21:34:52,157 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:34Z] INFO  21:34:52,158 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:34Z] INFO  21:34:52,189 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:34Z] samtools mpileup
[2015-09-30T20:34Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:34Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:35Z] INFO  21:35:02,446 VariantAnnotator - Processed 1950 loci.
[2015-09-30T20:35Z]
[2015-09-30T20:35Z] INFO  21:35:02,467 ProgressMeter -            done     14400.0    10.0 s      11.9 m      100.0%    10.0 s       0.0 s
[2015-09-30T20:35Z] INFO  21:35:02,467 ProgressMeter - Total runtime 10.31 secs, 0.17 min, 0.00 hours
[2015-09-30T20:35Z] INFO  21:35:02,468 MicroScheduler - 7309 reads were filtered out during the traversal out of approximately 154962 total reads (4.72%)
[2015-09-30T20:35Z] INFO  21:35:02,468 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:35Z] INFO  21:35:02,468 MicroScheduler -   -> 7279 reads (4.70% of total) failing DuplicateReadFilter
[2015-09-30T20:35Z] INFO  21:35:02,468 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:35Z] INFO  21:35:02,469 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:35Z] INFO  21:35:02,469 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:35Z] INFO  21:35:02,469 MicroScheduler -   -> 30 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:35Z] INFO  21:35:03,420 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:35Z] Genotyping with varscan: ('3', 186768753, 198022430) 1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam
[2015-09-30T20:35Z] samtools mpileup
[2015-09-30T20:35Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:35Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:35Z] samtools mpileup
[2015-09-30T20:35Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:35Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:35Z] Varscan
[2015-09-30T20:35Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpHMj5Gb/syn3-3_155652401_186761310-raw-normal.mpileup
[2015-09-30T20:35Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpHMj5Gb/syn3-3_155652401_186761310-raw-tumor.mpileup
[2015-09-30T20:35Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:35Z] Min reads2:	2
[2015-09-30T20:35Z] Min strands2:	1
[2015-09-30T20:35Z] Min var freq:	0.1
[2015-09-30T20:35Z] Min freq for hom:	0.75
[2015-09-30T20:35Z] Normal purity:	1.0
[2015-09-30T20:35Z] Tumor purity:	1.0
[2015-09-30T20:35Z] Min avg qual:	15
[2015-09-30T20:35Z] P-value thresh:	0.98
[2015-09-30T20:35Z] Somatic p-value:	0.05
[2015-09-30T20:35Z] Varscan
[2015-09-30T20:35Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpi5vhmV/syn3-3_186768753_198022430-raw-normal.mpileup
[2015-09-30T20:35Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/3/tx/tmpi5vhmV/syn3-3_186768753_198022430-raw-tumor.mpileup
[2015-09-30T20:35Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:35Z] Min reads2:	2
[2015-09-30T20:35Z] Min strands2:	1
[2015-09-30T20:35Z] Min var freq:	0.1
[2015-09-30T20:35Z] Min freq for hom:	0.75
[2015-09-30T20:35Z] Normal purity:	1.0
[2015-09-30T20:35Z] Tumor purity:	1.0
[2015-09-30T20:35Z] Min avg qual:	15
[2015-09-30T20:35Z] P-value thresh:	0.98
[2015-09-30T20:35Z] Somatic p-value:	0.05
[2015-09-30T20:35Z] 2629784 positions in tumor
[2015-09-30T20:35Z] 2629780 positions shared in normal
[2015-09-30T20:35Z] 2601176 had sufficient coverage for comparison
[2015-09-30T20:35Z] 2598931 were called Reference
[2015-09-30T20:35Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:35Z] 118 were removed by the strand filter
[2015-09-30T20:35Z] 2168 were called Germline
[2015-09-30T20:35Z] 12 were called LOH
[2015-09-30T20:35Z] 46 were called Somatic
[2015-09-30T20:35Z] 19 were called Unknown
[2015-09-30T20:35Z] 0 were called Variant
[2015-09-30T20:35Z] Varscan paired fix
[2015-09-30T20:35Z] Varscan paired fix
[2015-09-30T20:35Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:35Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:35Z] bgzip syn3-3_31494593_62516713-raw.snp.vcf
[2015-09-30T20:35Z] tabix index syn3-3_31494593_62516713-raw.snp.vcf.gz
[2015-09-30T20:35Z] bgzip syn3-3_31494593_62516713-raw.indel.vcf
[2015-09-30T20:35Z] tabix index syn3-3_31494593_62516713-raw.indel.vcf.gz
[2015-09-30T20:35Z] Combine variant files
[2015-09-30T20:35Z] INFO  21:35:59,114 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:35Z] INFO  21:35:59,117 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:35Z] INFO  21:35:59,117 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:35Z] INFO  21:35:59,117 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:35Z] INFO  21:35:59,120 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/3/tx/tmpOII6hM/tx/tmppwpWMT/syn3-3_31494593_62516713-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/3/tx/tmpOII6hM/syn3-3_31494593_62516713-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/3/tx/tmpOII6hM/syn3-3_31494593_62516713-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_31494593_62516713-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:35Z] INFO  21:35:59,126 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:35Z] INFO  21:35:59,126 HelpFormatter - Date/Time: 2015/09/30 21:35:59
[2015-09-30T20:35Z] INFO  21:35:59,126 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:35Z] INFO  21:35:59,127 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:35Z] INFO  21:35:59,206 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:35Z] INFO  21:35:59,356 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:35Z] INFO  21:35:59,525 IntervalUtils - Processing 2635478 bp from intervals
[2015-09-30T20:35Z] WARN  21:35:59,526 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:35Z] WARN  21:35:59,526 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:35Z] INFO  21:35:59,585 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:35Z] INFO  21:35:59,591 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:35Z] INFO  21:35:59,591 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:35Z] INFO  21:35:59,592 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:35Z] INFO  21:35:59,592 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:36Z] INFO  21:36:01,397 ProgressMeter -            done      2600.0     1.0 s      11.6 m       99.8%     1.0 s       0.0 s
[2015-09-30T20:36Z] INFO  21:36:01,398 ProgressMeter - Total runtime 1.81 secs, 0.03 min, 0.00 hours
[2015-09-30T20:36Z] bgzip syn3-3_31494593_62516713-raw.vcf
[2015-09-30T20:36Z] tabix index syn3-3_31494593_62516713-raw.vcf.gz
[2015-09-30T20:36Z] bgzip syn3-3_31494593_62516713-raw-rejectfix.vcf
[2015-09-30T20:36Z] tabix index syn3-3_31494593_62516713-raw-rejectfix.vcf.gz
[2015-09-30T20:36Z] GATK: VariantAnnotator
[2015-09-30T20:36Z] INFO  21:36:06,521 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:06,524 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:36Z] INFO  21:36:06,524 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:36Z] INFO  21:36:06,524 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:36Z] INFO  21:36:06,528 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/3/syn3-3_31494593_62516713-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/3/tx/tmporZs0D/syn3-3_31494593_62516713-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_31494593_62516713-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:36Z] INFO  21:36:06,533 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:36Z] INFO  21:36:06,534 HelpFormatter - Date/Time: 2015/09/30 21:36:06
[2015-09-30T20:36Z] INFO  21:36:06,534 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:06,534 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:06,612 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:36Z] INFO  21:36:06,691 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:36Z] INFO  21:36:06,699 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:36Z] INFO  21:36:06,740 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T20:36Z] INFO  21:36:07,149 IntervalUtils - Processing 2600 bp from intervals
[2015-09-30T20:36Z] WARN  21:36:07,153 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] WARN  21:36:07,153 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] INFO  21:36:07,347 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:36Z] INFO  21:36:07,595 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:36Z] INFO  21:36:07,596 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:36Z] INFO  21:36:07,596 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:36Z] INFO  21:36:07,596 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:36Z] INFO  21:36:07,629 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:36Z] 586993 positions in tumor
[2015-09-30T20:36Z] 586988 positions shared in normal
[2015-09-30T20:36Z] 576082 had sufficient coverage for comparison
[2015-09-30T20:36Z] 574445 were called Reference
[2015-09-30T20:36Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:36Z] 188 were removed by the strand filter
[2015-09-30T20:36Z] 1588 were called Germline
[2015-09-30T20:36Z] 6 were called LOH
[2015-09-30T20:36Z] 35 were called Somatic
[2015-09-30T20:36Z] 8 were called Unknown
[2015-09-30T20:36Z] 0 were called Variant
[2015-09-30T20:36Z] Varscan paired fix
[2015-09-30T20:36Z] Varscan paired fix
[2015-09-30T20:36Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:36Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:36Z] bgzip syn3-3_186768753_198022430-raw.snp.vcf
[2015-09-30T20:36Z] tabix index syn3-3_186768753_198022430-raw.snp.vcf.gz
[2015-09-30T20:36Z] bgzip syn3-3_186768753_198022430-raw.indel.vcf
[2015-09-30T20:36Z] tabix index syn3-3_186768753_198022430-raw.indel.vcf.gz
[2015-09-30T20:36Z] Combine variant files
[2015-09-30T20:36Z] INFO  21:36:18,176 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:18,178 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:36Z] INFO  21:36:18,178 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:36Z] INFO  21:36:18,179 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:36Z] INFO  21:36:18,182 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/3/tx/tmpi5vhmV/tx/tmp7qymb7/syn3-3_186768753_198022430-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/3/tx/tmpi5vhmV/syn3-3_186768753_198022430-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/3/tx/tmpi5vhmV/syn3-3_186768753_198022430-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_186768753_198022430-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:36Z] INFO  21:36:18,188 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:36Z] INFO  21:36:18,188 HelpFormatter - Date/Time: 2015/09/30 21:36:18
[2015-09-30T20:36Z] INFO  21:36:18,188 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:18,188 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:18,266 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:36Z] INFO  21:36:18,592 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:36Z] INFO  21:36:18,699 IntervalUtils - Processing 589876 bp from intervals
[2015-09-30T20:36Z] WARN  21:36:18,700 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] WARN  21:36:18,700 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] 1188425 positions in tumor
[2015-09-30T20:36Z] 1188417 positions shared in normal
[2015-09-30T20:36Z] 1149924 had sufficient coverage for comparison
[2015-09-30T20:36Z] 1148568 were called Reference
[2015-09-30T20:36Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:36Z] 92 were removed by the strand filter
[2015-09-30T20:36Z] 1301 were called Germline
[2015-09-30T20:36Z] 5 were called LOH
[2015-09-30T20:36Z] 32 were called Somatic
[2015-09-30T20:36Z] 18 were called Unknown
[2015-09-30T20:36Z] 0 were called Variant
[2015-09-30T20:36Z] Varscan paired fix
[2015-09-30T20:36Z] INFO  21:36:18,761 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:36Z] INFO  21:36:18,764 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:36Z] INFO  21:36:18,764 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:36Z] INFO  21:36:18,764 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:36Z] INFO  21:36:18,765 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:36Z] Varscan paired fix
[2015-09-30T20:36Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:36Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:36Z] bgzip syn3-3_155652401_186761310-raw.snp.vcf
[2015-09-30T20:36Z] tabix index syn3-3_155652401_186761310-raw.snp.vcf.gz
[2015-09-30T20:36Z] bgzip syn3-3_155652401_186761310-raw.indel.vcf
[2015-09-30T20:36Z] tabix index syn3-3_155652401_186761310-raw.indel.vcf.gz
[2015-09-30T20:36Z] Combine variant files
[2015-09-30T20:36Z] INFO  21:36:20,725 ProgressMeter -            done      1592.0     1.0 s      20.5 m       99.7%     1.0 s       0.0 s
[2015-09-30T20:36Z] INFO  21:36:20,725 ProgressMeter - Total runtime 1.96 secs, 0.03 min, 0.00 hours
[2015-09-30T20:36Z] INFO  21:36:20,805 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:20,807 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:36Z] INFO  21:36:20,807 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:36Z] INFO  21:36:20,807 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:36Z] INFO  21:36:20,811 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/3/tx/tmpHMj5Gb/tx/tmpEAiYkw/syn3-3_155652401_186761310-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/3/tx/tmpHMj5Gb/syn3-3_155652401_186761310-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/3/tx/tmpHMj5Gb/syn3-3_155652401_186761310-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_155652401_186761310-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:36Z] INFO  21:36:20,816 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:36Z] INFO  21:36:20,817 HelpFormatter - Date/Time: 2015/09/30 21:36:20
[2015-09-30T20:36Z] INFO  21:36:20,817 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:20,817 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:36Z] bgzip syn3-3_186768753_198022430-raw.vcf
[2015-09-30T20:36Z] INFO  21:36:20,898 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:36Z] tabix index syn3-3_186768753_198022430-raw.vcf.gz
[2015-09-30T20:36Z] INFO  21:36:21,042 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:36Z] INFO  21:36:21,163 IntervalUtils - Processing 1196842 bp from intervals
[2015-09-30T20:36Z] WARN  21:36:21,164 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] WARN  21:36:21,164 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] INFO  21:36:21,223 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:36Z] INFO  21:36:21,227 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:36Z] INFO  21:36:21,227 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:36Z] INFO  21:36:21,227 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:36Z] INFO  21:36:21,228 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:36Z] bgzip syn3-3_186768753_198022430-raw-rejectfix.vcf
[2015-09-30T20:36Z] INFO  21:36:21,332 VariantAnnotator - Processed 2117 loci.
[2015-09-30T20:36Z]
[2015-09-30T20:36Z] tabix index syn3-3_186768753_198022430-raw-rejectfix.vcf.gz
[2015-09-30T20:36Z] INFO  21:36:21,353 ProgressMeter -            done      9000.0    13.0 s      25.5 m      100.0%    13.0 s       0.0 s
[2015-09-30T20:36Z] INFO  21:36:21,353 ProgressMeter - Total runtime 13.76 secs, 0.23 min, 0.00 hours
[2015-09-30T20:36Z] INFO  21:36:21,353 MicroScheduler - 10062 reads were filtered out during the traversal out of approximately 202116 total reads (4.98%)
[2015-09-30T20:36Z] INFO  21:36:21,354 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:36Z] INFO  21:36:21,354 MicroScheduler -   -> 10020 reads (4.96% of total) failing DuplicateReadFilter
[2015-09-30T20:36Z] INFO  21:36:21,354 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:36Z] INFO  21:36:21,354 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:36Z] INFO  21:36:21,355 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:36Z] INFO  21:36:21,355 MicroScheduler -   -> 42 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:36Z] GATK: VariantAnnotator
[2015-09-30T20:36Z] INFO  21:36:22,517 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:36Z] Genotyping with varscan: ('4', 0, 31018607) 1_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam
[2015-09-30T20:36Z] INFO  21:36:22,803 ProgressMeter -            done      1484.0     1.0 s      17.7 m       99.8%     1.0 s       0.0 s
[2015-09-30T20:36Z] INFO  21:36:22,804 ProgressMeter - Total runtime 1.58 secs, 0.03 min, 0.00 hours
[2015-09-30T20:36Z] samtools mpileup
[2015-09-30T20:36Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:36Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:36Z] bgzip syn3-3_155652401_186761310-raw.vcf
[2015-09-30T20:36Z] tabix index syn3-3_155652401_186761310-raw.vcf.gz
[2015-09-30T20:36Z] INFO  21:36:23,180 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:23,182 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:36Z] INFO  21:36:23,183 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:36Z] INFO  21:36:23,183 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:36Z] INFO  21:36:23,186 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/3/syn3-3_186768753_198022430-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/3/tx/tmp9VicaP/syn3-3_186768753_198022430-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_186768753_198022430-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:36Z] INFO  21:36:23,192 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:36Z] INFO  21:36:23,192 HelpFormatter - Date/Time: 2015/09/30 21:36:23
[2015-09-30T20:36Z] INFO  21:36:23,192 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:23,192 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:23,326 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:36Z] INFO  21:36:23,576 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:36Z] INFO  21:36:23,584 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:36Z] bgzip syn3-3_155652401_186761310-raw-rejectfix.vcf
[2015-09-30T20:36Z] INFO  21:36:23,803 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.22
[2015-09-30T20:36Z] INFO  21:36:24,638 IntervalUtils - Processing 1608 bp from intervals
[2015-09-30T20:36Z] WARN  21:36:24,642 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] WARN  21:36:24,642 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] tabix index syn3-3_155652401_186761310-raw-rejectfix.vcf.gz
[2015-09-30T20:36Z] INFO  21:36:24,754 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:36Z] INFO  21:36:25,265 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:36Z] INFO  21:36:25,266 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:36Z] INFO  21:36:25,266 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:36Z] INFO  21:36:25,266 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:36Z] GATK: VariantAnnotator
[2015-09-30T20:36Z] INFO  21:36:25,299 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:36Z] INFO  21:36:27,028 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:27,030 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:36Z] INFO  21:36:27,030 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:36Z] INFO  21:36:27,030 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:36Z] INFO  21:36:27,034 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/3/syn3-3_155652401_186761310-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/3/tx/tmp49g8Wz/syn3-3_155652401_186761310-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/3/syn3-3_155652401_186761310-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:36Z] INFO  21:36:27,039 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:36Z] INFO  21:36:27,039 HelpFormatter - Date/Time: 2015/09/30 21:36:27
[2015-09-30T20:36Z] INFO  21:36:27,040 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:27,040 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:36Z] INFO  21:36:27,133 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:36Z] INFO  21:36:27,217 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:36Z] INFO  21:36:27,236 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:36Z] INFO  21:36:27,284 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T20:36Z] INFO  21:36:27,652 IntervalUtils - Processing 1484 bp from intervals
[2015-09-30T20:36Z] WARN  21:36:27,656 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] WARN  21:36:27,656 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:36Z] INFO  21:36:27,716 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:36Z] INFO  21:36:28,064 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:36Z] INFO  21:36:28,064 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:36Z] INFO  21:36:28,065 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:36Z] INFO  21:36:28,065 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:36Z] INFO  21:36:28,099 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:36Z] INFO  21:36:32,375 VariantAnnotator - Processed 1444 loci.
[2015-09-30T20:36Z]
[2015-09-30T20:36Z] INFO  21:36:32,469 ProgressMeter -            done     30901.0     7.0 s       3.9 m       99.9%     7.0 s       0.0 s
[2015-09-30T20:36Z] INFO  21:36:32,469 ProgressMeter - Total runtime 7.20 secs, 0.12 min, 0.00 hours
[2015-09-30T20:36Z] INFO  21:36:32,469 MicroScheduler - 5886 reads were filtered out during the traversal out of approximately 121120 total reads (4.86%)
[2015-09-30T20:36Z] INFO  21:36:32,470 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:36Z] INFO  21:36:32,470 MicroScheduler -   -> 5851 reads (4.83% of total) failing DuplicateReadFilter
[2015-09-30T20:36Z] INFO  21:36:32,470 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:36Z] INFO  21:36:32,470 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:36Z] INFO  21:36:32,471 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:36Z] INFO  21:36:32,471 MicroScheduler -   -> 35 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:36Z] INFO  21:36:33,485 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:36Z] Genotyping with varscan: ('4', 31031389, 62067173) 1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam
[2015-09-30T20:36Z] samtools mpileup
[2015-09-30T20:36Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:36Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:36Z] INFO  21:36:34,864 VariantAnnotator - Processed 1250 loci.
[2015-09-30T20:36Z]
[2015-09-30T20:36Z] INFO  21:36:34,905 ProgressMeter -            done      5398.0     6.0 s      21.1 m       99.9%     6.0 s       0.0 s
[2015-09-30T20:36Z] INFO  21:36:34,905 ProgressMeter - Total runtime 6.84 secs, 0.11 min, 0.00 hours
[2015-09-30T20:36Z] INFO  21:36:34,906 MicroScheduler - 4021 reads were filtered out during the traversal out of approximately 91627 total reads (4.39%)
[2015-09-30T20:36Z] INFO  21:36:34,906 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:36Z] INFO  21:36:34,906 MicroScheduler -   -> 3993 reads (4.36% of total) failing DuplicateReadFilter
[2015-09-30T20:36Z] INFO  21:36:34,906 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:36Z] INFO  21:36:34,907 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:36Z] INFO  21:36:34,907 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:36Z] INFO  21:36:34,907 MicroScheduler -   -> 28 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:36Z] INFO  21:36:35,827 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:36Z] Genotyping with varscan: ('4', 62292837, 93511697) 1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam
[2015-09-30T20:36Z] samtools mpileup
[2015-09-30T20:36Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:36Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:36Z] samtools mpileup
[2015-09-30T20:36Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:36Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:37Z] samtools mpileup
[2015-09-30T20:37Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:37Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:37Z] samtools mpileup
[2015-09-30T20:37Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:37Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:37Z] Varscan
[2015-09-30T20:37Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpVMblaD/syn3-4_31031389_62067173-raw-normal.mpileup
[2015-09-30T20:37Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpVMblaD/syn3-4_31031389_62067173-raw-tumor.mpileup
[2015-09-30T20:37Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:37Z] Min reads2:	2
[2015-09-30T20:37Z] Min strands2:	1
[2015-09-30T20:37Z] Min var freq:	0.1
[2015-09-30T20:37Z] Min freq for hom:	0.75
[2015-09-30T20:37Z] Normal purity:	1.0
[2015-09-30T20:37Z] Tumor purity:	1.0
[2015-09-30T20:37Z] Min avg qual:	15
[2015-09-30T20:37Z] P-value thresh:	0.98
[2015-09-30T20:37Z] Somatic p-value:	0.05
[2015-09-30T20:37Z] Varscan
[2015-09-30T20:37Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpgw8VtO/syn3-4_62292837_93511697-raw-normal.mpileup
[2015-09-30T20:37Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpgw8VtO/syn3-4_62292837_93511697-raw-tumor.mpileup
[2015-09-30T20:37Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:37Z] Min reads2:	2
[2015-09-30T20:37Z] Min strands2:	1
[2015-09-30T20:37Z] Min var freq:	0.1
[2015-09-30T20:37Z] Min freq for hom:	0.75
[2015-09-30T20:37Z] Normal purity:	1.0
[2015-09-30T20:37Z] Tumor purity:	1.0
[2015-09-30T20:37Z] Min avg qual:	15
[2015-09-30T20:37Z] P-value thresh:	0.98
[2015-09-30T20:37Z] Somatic p-value:	0.05
[2015-09-30T20:37Z] 845297 positions in tumor
[2015-09-30T20:37Z] 845289 positions shared in normal
[2015-09-30T20:37Z] 817736 had sufficient coverage for comparison
[2015-09-30T20:37Z] 816756 were called Reference
[2015-09-30T20:37Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:37Z] 53 were removed by the strand filter
[2015-09-30T20:37Z] 945 were called Germline
[2015-09-30T20:37Z] 5 were called LOH
[2015-09-30T20:37Z] 21 were called Somatic
[2015-09-30T20:37Z] 9 were called Unknown
[2015-09-30T20:37Z] 0 were called Variant
[2015-09-30T20:37Z] Varscan paired fix
[2015-09-30T20:37Z] Varscan paired fix
[2015-09-30T20:37Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:37Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:37Z] bgzip syn3-4_31031389_62067173-raw.snp.vcf
[2015-09-30T20:37Z] tabix index syn3-4_31031389_62067173-raw.snp.vcf.gz
[2015-09-30T20:37Z] bgzip syn3-4_31031389_62067173-raw.indel.vcf
[2015-09-30T20:38Z] tabix index syn3-4_31031389_62067173-raw.indel.vcf.gz
[2015-09-30T20:38Z] Combine variant files
[2015-09-30T20:38Z] INFO  21:38:02,318 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:02,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:38Z] INFO  21:38:02,320 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:38Z] INFO  21:38:02,320 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:38Z] INFO  21:38:02,323 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpVMblaD/tx/tmpc0Bm4i/syn3-4_31031389_62067173-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/4/tx/tmpVMblaD/syn3-4_31031389_62067173-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/4/tx/tmpVMblaD/syn3-4_31031389_62067173-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_31031389_62067173-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:38Z] INFO  21:38:02,330 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:38Z] INFO  21:38:02,330 HelpFormatter - Date/Time: 2015/09/30 21:38:02
[2015-09-30T20:38Z] INFO  21:38:02,330 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:02,331 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:02,404 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:38Z] Varscan
[2015-09-30T20:38Z] INFO  21:38:02,679 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:38Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmp1trv4R/syn3-4_0_31018607-raw-normal.mpileup
[2015-09-30T20:38Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmp1trv4R/syn3-4_0_31018607-raw-tumor.mpileup
[2015-09-30T20:38Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:38Z] Min reads2:	2
[2015-09-30T20:38Z] Min strands2:	1
[2015-09-30T20:38Z] Min var freq:	0.1
[2015-09-30T20:38Z] Min freq for hom:	0.75
[2015-09-30T20:38Z] Normal purity:	1.0
[2015-09-30T20:38Z] Tumor purity:	1.0
[2015-09-30T20:38Z] Min avg qual:	15
[2015-09-30T20:38Z] P-value thresh:	0.98
[2015-09-30T20:38Z] Somatic p-value:	0.05
[2015-09-30T20:38Z] INFO  21:38:02,780 IntervalUtils - Processing 850491 bp from intervals
[2015-09-30T20:38Z] WARN  21:38:02,781 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] WARN  21:38:02,782 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] INFO  21:38:02,837 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:38Z] INFO  21:38:02,840 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:38Z] INFO  21:38:02,840 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:38Z] INFO  21:38:02,841 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:38Z] INFO  21:38:02,841 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:38Z] INFO  21:38:03,873 ProgressMeter -            done      1064.0     1.0 s      16.2 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:38Z] INFO  21:38:03,874 ProgressMeter - Total runtime 1.03 secs, 0.02 min, 0.00 hours
[2015-09-30T20:38Z] bgzip syn3-4_31031389_62067173-raw.vcf
[2015-09-30T20:38Z] tabix index syn3-4_31031389_62067173-raw.vcf.gz
[2015-09-30T20:38Z] bgzip syn3-4_31031389_62067173-raw-rejectfix.vcf
[2015-09-30T20:38Z] tabix index syn3-4_31031389_62067173-raw-rejectfix.vcf.gz
[2015-09-30T20:38Z] GATK: VariantAnnotator
[2015-09-30T20:38Z] INFO  21:38:06,301 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:06,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:38Z] INFO  21:38:06,304 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:38Z] INFO  21:38:06,304 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:38Z] INFO  21:38:06,307 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/4/syn3-4_31031389_62067173-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/4/tx/tmp40Kr32/syn3-4_31031389_62067173-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_31031389_62067173-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:38Z] INFO  21:38:06,313 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:38Z] INFO  21:38:06,313 HelpFormatter - Date/Time: 2015/09/30 21:38:06
[2015-09-30T20:38Z] INFO  21:38:06,313 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:06,313 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:06,413 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:38Z] INFO  21:38:06,489 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:38Z] INFO  21:38:06,496 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:38Z] INFO  21:38:06,519 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:38Z] INFO  21:38:06,877 IntervalUtils - Processing 1064 bp from intervals
[2015-09-30T20:38Z] WARN  21:38:06,881 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] WARN  21:38:06,882 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] INFO  21:38:06,938 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:38Z] INFO  21:38:07,051 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:38Z] INFO  21:38:07,052 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:38Z] INFO  21:38:07,052 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:38Z] INFO  21:38:07,053 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:38Z] INFO  21:38:07,085 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:38Z] INFO  21:38:12,241 VariantAnnotator - Processed 920 loci.
[2015-09-30T20:38Z]
[2015-09-30T20:38Z] INFO  21:38:12,260 ProgressMeter -            done      3717.0     5.0 s      23.4 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:38Z] INFO  21:38:12,264 ProgressMeter - Total runtime 5.21 secs, 0.09 min, 0.00 hours
[2015-09-30T20:38Z] INFO  21:38:12,264 MicroScheduler - 2734 reads were filtered out during the traversal out of approximately 63449 total reads (4.31%)
[2015-09-30T20:38Z] INFO  21:38:12,265 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:38Z] INFO  21:38:12,265 MicroScheduler -   -> 2716 reads (4.28% of total) failing DuplicateReadFilter
[2015-09-30T20:38Z] INFO  21:38:12,265 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:38Z] INFO  21:38:12,265 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:38Z] INFO  21:38:12,266 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:38Z] INFO  21:38:12,266 MicroScheduler -   -> 18 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:38Z] INFO  21:38:13,298 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:38Z] Genotyping with varscan: ('4', 94005855, 125588163) 1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam
[2015-09-30T20:38Z] samtools mpileup
[2015-09-30T20:38Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:38Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:38Z] 1270334 positions in tumor
[2015-09-30T20:38Z] 1270327 positions shared in normal
[2015-09-30T20:38Z] 1223525 had sufficient coverage for comparison
[2015-09-30T20:38Z] 1222023 were called Reference
[2015-09-30T20:38Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:38Z] 74 were removed by the strand filter
[2015-09-30T20:38Z] 1444 were called Germline
[2015-09-30T20:38Z] 8 were called LOH
[2015-09-30T20:38Z] 37 were called Somatic
[2015-09-30T20:38Z] 13 were called Unknown
[2015-09-30T20:38Z] 0 were called Variant
[2015-09-30T20:38Z] Varscan paired fix
[2015-09-30T20:38Z] Varscan paired fix
[2015-09-30T20:38Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:38Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:38Z] bgzip syn3-4_62292837_93511697-raw.snp.vcf
[2015-09-30T20:38Z] tabix index syn3-4_62292837_93511697-raw.snp.vcf.gz
[2015-09-30T20:38Z] bgzip syn3-4_62292837_93511697-raw.indel.vcf
[2015-09-30T20:38Z] tabix index syn3-4_62292837_93511697-raw.indel.vcf.gz
[2015-09-30T20:38Z] Combine variant files
[2015-09-30T20:38Z] INFO  21:38:38,894 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:38,896 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:38Z] INFO  21:38:38,896 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:38Z] INFO  21:38:38,896 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:38Z] INFO  21:38:38,900 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpgw8VtO/tx/tmpI_Caix/syn3-4_62292837_93511697-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/4/tx/tmpgw8VtO/syn3-4_62292837_93511697-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/4/tx/tmpgw8VtO/syn3-4_62292837_93511697-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_62292837_93511697-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:38Z] INFO  21:38:38,905 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:38Z] INFO  21:38:38,905 HelpFormatter - Date/Time: 2015/09/30 21:38:38
[2015-09-30T20:38Z] INFO  21:38:38,906 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:38,906 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:38,981 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:38Z] INFO  21:38:39,127 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:38Z] INFO  21:38:39,246 IntervalUtils - Processing 1281025 bp from intervals
[2015-09-30T20:38Z] WARN  21:38:39,247 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] WARN  21:38:39,247 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] INFO  21:38:39,303 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:38Z] INFO  21:38:39,306 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:38Z] INFO  21:38:39,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:38Z] INFO  21:38:39,307 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:38Z] INFO  21:38:39,307 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:38Z] INFO  21:38:40,614 ProgressMeter -            done      1794.0     1.0 s      12.1 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:38Z] INFO  21:38:40,615 ProgressMeter - Total runtime 1.31 secs, 0.02 min, 0.00 hours
[2015-09-30T20:38Z] bgzip syn3-4_62292837_93511697-raw.vcf
[2015-09-30T20:38Z] tabix index syn3-4_62292837_93511697-raw.vcf.gz
[2015-09-30T20:38Z] bgzip syn3-4_62292837_93511697-raw-rejectfix.vcf
[2015-09-30T20:38Z] tabix index syn3-4_62292837_93511697-raw-rejectfix.vcf.gz
[2015-09-30T20:38Z] GATK: VariantAnnotator
[2015-09-30T20:38Z] samtools mpileup
[2015-09-30T20:38Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:38Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:38Z] INFO  21:38:43,354 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:43,356 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:38Z] INFO  21:38:43,356 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:38Z] INFO  21:38:43,356 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:38Z] INFO  21:38:43,360 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/4/syn3-4_62292837_93511697-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpPY3SD_/syn3-4_62292837_93511697-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_62292837_93511697-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:38Z] INFO  21:38:43,366 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:38Z] INFO  21:38:43,366 HelpFormatter - Date/Time: 2015/09/30 21:38:43
[2015-09-30T20:38Z] INFO  21:38:43,366 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:43,367 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:43,682 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:38Z] INFO  21:38:43,759 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:38Z] INFO  21:38:43,767 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:38Z] INFO  21:38:43,790 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:38Z] INFO  21:38:44,192 IntervalUtils - Processing 1794 bp from intervals
[2015-09-30T20:38Z] WARN  21:38:44,196 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] WARN  21:38:44,197 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] INFO  21:38:44,254 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:38Z] INFO  21:38:44,364 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:38Z] INFO  21:38:44,365 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:38Z] INFO  21:38:44,365 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:38Z] INFO  21:38:44,366 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:38Z] INFO  21:38:44,468 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:38Z] INFO  21:38:51,139 VariantAnnotator - Processed 1421 loci.
[2015-09-30T20:38Z]
[2015-09-30T20:38Z] INFO  21:38:51,175 ProgressMeter -            done      7743.0     6.0 s      14.7 m       99.9%     6.0 s       0.0 s
[2015-09-30T20:38Z] INFO  21:38:51,175 ProgressMeter - Total runtime 6.81 secs, 0.11 min, 0.00 hours
[2015-09-30T20:38Z] INFO  21:38:51,175 MicroScheduler - 3783 reads were filtered out during the traversal out of approximately 90817 total reads (4.17%)
[2015-09-30T20:38Z] INFO  21:38:51,175 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:38Z] INFO  21:38:51,176 MicroScheduler -   -> 3767 reads (4.15% of total) failing DuplicateReadFilter
[2015-09-30T20:38Z] INFO  21:38:51,176 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:38Z] INFO  21:38:51,176 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:38Z] INFO  21:38:51,176 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:38Z] INFO  21:38:51,177 MicroScheduler -   -> 16 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:38Z] INFO  21:38:52,148 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:38Z] Genotyping with varscan: ('4', 125589908, 156618518) 1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam
[2015-09-30T20:38Z] samtools mpileup
[2015-09-30T20:38Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:38Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:38Z] 1278734 positions in tumor
[2015-09-30T20:38Z] 1278719 positions shared in normal
[2015-09-30T20:38Z] 1257895 had sufficient coverage for comparison
[2015-09-30T20:38Z] 1255876 were called Reference
[2015-09-30T20:38Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:38Z] 94 were removed by the strand filter
[2015-09-30T20:38Z] 1966 were called Germline
[2015-09-30T20:38Z] 13 were called LOH
[2015-09-30T20:38Z] 32 were called Somatic
[2015-09-30T20:38Z] 8 were called Unknown
[2015-09-30T20:38Z] 0 were called Variant
[2015-09-30T20:38Z] Varscan paired fix
[2015-09-30T20:38Z] Varscan paired fix
[2015-09-30T20:38Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:38Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:38Z] bgzip syn3-4_0_31018607-raw.snp.vcf
[2015-09-30T20:38Z] tabix index syn3-4_0_31018607-raw.snp.vcf.gz
[2015-09-30T20:38Z] bgzip syn3-4_0_31018607-raw.indel.vcf
[2015-09-30T20:38Z] tabix index syn3-4_0_31018607-raw.indel.vcf.gz
[2015-09-30T20:38Z] Combine variant files
[2015-09-30T20:38Z] INFO  21:38:58,374 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:58,376 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:38Z] INFO  21:38:58,377 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:38Z] INFO  21:38:58,377 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:38Z] INFO  21:38:58,380 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/4/tx/tmp1trv4R/tx/tmpFouxRw/syn3-4_0_31018607-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/4/tx/tmp1trv4R/syn3-4_0_31018607-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/4/tx/tmp1trv4R/syn3-4_0_31018607-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_0_31018607-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:38Z] INFO  21:38:58,385 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:38Z] INFO  21:38:58,385 HelpFormatter - Date/Time: 2015/09/30 21:38:58
[2015-09-30T20:38Z] INFO  21:38:58,385 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:58,385 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:38Z] INFO  21:38:58,456 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:38Z] INFO  21:38:58,597 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:38Z] INFO  21:38:58,707 IntervalUtils - Processing 1291749 bp from intervals
[2015-09-30T20:38Z] WARN  21:38:58,708 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] WARN  21:38:58,708 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:38Z] INFO  21:38:58,763 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:38Z] INFO  21:38:58,766 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:38Z] INFO  21:38:58,767 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:38Z] INFO  21:38:58,767 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:38Z] INFO  21:38:58,767 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:39Z] INFO  21:39:00,476 ProgressMeter -            done      2239.0     1.0 s      12.7 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:39Z] INFO  21:39:00,477 ProgressMeter - Total runtime 1.71 secs, 0.03 min, 0.00 hours
[2015-09-30T20:39Z] bgzip syn3-4_0_31018607-raw.vcf
[2015-09-30T20:39Z] tabix index syn3-4_0_31018607-raw.vcf.gz
[2015-09-30T20:39Z] bgzip syn3-4_0_31018607-raw-rejectfix.vcf
[2015-09-30T20:39Z] tabix index syn3-4_0_31018607-raw-rejectfix.vcf.gz
[2015-09-30T20:39Z] GATK: VariantAnnotator
[2015-09-30T20:39Z] INFO  21:39:06,231 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:39Z] INFO  21:39:06,233 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:39Z] INFO  21:39:06,233 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:39Z] INFO  21:39:06,233 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:39Z] INFO  21:39:06,236 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/4/syn3-4_0_31018607-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpydn0ta/syn3-4_0_31018607-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_0_31018607-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:39Z] INFO  21:39:06,242 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:39Z] INFO  21:39:06,243 HelpFormatter - Date/Time: 2015/09/30 21:39:06
[2015-09-30T20:39Z] INFO  21:39:06,243 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:39Z] INFO  21:39:06,243 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:39Z] INFO  21:39:06,349 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:39Z] INFO  21:39:06,426 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:39Z] INFO  21:39:06,434 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:39Z] INFO  21:39:06,458 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:39Z] INFO  21:39:06,862 IntervalUtils - Processing 2239 bp from intervals
[2015-09-30T20:39Z] WARN  21:39:06,866 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:39Z] WARN  21:39:06,866 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:39Z] INFO  21:39:06,920 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:39Z] INFO  21:39:07,097 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:39Z] INFO  21:39:07,097 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:39Z] INFO  21:39:07,097 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:39Z] INFO  21:39:07,098 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:39Z] INFO  21:39:07,129 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:39Z] Varscan
[2015-09-30T20:39Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpUexsi1/syn3-4_94005855_125588163-raw-normal.mpileup
[2015-09-30T20:39Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpUexsi1/syn3-4_94005855_125588163-raw-tumor.mpileup
[2015-09-30T20:39Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:39Z] Min reads2:	2
[2015-09-30T20:39Z] Min strands2:	1
[2015-09-30T20:39Z] Min var freq:	0.1
[2015-09-30T20:39Z] Min freq for hom:	0.75
[2015-09-30T20:39Z] Normal purity:	1.0
[2015-09-30T20:39Z] Tumor purity:	1.0
[2015-09-30T20:39Z] Min avg qual:	15
[2015-09-30T20:39Z] P-value thresh:	0.98
[2015-09-30T20:39Z] Somatic p-value:	0.05
[2015-09-30T20:39Z] samtools mpileup
[2015-09-30T20:39Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:39Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:39Z] INFO  21:39:17,872 VariantAnnotator - Processed 1919 loci.
[2015-09-30T20:39Z]
[2015-09-30T20:39Z] INFO  21:39:17,921 ProgressMeter -            done     10842.0    10.0 s      16.6 m      100.0%    10.0 s       0.0 s
[2015-09-30T20:39Z] INFO  21:39:17,921 ProgressMeter - Total runtime 10.82 secs, 0.18 min, 0.00 hours
[2015-09-30T20:39Z] INFO  21:39:17,922 MicroScheduler - 9504 reads were filtered out during the traversal out of approximately 178327 total reads (5.33%)
[2015-09-30T20:39Z] INFO  21:39:17,922 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:39Z] INFO  21:39:17,922 MicroScheduler -   -> 9456 reads (5.30% of total) failing DuplicateReadFilter
[2015-09-30T20:39Z] INFO  21:39:17,922 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:39Z] INFO  21:39:17,923 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:39Z] INFO  21:39:17,923 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:39Z] INFO  21:39:17,923 MicroScheduler -   -> 48 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:39Z] INFO  21:39:18,856 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:39Z] Genotyping with varscan: ('4', 156624795, 188926424) 1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam
[2015-09-30T20:39Z] samtools mpileup
[2015-09-30T20:39Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:39Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:39Z] Varscan
[2015-09-30T20:39Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpY2QM8z/syn3-4_125589908_156618518-raw-normal.mpileup
[2015-09-30T20:39Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpY2QM8z/syn3-4_125589908_156618518-raw-tumor.mpileup
[2015-09-30T20:39Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:39Z] Min reads2:	2
[2015-09-30T20:39Z] Min strands2:	1
[2015-09-30T20:39Z] Min var freq:	0.1
[2015-09-30T20:39Z] Min freq for hom:	0.75
[2015-09-30T20:39Z] Normal purity:	1.0
[2015-09-30T20:39Z] Tumor purity:	1.0
[2015-09-30T20:39Z] Min avg qual:	15
[2015-09-30T20:39Z] P-value thresh:	0.98
[2015-09-30T20:39Z] Somatic p-value:	0.05
[2015-09-30T20:39Z] samtools mpileup
[2015-09-30T20:39Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:39Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:39Z] 1019455 positions in tumor
[2015-09-30T20:39Z] 1019442 positions shared in normal
[2015-09-30T20:39Z] 979851 had sufficient coverage for comparison
[2015-09-30T20:39Z] 978645 were called Reference
[2015-09-30T20:39Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:39Z] 111 were removed by the strand filter
[2015-09-30T20:39Z] 1164 were called Germline
[2015-09-30T20:39Z] 4 were called LOH
[2015-09-30T20:39Z] 31 were called Somatic
[2015-09-30T20:39Z] 7 were called Unknown
[2015-09-30T20:39Z] 0 were called Variant
[2015-09-30T20:39Z] Varscan paired fix
[2015-09-30T20:39Z] Varscan paired fix
[2015-09-30T20:39Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:39Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:39Z] bgzip syn3-4_94005855_125588163-raw.snp.vcf
[2015-09-30T20:39Z] tabix index syn3-4_94005855_125588163-raw.snp.vcf.gz
[2015-09-30T20:39Z] bgzip syn3-4_94005855_125588163-raw.indel.vcf
[2015-09-30T20:39Z] tabix index syn3-4_94005855_125588163-raw.indel.vcf.gz
[2015-09-30T20:39Z] Combine variant files
[2015-09-30T20:39Z] INFO  21:39:51,684 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:39Z] INFO  21:39:51,686 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:39Z] INFO  21:39:51,686 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:39Z] INFO  21:39:51,686 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:39Z] INFO  21:39:51,690 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpUexsi1/tx/tmpidxZx9/syn3-4_94005855_125588163-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/4/tx/tmpUexsi1/syn3-4_94005855_125588163-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/4/tx/tmpUexsi1/syn3-4_94005855_125588163-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_94005855_125588163-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:39Z] INFO  21:39:51,695 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:39Z] INFO  21:39:51,695 HelpFormatter - Date/Time: 2015/09/30 21:39:51
[2015-09-30T20:39Z] INFO  21:39:51,696 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:39Z] INFO  21:39:51,696 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:39Z] INFO  21:39:51,772 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:39Z] INFO  21:39:51,913 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:39Z] INFO  21:39:52,031 IntervalUtils - Processing 1026851 bp from intervals
[2015-09-30T20:39Z] WARN  21:39:52,032 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:39Z] WARN  21:39:52,032 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:39Z] INFO  21:39:52,088 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:39Z] INFO  21:39:52,091 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:39Z] INFO  21:39:52,091 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:39Z] INFO  21:39:52,091 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:39Z] INFO  21:39:52,092 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:39Z] INFO  21:39:53,241 ProgressMeter -            done      1269.0     1.0 s      15.1 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:39Z] INFO  21:39:53,241 ProgressMeter - Total runtime 1.15 secs, 0.02 min, 0.00 hours
[2015-09-30T20:39Z] bgzip syn3-4_94005855_125588163-raw.vcf
[2015-09-30T20:39Z] tabix index syn3-4_94005855_125588163-raw.vcf.gz
[2015-09-30T20:39Z] bgzip syn3-4_94005855_125588163-raw-rejectfix.vcf
[2015-09-30T20:39Z] tabix index syn3-4_94005855_125588163-raw-rejectfix.vcf.gz
[2015-09-30T20:39Z] GATK: VariantAnnotator
[2015-09-30T20:39Z] INFO  21:39:56,279 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:39Z] INFO  21:39:56,281 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:39Z] INFO  21:39:56,282 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:39Z] INFO  21:39:56,282 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:39Z] INFO  21:39:56,285 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/4/syn3-4_94005855_125588163-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/4/tx/tmp0rjP9p/syn3-4_94005855_125588163-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_94005855_125588163-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:39Z] INFO  21:39:56,291 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:39Z] INFO  21:39:56,291 HelpFormatter - Date/Time: 2015/09/30 21:39:56
[2015-09-30T20:39Z] INFO  21:39:56,291 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:39Z] INFO  21:39:56,292 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:39Z] INFO  21:39:56,389 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:39Z] INFO  21:39:56,465 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:39Z] INFO  21:39:56,473 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:39Z] INFO  21:39:56,494 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:39Z] INFO  21:39:56,962 IntervalUtils - Processing 1269 bp from intervals
[2015-09-30T20:39Z] WARN  21:39:56,966 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:39Z] WARN  21:39:56,966 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:39Z] INFO  21:39:57,022 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:39Z] INFO  21:39:57,415 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:39Z] INFO  21:39:57,415 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:39Z] INFO  21:39:57,415 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:39Z] INFO  21:39:57,416 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:39Z] INFO  21:39:57,507 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:40Z] INFO  21:40:03,114 VariantAnnotator - Processed 1092 loci.
[2015-09-30T20:40Z]
[2015-09-30T20:40Z] INFO  21:40:03,139 ProgressMeter -            done      3979.0     5.0 s      24.0 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:40Z] INFO  21:40:03,139 ProgressMeter - Total runtime 5.72 secs, 0.10 min, 0.00 hours
[2015-09-30T20:40Z] INFO  21:40:03,140 MicroScheduler - 2816 reads were filtered out during the traversal out of approximately 68953 total reads (4.08%)
[2015-09-30T20:40Z] INFO  21:40:03,140 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:40Z] INFO  21:40:03,140 MicroScheduler -   -> 2796 reads (4.05% of total) failing DuplicateReadFilter
[2015-09-30T20:40Z] INFO  21:40:03,140 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:40Z] INFO  21:40:03,140 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:40Z] INFO  21:40:03,141 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:40Z] INFO  21:40:03,141 MicroScheduler -   -> 20 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:40Z] INFO  21:40:04,079 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:40Z] Genotyping with varscan: ('4', 189012293, 191154276) 1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam
[2015-09-30T20:40Z] samtools mpileup
[2015-09-30T20:40Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:40Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:40Z] Varscan
[2015-09-30T20:40Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpjx9YZH/syn3-4_156624795_188926424-raw-normal.mpileup
[2015-09-30T20:40Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpjx9YZH/syn3-4_156624795_188926424-raw-tumor.mpileup
[2015-09-30T20:40Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:40Z] Min reads2:	2
[2015-09-30T20:40Z] Min strands2:	1
[2015-09-30T20:40Z] Min var freq:	0.1
[2015-09-30T20:40Z] Min freq for hom:	0.75
[2015-09-30T20:40Z] Normal purity:	1.0
[2015-09-30T20:40Z] Tumor purity:	1.0
[2015-09-30T20:40Z] Min avg qual:	15
[2015-09-30T20:40Z] P-value thresh:	0.98
[2015-09-30T20:40Z] Somatic p-value:	0.05
[2015-09-30T20:40Z] samtools mpileup
[2015-09-30T20:40Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:40Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:40Z] 787390 positions in tumor
[2015-09-30T20:40Z] 787380 positions shared in normal
[2015-09-30T20:40Z] 759376 had sufficient coverage for comparison
[2015-09-30T20:40Z] 758539 were called Reference
[2015-09-30T20:40Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:40Z] 59 were removed by the strand filter
[2015-09-30T20:40Z] 805 were called Germline
[2015-09-30T20:40Z] 3 were called LOH
[2015-09-30T20:40Z] 20 were called Somatic
[2015-09-30T20:40Z] 9 were called Unknown
[2015-09-30T20:40Z] 0 were called Variant
[2015-09-30T20:40Z] Varscan paired fix
[2015-09-30T20:40Z] Varscan paired fix
[2015-09-30T20:40Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:40Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:40Z] bgzip syn3-4_125589908_156618518-raw.snp.vcf
[2015-09-30T20:40Z] tabix index syn3-4_125589908_156618518-raw.snp.vcf.gz
[2015-09-30T20:40Z] bgzip syn3-4_125589908_156618518-raw.indel.vcf
[2015-09-30T20:40Z] tabix index syn3-4_125589908_156618518-raw.indel.vcf.gz
[2015-09-30T20:40Z] Combine variant files
[2015-09-30T20:40Z] Varscan
[2015-09-30T20:40Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpP4FTOn/syn3-4_189012293_191154276-raw-normal.mpileup
[2015-09-30T20:40Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/4/tx/tmpP4FTOn/syn3-4_189012293_191154276-raw-tumor.mpileup
[2015-09-30T20:40Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:40Z] Min reads2:	2
[2015-09-30T20:40Z] Min strands2:	1
[2015-09-30T20:40Z] Min var freq:	0.1
[2015-09-30T20:40Z] Min freq for hom:	0.75
[2015-09-30T20:40Z] Normal purity:	1.0
[2015-09-30T20:40Z] Tumor purity:	1.0
[2015-09-30T20:40Z] Min avg qual:	15
[2015-09-30T20:40Z] P-value thresh:	0.98
[2015-09-30T20:40Z] Somatic p-value:	0.05
[2015-09-30T20:40Z] INFO  21:40:10,858 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:10,860 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:40Z] INFO  21:40:10,861 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:40Z] INFO  21:40:10,861 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:40Z] INFO  21:40:10,864 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpY2QM8z/tx/tmpckdfxj/syn3-4_125589908_156618518-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/4/tx/tmpY2QM8z/syn3-4_125589908_156618518-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/4/tx/tmpY2QM8z/syn3-4_125589908_156618518-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_125589908_156618518-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:40Z] INFO  21:40:10,870 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:40Z] INFO  21:40:10,870 HelpFormatter - Date/Time: 2015/09/30 21:40:10
[2015-09-30T20:40Z] INFO  21:40:10,870 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:10,870 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:10,949 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:40Z] INFO  21:40:11,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:40Z] INFO  21:40:11,395 IntervalUtils - Processing 792406 bp from intervals
[2015-09-30T20:40Z] WARN  21:40:11,396 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] WARN  21:40:11,397 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] INFO  21:40:11,455 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:40Z] INFO  21:40:11,458 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:40Z] INFO  21:40:11,458 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:40Z] INFO  21:40:11,459 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:40Z] INFO  21:40:11,459 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:40Z] INFO  21:40:12,381 ProgressMeter -            done       931.0     0.0 s      16.5 m       99.8%     0.0 s       0.0 s
[2015-09-30T20:40Z] INFO  21:40:12,382 ProgressMeter - Total runtime 0.92 secs, 0.02 min, 0.00 hours
[2015-09-30T20:40Z] bgzip syn3-4_125589908_156618518-raw.vcf
[2015-09-30T20:40Z] tabix index syn3-4_125589908_156618518-raw.vcf.gz
[2015-09-30T20:40Z] bgzip syn3-4_125589908_156618518-raw-rejectfix.vcf
[2015-09-30T20:40Z] tabix index syn3-4_125589908_156618518-raw-rejectfix.vcf.gz
[2015-09-30T20:40Z] GATK: VariantAnnotator
[2015-09-30T20:40Z] 26811 positions in tumor
[2015-09-30T20:40Z] 26811 positions shared in normal
[2015-09-30T20:40Z] 26353 had sufficient coverage for comparison
[2015-09-30T20:40Z] 26035 were called Reference
[2015-09-30T20:40Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:40Z] 113 were removed by the strand filter
[2015-09-30T20:40Z] 294 were called Germline
[2015-09-30T20:40Z] 3 were called LOH
[2015-09-30T20:40Z] 21 were called Somatic
[2015-09-30T20:40Z] 0 were called Unknown
[2015-09-30T20:40Z] 0 were called Variant
[2015-09-30T20:40Z] Varscan paired fix
[2015-09-30T20:40Z] Varscan paired fix
[2015-09-30T20:40Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:40Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:40Z] bgzip syn3-4_189012293_191154276-raw.snp.vcf
[2015-09-30T20:40Z] tabix index syn3-4_189012293_191154276-raw.snp.vcf.gz
[2015-09-30T20:40Z] bgzip syn3-4_189012293_191154276-raw.indel.vcf
[2015-09-30T20:40Z] tabix index syn3-4_189012293_191154276-raw.indel.vcf.gz
[2015-09-30T20:40Z] Combine variant files
[2015-09-30T20:40Z] INFO  21:40:14,675 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:14,677 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:40Z] INFO  21:40:14,677 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:40Z] INFO  21:40:14,677 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:40Z] INFO  21:40:14,681 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/4/syn3-4_125589908_156618518-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpoktgNm/syn3-4_125589908_156618518-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_125589908_156618518-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:40Z] INFO  21:40:14,686 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:40Z] INFO  21:40:14,686 HelpFormatter - Date/Time: 2015/09/30 21:40:14
[2015-09-30T20:40Z] INFO  21:40:14,687 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:14,687 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:14,783 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:40Z] INFO  21:40:14,860 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:40Z] INFO  21:40:14,868 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:40Z] INFO  21:40:14,891 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:40Z] INFO  21:40:15,219 IntervalUtils - Processing 952 bp from intervals
[2015-09-30T20:40Z] WARN  21:40:15,224 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] WARN  21:40:15,224 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] INFO  21:40:15,284 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:40Z] INFO  21:40:15,386 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:40Z] INFO  21:40:15,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:40Z] INFO  21:40:15,386 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:40Z] INFO  21:40:15,387 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:40Z] INFO  21:40:15,420 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:40Z] INFO  21:40:16,295 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:16,297 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:40Z] INFO  21:40:16,297 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:40Z] INFO  21:40:16,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:40Z] INFO  21:40:16,301 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpP4FTOn/tx/tmpLLLhSA/syn3-4_189012293_191154276-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/4/tx/tmpP4FTOn/syn3-4_189012293_191154276-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/4/tx/tmpP4FTOn/syn3-4_189012293_191154276-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_189012293_191154276-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:40Z] INFO  21:40:16,306 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:40Z] INFO  21:40:16,307 HelpFormatter - Date/Time: 2015/09/30 21:40:16
[2015-09-30T20:40Z] INFO  21:40:16,307 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:16,307 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:16,386 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:40Z] INFO  21:40:16,525 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:40Z] INFO  21:40:16,608 IntervalUtils - Processing 26832 bp from intervals
[2015-09-30T20:40Z] WARN  21:40:16,609 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] WARN  21:40:16,609 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] INFO  21:40:16,670 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:40Z] INFO  21:40:16,671 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:40Z] INFO  21:40:16,671 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:40Z] INFO  21:40:16,672 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:40Z] INFO  21:40:16,672 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:40Z] INFO  21:40:17,043 ProgressMeter -            done       234.0     0.0 s      26.4 m       98.4%     0.0 s       0.0 s
[2015-09-30T20:40Z] INFO  21:40:17,044 ProgressMeter - Total runtime 0.37 secs, 0.01 min, 0.00 hours
[2015-09-30T20:40Z] bgzip syn3-4_189012293_191154276-raw.vcf
[2015-09-30T20:40Z] tabix index syn3-4_189012293_191154276-raw.vcf.gz
[2015-09-30T20:40Z] bgzip syn3-4_189012293_191154276-raw-rejectfix.vcf
[2015-09-30T20:40Z] tabix index syn3-4_189012293_191154276-raw-rejectfix.vcf.gz
[2015-09-30T20:40Z] GATK: VariantAnnotator
[2015-09-30T20:40Z] INFO  21:40:19,192 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:19,194 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:40Z] INFO  21:40:19,194 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:40Z] INFO  21:40:19,194 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:40Z] INFO  21:40:19,198 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/4/syn3-4_189012293_191154276-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpR64Bq5/syn3-4_189012293_191154276-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_189012293_191154276-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:40Z] INFO  21:40:19,204 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:40Z] INFO  21:40:19,204 HelpFormatter - Date/Time: 2015/09/30 21:40:19
[2015-09-30T20:40Z] INFO  21:40:19,204 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:19,204 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:19,301 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:40Z] INFO  21:40:19,379 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:40Z] INFO  21:40:19,387 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:40Z] INFO  21:40:19,411 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:40Z] INFO  21:40:19,735 IntervalUtils - Processing 234 bp from intervals
[2015-09-30T20:40Z] WARN  21:40:19,739 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] WARN  21:40:19,739 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] INFO  21:40:19,799 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:40Z] INFO  21:40:19,839 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:40Z] INFO  21:40:19,840 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:40Z] INFO  21:40:19,840 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:40Z] INFO  21:40:19,841 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:40Z] INFO  21:40:19,875 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:40Z] INFO  21:40:20,086 VariantAnnotator - Processed 775 loci.
[2015-09-30T20:40Z]
[2015-09-30T20:40Z] INFO  21:40:20,118 ProgressMeter -            done      2810.0     4.0 s      28.1 m       99.9%     4.0 s       0.0 s
[2015-09-30T20:40Z] INFO  21:40:20,118 ProgressMeter - Total runtime 4.73 secs, 0.08 min, 0.00 hours
[2015-09-30T20:40Z] INFO  21:40:20,118 MicroScheduler - 2212 reads were filtered out during the traversal out of approximately 52278 total reads (4.23%)
[2015-09-30T20:40Z] INFO  21:40:20,119 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:40Z] INFO  21:40:20,119 MicroScheduler -   -> 2190 reads (4.19% of total) failing DuplicateReadFilter
[2015-09-30T20:40Z] INFO  21:40:20,119 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:40Z] INFO  21:40:20,119 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:40Z] INFO  21:40:20,120 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:40Z] INFO  21:40:20,120 MicroScheduler -   -> 22 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T20:40Z] INFO  21:40:21,054 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:40Z] Genotyping with varscan: ('5', 0, 31268043) 1_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam
[2015-09-30T20:40Z] samtools mpileup
[2015-09-30T20:40Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:40Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:40Z] INFO  21:40:22,009 VariantAnnotator - Processed 205 loci.
[2015-09-30T20:40Z]
[2015-09-30T20:40Z] INFO  21:40:22,031 ProgressMeter -            done      3919.0     2.0 s       9.3 m       99.6%     2.0 s       0.0 s
[2015-09-30T20:40Z] INFO  21:40:22,031 ProgressMeter - Total runtime 2.19 secs, 0.04 min, 0.00 hours
[2015-09-30T20:40Z] INFO  21:40:22,032 MicroScheduler - 799 reads were filtered out during the traversal out of approximately 11559 total reads (6.91%)
[2015-09-30T20:40Z] INFO  21:40:22,032 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:40Z] INFO  21:40:22,032 MicroScheduler -   -> 781 reads (6.76% of total) failing DuplicateReadFilter
[2015-09-30T20:40Z] INFO  21:40:22,033 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:40Z] INFO  21:40:22,033 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:40Z] INFO  21:40:22,033 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:40Z] INFO  21:40:22,033 MicroScheduler -   -> 18 reads (0.16% of total) failing UnmappedReadFilter
[2015-09-30T20:40Z] INFO  21:40:22,954 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:40Z] Genotyping with varscan: ('5', 31293868, 62597714) 1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam
[2015-09-30T20:40Z] samtools mpileup
[2015-09-30T20:40Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:40Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:40Z] 806476 positions in tumor
[2015-09-30T20:40Z] 806467 positions shared in normal
[2015-09-30T20:40Z] 775910 had sufficient coverage for comparison
[2015-09-30T20:40Z] 774926 were called Reference
[2015-09-30T20:40Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:40Z] 48 were removed by the strand filter
[2015-09-30T20:40Z] 958 were called Germline
[2015-09-30T20:40Z] 3 were called LOH
[2015-09-30T20:40Z] 13 were called Somatic
[2015-09-30T20:40Z] 10 were called Unknown
[2015-09-30T20:40Z] 0 were called Variant
[2015-09-30T20:40Z] Varscan paired fix
[2015-09-30T20:40Z] Varscan paired fix
[2015-09-30T20:40Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:40Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:40Z] bgzip syn3-4_156624795_188926424-raw.snp.vcf
[2015-09-30T20:40Z] tabix index syn3-4_156624795_188926424-raw.snp.vcf.gz
[2015-09-30T20:40Z] bgzip syn3-4_156624795_188926424-raw.indel.vcf
[2015-09-30T20:40Z] tabix index syn3-4_156624795_188926424-raw.indel.vcf.gz
[2015-09-30T20:40Z] Combine variant files
[2015-09-30T20:40Z] INFO  21:40:39,276 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:39,278 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:40Z] INFO  21:40:39,278 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:40Z] INFO  21:40:39,278 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:40Z] INFO  21:40:39,281 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/4/tx/tmpjx9YZH/tx/tmpcfubsT/syn3-4_156624795_188926424-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/4/tx/tmpjx9YZH/syn3-4_156624795_188926424-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/4/tx/tmpjx9YZH/syn3-4_156624795_188926424-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_156624795_188926424-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:40Z] INFO  21:40:39,287 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:40Z] INFO  21:40:39,287 HelpFormatter - Date/Time: 2015/09/30 21:40:39
[2015-09-30T20:40Z] INFO  21:40:39,287 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:39,287 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:39,361 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:40Z] INFO  21:40:39,627 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:40Z] INFO  21:40:39,733 IntervalUtils - Processing 813870 bp from intervals
[2015-09-30T20:40Z] WARN  21:40:39,734 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] WARN  21:40:39,734 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] INFO  21:40:39,788 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:40Z] INFO  21:40:39,791 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:40Z] INFO  21:40:39,791 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:40Z] INFO  21:40:39,791 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:40Z] INFO  21:40:39,792 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:40Z] INFO  21:40:40,869 ProgressMeter -            done      1099.0     1.0 s      16.3 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:40Z] INFO  21:40:40,869 ProgressMeter - Total runtime 1.08 secs, 0.02 min, 0.00 hours
[2015-09-30T20:40Z] bgzip syn3-4_156624795_188926424-raw.vcf
[2015-09-30T20:40Z] tabix index syn3-4_156624795_188926424-raw.vcf.gz
[2015-09-30T20:40Z] bgzip syn3-4_156624795_188926424-raw-rejectfix.vcf
[2015-09-30T20:40Z] tabix index syn3-4_156624795_188926424-raw-rejectfix.vcf.gz
[2015-09-30T20:40Z] GATK: VariantAnnotator
[2015-09-30T20:40Z] INFO  21:40:43,137 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:43,139 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:40Z] INFO  21:40:43,139 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:40Z] INFO  21:40:43,140 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:40Z] INFO  21:40:43,143 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/4/syn3-4_156624795_188926424-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/4/tx/tmplubiMB/syn3-4_156624795_188926424-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/4/syn3-4_156624795_188926424-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:40Z] INFO  21:40:43,148 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:40Z] INFO  21:40:43,149 HelpFormatter - Date/Time: 2015/09/30 21:40:43
[2015-09-30T20:40Z] INFO  21:40:43,149 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:43,149 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:40Z] INFO  21:40:43,221 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:40Z] INFO  21:40:43,303 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:40Z] INFO  21:40:43,310 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:40Z] INFO  21:40:43,944 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.63
[2015-09-30T20:40Z] INFO  21:40:44,311 IntervalUtils - Processing 1102 bp from intervals
[2015-09-30T20:40Z] WARN  21:40:44,315 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] WARN  21:40:44,315 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:40Z] INFO  21:40:44,371 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:40Z] INFO  21:40:44,552 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:40Z] INFO  21:40:44,553 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:40Z] INFO  21:40:44,553 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:40Z] INFO  21:40:44,553 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:40Z] INFO  21:40:44,585 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:40Z] samtools mpileup
[2015-09-30T20:40Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:40Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:40Z] INFO  21:40:49,802 VariantAnnotator - Processed 931 loci.
[2015-09-30T20:40Z]
[2015-09-30T20:40Z] INFO  21:40:49,830 ProgressMeter -            done      3577.0     5.0 s      24.6 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:40Z] INFO  21:40:49,831 ProgressMeter - Total runtime 5.28 secs, 0.09 min, 0.00 hours
[2015-09-30T20:40Z] INFO  21:40:49,831 MicroScheduler - 2713 reads were filtered out during the traversal out of approximately 63014 total reads (4.31%)
[2015-09-30T20:40Z] INFO  21:40:49,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:40Z] INFO  21:40:49,831 MicroScheduler -   -> 2703 reads (4.29% of total) failing DuplicateReadFilter
[2015-09-30T20:40Z] INFO  21:40:49,832 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:40Z] INFO  21:40:49,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:40Z] INFO  21:40:49,832 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:40Z] INFO  21:40:49,832 MicroScheduler -   -> 10 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:40Z] INFO  21:40:50,791 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:40Z] Genotyping with varscan: ('5', 63256014, 94276127) 1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam
[2015-09-30T20:40Z] samtools mpileup
[2015-09-30T20:40Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:40Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:40Z] samtools mpileup
[2015-09-30T20:40Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:40Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:41Z] Varscan
[2015-09-30T20:41Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpzT08N3/syn3-5_0_31268043-raw-normal.mpileup
[2015-09-30T20:41Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpzT08N3/syn3-5_0_31268043-raw-tumor.mpileup
[2015-09-30T20:41Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:41Z] Min reads2:	2
[2015-09-30T20:41Z] Min strands2:	1
[2015-09-30T20:41Z] Min var freq:	0.1
[2015-09-30T20:41Z] Min freq for hom:	0.75
[2015-09-30T20:41Z] Normal purity:	1.0
[2015-09-30T20:41Z] Tumor purity:	1.0
[2015-09-30T20:41Z] Min avg qual:	15
[2015-09-30T20:41Z] P-value thresh:	0.98
[2015-09-30T20:41Z] Somatic p-value:	0.05
[2015-09-30T20:41Z] samtools mpileup
[2015-09-30T20:41Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:41Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:41Z] Varscan
[2015-09-30T20:41Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmp3IAB1v/syn3-5_31293868_62597714-raw-normal.mpileup
[2015-09-30T20:41Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmp3IAB1v/syn3-5_31293868_62597714-raw-tumor.mpileup
[2015-09-30T20:41Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:41Z] Min reads2:	2
[2015-09-30T20:41Z] Min strands2:	1
[2015-09-30T20:41Z] Min var freq:	0.1
[2015-09-30T20:41Z] Min freq for hom:	0.75
[2015-09-30T20:41Z] Normal purity:	1.0
[2015-09-30T20:41Z] Tumor purity:	1.0
[2015-09-30T20:41Z] Min avg qual:	15
[2015-09-30T20:41Z] P-value thresh:	0.98
[2015-09-30T20:41Z] Somatic p-value:	0.05
[2015-09-30T20:41Z] 652712 positions in tumor
[2015-09-30T20:41Z] 652710 positions shared in normal
[2015-09-30T20:41Z] 642842 had sufficient coverage for comparison
[2015-09-30T20:41Z] 641726 were called Reference
[2015-09-30T20:41Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:41Z] 108 were removed by the strand filter
[2015-09-30T20:41Z] 1082 were called Germline
[2015-09-30T20:41Z] 6 were called LOH
[2015-09-30T20:41Z] 23 were called Somatic
[2015-09-30T20:41Z] 5 were called Unknown
[2015-09-30T20:41Z] 0 were called Variant
[2015-09-30T20:41Z] Varscan paired fix
[2015-09-30T20:41Z] Varscan paired fix
[2015-09-30T20:41Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:41Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:41Z] bgzip syn3-5_0_31268043-raw.snp.vcf
[2015-09-30T20:41Z] tabix index syn3-5_0_31268043-raw.snp.vcf.gz
[2015-09-30T20:41Z] bgzip syn3-5_0_31268043-raw.indel.vcf
[2015-09-30T20:41Z] tabix index syn3-5_0_31268043-raw.indel.vcf.gz
[2015-09-30T20:41Z] Combine variant files
[2015-09-30T20:41Z] INFO  21:41:45,057 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:41Z] INFO  21:41:45,059 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:41Z] INFO  21:41:45,059 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:41Z] INFO  21:41:45,059 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:41Z] INFO  21:41:45,063 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpzT08N3/tx/tmpogiEzB/syn3-5_0_31268043-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/5/tx/tmpzT08N3/syn3-5_0_31268043-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/5/tx/tmpzT08N3/syn3-5_0_31268043-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_0_31268043-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:41Z] INFO  21:41:45,070 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:41Z] INFO  21:41:45,070 HelpFormatter - Date/Time: 2015/09/30 21:41:45
[2015-09-30T20:41Z] INFO  21:41:45,071 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:41Z] INFO  21:41:45,071 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:41Z] INFO  21:41:45,147 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:41Z] INFO  21:41:45,432 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:41Z] INFO  21:41:45,519 IntervalUtils - Processing 657750 bp from intervals
[2015-09-30T20:41Z] WARN  21:41:45,520 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:41Z] WARN  21:41:45,520 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:41Z] INFO  21:41:45,578 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:41Z] INFO  21:41:45,580 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:41Z] INFO  21:41:45,581 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:41Z] INFO  21:41:45,581 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:41Z] INFO  21:41:45,581 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:41Z] INFO  21:41:46,522 ProgressMeter -            done      1223.0     0.0 s      12.8 m       99.9%     0.0 s       0.0 s
[2015-09-30T20:41Z] INFO  21:41:46,522 ProgressMeter - Total runtime 0.94 secs, 0.02 min, 0.00 hours
[2015-09-30T20:41Z] bgzip syn3-5_0_31268043-raw.vcf
[2015-09-30T20:41Z] tabix index syn3-5_0_31268043-raw.vcf.gz
[2015-09-30T20:41Z] bgzip syn3-5_0_31268043-raw-rejectfix.vcf
[2015-09-30T20:41Z] tabix index syn3-5_0_31268043-raw-rejectfix.vcf.gz
[2015-09-30T20:41Z] GATK: VariantAnnotator
[2015-09-30T20:41Z] INFO  21:41:48,806 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:41Z] INFO  21:41:48,808 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:41Z] INFO  21:41:48,808 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:41Z] INFO  21:41:48,808 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:41Z] INFO  21:41:48,812 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/5/syn3-5_0_31268043-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/5/tx/tmppLRtSf/syn3-5_0_31268043-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_0_31268043-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:41Z] INFO  21:41:48,817 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:41Z] INFO  21:41:48,817 HelpFormatter - Date/Time: 2015/09/30 21:41:48
[2015-09-30T20:41Z] INFO  21:41:48,817 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:41Z] INFO  21:41:48,818 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:41Z] INFO  21:41:48,889 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:41Z] INFO  21:41:48,982 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:41Z] INFO  21:41:48,989 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:41Z] INFO  21:41:49,011 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:41Z] INFO  21:41:49,332 IntervalUtils - Processing 1223 bp from intervals
[2015-09-30T20:41Z] WARN  21:41:49,336 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:41Z] WARN  21:41:49,336 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:41Z] INFO  21:41:49,389 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:41Z] INFO  21:41:49,510 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:41Z] INFO  21:41:49,511 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:41Z] INFO  21:41:49,511 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:41Z] INFO  21:41:49,511 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:41Z] INFO  21:41:49,609 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:41Z] INFO  21:41:55,401 VariantAnnotator - Processed 1006 loci.
[2015-09-30T20:41Z]
[2015-09-30T20:41Z] INFO  21:41:55,420 ProgressMeter -            done      7028.0     5.0 s      14.0 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:41Z] INFO  21:41:55,420 ProgressMeter - Total runtime 5.91 secs, 0.10 min, 0.00 hours
[2015-09-30T20:41Z] INFO  21:41:55,421 MicroScheduler - 4437 reads were filtered out during the traversal out of approximately 86830 total reads (5.11%)
[2015-09-30T20:41Z] INFO  21:41:55,421 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:41Z] INFO  21:41:55,421 MicroScheduler -   -> 4415 reads (5.08% of total) failing DuplicateReadFilter
[2015-09-30T20:41Z] INFO  21:41:55,421 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:41Z] INFO  21:41:55,422 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:41Z] INFO  21:41:55,422 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:41Z] INFO  21:41:55,422 MicroScheduler -   -> 22 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:41Z] INFO  21:41:56,334 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:41Z] Genotyping with varscan: ('5', 94277739, 125696417) 1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam
[2015-09-30T20:41Z] samtools mpileup
[2015-09-30T20:41Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:41Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:42Z] Varscan
[2015-09-30T20:42Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpcBMAyD/syn3-5_63256014_94276127-raw-normal.mpileup
[2015-09-30T20:42Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpcBMAyD/syn3-5_63256014_94276127-raw-tumor.mpileup
[2015-09-30T20:42Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:42Z] Min reads2:	2
[2015-09-30T20:42Z] Min strands2:	1
[2015-09-30T20:42Z] Min var freq:	0.1
[2015-09-30T20:42Z] Min freq for hom:	0.75
[2015-09-30T20:42Z] Normal purity:	1.0
[2015-09-30T20:42Z] Tumor purity:	1.0
[2015-09-30T20:42Z] Min avg qual:	15
[2015-09-30T20:42Z] P-value thresh:	0.98
[2015-09-30T20:42Z] Somatic p-value:	0.05
[2015-09-30T20:42Z] 1108612 positions in tumor
[2015-09-30T20:42Z] 1108604 positions shared in normal
[2015-09-30T20:42Z] 1074501 had sufficient coverage for comparison
[2015-09-30T20:42Z] 1073250 were called Reference
[2015-09-30T20:42Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:42Z] 56 were removed by the strand filter
[2015-09-30T20:42Z] 1225 were called Germline
[2015-09-30T20:42Z] 2 were called LOH
[2015-09-30T20:42Z] 15 were called Somatic
[2015-09-30T20:42Z] 9 were called Unknown
[2015-09-30T20:42Z] 0 were called Variant
[2015-09-30T20:42Z] Varscan paired fix
[2015-09-30T20:42Z] Varscan paired fix
[2015-09-30T20:42Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:42Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:42Z] bgzip syn3-5_31293868_62597714-raw.snp.vcf
[2015-09-30T20:42Z] tabix index syn3-5_31293868_62597714-raw.snp.vcf.gz
[2015-09-30T20:42Z] bgzip syn3-5_31293868_62597714-raw.indel.vcf
[2015-09-30T20:42Z] tabix index syn3-5_31293868_62597714-raw.indel.vcf.gz
[2015-09-30T20:42Z] Combine variant files
[2015-09-30T20:42Z] samtools mpileup
[2015-09-30T20:42Z] INFO  21:42:17,092 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:42Z] INFO  21:42:17,095 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:42Z] INFO  21:42:17,095 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:42Z] INFO  21:42:17,095 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:42Z] INFO  21:42:17,098 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/5/tx/tmp3IAB1v/tx/tmpdYwG2v/syn3-5_31293868_62597714-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/5/tx/tmp3IAB1v/syn3-5_31293868_62597714-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/5/tx/tmp3IAB1v/syn3-5_31293868_62597714-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_31293868_62597714-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:42Z] INFO  21:42:17,104 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:42Z] INFO  21:42:17,104 HelpFormatter - Date/Time: 2015/09/30 21:42:17
[2015-09-30T20:42Z] INFO  21:42:17,104 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:42Z] INFO  21:42:17,105 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:42Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:42Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:42Z] INFO  21:42:17,181 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:42Z] INFO  21:42:17,310 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:42Z] INFO  21:42:17,419 IntervalUtils - Processing 1117535 bp from intervals
[2015-09-30T20:42Z] WARN  21:42:17,420 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:42Z] WARN  21:42:17,420 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:42Z] INFO  21:42:17,477 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:42Z] INFO  21:42:17,480 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:42Z] INFO  21:42:17,481 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:42Z] INFO  21:42:17,481 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:42Z] INFO  21:42:17,481 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:42Z] INFO  21:42:18,621 ProgressMeter -            done      1430.0     1.0 s      13.3 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:42Z] INFO  21:42:18,621 ProgressMeter - Total runtime 1.14 secs, 0.02 min, 0.00 hours
[2015-09-30T20:42Z] bgzip syn3-5_31293868_62597714-raw.vcf
[2015-09-30T20:42Z] tabix index syn3-5_31293868_62597714-raw.vcf.gz
[2015-09-30T20:42Z] bgzip syn3-5_31293868_62597714-raw-rejectfix.vcf
[2015-09-30T20:42Z] tabix index syn3-5_31293868_62597714-raw-rejectfix.vcf.gz
[2015-09-30T20:42Z] GATK: VariantAnnotator
[2015-09-30T20:42Z] INFO  21:42:21,096 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:42Z] INFO  21:42:21,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:42Z] INFO  21:42:21,098 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:42Z] INFO  21:42:21,098 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:42Z] INFO  21:42:21,102 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/5/syn3-5_31293868_62597714-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpnHqKN2/syn3-5_31293868_62597714-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_31293868_62597714-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:42Z] INFO  21:42:21,107 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:42Z] INFO  21:42:21,107 HelpFormatter - Date/Time: 2015/09/30 21:42:21
[2015-09-30T20:42Z] INFO  21:42:21,107 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:42Z] INFO  21:42:21,108 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:42Z] INFO  21:42:21,198 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:42Z] INFO  21:42:21,277 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:42Z] INFO  21:42:21,284 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:42Z] INFO  21:42:21,307 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:42Z] INFO  21:42:21,687 IntervalUtils - Processing 1430 bp from intervals
[2015-09-30T20:42Z] WARN  21:42:21,691 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:42Z] WARN  21:42:21,691 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:42Z] INFO  21:42:21,748 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:42Z] INFO  21:42:21,842 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:42Z] INFO  21:42:21,843 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:42Z] INFO  21:42:21,843 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:42Z] INFO  21:42:21,843 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:42Z] INFO  21:42:21,931 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:42Z] INFO  21:42:28,289 VariantAnnotator - Processed 1189 loci.
[2015-09-30T20:42Z]
[2015-09-30T20:42Z] INFO  21:42:28,310 ProgressMeter -            done      4667.0     6.0 s      23.1 m       99.8%     6.0 s       0.0 s
[2015-09-30T20:42Z] INFO  21:42:28,311 ProgressMeter - Total runtime 6.47 secs, 0.11 min, 0.00 hours
[2015-09-30T20:42Z] INFO  21:42:28,311 MicroScheduler - 3703 reads were filtered out during the traversal out of approximately 86115 total reads (4.30%)
[2015-09-30T20:42Z] INFO  21:42:28,311 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:42Z] INFO  21:42:28,312 MicroScheduler -   -> 3687 reads (4.28% of total) failing DuplicateReadFilter
[2015-09-30T20:42Z] INFO  21:42:28,312 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:42Z] INFO  21:42:28,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:42Z] INFO  21:42:28,312 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:42Z] INFO  21:42:28,313 MicroScheduler -   -> 16 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:42Z] INFO  21:42:29,236 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:42Z] Genotyping with varscan: ('5', 125759062, 156781785) 1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam
[2015-09-30T20:42Z] samtools mpileup
[2015-09-30T20:42Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:42Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:42Z] Varscan
[2015-09-30T20:42Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpCPRo5S/syn3-5_94277739_125696417-raw-normal.mpileup
[2015-09-30T20:42Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpCPRo5S/syn3-5_94277739_125696417-raw-tumor.mpileup
[2015-09-30T20:42Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:42Z] Min reads2:	2
[2015-09-30T20:42Z] Min strands2:	1
[2015-09-30T20:42Z] Min var freq:	0.1
[2015-09-30T20:42Z] Min freq for hom:	0.75
[2015-09-30T20:42Z] Normal purity:	1.0
[2015-09-30T20:42Z] Tumor purity:	1.0
[2015-09-30T20:42Z] Min avg qual:	15
[2015-09-30T20:42Z] P-value thresh:	0.98
[2015-09-30T20:42Z] Somatic p-value:	0.05
[2015-09-30T20:42Z] 1259065 positions in tumor
[2015-09-30T20:42Z] 1258935 positions shared in normal
[2015-09-30T20:42Z] 1198733 had sufficient coverage for comparison
[2015-09-30T20:42Z] 1197390 were called Reference
[2015-09-30T20:42Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:42Z] 131 were removed by the strand filter
[2015-09-30T20:42Z] 1302 were called Germline
[2015-09-30T20:42Z] 2 were called LOH
[2015-09-30T20:42Z] 28 were called Somatic
[2015-09-30T20:42Z] 11 were called Unknown
[2015-09-30T20:42Z] 0 were called Variant
[2015-09-30T20:42Z] Varscan paired fix
[2015-09-30T20:42Z] Varscan paired fix
[2015-09-30T20:42Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:42Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:42Z] bgzip syn3-5_63256014_94276127-raw.snp.vcf
[2015-09-30T20:42Z] tabix index syn3-5_63256014_94276127-raw.snp.vcf.gz
[2015-09-30T20:42Z] bgzip syn3-5_63256014_94276127-raw.indel.vcf
[2015-09-30T20:42Z] tabix index syn3-5_63256014_94276127-raw.indel.vcf.gz
[2015-09-30T20:42Z] Combine variant files
[2015-09-30T20:42Z] INFO  21:42:56,702 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:42Z] INFO  21:42:56,704 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:42Z] INFO  21:42:56,704 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:42Z] INFO  21:42:56,704 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:42Z] INFO  21:42:56,708 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpcBMAyD/tx/tmpoSC3KK/syn3-5_63256014_94276127-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/5/tx/tmpcBMAyD/syn3-5_63256014_94276127-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/5/tx/tmpcBMAyD/syn3-5_63256014_94276127-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_63256014_94276127-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:42Z] INFO  21:42:56,714 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:42Z] INFO  21:42:56,714 HelpFormatter - Date/Time: 2015/09/30 21:42:56
[2015-09-30T20:42Z] INFO  21:42:56,714 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:42Z] INFO  21:42:56,714 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:42Z] INFO  21:42:56,788 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:42Z] INFO  21:42:57,170 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:42Z] INFO  21:42:57,287 IntervalUtils - Processing 1272246 bp from intervals
[2015-09-30T20:42Z] WARN  21:42:57,288 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:42Z] WARN  21:42:57,288 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:42Z] INFO  21:42:57,344 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:42Z] INFO  21:42:57,347 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:42Z] INFO  21:42:57,347 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:42Z] INFO  21:42:57,348 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:42Z] INFO  21:42:57,348 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:42Z] INFO  21:42:58,523 ProgressMeter -            done      1391.0     1.0 s      14.1 m       99.6%     1.0 s       0.0 s
[2015-09-30T20:42Z] INFO  21:42:58,524 ProgressMeter - Total runtime 1.18 secs, 0.02 min, 0.00 hours
[2015-09-30T20:42Z] bgzip syn3-5_63256014_94276127-raw.vcf
[2015-09-30T20:42Z] tabix index syn3-5_63256014_94276127-raw.vcf.gz
[2015-09-30T20:42Z] bgzip syn3-5_63256014_94276127-raw-rejectfix.vcf
[2015-09-30T20:42Z] tabix index syn3-5_63256014_94276127-raw-rejectfix.vcf.gz
[2015-09-30T20:42Z] GATK: VariantAnnotator
[2015-09-30T20:43Z] INFO  21:43:02,240 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:43Z] INFO  21:43:02,242 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:43Z] INFO  21:43:02,242 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:43Z] INFO  21:43:02,243 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:43Z] INFO  21:43:02,246 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/5/syn3-5_63256014_94276127-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpVkzYsJ/syn3-5_63256014_94276127-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_63256014_94276127-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:43Z] INFO  21:43:02,253 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:43Z] INFO  21:43:02,253 HelpFormatter - Date/Time: 2015/09/30 21:43:02
[2015-09-30T20:43Z] INFO  21:43:02,253 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:43Z] INFO  21:43:02,253 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:43Z] INFO  21:43:02,973 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:43Z] INFO  21:43:03,047 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:43Z] INFO  21:43:03,054 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:43Z] INFO  21:43:03,076 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:43Z] INFO  21:43:03,468 IntervalUtils - Processing 1392 bp from intervals
[2015-09-30T20:43Z] WARN  21:43:03,472 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:43Z] WARN  21:43:03,472 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:43Z] INFO  21:43:03,529 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:43Z] INFO  21:43:04,091 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:43Z] INFO  21:43:04,091 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:43Z] INFO  21:43:04,092 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:43Z] INFO  21:43:04,092 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:43Z] INFO  21:43:04,123 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:43Z] 721441 positions in tumor
[2015-09-30T20:43Z] 721437 positions shared in normal
[2015-09-30T20:43Z] 688976 had sufficient coverage for comparison
[2015-09-30T20:43Z] 688115 were called Reference
[2015-09-30T20:43Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:43Z] 77 were removed by the strand filter
[2015-09-30T20:43Z] 836 were called Germline
[2015-09-30T20:43Z] 5 were called LOH
[2015-09-30T20:43Z] 18 were called Somatic
[2015-09-30T20:43Z] 2 were called Unknown
[2015-09-30T20:43Z] 0 were called Variant
[2015-09-30T20:43Z] Varscan paired fix
[2015-09-30T20:43Z] Varscan paired fix
[2015-09-30T20:43Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:43Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:43Z] bgzip syn3-5_94277739_125696417-raw.snp.vcf
[2015-09-30T20:43Z] tabix index syn3-5_94277739_125696417-raw.snp.vcf.gz
[2015-09-30T20:43Z] bgzip syn3-5_94277739_125696417-raw.indel.vcf
[2015-09-30T20:43Z] tabix index syn3-5_94277739_125696417-raw.indel.vcf.gz
[2015-09-30T20:43Z] Combine variant files
[2015-09-30T20:43Z] INFO  21:43:08,564 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:43Z] INFO  21:43:08,566 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:43Z] INFO  21:43:08,566 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:43Z] INFO  21:43:08,566 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:43Z] INFO  21:43:08,570 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpCPRo5S/tx/tmpTNFpof/syn3-5_94277739_125696417-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/5/tx/tmpCPRo5S/syn3-5_94277739_125696417-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/5/tx/tmpCPRo5S/syn3-5_94277739_125696417-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_94277739_125696417-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:43Z] INFO  21:43:08,575 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:43Z] INFO  21:43:08,575 HelpFormatter - Date/Time: 2015/09/30 21:43:08
[2015-09-30T20:43Z] INFO  21:43:08,576 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:43Z] INFO  21:43:08,576 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:43Z] INFO  21:43:08,820 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:43Z] INFO  21:43:08,963 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:43Z] INFO  21:43:09,121 IntervalUtils - Processing 727022 bp from intervals
[2015-09-30T20:43Z] WARN  21:43:09,121 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:43Z] WARN  21:43:09,122 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:43Z] INFO  21:43:09,178 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:43Z] INFO  21:43:09,180 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:43Z] INFO  21:43:09,180 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:43Z] INFO  21:43:09,181 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:43Z] INFO  21:43:09,181 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:43Z] INFO  21:43:10,347 ProgressMeter -            done       954.0     1.0 s      20.4 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:43Z] INFO  21:43:10,347 ProgressMeter - Total runtime 1.17 secs, 0.02 min, 0.00 hours
[2015-09-30T20:43Z] INFO  21:43:10,420 VariantAnnotator - Processed 1203 loci.
[2015-09-30T20:43Z]
[2015-09-30T20:43Z] INFO  21:43:10,448 ProgressMeter -            done      4723.0     6.0 s      22.4 m       99.9%     6.0 s       0.0 s
[2015-09-30T20:43Z] INFO  21:43:10,448 ProgressMeter - Total runtime 6.36 secs, 0.11 min, 0.00 hours
[2015-09-30T20:43Z] INFO  21:43:10,448 MicroScheduler - 3609 reads were filtered out during the traversal out of approximately 90158 total reads (4.00%)
[2015-09-30T20:43Z] INFO  21:43:10,449 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:43Z] INFO  21:43:10,449 MicroScheduler -   -> 3587 reads (3.98% of total) failing DuplicateReadFilter
[2015-09-30T20:43Z] INFO  21:43:10,449 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:43Z] INFO  21:43:10,449 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:43Z] INFO  21:43:10,450 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:43Z] INFO  21:43:10,450 MicroScheduler -   -> 22 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:43Z] bgzip syn3-5_94277739_125696417-raw.vcf
[2015-09-30T20:43Z] tabix index syn3-5_94277739_125696417-raw.vcf.gz
[2015-09-30T20:43Z] bgzip syn3-5_94277739_125696417-raw-rejectfix.vcf
[2015-09-30T20:43Z] tabix index syn3-5_94277739_125696417-raw-rejectfix.vcf.gz
[2015-09-30T20:43Z] GATK: VariantAnnotator
[2015-09-30T20:43Z] INFO  21:43:11,425 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:43Z] Genotyping with varscan: ('5', 156785743, 180915260) 1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam
[2015-09-30T20:43Z] INFO  21:43:12,483 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:43Z] INFO  21:43:12,485 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:43Z] INFO  21:43:12,485 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:43Z] INFO  21:43:12,486 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:43Z] INFO  21:43:12,489 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/5/syn3-5_94277739_125696417-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpA4DaGz/syn3-5_94277739_125696417-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_94277739_125696417-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:43Z] INFO  21:43:12,495 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:43Z] INFO  21:43:12,495 HelpFormatter - Date/Time: 2015/09/30 21:43:12
[2015-09-30T20:43Z] INFO  21:43:12,495 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:43Z] INFO  21:43:12,495 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:43Z] samtools mpileup
[2015-09-30T20:43Z] INFO  21:43:12,585 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:43Z] INFO  21:43:12,659 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:43Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:43Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:43Z] INFO  21:43:12,667 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:43Z] INFO  21:43:12,689 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:43Z] INFO  21:43:13,079 IntervalUtils - Processing 954 bp from intervals
[2015-09-30T20:43Z] WARN  21:43:13,084 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:43Z] WARN  21:43:13,084 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:43Z] INFO  21:43:13,138 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:43Z] INFO  21:43:13,222 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:43Z] INFO  21:43:13,223 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:43Z] INFO  21:43:13,223 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:43Z] INFO  21:43:13,223 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:43Z] INFO  21:43:13,255 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:43Z] INFO  21:43:17,805 VariantAnnotator - Processed 782 loci.
[2015-09-30T20:43Z]
[2015-09-30T20:43Z] INFO  21:43:17,831 ProgressMeter -            done      3629.0     4.0 s      21.2 m       99.9%     4.0 s       0.0 s
[2015-09-30T20:43Z] INFO  21:43:17,831 ProgressMeter - Total runtime 4.61 secs, 0.08 min, 0.00 hours
[2015-09-30T20:43Z] INFO  21:43:17,831 MicroScheduler - 2280 reads were filtered out during the traversal out of approximately 53289 total reads (4.28%)
[2015-09-30T20:43Z] INFO  21:43:17,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:43Z] INFO  21:43:17,832 MicroScheduler -   -> 2266 reads (4.25% of total) failing DuplicateReadFilter
[2015-09-30T20:43Z] INFO  21:43:17,832 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:43Z] INFO  21:43:17,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:43Z] INFO  21:43:17,832 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:43Z] INFO  21:43:17,833 MicroScheduler -   -> 14 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:43Z] INFO  21:43:18,758 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:43Z] Genotyping with varscan: ('6', 0, 31080572) 1_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam
[2015-09-30T20:43Z] samtools mpileup
[2015-09-30T20:43Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:43Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:43Z] samtools mpileup
[2015-09-30T20:43Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:43Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:43Z] samtools mpileup
[2015-09-30T20:43Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:43Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:44Z] samtools mpileup
[2015-09-30T20:44Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:44Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:44Z] Varscan
[2015-09-30T20:44Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpRX8haq/syn3-5_156785743_180915260-raw-normal.mpileup
[2015-09-30T20:44Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpRX8haq/syn3-5_156785743_180915260-raw-tumor.mpileup
[2015-09-30T20:44Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:44Z] Min reads2:	2
[2015-09-30T20:44Z] Min strands2:	1
[2015-09-30T20:44Z] Min var freq:	0.1
[2015-09-30T20:44Z] Min freq for hom:	0.75
[2015-09-30T20:44Z] Normal purity:	1.0
[2015-09-30T20:44Z] Tumor purity:	1.0
[2015-09-30T20:44Z] Min avg qual:	15
[2015-09-30T20:44Z] P-value thresh:	0.98
[2015-09-30T20:44Z] Somatic p-value:	0.05
[2015-09-30T20:44Z] Varscan
[2015-09-30T20:44Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpbRZKqB/syn3-6_0_31080572-raw-normal.mpileup
[2015-09-30T20:44Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpbRZKqB/syn3-6_0_31080572-raw-tumor.mpileup
[2015-09-30T20:44Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:44Z] Min reads2:	2
[2015-09-30T20:44Z] Min strands2:	1
[2015-09-30T20:44Z] Min var freq:	0.1
[2015-09-30T20:44Z] Min freq for hom:	0.75
[2015-09-30T20:44Z] Normal purity:	1.0
[2015-09-30T20:44Z] Tumor purity:	1.0
[2015-09-30T20:44Z] Min avg qual:	15
[2015-09-30T20:44Z] P-value thresh:	0.98
[2015-09-30T20:44Z] Somatic p-value:	0.05
[2015-09-30T20:45Z] Varscan
[2015-09-30T20:45Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpWAy9Lt/syn3-5_125759062_156781785-raw-normal.mpileup
[2015-09-30T20:45Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/5/tx/tmpWAy9Lt/syn3-5_125759062_156781785-raw-tumor.mpileup
[2015-09-30T20:45Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:45Z] Min reads2:	2
[2015-09-30T20:45Z] Min strands2:	1
[2015-09-30T20:45Z] Min var freq:	0.1
[2015-09-30T20:45Z] Min freq for hom:	0.75
[2015-09-30T20:45Z] Normal purity:	1.0
[2015-09-30T20:45Z] Tumor purity:	1.0
[2015-09-30T20:45Z] Min avg qual:	15
[2015-09-30T20:45Z] P-value thresh:	0.98
[2015-09-30T20:45Z] Somatic p-value:	0.05
[2015-09-30T20:45Z] 1146108 positions in tumor
[2015-09-30T20:45Z] 1146099 positions shared in normal
[2015-09-30T20:45Z] 1134019 had sufficient coverage for comparison
[2015-09-30T20:45Z] 1132448 were called Reference
[2015-09-30T20:45Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:45Z] 78 were removed by the strand filter
[2015-09-30T20:45Z] 1532 were called Germline
[2015-09-30T20:45Z] 3 were called LOH
[2015-09-30T20:45Z] 30 were called Somatic
[2015-09-30T20:45Z] 6 were called Unknown
[2015-09-30T20:45Z] 0 were called Variant
[2015-09-30T20:45Z] Varscan paired fix
[2015-09-30T20:45Z] Varscan paired fix
[2015-09-30T20:45Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:45Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:45Z] bgzip syn3-5_156785743_180915260-raw.snp.vcf
[2015-09-30T20:45Z] tabix index syn3-5_156785743_180915260-raw.snp.vcf.gz
[2015-09-30T20:45Z] bgzip syn3-5_156785743_180915260-raw.indel.vcf
[2015-09-30T20:45Z] tabix index syn3-5_156785743_180915260-raw.indel.vcf.gz
[2015-09-30T20:45Z] Combine variant files
[2015-09-30T20:45Z] INFO  21:45:34,789 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:34,791 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:45Z] INFO  21:45:34,791 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:45Z] INFO  21:45:34,791 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:45Z] INFO  21:45:34,795 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpRX8haq/tx/tmpeGMvLj/syn3-5_156785743_180915260-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/5/tx/tmpRX8haq/syn3-5_156785743_180915260-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/5/tx/tmpRX8haq/syn3-5_156785743_180915260-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_156785743_180915260-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:45Z] INFO  21:45:34,800 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:45Z] INFO  21:45:34,801 HelpFormatter - Date/Time: 2015/09/30 21:45:34
[2015-09-30T20:45Z] INFO  21:45:34,801 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:34,801 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:34,878 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:45Z] INFO  21:45:35,023 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:45Z] INFO  21:45:35,141 IntervalUtils - Processing 1149697 bp from intervals
[2015-09-30T20:45Z] WARN  21:45:35,142 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:45Z] WARN  21:45:35,142 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:45Z] INFO  21:45:35,200 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:45Z] INFO  21:45:35,203 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:45Z] INFO  21:45:35,204 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:45Z] INFO  21:45:35,204 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:45Z] INFO  21:45:35,205 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:45Z] INFO  21:45:36,612 ProgressMeter -            done      1737.0     1.0 s      13.5 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:45Z] INFO  21:45:36,612 ProgressMeter - Total runtime 1.41 secs, 0.02 min, 0.00 hours
[2015-09-30T20:45Z] bgzip syn3-5_156785743_180915260-raw.vcf
[2015-09-30T20:45Z] tabix index syn3-5_156785743_180915260-raw.vcf.gz
[2015-09-30T20:45Z] bgzip syn3-5_156785743_180915260-raw-rejectfix.vcf
[2015-09-30T20:45Z] tabix index syn3-5_156785743_180915260-raw-rejectfix.vcf.gz
[2015-09-30T20:45Z] GATK: VariantAnnotator
[2015-09-30T20:45Z] INFO  21:45:39,397 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:39,399 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:45Z] INFO  21:45:39,399 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:45Z] INFO  21:45:39,399 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:45Z] INFO  21:45:39,403 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/5/syn3-5_156785743_180915260-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpRMhEni/syn3-5_156785743_180915260-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_156785743_180915260-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:45Z] INFO  21:45:39,409 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:45Z] INFO  21:45:39,409 HelpFormatter - Date/Time: 2015/09/30 21:45:39
[2015-09-30T20:45Z] INFO  21:45:39,409 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:39,409 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:39,505 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:45Z] INFO  21:45:39,583 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:45Z] INFO  21:45:39,591 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:45Z] INFO  21:45:39,613 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:45Z] INFO  21:45:39,997 IntervalUtils - Processing 1737 bp from intervals
[2015-09-30T20:45Z] WARN  21:45:40,002 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:45Z] WARN  21:45:40,002 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:45Z] INFO  21:45:40,061 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:45Z] INFO  21:45:40,249 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:45Z] INFO  21:45:40,249 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:45Z] INFO  21:45:40,250 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:45Z] INFO  21:45:40,250 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:45Z] INFO  21:45:40,283 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:45Z] INFO  21:45:48,659 VariantAnnotator - Processed 1488 loci.
[2015-09-30T20:45Z]
[2015-09-30T20:45Z] INFO  21:45:48,683 ProgressMeter -            done      8769.0     8.0 s      16.0 m       99.9%     8.0 s       0.0 s
[2015-09-30T20:45Z] INFO  21:45:48,683 ProgressMeter - Total runtime 8.43 secs, 0.14 min, 0.00 hours
[2015-09-30T20:45Z] INFO  21:45:48,684 MicroScheduler - 6980 reads were filtered out during the traversal out of approximately 135113 total reads (5.17%)
[2015-09-30T20:45Z] INFO  21:45:48,684 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:45Z] INFO  21:45:48,684 MicroScheduler -   -> 6942 reads (5.14% of total) failing DuplicateReadFilter
[2015-09-30T20:45Z] INFO  21:45:48,685 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:45Z] INFO  21:45:48,685 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:45Z] INFO  21:45:48,685 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:45Z] INFO  21:45:48,685 MicroScheduler -   -> 38 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:45Z] 1370643 positions in tumor
[2015-09-30T20:45Z] 1370641 positions shared in normal
[2015-09-30T20:45Z] 1351904 had sufficient coverage for comparison
[2015-09-30T20:45Z] 1349517 were called Reference
[2015-09-30T20:45Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:45Z] 150 were removed by the strand filter
[2015-09-30T20:45Z] 2344 were called Germline
[2015-09-30T20:45Z] 2 were called LOH
[2015-09-30T20:45Z] 30 were called Somatic
[2015-09-30T20:45Z] 11 were called Unknown
[2015-09-30T20:45Z] 0 were called Variant
[2015-09-30T20:45Z] Varscan paired fix
[2015-09-30T20:45Z] Varscan paired fix
[2015-09-30T20:45Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:45Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:45Z] bgzip syn3-6_0_31080572-raw.snp.vcf
[2015-09-30T20:45Z] tabix index syn3-6_0_31080572-raw.snp.vcf.gz
[2015-09-30T20:45Z] bgzip syn3-6_0_31080572-raw.indel.vcf
[2015-09-30T20:45Z] tabix index syn3-6_0_31080572-raw.indel.vcf.gz
[2015-09-30T20:45Z] Combine variant files
[2015-09-30T20:45Z] INFO  21:45:49,654 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:45Z] Genotyping with varscan: ('6', 31082315, 62284583) 1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam
[2015-09-30T20:45Z] samtools mpileup
[2015-09-30T20:45Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:45Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:45Z] INFO  21:45:51,220 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:51,222 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:45Z] INFO  21:45:51,223 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:45Z] INFO  21:45:51,223 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:45Z] INFO  21:45:51,226 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/6/tx/tmpbRZKqB/tx/tmplmjtBN/syn3-6_0_31080572-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/6/tx/tmpbRZKqB/syn3-6_0_31080572-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/6/tx/tmpbRZKqB/syn3-6_0_31080572-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_0_31080572-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:45Z] INFO  21:45:51,232 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:45Z] INFO  21:45:51,232 HelpFormatter - Date/Time: 2015/09/30 21:45:51
[2015-09-30T20:45Z] INFO  21:45:51,232 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:51,233 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:51,310 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:45Z] INFO  21:45:51,704 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:45Z] INFO  21:45:51,832 IntervalUtils - Processing 1374885 bp from intervals
[2015-09-30T20:45Z] WARN  21:45:51,833 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:45Z] WARN  21:45:51,833 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:45Z] INFO  21:45:51,890 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:45Z] INFO  21:45:51,893 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:45Z] INFO  21:45:51,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:45Z] INFO  21:45:51,894 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:45Z] INFO  21:45:51,895 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:45Z] INFO  21:45:53,458 ProgressMeter -            done      2483.0     1.0 s      10.5 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:45Z] INFO  21:45:53,459 ProgressMeter - Total runtime 1.56 secs, 0.03 min, 0.00 hours
[2015-09-30T20:45Z] bgzip syn3-6_0_31080572-raw.vcf
[2015-09-30T20:45Z] tabix index syn3-6_0_31080572-raw.vcf.gz
[2015-09-30T20:45Z] bgzip syn3-6_0_31080572-raw-rejectfix.vcf
[2015-09-30T20:45Z] tabix index syn3-6_0_31080572-raw-rejectfix.vcf.gz
[2015-09-30T20:45Z] GATK: VariantAnnotator
[2015-09-30T20:45Z] INFO  21:45:55,912 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:55,914 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:45Z] INFO  21:45:55,915 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:45Z] INFO  21:45:55,915 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:45Z] INFO  21:45:55,918 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/6/syn3-6_0_31080572-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/6/tx/tmpA2br8n/syn3-6_0_31080572-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_0_31080572-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:45Z] INFO  21:45:55,924 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:45Z] INFO  21:45:55,924 HelpFormatter - Date/Time: 2015/09/30 21:45:55
[2015-09-30T20:45Z] INFO  21:45:55,924 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:55,924 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:45Z] INFO  21:45:56,243 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:45Z] INFO  21:45:56,322 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:45Z] INFO  21:45:56,330 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:45Z] INFO  21:45:56,353 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:45Z] INFO  21:45:56,739 IntervalUtils - Processing 2483 bp from intervals
[2015-09-30T20:45Z] WARN  21:45:56,743 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:45Z] WARN  21:45:56,743 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:45Z] INFO  21:45:56,801 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:45Z] INFO  21:45:56,968 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:45Z] INFO  21:45:56,969 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:45Z] INFO  21:45:56,969 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:45Z] INFO  21:45:56,969 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:45Z] INFO  21:45:57,002 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:46Z] INFO  21:46:08,324 VariantAnnotator - Processed 2228 loci.
[2015-09-30T20:46Z]
[2015-09-30T20:46Z] INFO  21:46:08,343 ProgressMeter -            done     35604.0    11.0 s       5.3 m      100.0%    11.0 s       0.0 s
[2015-09-30T20:46Z] INFO  21:46:08,343 ProgressMeter - Total runtime 11.37 secs, 0.19 min, 0.00 hours
[2015-09-30T20:46Z] INFO  21:46:08,343 MicroScheduler - 7911 reads were filtered out during the traversal out of approximately 163585 total reads (4.84%)
[2015-09-30T20:46Z] INFO  21:46:08,344 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:46Z] INFO  21:46:08,344 MicroScheduler -   -> 7860 reads (4.80% of total) failing DuplicateReadFilter
[2015-09-30T20:46Z] INFO  21:46:08,344 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:46Z] INFO  21:46:08,344 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:46Z] INFO  21:46:08,345 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:46Z] INFO  21:46:08,345 MicroScheduler -   -> 51 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:46Z] INFO  21:46:09,305 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:46Z] Genotyping with varscan: ('6', 62389878, 93953543) 1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam
[2015-09-30T20:46Z] samtools mpileup
[2015-09-30T20:46Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:46Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:46Z] 2007443 positions in tumor
[2015-09-30T20:46Z] 2007435 positions shared in normal
[2015-09-30T20:46Z] 1981611 had sufficient coverage for comparison
[2015-09-30T20:46Z] 1979579 were called Reference
[2015-09-30T20:46Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:46Z] 77 were removed by the strand filter
[2015-09-30T20:46Z] 1974 were called Germline
[2015-09-30T20:46Z] 11 were called LOH
[2015-09-30T20:46Z] 38 were called Somatic
[2015-09-30T20:46Z] 9 were called Unknown
[2015-09-30T20:46Z] 0 were called Variant
[2015-09-30T20:46Z] Varscan paired fix
[2015-09-30T20:46Z] Varscan paired fix
[2015-09-30T20:46Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:46Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:46Z] bgzip syn3-5_125759062_156781785-raw.snp.vcf
[2015-09-30T20:46Z] tabix index syn3-5_125759062_156781785-raw.snp.vcf.gz
[2015-09-30T20:46Z] bgzip syn3-5_125759062_156781785-raw.indel.vcf
[2015-09-30T20:46Z] tabix index syn3-5_125759062_156781785-raw.indel.vcf.gz
[2015-09-30T20:46Z] Combine variant files
[2015-09-30T20:46Z] INFO  21:46:26,431 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:46Z] INFO  21:46:26,433 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:46Z] INFO  21:46:26,433 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:46Z] INFO  21:46:26,434 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:46Z] INFO  21:46:26,437 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpWAy9Lt/tx/tmpalxxcS/syn3-5_125759062_156781785-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/5/tx/tmpWAy9Lt/syn3-5_125759062_156781785-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/5/tx/tmpWAy9Lt/syn3-5_125759062_156781785-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_125759062_156781785-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:46Z] INFO  21:46:26,443 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:46Z] INFO  21:46:26,443 HelpFormatter - Date/Time: 2015/09/30 21:46:26
[2015-09-30T20:46Z] INFO  21:46:26,444 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:46Z] INFO  21:46:26,444 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:46Z] INFO  21:46:26,517 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:46Z] INFO  21:46:26,654 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:46Z] INFO  21:46:26,783 IntervalUtils - Processing 2012098 bp from intervals
[2015-09-30T20:46Z] WARN  21:46:26,784 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:46Z] WARN  21:46:26,784 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:46Z] INFO  21:46:26,838 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:46Z] INFO  21:46:26,842 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:46Z] INFO  21:46:26,842 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:46Z] INFO  21:46:26,843 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:46Z] INFO  21:46:26,843 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:46Z] INFO  21:46:28,509 ProgressMeter -            done      2448.0     1.0 s      11.3 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:46Z] INFO  21:46:28,510 ProgressMeter - Total runtime 1.67 secs, 0.03 min, 0.00 hours
[2015-09-30T20:46Z] bgzip syn3-5_125759062_156781785-raw.vcf
[2015-09-30T20:46Z] tabix index syn3-5_125759062_156781785-raw.vcf.gz
[2015-09-30T20:46Z] bgzip syn3-5_125759062_156781785-raw-rejectfix.vcf
[2015-09-30T20:46Z] tabix index syn3-5_125759062_156781785-raw-rejectfix.vcf.gz
[2015-09-30T20:46Z] GATK: VariantAnnotator
[2015-09-30T20:46Z] INFO  21:46:31,136 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:46Z] INFO  21:46:31,138 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:46Z] INFO  21:46:31,138 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:46Z] INFO  21:46:31,139 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:46Z] INFO  21:46:31,142 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/5/syn3-5_125759062_156781785-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/5/tx/tmpJVXPB9/syn3-5_125759062_156781785-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/5/syn3-5_125759062_156781785-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:46Z] INFO  21:46:31,147 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:46Z] INFO  21:46:31,148 HelpFormatter - Date/Time: 2015/09/30 21:46:31
[2015-09-30T20:46Z] INFO  21:46:31,148 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:46Z] INFO  21:46:31,148 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:46Z] INFO  21:46:31,257 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:46Z] INFO  21:46:31,439 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:46Z] INFO  21:46:31,447 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:46Z] INFO  21:46:31,678 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.23
[2015-09-30T20:46Z] INFO  21:46:32,715 IntervalUtils - Processing 2449 bp from intervals
[2015-09-30T20:46Z] WARN  21:46:32,731 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:46Z] WARN  21:46:32,732 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:46Z] INFO  21:46:32,813 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:46Z] INFO  21:46:33,386 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:46Z] INFO  21:46:33,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:46Z] INFO  21:46:33,387 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:46Z] INFO  21:46:33,387 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:46Z] INFO  21:46:33,420 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:46Z] samtools mpileup
[2015-09-30T20:46Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:46Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:46Z] INFO  21:46:44,555 VariantAnnotator - Processed 1950 loci.
[2015-09-30T20:46Z]
[2015-09-30T20:46Z] INFO  21:46:44,613 ProgressMeter -            done     11820.0    11.0 s      15.8 m      100.0%    11.0 s       0.0 s
[2015-09-30T20:46Z] INFO  21:46:44,613 ProgressMeter - Total runtime 11.23 secs, 0.19 min, 0.00 hours
[2015-09-30T20:46Z] INFO  21:46:44,614 MicroScheduler - 8080 reads were filtered out during the traversal out of approximately 168662 total reads (4.79%)
[2015-09-30T20:46Z] INFO  21:46:44,614 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:46Z] INFO  21:46:44,614 MicroScheduler -   -> 8043 reads (4.77% of total) failing DuplicateReadFilter
[2015-09-30T20:46Z] INFO  21:46:44,614 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:46Z] INFO  21:46:44,615 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:46Z] INFO  21:46:44,615 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:46Z] INFO  21:46:44,615 MicroScheduler -   -> 37 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:46Z] INFO  21:46:45,553 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:46Z] Genotyping with varscan: ('6', 93954776, 124979769) 1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam
[2015-09-30T20:46Z] samtools mpileup
[2015-09-30T20:46Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:46Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:47Z] Varscan
[2015-09-30T20:47Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpzi0R3Z/syn3-6_62389878_93953543-raw-normal.mpileup
[2015-09-30T20:47Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpzi0R3Z/syn3-6_62389878_93953543-raw-tumor.mpileup
[2015-09-30T20:47Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:47Z] Min reads2:	2
[2015-09-30T20:47Z] Min strands2:	1
[2015-09-30T20:47Z] Min var freq:	0.1
[2015-09-30T20:47Z] Min freq for hom:	0.75
[2015-09-30T20:47Z] Normal purity:	1.0
[2015-09-30T20:47Z] Tumor purity:	1.0
[2015-09-30T20:47Z] Min avg qual:	15
[2015-09-30T20:47Z] P-value thresh:	0.98
[2015-09-30T20:47Z] Somatic p-value:	0.05
[2015-09-30T20:47Z] samtools mpileup
[2015-09-30T20:47Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:47Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:47Z] samtools mpileup
[2015-09-30T20:47Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:47Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:47Z] 916464 positions in tumor
[2015-09-30T20:47Z] 916454 positions shared in normal
[2015-09-30T20:47Z] 876871 had sufficient coverage for comparison
[2015-09-30T20:47Z] 875967 were called Reference
[2015-09-30T20:47Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:47Z] 40 were removed by the strand filter
[2015-09-30T20:47Z] 878 were called Germline
[2015-09-30T20:47Z] 5 were called LOH
[2015-09-30T20:47Z] 13 were called Somatic
[2015-09-30T20:47Z] 8 were called Unknown
[2015-09-30T20:47Z] 0 were called Variant
[2015-09-30T20:47Z] Varscan paired fix
[2015-09-30T20:47Z] Varscan paired fix
[2015-09-30T20:47Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:47Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:47Z] bgzip syn3-6_62389878_93953543-raw.snp.vcf
[2015-09-30T20:47Z] tabix index syn3-6_62389878_93953543-raw.snp.vcf.gz
[2015-09-30T20:47Z] bgzip syn3-6_62389878_93953543-raw.indel.vcf
[2015-09-30T20:47Z] tabix index syn3-6_62389878_93953543-raw.indel.vcf.gz
[2015-09-30T20:47Z] Combine variant files
[2015-09-30T20:47Z] INFO  21:47:36,931 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:47Z] INFO  21:47:36,933 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:47Z] INFO  21:47:36,933 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:47Z] INFO  21:47:36,933 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:47Z] INFO  21:47:36,936 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/6/tx/tmpzi0R3Z/tx/tmp8lEdVc/syn3-6_62389878_93953543-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/6/tx/tmpzi0R3Z/syn3-6_62389878_93953543-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/6/tx/tmpzi0R3Z/syn3-6_62389878_93953543-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_62389878_93953543-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:47Z] INFO  21:47:36,942 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:47Z] INFO  21:47:36,943 HelpFormatter - Date/Time: 2015/09/30 21:47:36
[2015-09-30T20:47Z] INFO  21:47:36,943 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:47Z] INFO  21:47:36,943 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:47Z] INFO  21:47:37,015 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:47Z] INFO  21:47:37,336 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:47Z] INFO  21:47:37,453 IntervalUtils - Processing 924860 bp from intervals
[2015-09-30T20:47Z] WARN  21:47:37,454 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:47Z] WARN  21:47:37,454 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:47Z] INFO  21:47:37,512 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:47Z] INFO  21:47:37,515 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:47Z] INFO  21:47:37,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:47Z] INFO  21:47:37,516 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:47Z] INFO  21:47:37,516 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:47Z] INFO  21:47:38,532 ProgressMeter -            done       958.0     1.0 s      17.7 m       99.7%     1.0 s       0.0 s
[2015-09-30T20:47Z] INFO  21:47:38,533 ProgressMeter - Total runtime 1.02 secs, 0.02 min, 0.00 hours
[2015-09-30T20:47Z] bgzip syn3-6_62389878_93953543-raw.vcf
[2015-09-30T20:47Z] tabix index syn3-6_62389878_93953543-raw.vcf.gz
[2015-09-30T20:47Z] bgzip syn3-6_62389878_93953543-raw-rejectfix.vcf
[2015-09-30T20:47Z] tabix index syn3-6_62389878_93953543-raw-rejectfix.vcf.gz
[2015-09-30T20:47Z] GATK: VariantAnnotator
[2015-09-30T20:47Z] INFO  21:47:40,763 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:47Z] INFO  21:47:40,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:47Z] INFO  21:47:40,765 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:47Z] INFO  21:47:40,766 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:47Z] INFO  21:47:40,769 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/6/syn3-6_62389878_93953543-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/6/tx/tmp0yaji3/syn3-6_62389878_93953543-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_62389878_93953543-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:47Z] INFO  21:47:40,774 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:47Z] INFO  21:47:40,775 HelpFormatter - Date/Time: 2015/09/30 21:47:40
[2015-09-30T20:47Z] INFO  21:47:40,775 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:47Z] INFO  21:47:40,775 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:47Z] INFO  21:47:40,868 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:47Z] INFO  21:47:40,940 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:47Z] INFO  21:47:40,948 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:47Z] INFO  21:47:40,969 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:47Z] INFO  21:47:41,283 IntervalUtils - Processing 958 bp from intervals
[2015-09-30T20:47Z] WARN  21:47:41,287 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:47Z] WARN  21:47:41,287 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:47Z] INFO  21:47:41,341 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:47Z] INFO  21:47:41,435 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:47Z] INFO  21:47:41,435 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:47Z] INFO  21:47:41,435 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:47Z] INFO  21:47:41,436 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:47Z] INFO  21:47:41,466 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:47Z] Varscan
[2015-09-30T20:47Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpfYtE3L/syn3-6_93954776_124979769-raw-normal.mpileup
[2015-09-30T20:47Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpfYtE3L/syn3-6_93954776_124979769-raw-tumor.mpileup
[2015-09-30T20:47Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:47Z] Min reads2:	2
[2015-09-30T20:47Z] Min strands2:	1
[2015-09-30T20:47Z] Min var freq:	0.1
[2015-09-30T20:47Z] Min freq for hom:	0.75
[2015-09-30T20:47Z] Normal purity:	1.0
[2015-09-30T20:47Z] Tumor purity:	1.0
[2015-09-30T20:47Z] Min avg qual:	15
[2015-09-30T20:47Z] P-value thresh:	0.98
[2015-09-30T20:47Z] Somatic p-value:	0.05
[2015-09-30T20:47Z] INFO  21:47:46,626 VariantAnnotator - Processed 858 loci.
[2015-09-30T20:47Z]
[2015-09-30T20:47Z] INFO  21:47:46,658 ProgressMeter -            done      3041.0     5.0 s      28.6 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:47Z] INFO  21:47:46,658 ProgressMeter - Total runtime 5.22 secs, 0.09 min, 0.00 hours
[2015-09-30T20:47Z] INFO  21:47:46,658 MicroScheduler - 2482 reads were filtered out during the traversal out of approximately 59027 total reads (4.20%)
[2015-09-30T20:47Z] INFO  21:47:46,658 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:47Z] INFO  21:47:46,659 MicroScheduler -   -> 2471 reads (4.19% of total) failing DuplicateReadFilter
[2015-09-30T20:47Z] INFO  21:47:46,659 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:47Z] INFO  21:47:46,659 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:47Z] INFO  21:47:46,659 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:47Z] INFO  21:47:46,660 MicroScheduler -   -> 11 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:47Z] INFO  21:47:47,607 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:47Z] Genotyping with varscan: ('6', 125064552, 156268261) 1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam
[2015-09-30T20:47Z] samtools mpileup
[2015-09-30T20:47Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:47Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:48Z] 957068 positions in tumor
[2015-09-30T20:48Z] 957059 positions shared in normal
[2015-09-30T20:48Z] 922232 had sufficient coverage for comparison
[2015-09-30T20:48Z] 921137 were called Reference
[2015-09-30T20:48Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:48Z] 37 were removed by the strand filter
[2015-09-30T20:48Z] 1069 were called Germline
[2015-09-30T20:48Z] 0 were called LOH
[2015-09-30T20:48Z] 18 were called Somatic
[2015-09-30T20:48Z] 8 were called Unknown
[2015-09-30T20:48Z] 0 were called Variant
[2015-09-30T20:48Z] Varscan paired fix
[2015-09-30T20:48Z] Varscan paired fix
[2015-09-30T20:48Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:48Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:48Z] bgzip syn3-6_93954776_124979769-raw.snp.vcf
[2015-09-30T20:48Z] tabix index syn3-6_93954776_124979769-raw.snp.vcf.gz
[2015-09-30T20:48Z] bgzip syn3-6_93954776_124979769-raw.indel.vcf
[2015-09-30T20:48Z] tabix index syn3-6_93954776_124979769-raw.indel.vcf.gz
[2015-09-30T20:48Z] Combine variant files
[2015-09-30T20:48Z] INFO  21:48:20,008 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:48Z] INFO  21:48:20,010 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:48Z] INFO  21:48:20,010 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:48Z] INFO  21:48:20,010 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:48Z] INFO  21:48:20,014 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/6/tx/tmpfYtE3L/tx/tmpyjttGi/syn3-6_93954776_124979769-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/6/tx/tmpfYtE3L/syn3-6_93954776_124979769-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/6/tx/tmpfYtE3L/syn3-6_93954776_124979769-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_93954776_124979769-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:48Z] INFO  21:48:20,019 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:48Z] INFO  21:48:20,019 HelpFormatter - Date/Time: 2015/09/30 21:48:20
[2015-09-30T20:48Z] INFO  21:48:20,019 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:48Z] INFO  21:48:20,019 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:48Z] INFO  21:48:20,094 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:48Z] INFO  21:48:20,234 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:48Z] INFO  21:48:20,353 IntervalUtils - Processing 964242 bp from intervals
[2015-09-30T20:48Z] WARN  21:48:20,354 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:48Z] WARN  21:48:20,354 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:48Z] INFO  21:48:20,411 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:48Z] INFO  21:48:20,414 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:48Z] INFO  21:48:20,414 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:48Z] INFO  21:48:20,415 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:48Z] INFO  21:48:20,415 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:48Z] INFO  21:48:21,555 ProgressMeter -            done      1265.0     1.0 s      15.0 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:48Z] INFO  21:48:21,555 ProgressMeter - Total runtime 1.14 secs, 0.02 min, 0.00 hours
[2015-09-30T20:48Z] bgzip syn3-6_93954776_124979769-raw.vcf
[2015-09-30T20:48Z] tabix index syn3-6_93954776_124979769-raw.vcf.gz
[2015-09-30T20:48Z] bgzip syn3-6_93954776_124979769-raw-rejectfix.vcf
[2015-09-30T20:48Z] tabix index syn3-6_93954776_124979769-raw-rejectfix.vcf.gz
[2015-09-30T20:48Z] GATK: VariantAnnotator
[2015-09-30T20:48Z] INFO  21:48:24,205 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:48Z] INFO  21:48:24,207 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:48Z] INFO  21:48:24,207 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:48Z] INFO  21:48:24,208 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:48Z] INFO  21:48:24,211 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/6/syn3-6_93954776_124979769-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/6/tx/tmpdGMeMS/syn3-6_93954776_124979769-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_93954776_124979769-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:48Z] INFO  21:48:24,216 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:48Z] INFO  21:48:24,216 HelpFormatter - Date/Time: 2015/09/30 21:48:24
[2015-09-30T20:48Z] INFO  21:48:24,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:48Z] INFO  21:48:24,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:48Z] INFO  21:48:24,301 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:48Z] INFO  21:48:24,373 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:48Z] INFO  21:48:24,381 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:48Z] INFO  21:48:24,402 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:48Z] INFO  21:48:24,705 IntervalUtils - Processing 1267 bp from intervals
[2015-09-30T20:48Z] WARN  21:48:24,709 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:48Z] WARN  21:48:24,709 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:48Z] INFO  21:48:24,762 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:48Z] INFO  21:48:24,899 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:48Z] INFO  21:48:24,899 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:48Z] INFO  21:48:24,899 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:48Z] INFO  21:48:24,900 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:48Z] INFO  21:48:24,983 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:48Z] samtools mpileup
[2015-09-30T20:48Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:48Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:48Z] INFO  21:48:30,316 VariantAnnotator - Processed 1053 loci.
[2015-09-30T20:48Z]
[2015-09-30T20:48Z] INFO  21:48:30,336 ProgressMeter -            done      4540.0     5.0 s      20.0 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:48Z] INFO  21:48:30,336 ProgressMeter - Total runtime 5.44 secs, 0.09 min, 0.00 hours
[2015-09-30T20:48Z] INFO  21:48:30,337 MicroScheduler - 3094 reads were filtered out during the traversal out of approximately 70587 total reads (4.38%)
[2015-09-30T20:48Z] INFO  21:48:30,337 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:48Z] INFO  21:48:30,337 MicroScheduler -   -> 3085 reads (4.37% of total) failing DuplicateReadFilter
[2015-09-30T20:48Z] INFO  21:48:30,337 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:48Z] INFO  21:48:30,338 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:48Z] INFO  21:48:30,338 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:48Z] INFO  21:48:30,338 MicroScheduler -   -> 9 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T20:48Z] INFO  21:48:31,490 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:48Z] Genotyping with varscan: ('6', 156275378, 171115067) 1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam
[2015-09-30T20:48Z] samtools mpileup
[2015-09-30T20:48Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:48Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:48Z] samtools mpileup
[2015-09-30T20:48Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:48Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:48Z] Varscan
[2015-09-30T20:48Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmp9Xvval/syn3-6_31082315_62284583-raw-normal.mpileup
[2015-09-30T20:48Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmp9Xvval/syn3-6_31082315_62284583-raw-tumor.mpileup
[2015-09-30T20:48Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:48Z] Min reads2:	2
[2015-09-30T20:48Z] Min strands2:	1
[2015-09-30T20:48Z] Min var freq:	0.1
[2015-09-30T20:48Z] Min freq for hom:	0.75
[2015-09-30T20:48Z] Normal purity:	1.0
[2015-09-30T20:48Z] Tumor purity:	1.0
[2015-09-30T20:48Z] Min avg qual:	15
[2015-09-30T20:48Z] P-value thresh:	0.98
[2015-09-30T20:48Z] Somatic p-value:	0.05
[2015-09-30T20:49Z] Varscan
[2015-09-30T20:49Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpMc1uKE/syn3-6_125064552_156268261-raw-normal.mpileup
[2015-09-30T20:49Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpMc1uKE/syn3-6_125064552_156268261-raw-tumor.mpileup
[2015-09-30T20:49Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:49Z] Min reads2:	2
[2015-09-30T20:49Z] Min strands2:	1
[2015-09-30T20:49Z] Min var freq:	0.1
[2015-09-30T20:49Z] Min freq for hom:	0.75
[2015-09-30T20:49Z] Normal purity:	1.0
[2015-09-30T20:49Z] Tumor purity:	1.0
[2015-09-30T20:49Z] Min avg qual:	15
[2015-09-30T20:49Z] P-value thresh:	0.98
[2015-09-30T20:49Z] Somatic p-value:	0.05
[2015-09-30T20:49Z] Varscan
[2015-09-30T20:49Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpf5vGYC/syn3-6_156275378_171115067-raw-normal.mpileup
[2015-09-30T20:49Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/6/tx/tmpf5vGYC/syn3-6_156275378_171115067-raw-tumor.mpileup
[2015-09-30T20:49Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:49Z] Min reads2:	2
[2015-09-30T20:49Z] Min strands2:	1
[2015-09-30T20:49Z] Min var freq:	0.1
[2015-09-30T20:49Z] Min freq for hom:	0.75
[2015-09-30T20:49Z] Normal purity:	1.0
[2015-09-30T20:49Z] Tumor purity:	1.0
[2015-09-30T20:49Z] Min avg qual:	15
[2015-09-30T20:49Z] P-value thresh:	0.98
[2015-09-30T20:49Z] Somatic p-value:	0.05
[2015-09-30T20:49Z] 626097 positions in tumor
[2015-09-30T20:49Z] 626086 positions shared in normal
[2015-09-30T20:49Z] 614276 had sufficient coverage for comparison
[2015-09-30T20:49Z] 613315 were called Reference
[2015-09-30T20:49Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:49Z] 60 were removed by the strand filter
[2015-09-30T20:49Z] 942 were called Germline
[2015-09-30T20:49Z] 1 were called LOH
[2015-09-30T20:49Z] 15 were called Somatic
[2015-09-30T20:49Z] 3 were called Unknown
[2015-09-30T20:49Z] 0 were called Variant
[2015-09-30T20:49Z] Varscan paired fix
[2015-09-30T20:49Z] Varscan paired fix
[2015-09-30T20:49Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:49Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:49Z] bgzip syn3-6_156275378_171115067-raw.snp.vcf
[2015-09-30T20:49Z] tabix index syn3-6_156275378_171115067-raw.snp.vcf.gz
[2015-09-30T20:49Z] bgzip syn3-6_156275378_171115067-raw.indel.vcf
[2015-09-30T20:49Z] tabix index syn3-6_156275378_171115067-raw.indel.vcf.gz
[2015-09-30T20:49Z] Combine variant files
[2015-09-30T20:49Z] INFO  21:49:52,176 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:49Z] INFO  21:49:52,178 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:49Z] INFO  21:49:52,178 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:49Z] INFO  21:49:52,178 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:49Z] INFO  21:49:52,182 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/6/tx/tmpf5vGYC/tx/tmpJqIhD0/syn3-6_156275378_171115067-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/6/tx/tmpf5vGYC/syn3-6_156275378_171115067-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/6/tx/tmpf5vGYC/syn3-6_156275378_171115067-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_156275378_171115067-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:49Z] INFO  21:49:52,189 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:49Z] INFO  21:49:52,189 HelpFormatter - Date/Time: 2015/09/30 21:49:52
[2015-09-30T20:49Z] INFO  21:49:52,189 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:49Z] INFO  21:49:52,189 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:49Z] INFO  21:49:52,270 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:49Z] INFO  21:49:52,407 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:49Z] INFO  21:49:52,515 IntervalUtils - Processing 630229 bp from intervals
[2015-09-30T20:49Z] WARN  21:49:52,516 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:49Z] WARN  21:49:52,516 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:49Z] INFO  21:49:52,577 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:49Z] INFO  21:49:52,579 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:49Z] INFO  21:49:52,580 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:49Z] INFO  21:49:52,580 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:49Z] INFO  21:49:52,580 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:49Z] INFO  21:49:53,755 ProgressMeter -            done      1156.0     1.0 s      16.9 m       99.9%     1.0 s       0.0 s
[2015-09-30T20:49Z] INFO  21:49:53,756 ProgressMeter - Total runtime 1.18 secs, 0.02 min, 0.00 hours
[2015-09-30T20:49Z] bgzip syn3-6_156275378_171115067-raw.vcf
[2015-09-30T20:49Z] tabix index syn3-6_156275378_171115067-raw.vcf.gz
[2015-09-30T20:49Z] bgzip syn3-6_156275378_171115067-raw-rejectfix.vcf
[2015-09-30T20:49Z] tabix index syn3-6_156275378_171115067-raw-rejectfix.vcf.gz
[2015-09-30T20:49Z] GATK: VariantAnnotator
[2015-09-30T20:49Z] 1256366 positions in tumor
[2015-09-30T20:49Z] 1256355 positions shared in normal
[2015-09-30T20:49Z] 1221240 had sufficient coverage for comparison
[2015-09-30T20:49Z] 1219917 were called Reference
[2015-09-30T20:49Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:49Z] 73 were removed by the strand filter
[2015-09-30T20:49Z] 1287 were called Germline
[2015-09-30T20:49Z] 4 were called LOH
[2015-09-30T20:49Z] 22 were called Somatic
[2015-09-30T20:49Z] 10 were called Unknown
[2015-09-30T20:49Z] 0 were called Variant
[2015-09-30T20:49Z] Varscan paired fix
[2015-09-30T20:49Z] Varscan paired fix
[2015-09-30T20:49Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:49Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:49Z] bgzip syn3-6_125064552_156268261-raw.snp.vcf
[2015-09-30T20:49Z] tabix index syn3-6_125064552_156268261-raw.snp.vcf.gz
[2015-09-30T20:49Z] bgzip syn3-6_125064552_156268261-raw.indel.vcf
[2015-09-30T20:49Z] INFO  21:49:56,727 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:49Z] INFO  21:49:56,730 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:49Z] tabix index syn3-6_125064552_156268261-raw.indel.vcf.gz
[2015-09-30T20:49Z] INFO  21:49:56,730 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:49Z] INFO  21:49:56,730 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:49Z] INFO  21:49:56,734 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/6/syn3-6_156275378_171115067-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/6/tx/tmpnSvXXi/syn3-6_156275378_171115067-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_156275378_171115067-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:49Z] INFO  21:49:56,739 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:49Z] INFO  21:49:56,740 HelpFormatter - Date/Time: 2015/09/30 21:49:56
[2015-09-30T20:49Z] INFO  21:49:56,740 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:49Z] INFO  21:49:56,740 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:49Z] INFO  21:49:56,835 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:49Z] Combine variant files
[2015-09-30T20:49Z] INFO  21:49:56,917 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:49Z] INFO  21:49:56,925 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:49Z] INFO  21:49:56,949 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:49Z] INFO  21:49:57,280 IntervalUtils - Processing 1156 bp from intervals
[2015-09-30T20:49Z] WARN  21:49:57,284 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:49Z] WARN  21:49:57,285 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:49Z] INFO  21:49:57,344 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:49Z] INFO  21:49:57,444 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:49Z] INFO  21:49:57,444 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:49Z] INFO  21:49:57,445 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:49Z] INFO  21:49:57,445 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:49Z] INFO  21:49:57,535 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:50Z] INFO  21:50:00,405 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:00,407 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:50Z] INFO  21:50:00,408 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:50Z] INFO  21:50:00,408 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:50Z] INFO  21:50:00,411 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/6/tx/tmpMc1uKE/tx/tmpHEjoBX/syn3-6_125064552_156268261-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/6/tx/tmpMc1uKE/syn3-6_125064552_156268261-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/6/tx/tmpMc1uKE/syn3-6_125064552_156268261-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_125064552_156268261-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:50Z] INFO  21:50:00,417 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:50Z] INFO  21:50:00,417 HelpFormatter - Date/Time: 2015/09/30 21:50:00
[2015-09-30T20:50Z] INFO  21:50:00,417 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:00,418 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:00,498 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:50Z] INFO  21:50:00,640 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:50Z] INFO  21:50:00,766 IntervalUtils - Processing 1262148 bp from intervals
[2015-09-30T20:50Z] WARN  21:50:00,767 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:50Z] WARN  21:50:00,768 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:50Z] INFO  21:50:00,829 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:50Z] INFO  21:50:00,832 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:50Z] INFO  21:50:00,833 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:50Z] INFO  21:50:00,833 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:50Z] INFO  21:50:00,833 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:50Z] INFO  21:50:02,199 ProgressMeter -            done      1490.0     1.0 s      15.3 m       99.7%     1.0 s       0.0 s
[2015-09-30T20:50Z] INFO  21:50:02,199 ProgressMeter - Total runtime 1.37 secs, 0.02 min, 0.00 hours
[2015-09-30T20:50Z] bgzip syn3-6_125064552_156268261-raw.vcf
[2015-09-30T20:50Z] INFO  21:50:03,856 VariantAnnotator - Processed 899 loci.
[2015-09-30T20:50Z]
[2015-09-30T20:50Z] INFO  21:50:04,034 ProgressMeter -            done      5239.0     6.0 s      21.0 m       99.9%     6.0 s       0.0 s
[2015-09-30T20:50Z] INFO  21:50:04,034 ProgressMeter - Total runtime 6.59 secs, 0.11 min, 0.00 hours
[2015-09-30T20:50Z] INFO  21:50:04,034 MicroScheduler - 3937 reads were filtered out during the traversal out of approximately 78138 total reads (5.04%)
[2015-09-30T20:50Z] INFO  21:50:04,035 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:50Z] INFO  21:50:04,035 MicroScheduler -   -> 3920 reads (5.02% of total) failing DuplicateReadFilter
[2015-09-30T20:50Z] INFO  21:50:04,035 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:50Z] INFO  21:50:04,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:50Z] INFO  21:50:04,036 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:50Z] INFO  21:50:04,036 MicroScheduler -   -> 17 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:50Z] tabix index syn3-6_125064552_156268261-raw.vcf.gz
[2015-09-30T20:50Z] bgzip syn3-6_125064552_156268261-raw-rejectfix.vcf
[2015-09-30T20:50Z] tabix index syn3-6_125064552_156268261-raw-rejectfix.vcf.gz
[2015-09-30T20:50Z] GATK: VariantAnnotator
[2015-09-30T20:50Z] INFO  21:50:04,973 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:50Z] Genotyping with varscan: ('7', 0, 31019109) 1_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam
[2015-09-30T20:50Z] samtools mpileup
[2015-09-30T20:50Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:50Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:50Z] INFO  21:50:08,330 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:08,332 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:50Z] INFO  21:50:08,332 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:50Z] INFO  21:50:08,332 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:50Z] INFO  21:50:08,336 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/6/syn3-6_125064552_156268261-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/6/tx/tmp19ZRP2/syn3-6_125064552_156268261-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_125064552_156268261-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:50Z] INFO  21:50:08,342 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:50Z] INFO  21:50:08,342 HelpFormatter - Date/Time: 2015/09/30 21:50:08
[2015-09-30T20:50Z] INFO  21:50:08,342 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:08,342 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:08,447 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:50Z] INFO  21:50:08,527 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:50Z] INFO  21:50:08,534 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:50Z] INFO  21:50:08,563 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T20:50Z] INFO  21:50:09,073 IntervalUtils - Processing 1490 bp from intervals
[2015-09-30T20:50Z] WARN  21:50:09,078 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:50Z] WARN  21:50:09,078 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:50Z] INFO  21:50:09,148 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:50Z] INFO  21:50:09,438 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:50Z] INFO  21:50:09,439 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:50Z] INFO  21:50:09,439 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:50Z] INFO  21:50:09,440 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:50Z] INFO  21:50:09,529 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:50Z] INFO  21:50:16,407 VariantAnnotator - Processed 1243 loci.
[2015-09-30T20:50Z]
[2015-09-30T20:50Z] INFO  21:50:16,437 ProgressMeter -            done      4536.0     6.0 s      25.7 m       99.9%     6.0 s       0.0 s
[2015-09-30T20:50Z] INFO  21:50:16,437 ProgressMeter - Total runtime 7.00 secs, 0.12 min, 0.00 hours
[2015-09-30T20:50Z] INFO  21:50:16,438 MicroScheduler - 3773 reads were filtered out during the traversal out of approximately 88373 total reads (4.27%)
[2015-09-30T20:50Z] INFO  21:50:16,438 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:50Z] INFO  21:50:16,438 MicroScheduler -   -> 3755 reads (4.25% of total) failing DuplicateReadFilter
[2015-09-30T20:50Z] INFO  21:50:16,438 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:50Z] INFO  21:50:16,439 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:50Z] INFO  21:50:16,439 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:50Z] INFO  21:50:16,439 MicroScheduler -   -> 18 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:50Z] INFO  21:50:17,357 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:50Z] Genotyping with varscan: ('7', 31022897, 62585293) 1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam
[2015-09-30T20:50Z] samtools mpileup
[2015-09-30T20:50Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:50Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:50Z] 2320194 positions in tumor
[2015-09-30T20:50Z] 2320189 positions shared in normal
[2015-09-30T20:50Z] 2292143 had sufficient coverage for comparison
[2015-09-30T20:50Z] 2287210 were called Reference
[2015-09-30T20:50Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:50Z] 392 were removed by the strand filter
[2015-09-30T20:50Z] 4846 were called Germline
[2015-09-30T20:50Z] 7 were called LOH
[2015-09-30T20:50Z] 57 were called Somatic
[2015-09-30T20:50Z] 23 were called Unknown
[2015-09-30T20:50Z] 0 were called Variant
[2015-09-30T20:50Z] Varscan paired fix
[2015-09-30T20:50Z] Varscan paired fix
[2015-09-30T20:50Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:50Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:50Z] bgzip syn3-6_31082315_62284583-raw.snp.vcf
[2015-09-30T20:50Z] tabix index syn3-6_31082315_62284583-raw.snp.vcf.gz
[2015-09-30T20:50Z] bgzip syn3-6_31082315_62284583-raw.indel.vcf
[2015-09-30T20:50Z] tabix index syn3-6_31082315_62284583-raw.indel.vcf.gz
[2015-09-30T20:50Z] Combine variant files
[2015-09-30T20:50Z] INFO  21:50:41,946 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:41,948 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:50Z] INFO  21:50:41,948 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:50Z] INFO  21:50:41,948 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:50Z] INFO  21:50:41,952 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/6/tx/tmp9Xvval/tx/tmpHN_u6V/syn3-6_31082315_62284583-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/6/tx/tmp9Xvval/syn3-6_31082315_62284583-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/6/tx/tmp9Xvval/syn3-6_31082315_62284583-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_31082315_62284583-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:50Z] INFO  21:50:41,957 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:50Z] INFO  21:50:41,957 HelpFormatter - Date/Time: 2015/09/30 21:50:41
[2015-09-30T20:50Z] INFO  21:50:41,957 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:41,957 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:42,030 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:50Z] INFO  21:50:42,166 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:50Z] INFO  21:50:42,296 IntervalUtils - Processing 2326318 bp from intervals
[2015-09-30T20:50Z] WARN  21:50:42,297 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:50Z] WARN  21:50:42,297 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:50Z] INFO  21:50:42,352 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:50Z] INFO  21:50:42,356 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:50Z] INFO  21:50:42,356 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:50Z] INFO  21:50:42,357 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:50Z] INFO  21:50:42,357 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:50Z] INFO  21:50:44,805 ProgressMeter -            done      5084.0     2.0 s       8.0 m      100.0%     2.0 s       0.0 s
[2015-09-30T20:50Z] INFO  21:50:44,805 ProgressMeter - Total runtime 2.45 secs, 0.04 min, 0.00 hours
[2015-09-30T20:50Z] bgzip syn3-6_31082315_62284583-raw.vcf
[2015-09-30T20:50Z] tabix index syn3-6_31082315_62284583-raw.vcf.gz
[2015-09-30T20:50Z] bgzip syn3-6_31082315_62284583-raw-rejectfix.vcf
[2015-09-30T20:50Z] tabix index syn3-6_31082315_62284583-raw-rejectfix.vcf.gz
[2015-09-30T20:50Z] GATK: VariantAnnotator
[2015-09-30T20:50Z] INFO  21:50:48,639 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:48,641 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:50Z] INFO  21:50:48,641 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:50Z] INFO  21:50:48,641 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:50Z] INFO  21:50:48,645 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/6/syn3-6_31082315_62284583-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/6/tx/tmpaFsVXV/syn3-6_31082315_62284583-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/6/syn3-6_31082315_62284583-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:50Z] INFO  21:50:48,650 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:50Z] INFO  21:50:48,650 HelpFormatter - Date/Time: 2015/09/30 21:50:48
[2015-09-30T20:50Z] INFO  21:50:48,650 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:48,650 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:50Z] INFO  21:50:48,739 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:50Z] INFO  21:50:48,815 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:50Z] INFO  21:50:48,822 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:50Z] INFO  21:50:48,844 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:50Z] INFO  21:50:49,407 IntervalUtils - Processing 5086 bp from intervals
[2015-09-30T20:50Z] WARN  21:50:49,412 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:50Z] WARN  21:50:49,412 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:50Z] INFO  21:50:49,468 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:50Z] INFO  21:50:49,620 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:50Z] INFO  21:50:49,621 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:50Z] INFO  21:50:49,621 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:50Z] INFO  21:50:49,621 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:50Z] INFO  21:50:49,651 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:50Z] samtools mpileup
[2015-09-30T20:50Z] samtools mpileup
[2015-09-30T20:50Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:50Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:50Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:50Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:51Z] INFO  21:51:10,383 VariantAnnotator - Processed 4525 loci.
[2015-09-30T20:51Z]
[2015-09-30T20:51Z] INFO  21:51:10,612 ProgressMeter -            done    159910.0    20.0 s       2.2 m      100.0%    20.0 s       0.0 s
[2015-09-30T20:51Z] INFO  21:51:10,612 ProgressMeter - Total runtime 20.99 secs, 0.35 min, 0.01 hours
[2015-09-30T20:51Z] INFO  21:51:10,612 MicroScheduler - 14134 reads were filtered out during the traversal out of approximately 288314 total reads (4.90%)
[2015-09-30T20:51Z] INFO  21:51:10,613 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:51Z] INFO  21:51:10,613 MicroScheduler -   -> 14037 reads (4.87% of total) failing DuplicateReadFilter
[2015-09-30T20:51Z] INFO  21:51:10,613 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:51Z] INFO  21:51:10,613 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:51Z] INFO  21:51:10,614 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:51Z] INFO  21:51:10,614 MicroScheduler -   -> 97 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:51Z] INFO  21:51:11,546 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:51Z] Genotyping with varscan: ('7', 62708318, 93925745) 1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam
[2015-09-30T20:51Z] samtools mpileup
[2015-09-30T20:51Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:51Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:51Z] Varscan
[2015-09-30T20:51Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpPSriro/syn3-7_31022897_62585293-raw-normal.mpileup
[2015-09-30T20:51Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpPSriro/syn3-7_31022897_62585293-raw-tumor.mpileup
[2015-09-30T20:51Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:51Z] Min reads2:	2
[2015-09-30T20:51Z] Min strands2:	1
[2015-09-30T20:51Z] Min var freq:	0.1
[2015-09-30T20:51Z] Min freq for hom:	0.75
[2015-09-30T20:51Z] Normal purity:	1.0
[2015-09-30T20:51Z] Tumor purity:	1.0
[2015-09-30T20:51Z] Min avg qual:	15
[2015-09-30T20:51Z] P-value thresh:	0.98
[2015-09-30T20:51Z] Somatic p-value:	0.05
[2015-09-30T20:51Z] Varscan
[2015-09-30T20:51Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpHEbRrl/syn3-7_0_31019109-raw-normal.mpileup
[2015-09-30T20:51Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpHEbRrl/syn3-7_0_31019109-raw-tumor.mpileup
[2015-09-30T20:51Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:51Z] Min reads2:	2
[2015-09-30T20:51Z] Min strands2:	1
[2015-09-30T20:51Z] Min var freq:	0.1
[2015-09-30T20:51Z] Min freq for hom:	0.75
[2015-09-30T20:51Z] Normal purity:	1.0
[2015-09-30T20:51Z] Tumor purity:	1.0
[2015-09-30T20:51Z] Min avg qual:	15
[2015-09-30T20:51Z] P-value thresh:	0.98
[2015-09-30T20:51Z] Somatic p-value:	0.05
[2015-09-30T20:52Z] samtools mpileup
[2015-09-30T20:52Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:52Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:52Z] 1029784 positions in tumor
[2015-09-30T20:52Z] 1029779 positions shared in normal
[2015-09-30T20:52Z] 1010764 had sufficient coverage for comparison
[2015-09-30T20:52Z] 1008973 were called Reference
[2015-09-30T20:52Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:52Z] 145 were removed by the strand filter
[2015-09-30T20:52Z] 1734 were called Germline
[2015-09-30T20:52Z] 12 were called LOH
[2015-09-30T20:52Z] 27 were called Somatic
[2015-09-30T20:52Z] 18 were called Unknown
[2015-09-30T20:52Z] 0 were called Variant
[2015-09-30T20:52Z] Varscan paired fix
[2015-09-30T20:52Z] Varscan paired fix
[2015-09-30T20:52Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:52Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:52Z] bgzip syn3-7_31022897_62585293-raw.snp.vcf
[2015-09-30T20:52Z] tabix index syn3-7_31022897_62585293-raw.snp.vcf.gz
[2015-09-30T20:52Z] bgzip syn3-7_31022897_62585293-raw.indel.vcf
[2015-09-30T20:52Z] tabix index syn3-7_31022897_62585293-raw.indel.vcf.gz
[2015-09-30T20:52Z] Combine variant files
[2015-09-30T20:52Z] INFO  21:52:20,066 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:20,068 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:52Z] INFO  21:52:20,068 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:52Z] INFO  21:52:20,068 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:52Z] INFO  21:52:20,072 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpPSriro/tx/tmpoqAw11/syn3-7_31022897_62585293-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/7/tx/tmpPSriro/syn3-7_31022897_62585293-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/7/tx/tmpPSriro/syn3-7_31022897_62585293-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_31022897_62585293-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:52Z] INFO  21:52:20,077 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:52Z] INFO  21:52:20,077 HelpFormatter - Date/Time: 2015/09/30 21:52:20
[2015-09-30T20:52Z] INFO  21:52:20,078 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:20,078 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:20,154 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:52Z] INFO  21:52:20,294 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:52Z] INFO  21:52:20,402 IntervalUtils - Processing 1035831 bp from intervals
[2015-09-30T20:52Z] WARN  21:52:20,403 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:52Z] WARN  21:52:20,404 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:52Z] INFO  21:52:20,460 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:52Z] INFO  21:52:20,463 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:52Z] INFO  21:52:20,464 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:52Z] INFO  21:52:20,464 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:52Z] INFO  21:52:20,464 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:52Z] INFO  21:52:21,802 ProgressMeter -            done      1860.0     1.0 s      12.0 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:52Z] INFO  21:52:21,803 ProgressMeter - Total runtime 1.34 secs, 0.02 min, 0.00 hours
[2015-09-30T20:52Z] bgzip syn3-7_31022897_62585293-raw.vcf
[2015-09-30T20:52Z] tabix index syn3-7_31022897_62585293-raw.vcf.gz
[2015-09-30T20:52Z] bgzip syn3-7_31022897_62585293-raw-rejectfix.vcf
[2015-09-30T20:52Z] tabix index syn3-7_31022897_62585293-raw-rejectfix.vcf.gz
[2015-09-30T20:52Z] GATK: VariantAnnotator
[2015-09-30T20:52Z] INFO  21:52:24,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:24,360 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:52Z] INFO  21:52:24,360 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:52Z] INFO  21:52:24,361 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:52Z] INFO  21:52:24,364 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/7/syn3-7_31022897_62585293-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpT4Mu14/syn3-7_31022897_62585293-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_31022897_62585293-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:52Z] INFO  21:52:24,370 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:52Z] INFO  21:52:24,370 HelpFormatter - Date/Time: 2015/09/30 21:52:24
[2015-09-30T20:52Z] INFO  21:52:24,370 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:24,370 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:24,447 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:52Z] INFO  21:52:24,548 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:52Z] INFO  21:52:24,556 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:52Z] INFO  21:52:24,579 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:52Z] INFO  21:52:24,970 IntervalUtils - Processing 1860 bp from intervals
[2015-09-30T20:52Z] WARN  21:52:24,974 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:52Z] WARN  21:52:24,975 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:52Z] INFO  21:52:25,031 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:52Z] INFO  21:52:25,193 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:52Z] INFO  21:52:25,194 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:52Z] INFO  21:52:25,194 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:52Z] INFO  21:52:25,195 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:52Z] INFO  21:52:25,228 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:52Z] INFO  21:52:33,183 VariantAnnotator - Processed 1632 loci.
[2015-09-30T20:52Z]
[2015-09-30T20:52Z] INFO  21:52:33,668 ProgressMeter -            done     13400.0     8.0 s      10.5 m       99.9%     8.0 s       0.0 s
[2015-09-30T20:52Z] INFO  21:52:33,669 ProgressMeter - Total runtime 8.48 secs, 0.14 min, 0.00 hours
[2015-09-30T20:52Z] INFO  21:52:33,669 MicroScheduler - 6654 reads were filtered out during the traversal out of approximately 133974 total reads (4.97%)
[2015-09-30T20:52Z] INFO  21:52:33,669 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:52Z] INFO  21:52:33,670 MicroScheduler -   -> 6613 reads (4.94% of total) failing DuplicateReadFilter
[2015-09-30T20:52Z] INFO  21:52:33,670 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:52Z] INFO  21:52:33,670 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:52Z] INFO  21:52:33,670 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:52Z] INFO  21:52:33,671 MicroScheduler -   -> 41 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:52Z] INFO  21:52:34,731 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:52Z] Genotyping with varscan: ('7', 94024041, 125680568) 1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam
[2015-09-30T20:52Z] samtools mpileup
[2015-09-30T20:52Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:52Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:52Z] 1418130 positions in tumor
[2015-09-30T20:52Z] 1418119 positions shared in normal
[2015-09-30T20:52Z] 1389633 had sufficient coverage for comparison
[2015-09-30T20:52Z] 1387377 were called Reference
[2015-09-30T20:52Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:52Z] 131 were removed by the strand filter
[2015-09-30T20:52Z] 2203 were called Germline
[2015-09-30T20:52Z] 4 were called LOH
[2015-09-30T20:52Z] 39 were called Somatic
[2015-09-30T20:52Z] 10 were called Unknown
[2015-09-30T20:52Z] 0 were called Variant
[2015-09-30T20:52Z] Varscan paired fix
[2015-09-30T20:52Z] Varscan paired fix
[2015-09-30T20:52Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:52Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:52Z] bgzip syn3-7_0_31019109-raw.snp.vcf
[2015-09-30T20:52Z] tabix index syn3-7_0_31019109-raw.snp.vcf.gz
[2015-09-30T20:52Z] bgzip syn3-7_0_31019109-raw.indel.vcf
[2015-09-30T20:52Z] tabix index syn3-7_0_31019109-raw.indel.vcf.gz
[2015-09-30T20:52Z] Combine variant files
[2015-09-30T20:52Z] INFO  21:52:41,729 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:41,731 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:52Z] INFO  21:52:41,731 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:52Z] INFO  21:52:41,731 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:52Z] INFO  21:52:41,735 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpHEbRrl/tx/tmptWD75S/syn3-7_0_31019109-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/7/tx/tmpHEbRrl/syn3-7_0_31019109-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/7/tx/tmpHEbRrl/syn3-7_0_31019109-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_0_31019109-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:52Z] INFO  21:52:41,740 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:52Z] INFO  21:52:41,741 HelpFormatter - Date/Time: 2015/09/30 21:52:41
[2015-09-30T20:52Z] INFO  21:52:41,741 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:41,741 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:41,817 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:52Z] INFO  21:52:42,048 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:52Z] INFO  21:52:42,163 IntervalUtils - Processing 1428141 bp from intervals
[2015-09-30T20:52Z] WARN  21:52:42,164 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:52Z] WARN  21:52:42,164 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:52Z] INFO  21:52:42,221 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:52Z] INFO  21:52:42,225 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:52Z] INFO  21:52:42,225 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:52Z] INFO  21:52:42,226 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:52Z] INFO  21:52:42,226 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:52Z] INFO  21:52:43,779 ProgressMeter -            done      2580.0     1.0 s      10.0 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:52Z] INFO  21:52:43,780 ProgressMeter - Total runtime 1.55 secs, 0.03 min, 0.00 hours
[2015-09-30T20:52Z] bgzip syn3-7_0_31019109-raw.vcf
[2015-09-30T20:52Z] tabix index syn3-7_0_31019109-raw.vcf.gz
[2015-09-30T20:52Z] bgzip syn3-7_0_31019109-raw-rejectfix.vcf
[2015-09-30T20:52Z] tabix index syn3-7_0_31019109-raw-rejectfix.vcf.gz
[2015-09-30T20:52Z] GATK: VariantAnnotator
[2015-09-30T20:52Z] INFO  21:52:46,329 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:46,331 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:52Z] INFO  21:52:46,331 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:52Z] INFO  21:52:46,331 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:52Z] INFO  21:52:46,335 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/7/syn3-7_0_31019109-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpdvTMT4/syn3-7_0_31019109-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_0_31019109-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:52Z] INFO  21:52:46,340 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:52Z] INFO  21:52:46,340 HelpFormatter - Date/Time: 2015/09/30 21:52:46
[2015-09-30T20:52Z] INFO  21:52:46,340 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:46,341 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:52Z] INFO  21:52:46,434 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:52Z] INFO  21:52:46,510 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:52Z] INFO  21:52:46,518 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:52Z] INFO  21:52:46,540 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:52Z] INFO  21:52:46,956 IntervalUtils - Processing 2581 bp from intervals
[2015-09-30T20:52Z] WARN  21:52:46,960 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:52Z] WARN  21:52:46,961 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:52Z] INFO  21:52:47,017 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:52Z] INFO  21:52:47,198 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:52Z] INFO  21:52:47,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:52Z] INFO  21:52:47,199 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:52Z] INFO  21:52:47,199 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:52Z] INFO  21:52:47,231 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:52Z] Varscan
[2015-09-30T20:52Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpYiV4zK/syn3-7_62708318_93925745-raw-normal.mpileup
[2015-09-30T20:52Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpYiV4zK/syn3-7_62708318_93925745-raw-tumor.mpileup
[2015-09-30T20:52Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:52Z] Min reads2:	2
[2015-09-30T20:52Z] Min strands2:	1
[2015-09-30T20:52Z] Min var freq:	0.1
[2015-09-30T20:52Z] Min freq for hom:	0.75
[2015-09-30T20:52Z] Normal purity:	1.0
[2015-09-30T20:52Z] Tumor purity:	1.0
[2015-09-30T20:52Z] Min avg qual:	15
[2015-09-30T20:52Z] P-value thresh:	0.98
[2015-09-30T20:52Z] Somatic p-value:	0.05
[2015-09-30T20:52Z] INFO  21:52:57,145 VariantAnnotator - Processed 2118 loci.
[2015-09-30T20:52Z]
[2015-09-30T20:52Z] INFO  21:52:57,168 ProgressMeter -            done     12650.0     9.0 s      13.1 m      100.0%     9.0 s       0.0 s
[2015-09-30T20:52Z] INFO  21:52:57,168 ProgressMeter - Total runtime 9.97 secs, 0.17 min, 0.00 hours
[2015-09-30T20:52Z] INFO  21:52:57,168 MicroScheduler - 8806 reads were filtered out during the traversal out of approximately 177333 total reads (4.97%)
[2015-09-30T20:52Z] INFO  21:52:57,169 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:52Z] INFO  21:52:57,169 MicroScheduler -   -> 8766 reads (4.94% of total) failing DuplicateReadFilter
[2015-09-30T20:52Z] INFO  21:52:57,169 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:52Z] INFO  21:52:57,169 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:52Z] INFO  21:52:57,169 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:52Z] INFO  21:52:57,170 MicroScheduler -   -> 40 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:52Z] INFO  21:52:58,139 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:52Z] Genotyping with varscan: ('7', 126078434, 157151579) 1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam
[2015-09-30T20:52Z] samtools mpileup
[2015-09-30T20:52Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:52Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:53Z] samtools mpileup
[2015-09-30T20:53Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:53Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:53Z] 1458076 positions in tumor
[2015-09-30T20:53Z] 1458057 positions shared in normal
[2015-09-30T20:53Z] 1418154 had sufficient coverage for comparison
[2015-09-30T20:53Z] 1416255 were called Reference
[2015-09-30T20:53Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:53Z] 223 were removed by the strand filter
[2015-09-30T20:53Z] 1818 were called Germline
[2015-09-30T20:53Z] 9 were called LOH
[2015-09-30T20:53Z] 58 were called Somatic
[2015-09-30T20:53Z] 14 were called Unknown
[2015-09-30T20:53Z] 0 were called Variant
[2015-09-30T20:53Z] Varscan paired fix
[2015-09-30T20:53Z] Varscan paired fix
[2015-09-30T20:53Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:53Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:53Z] bgzip syn3-7_62708318_93925745-raw.snp.vcf
[2015-09-30T20:53Z] tabix index syn3-7_62708318_93925745-raw.snp.vcf.gz
[2015-09-30T20:53Z] bgzip syn3-7_62708318_93925745-raw.indel.vcf
[2015-09-30T20:53Z] tabix index syn3-7_62708318_93925745-raw.indel.vcf.gz
[2015-09-30T20:53Z] Combine variant files
[2015-09-30T20:53Z] INFO  21:53:53,071 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:53Z] INFO  21:53:53,073 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:53Z] INFO  21:53:53,073 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:53Z] INFO  21:53:53,074 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:53Z] INFO  21:53:53,077 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpYiV4zK/tx/tmppywM1x/syn3-7_62708318_93925745-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/7/tx/tmpYiV4zK/syn3-7_62708318_93925745-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/7/tx/tmpYiV4zK/syn3-7_62708318_93925745-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_62708318_93925745-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:53Z] INFO  21:53:53,082 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:53Z] INFO  21:53:53,083 HelpFormatter - Date/Time: 2015/09/30 21:53:53
[2015-09-30T20:53Z] INFO  21:53:53,083 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:53Z] INFO  21:53:53,083 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:53Z] INFO  21:53:53,162 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:53Z] INFO  21:53:53,483 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:53Z] INFO  21:53:53,612 IntervalUtils - Processing 1466050 bp from intervals
[2015-09-30T20:53Z] WARN  21:53:53,613 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:53Z] WARN  21:53:53,613 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:53Z] INFO  21:53:53,670 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:53Z] INFO  21:53:53,674 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:53Z] INFO  21:53:53,675 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:53Z] INFO  21:53:53,675 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:53Z] INFO  21:53:53,675 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:53Z] INFO  21:53:55,132 ProgressMeter -            done      1947.0     1.0 s      12.5 m       99.6%     1.0 s       0.0 s
[2015-09-30T20:53Z] INFO  21:53:55,132 ProgressMeter - Total runtime 1.46 secs, 0.02 min, 0.00 hours
[2015-09-30T20:53Z] bgzip syn3-7_62708318_93925745-raw.vcf
[2015-09-30T20:53Z] tabix index syn3-7_62708318_93925745-raw.vcf.gz
[2015-09-30T20:53Z] bgzip syn3-7_62708318_93925745-raw-rejectfix.vcf
[2015-09-30T20:53Z] tabix index syn3-7_62708318_93925745-raw-rejectfix.vcf.gz
[2015-09-30T20:53Z] GATK: VariantAnnotator
[2015-09-30T20:53Z] INFO  21:53:57,587 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:53Z] INFO  21:53:57,589 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:53Z] INFO  21:53:57,589 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:53Z] INFO  21:53:57,590 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:53Z] INFO  21:53:57,593 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/7/syn3-7_62708318_93925745-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpPGQYJC/syn3-7_62708318_93925745-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_62708318_93925745-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:53Z] INFO  21:53:57,599 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:53Z] INFO  21:53:57,599 HelpFormatter - Date/Time: 2015/09/30 21:53:57
[2015-09-30T20:53Z] INFO  21:53:57,599 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:53Z] INFO  21:53:57,599 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:53Z] INFO  21:53:57,698 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:53Z] INFO  21:53:57,775 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:53Z] INFO  21:53:57,783 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:53Z] INFO  21:53:57,805 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:53Z] INFO  21:53:58,219 IntervalUtils - Processing 1947 bp from intervals
[2015-09-30T20:53Z] WARN  21:53:58,224 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:53Z] WARN  21:53:58,224 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:53Z] INFO  21:53:58,281 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:53Z] INFO  21:53:58,464 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:53Z] INFO  21:53:58,465 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:53Z] INFO  21:53:58,465 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:53Z] INFO  21:53:58,465 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:53Z] INFO  21:53:58,498 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:54Z] INFO  21:54:06,780 VariantAnnotator - Processed 1669 loci.
[2015-09-30T20:54Z]
[2015-09-30T20:54Z] INFO  21:54:06,829 ProgressMeter -            done      9551.0     8.0 s      14.6 m       99.9%     8.0 s       0.0 s
[2015-09-30T20:54Z] INFO  21:54:06,830 ProgressMeter - Total runtime 8.37 secs, 0.14 min, 0.00 hours
[2015-09-30T20:54Z] INFO  21:54:06,830 MicroScheduler - 6204 reads were filtered out during the traversal out of approximately 137843 total reads (4.50%)
[2015-09-30T20:54Z] INFO  21:54:06,830 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:54Z] INFO  21:54:06,830 MicroScheduler -   -> 6175 reads (4.48% of total) failing DuplicateReadFilter
[2015-09-30T20:54Z] INFO  21:54:06,831 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:54Z] INFO  21:54:06,831 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:54Z] INFO  21:54:06,831 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:54Z] INFO  21:54:06,831 MicroScheduler -   -> 29 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:54Z] INFO  21:54:07,878 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:54Z] Genotyping with varscan: ('7', 157155595, 159138663) 1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam
[2015-09-30T20:54Z] samtools mpileup
[2015-09-30T20:54Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:54Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:54Z] samtools mpileup
[2015-09-30T20:54Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:54Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:54Z] samtools mpileup
[2015-09-30T20:54Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:54Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:54Z] Varscan
[2015-09-30T20:54Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpiP5bQ3/syn3-7_157155595_159138663-raw-normal.mpileup
[2015-09-30T20:54Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpiP5bQ3/syn3-7_157155595_159138663-raw-tumor.mpileup
[2015-09-30T20:54Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:54Z] Min reads2:	2
[2015-09-30T20:54Z] Min strands2:	1
[2015-09-30T20:54Z] Min var freq:	0.1
[2015-09-30T20:54Z] Min freq for hom:	0.75
[2015-09-30T20:54Z] Normal purity:	1.0
[2015-09-30T20:54Z] Tumor purity:	1.0
[2015-09-30T20:54Z] Min avg qual:	15
[2015-09-30T20:54Z] P-value thresh:	0.98
[2015-09-30T20:54Z] Somatic p-value:	0.05
[2015-09-30T20:54Z] 102781 positions in tumor
[2015-09-30T20:54Z] 102781 positions shared in normal
[2015-09-30T20:54Z] 101527 had sufficient coverage for comparison
[2015-09-30T20:54Z] 101179 were called Reference
[2015-09-30T20:54Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:54Z] 60 were removed by the strand filter
[2015-09-30T20:54Z] 329 were called Germline
[2015-09-30T20:54Z] 4 were called LOH
[2015-09-30T20:54Z] 14 were called Somatic
[2015-09-30T20:54Z] 1 were called Unknown
[2015-09-30T20:54Z] 0 were called Variant
[2015-09-30T20:54Z] Varscan paired fix
[2015-09-30T20:54Z] Varscan paired fix
[2015-09-30T20:54Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:54Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:54Z] bgzip syn3-7_157155595_159138663-raw.snp.vcf
[2015-09-30T20:54Z] tabix index syn3-7_157155595_159138663-raw.snp.vcf.gz
[2015-09-30T20:54Z] bgzip syn3-7_157155595_159138663-raw.indel.vcf
[2015-09-30T20:54Z] tabix index syn3-7_157155595_159138663-raw.indel.vcf.gz
[2015-09-30T20:54Z] Combine variant files
[2015-09-30T20:54Z] INFO  21:54:31,527 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:54Z] INFO  21:54:31,529 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:54Z] INFO  21:54:31,530 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:54Z] INFO  21:54:31,530 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:54Z] INFO  21:54:31,533 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpiP5bQ3/tx/tmpJEpfRR/syn3-7_157155595_159138663-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/7/tx/tmpiP5bQ3/syn3-7_157155595_159138663-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/7/tx/tmpiP5bQ3/syn3-7_157155595_159138663-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_157155595_159138663-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:54Z] INFO  21:54:31,539 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:54Z] INFO  21:54:31,539 HelpFormatter - Date/Time: 2015/09/30 21:54:31
[2015-09-30T20:54Z] INFO  21:54:31,540 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:54Z] INFO  21:54:31,540 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:54Z] INFO  21:54:31,615 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:54Z] INFO  21:54:31,903 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:54Z] INFO  21:54:31,986 IntervalUtils - Processing 103094 bp from intervals
[2015-09-30T20:54Z] WARN  21:54:31,987 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:54Z] WARN  21:54:31,987 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:54Z] INFO  21:54:32,044 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:54Z] INFO  21:54:32,045 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:54Z] INFO  21:54:32,045 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:54Z] INFO  21:54:32,046 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:54Z] INFO  21:54:32,046 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:54Z] INFO  21:54:32,462 ProgressMeter -            done       314.0     0.0 s      22.1 m       99.9%     0.0 s       0.0 s
[2015-09-30T20:54Z] INFO  21:54:32,462 ProgressMeter - Total runtime 0.42 secs, 0.01 min, 0.00 hours
[2015-09-30T20:54Z] bgzip syn3-7_157155595_159138663-raw.vcf
[2015-09-30T20:54Z] tabix index syn3-7_157155595_159138663-raw.vcf.gz
[2015-09-30T20:54Z] bgzip syn3-7_157155595_159138663-raw-rejectfix.vcf
[2015-09-30T20:54Z] tabix index syn3-7_157155595_159138663-raw-rejectfix.vcf.gz
[2015-09-30T20:54Z] GATK: VariantAnnotator
[2015-09-30T20:54Z] INFO  21:54:34,734 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:54Z] INFO  21:54:34,736 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:54Z] INFO  21:54:34,736 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:54Z] INFO  21:54:34,736 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:54Z] INFO  21:54:34,740 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/7/syn3-7_157155595_159138663-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpSKtgug/syn3-7_157155595_159138663-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_157155595_159138663-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:54Z] INFO  21:54:34,745 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:54Z] INFO  21:54:34,746 HelpFormatter - Date/Time: 2015/09/30 21:54:34
[2015-09-30T20:54Z] INFO  21:54:34,746 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:54Z] INFO  21:54:34,746 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:54Z] INFO  21:54:35,096 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:54Z] INFO  21:54:35,265 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:54Z] INFO  21:54:35,273 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:54Z] INFO  21:54:35,458 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.18
[2015-09-30T20:54Z] INFO  21:54:35,827 IntervalUtils - Processing 314 bp from intervals
[2015-09-30T20:54Z] WARN  21:54:35,831 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:54Z] WARN  21:54:35,831 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:54Z] INFO  21:54:35,886 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:54Z] INFO  21:54:35,930 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:54Z] INFO  21:54:35,930 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:54Z] INFO  21:54:35,930 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:54Z] INFO  21:54:35,931 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:54Z] INFO  21:54:35,964 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:54Z] INFO  21:54:38,368 VariantAnnotator - Processed 288 loci.
[2015-09-30T20:54Z]
[2015-09-30T20:54Z] INFO  21:54:38,390 ProgressMeter -            done      2583.0     2.0 s      15.9 m       99.7%     2.0 s       0.0 s
[2015-09-30T20:54Z] INFO  21:54:38,390 ProgressMeter - Total runtime 2.46 secs, 0.04 min, 0.00 hours
[2015-09-30T20:54Z] INFO  21:54:38,391 MicroScheduler - 1001 reads were filtered out during the traversal out of approximately 19602 total reads (5.11%)
[2015-09-30T20:54Z] INFO  21:54:38,391 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:54Z] INFO  21:54:38,391 MicroScheduler -   -> 995 reads (5.08% of total) failing DuplicateReadFilter
[2015-09-30T20:54Z] INFO  21:54:38,391 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:54Z] INFO  21:54:38,392 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:54Z] INFO  21:54:38,392 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:54Z] INFO  21:54:38,392 MicroScheduler -   -> 6 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:54Z] INFO  21:54:39,386 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:54Z] Genotyping with varscan: ('8', 0, 31024990) 1_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam
[2015-09-30T20:54Z] samtools mpileup
[2015-09-30T20:54Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:54Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:54Z] Varscan
[2015-09-30T20:54Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmp85W460/syn3-7_94024041_125680568-raw-normal.mpileup
[2015-09-30T20:54Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmp85W460/syn3-7_94024041_125680568-raw-tumor.mpileup
[2015-09-30T20:54Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:54Z] Min reads2:	2
[2015-09-30T20:54Z] Min strands2:	1
[2015-09-30T20:54Z] Min var freq:	0.1
[2015-09-30T20:54Z] Min freq for hom:	0.75
[2015-09-30T20:54Z] Normal purity:	1.0
[2015-09-30T20:54Z] Tumor purity:	1.0
[2015-09-30T20:54Z] Min avg qual:	15
[2015-09-30T20:54Z] P-value thresh:	0.98
[2015-09-30T20:54Z] Somatic p-value:	0.05
[2015-09-30T20:55Z] samtools mpileup
[2015-09-30T20:55Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:55Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:55Z] Varscan
[2015-09-30T20:55Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpDesbey/syn3-7_126078434_157151579-raw-normal.mpileup
[2015-09-30T20:55Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/7/tx/tmpDesbey/syn3-7_126078434_157151579-raw-tumor.mpileup
[2015-09-30T20:55Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:55Z] Min reads2:	2
[2015-09-30T20:55Z] Min strands2:	1
[2015-09-30T20:55Z] Min var freq:	0.1
[2015-09-30T20:55Z] Min freq for hom:	0.75
[2015-09-30T20:55Z] Normal purity:	1.0
[2015-09-30T20:55Z] Tumor purity:	1.0
[2015-09-30T20:55Z] Min avg qual:	15
[2015-09-30T20:55Z] P-value thresh:	0.98
[2015-09-30T20:55Z] Somatic p-value:	0.05
[2015-09-30T20:56Z] 1760424 positions in tumor
[2015-09-30T20:56Z] 1760414 positions shared in normal
[2015-09-30T20:56Z] 1725386 had sufficient coverage for comparison
[2015-09-30T20:56Z] 1722866 were called Reference
[2015-09-30T20:56Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:56Z] 232 were removed by the strand filter
[2015-09-30T20:56Z] 2458 were called Germline
[2015-09-30T20:56Z] 3 were called LOH
[2015-09-30T20:56Z] 30 were called Somatic
[2015-09-30T20:56Z] 29 were called Unknown
[2015-09-30T20:56Z] 0 were called Variant
[2015-09-30T20:56Z] Varscan paired fix
[2015-09-30T20:56Z] Varscan paired fix
[2015-09-30T20:56Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:56Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:56Z] bgzip syn3-7_94024041_125680568-raw.snp.vcf
[2015-09-30T20:56Z] tabix index syn3-7_94024041_125680568-raw.snp.vcf.gz
[2015-09-30T20:56Z] bgzip syn3-7_94024041_125680568-raw.indel.vcf
[2015-09-30T20:56Z] tabix index syn3-7_94024041_125680568-raw.indel.vcf.gz
[2015-09-30T20:56Z] Combine variant files
[2015-09-30T20:56Z] INFO  21:56:11,226 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:11,228 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:56Z] INFO  21:56:11,229 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:56Z] INFO  21:56:11,229 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:56Z] INFO  21:56:11,232 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/7/tx/tmp85W460/tx/tmp4dXQUW/syn3-7_94024041_125680568-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/7/tx/tmp85W460/syn3-7_94024041_125680568-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/7/tx/tmp85W460/syn3-7_94024041_125680568-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_94024041_125680568-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:56Z] INFO  21:56:11,238 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:56Z] INFO  21:56:11,238 HelpFormatter - Date/Time: 2015/09/30 21:56:11
[2015-09-30T20:56Z] INFO  21:56:11,239 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:11,239 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:11,324 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:56Z] INFO  21:56:11,497 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:56Z] INFO  21:56:11,636 IntervalUtils - Processing 1767772 bp from intervals
[2015-09-30T20:56Z] WARN  21:56:11,637 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:56Z] WARN  21:56:11,637 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:56Z] INFO  21:56:11,696 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:56Z] INFO  21:56:11,700 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:56Z] INFO  21:56:11,701 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:56Z] INFO  21:56:11,701 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:56Z] INFO  21:56:11,701 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:56Z] Varscan
[2015-09-30T20:56Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmpHWM9iT/syn3-8_0_31024990-raw-normal.mpileup
[2015-09-30T20:56Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmpHWM9iT/syn3-8_0_31024990-raw-tumor.mpileup
[2015-09-30T20:56Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:56Z] Min reads2:	2
[2015-09-30T20:56Z] Min strands2:	1
[2015-09-30T20:56Z] Min var freq:	0.1
[2015-09-30T20:56Z] Min freq for hom:	0.75
[2015-09-30T20:56Z] Normal purity:	1.0
[2015-09-30T20:56Z] Tumor purity:	1.0
[2015-09-30T20:56Z] Min avg qual:	15
[2015-09-30T20:56Z] P-value thresh:	0.98
[2015-09-30T20:56Z] Somatic p-value:	0.05
[2015-09-30T20:56Z] INFO  21:56:14,415 ProgressMeter -            done      2725.0     2.0 s      16.6 m      100.0%     2.0 s       0.0 s
[2015-09-30T20:56Z] INFO  21:56:14,416 ProgressMeter - Total runtime 2.71 secs, 0.05 min, 0.00 hours
[2015-09-30T20:56Z] bgzip syn3-7_94024041_125680568-raw.vcf
[2015-09-30T20:56Z] tabix index syn3-7_94024041_125680568-raw.vcf.gz
[2015-09-30T20:56Z] bgzip syn3-7_94024041_125680568-raw-rejectfix.vcf
[2015-09-30T20:56Z] tabix index syn3-7_94024041_125680568-raw-rejectfix.vcf.gz
[2015-09-30T20:56Z] GATK: VariantAnnotator
[2015-09-30T20:56Z] INFO  21:56:17,233 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:17,235 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:56Z] INFO  21:56:17,235 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:56Z] INFO  21:56:17,235 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:56Z] INFO  21:56:17,239 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/7/syn3-7_94024041_125680568-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpXy2Si8/syn3-7_94024041_125680568-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_94024041_125680568-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:56Z] INFO  21:56:17,244 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:56Z] INFO  21:56:17,244 HelpFormatter - Date/Time: 2015/09/30 21:56:17
[2015-09-30T20:56Z] INFO  21:56:17,244 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:17,244 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:17,341 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:56Z] INFO  21:56:17,419 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:56Z] INFO  21:56:17,427 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:56Z] INFO  21:56:17,450 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:56Z] INFO  21:56:17,908 IntervalUtils - Processing 2725 bp from intervals
[2015-09-30T20:56Z] WARN  21:56:17,912 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:56Z] WARN  21:56:17,912 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:56Z] INFO  21:56:17,969 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:56Z] INFO  21:56:18,227 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:56Z] INFO  21:56:18,227 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:56Z] INFO  21:56:18,228 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:56Z] INFO  21:56:18,228 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:56Z] INFO  21:56:18,261 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:56Z] INFO  21:56:30,723 VariantAnnotator - Processed 2268 loci.
[2015-09-30T20:56Z]
[2015-09-30T20:56Z] INFO  21:56:30,750 ProgressMeter -            done     55967.0    12.0 s       3.7 m      100.0%    12.0 s       0.0 s
[2015-09-30T20:56Z] INFO  21:56:30,751 ProgressMeter - Total runtime 12.52 secs, 0.21 min, 0.00 hours
[2015-09-30T20:56Z] INFO  21:56:30,751 MicroScheduler - 17130 reads were filtered out during the traversal out of approximately 230076 total reads (7.45%)
[2015-09-30T20:56Z] INFO  21:56:30,751 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:56Z] INFO  21:56:30,751 MicroScheduler -   -> 16729 reads (7.27% of total) failing DuplicateReadFilter
[2015-09-30T20:56Z] INFO  21:56:30,752 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:56Z] INFO  21:56:30,752 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:56Z] INFO  21:56:30,752 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:56Z] INFO  21:56:30,752 MicroScheduler -   -> 401 reads (0.17% of total) failing UnmappedReadFilter
[2015-09-30T20:56Z] INFO  21:56:31,914 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:56Z] Genotyping with varscan: ('8', 31030285, 62213090) 1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam
[2015-09-30T20:56Z] samtools mpileup
[2015-09-30T20:56Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:56Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:56Z] 1886692 positions in tumor
[2015-09-30T20:56Z] 1886681 positions shared in normal
[2015-09-30T20:56Z] 1864922 had sufficient coverage for comparison
[2015-09-30T20:56Z] 1861847 were called Reference
[2015-09-30T20:56Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:56Z] 465 were removed by the strand filter
[2015-09-30T20:56Z] 3003 were called Germline
[2015-09-30T20:56Z] 10 were called LOH
[2015-09-30T20:56Z] 49 were called Somatic
[2015-09-30T20:56Z] 13 were called Unknown
[2015-09-30T20:56Z] 0 were called Variant
[2015-09-30T20:56Z] Varscan paired fix
[2015-09-30T20:56Z] Varscan paired fix
[2015-09-30T20:56Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:56Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:56Z] bgzip syn3-7_126078434_157151579-raw.snp.vcf
[2015-09-30T20:56Z] tabix index syn3-7_126078434_157151579-raw.snp.vcf.gz
[2015-09-30T20:56Z] bgzip syn3-7_126078434_157151579-raw.indel.vcf
[2015-09-30T20:56Z] tabix index syn3-7_126078434_157151579-raw.indel.vcf.gz
[2015-09-30T20:56Z] Combine variant files
[2015-09-30T20:56Z] INFO  21:56:48,699 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:48,701 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:56Z] INFO  21:56:48,702 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:56Z] INFO  21:56:48,702 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:56Z] INFO  21:56:48,705 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpDesbey/tx/tmpTnneTs/syn3-7_126078434_157151579-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/7/tx/tmpDesbey/syn3-7_126078434_157151579-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/7/tx/tmpDesbey/syn3-7_126078434_157151579-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_126078434_157151579-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:56Z] INFO  21:56:48,711 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:56Z] INFO  21:56:48,711 HelpFormatter - Date/Time: 2015/09/30 21:56:48
[2015-09-30T20:56Z] INFO  21:56:48,711 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:48,712 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:48,789 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:56Z] INFO  21:56:48,927 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:56Z] INFO  21:56:49,064 IntervalUtils - Processing 1895508 bp from intervals
[2015-09-30T20:56Z] WARN  21:56:49,065 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:56Z] WARN  21:56:49,066 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:56Z] INFO  21:56:49,123 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:56Z] INFO  21:56:49,127 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:56Z] INFO  21:56:49,128 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:56Z] INFO  21:56:49,128 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:56Z] INFO  21:56:49,128 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:56Z] INFO  21:56:51,282 ProgressMeter -            done      3073.0     2.0 s      11.7 m      100.0%     2.0 s       0.0 s
[2015-09-30T20:56Z] INFO  21:56:51,283 ProgressMeter - Total runtime 2.16 secs, 0.04 min, 0.00 hours
[2015-09-30T20:56Z] bgzip syn3-7_126078434_157151579-raw.vcf
[2015-09-30T20:56Z] tabix index syn3-7_126078434_157151579-raw.vcf.gz
[2015-09-30T20:56Z] bgzip syn3-7_126078434_157151579-raw-rejectfix.vcf
[2015-09-30T20:56Z] tabix index syn3-7_126078434_157151579-raw-rejectfix.vcf.gz
[2015-09-30T20:56Z] GATK: VariantAnnotator
[2015-09-30T20:56Z] INFO  21:56:53,972 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:53,974 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:56Z] INFO  21:56:53,974 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:56Z] INFO  21:56:53,974 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:56Z] INFO  21:56:53,978 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/7/syn3-7_126078434_157151579-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/7/tx/tmpyVd3UL/syn3-7_126078434_157151579-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/7/syn3-7_126078434_157151579-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:56Z] INFO  21:56:53,983 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:56Z] INFO  21:56:53,984 HelpFormatter - Date/Time: 2015/09/30 21:56:53
[2015-09-30T20:56Z] INFO  21:56:53,984 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:53,984 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:56Z] INFO  21:56:54,481 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:56Z] INFO  21:56:54,556 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:56Z] INFO  21:56:54,564 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:56Z] INFO  21:56:54,586 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:56Z] INFO  21:56:55,009 IntervalUtils - Processing 3073 bp from intervals
[2015-09-30T20:56Z] WARN  21:56:55,014 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:56Z] WARN  21:56:55,014 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:56Z] INFO  21:56:55,135 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:56Z] INFO  21:56:55,292 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:56Z] INFO  21:56:55,292 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:56Z] INFO  21:56:55,292 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:56Z] INFO  21:56:55,293 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:56Z] INFO  21:56:55,325 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:57Z] samtools mpileup
[2015-09-30T20:57Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:57Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:57Z] INFO  21:57:08,097 VariantAnnotator - Processed 2601 loci.
[2015-09-30T20:57Z]
[2015-09-30T20:57Z] INFO  21:57:08,775 ProgressMeter -            done     23199.0    13.0 s       9.7 m      100.0%    13.0 s       0.0 s
[2015-09-30T20:57Z] INFO  21:57:08,775 ProgressMeter - Total runtime 13.48 secs, 0.22 min, 0.00 hours
[2015-09-30T20:57Z] INFO  21:57:08,775 MicroScheduler - 10872 reads were filtered out during the traversal out of approximately 214695 total reads (5.06%)
[2015-09-30T20:57Z] INFO  21:57:08,776 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:57Z] INFO  21:57:08,776 MicroScheduler -   -> 10805 reads (5.03% of total) failing DuplicateReadFilter
[2015-09-30T20:57Z] INFO  21:57:08,776 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:57Z] INFO  21:57:08,776 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:57Z] INFO  21:57:08,777 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:57Z] INFO  21:57:08,777 MicroScheduler -   -> 67 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T20:57Z] INFO  21:57:09,736 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:57Z] Genotyping with varscan: ('8', 62288979, 93648031) 1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam
[2015-09-30T20:57Z] samtools mpileup
[2015-09-30T20:57Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:57Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:57Z] 1412225 positions in tumor
[2015-09-30T20:57Z] 1412211 positions shared in normal
[2015-09-30T20:57Z] 1384916 had sufficient coverage for comparison
[2015-09-30T20:57Z] 1381816 were called Reference
[2015-09-30T20:57Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:57Z] 241 were removed by the strand filter
[2015-09-30T20:57Z] 3010 were called Germline
[2015-09-30T20:57Z] 12 were called LOH
[2015-09-30T20:57Z] 63 were called Somatic
[2015-09-30T20:57Z] 15 were called Unknown
[2015-09-30T20:57Z] 0 were called Variant
[2015-09-30T20:57Z] Varscan paired fix
[2015-09-30T20:57Z] Varscan paired fix
[2015-09-30T20:57Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:57Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:57Z] bgzip syn3-8_0_31024990-raw.snp.vcf
[2015-09-30T20:57Z] tabix index syn3-8_0_31024990-raw.snp.vcf.gz
[2015-09-30T20:57Z] bgzip syn3-8_0_31024990-raw.indel.vcf
[2015-09-30T20:57Z] tabix index syn3-8_0_31024990-raw.indel.vcf.gz
[2015-09-30T20:57Z] Combine variant files
[2015-09-30T20:57Z] INFO  21:57:14,894 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:57Z] INFO  21:57:14,896 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:57Z] INFO  21:57:14,896 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:57Z] INFO  21:57:14,896 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:57Z] INFO  21:57:14,900 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/8/tx/tmpHWM9iT/tx/tmpAGTJpi/syn3-8_0_31024990-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/8/tx/tmpHWM9iT/syn3-8_0_31024990-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/8/tx/tmpHWM9iT/syn3-8_0_31024990-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_0_31024990-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:57Z] INFO  21:57:14,905 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:57Z] INFO  21:57:14,906 HelpFormatter - Date/Time: 2015/09/30 21:57:14
[2015-09-30T20:57Z] INFO  21:57:14,906 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:57Z] INFO  21:57:14,906 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:57Z] INFO  21:57:14,980 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:57Z] INFO  21:57:15,317 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:57Z] INFO  21:57:15,431 IntervalUtils - Processing 1421167 bp from intervals
[2015-09-30T20:57Z] WARN  21:57:15,432 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:57Z] WARN  21:57:15,432 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:57Z] INFO  21:57:15,489 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:57Z] INFO  21:57:15,492 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:57Z] INFO  21:57:15,493 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:57Z] INFO  21:57:15,493 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:57Z] INFO  21:57:15,493 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:57Z] INFO  21:57:17,409 ProgressMeter -            done      3223.0     1.0 s       9.9 m       99.8%     1.0 s       0.0 s
[2015-09-30T20:57Z] INFO  21:57:17,410 ProgressMeter - Total runtime 1.92 secs, 0.03 min, 0.00 hours
[2015-09-30T20:57Z] bgzip syn3-8_0_31024990-raw.vcf
[2015-09-30T20:57Z] tabix index syn3-8_0_31024990-raw.vcf.gz
[2015-09-30T20:57Z] bgzip syn3-8_0_31024990-raw-rejectfix.vcf
[2015-09-30T20:57Z] tabix index syn3-8_0_31024990-raw-rejectfix.vcf.gz
[2015-09-30T20:57Z] GATK: VariantAnnotator
[2015-09-30T20:57Z] INFO  21:57:20,071 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:57Z] INFO  21:57:20,073 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:57Z] INFO  21:57:20,074 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:57Z] INFO  21:57:20,074 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:57Z] INFO  21:57:20,077 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/8/syn3-8_0_31024990-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/8/tx/tmpPCo87a/syn3-8_0_31024990-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_0_31024990-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:57Z] INFO  21:57:20,083 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:57Z] INFO  21:57:20,083 HelpFormatter - Date/Time: 2015/09/30 21:57:20
[2015-09-30T20:57Z] INFO  21:57:20,083 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:57Z] INFO  21:57:20,083 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:57Z] INFO  21:57:20,175 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:57Z] INFO  21:57:20,249 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:57Z] INFO  21:57:20,256 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:57Z] INFO  21:57:20,278 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:57Z] INFO  21:57:20,681 IntervalUtils - Processing 3228 bp from intervals
[2015-09-30T20:57Z] WARN  21:57:20,685 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:57Z] WARN  21:57:20,685 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:57Z] INFO  21:57:20,807 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:57Z] INFO  21:57:20,936 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:57Z] INFO  21:57:20,937 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:57Z] INFO  21:57:20,937 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:57Z] INFO  21:57:20,937 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:57Z] INFO  21:57:20,969 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:57Z] Varscan
[2015-09-30T20:57Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmp33rw38/syn3-8_31030285_62213090-raw-normal.mpileup
[2015-09-30T20:57Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmp33rw38/syn3-8_31030285_62213090-raw-tumor.mpileup
[2015-09-30T20:57Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:57Z] Min reads2:	2
[2015-09-30T20:57Z] Min strands2:	1
[2015-09-30T20:57Z] Min var freq:	0.1
[2015-09-30T20:57Z] Min freq for hom:	0.75
[2015-09-30T20:57Z] Normal purity:	1.0
[2015-09-30T20:57Z] Tumor purity:	1.0
[2015-09-30T20:57Z] Min avg qual:	15
[2015-09-30T20:57Z] P-value thresh:	0.98
[2015-09-30T20:57Z] Somatic p-value:	0.05
[2015-09-30T20:57Z] INFO  21:57:32,989 VariantAnnotator - Processed 2846 loci.
[2015-09-30T20:57Z]
[2015-09-30T20:57Z] INFO  21:57:33,009 ProgressMeter -            done     22207.0    12.0 s       9.1 m      100.0%    12.0 s       0.0 s
[2015-09-30T20:57Z] INFO  21:57:33,010 ProgressMeter - Total runtime 12.07 secs, 0.20 min, 0.00 hours
[2015-09-30T20:57Z] INFO  21:57:33,010 MicroScheduler - 10527 reads were filtered out during the traversal out of approximately 228871 total reads (4.60%)
[2015-09-30T20:57Z] INFO  21:57:33,010 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:57Z] INFO  21:57:33,011 MicroScheduler -   -> 10470 reads (4.57% of total) failing DuplicateReadFilter
[2015-09-30T20:57Z] INFO  21:57:33,011 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:57Z] INFO  21:57:33,011 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:57Z] INFO  21:57:33,011 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:57Z] INFO  21:57:33,011 MicroScheduler -   -> 57 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:57Z] INFO  21:57:34,111 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:57Z] Genotyping with varscan: ('8', 93896832, 124968568) 1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam
[2015-09-30T20:57Z] samtools mpileup
[2015-09-30T20:57Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:57Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:57Z] samtools mpileup
[2015-09-30T20:57Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:57Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:58Z] samtools mpileup
[2015-09-30T20:58Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:58Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:58Z] 894465 positions in tumor
[2015-09-30T20:58Z] 894457 positions shared in normal
[2015-09-30T20:58Z] 864716 had sufficient coverage for comparison
[2015-09-30T20:58Z] 864018 were called Reference
[2015-09-30T20:58Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:58Z] 42 were removed by the strand filter
[2015-09-30T20:58Z] 662 were called Germline
[2015-09-30T20:58Z] 3 were called LOH
[2015-09-30T20:58Z] 25 were called Somatic
[2015-09-30T20:58Z] 8 were called Unknown
[2015-09-30T20:58Z] 0 were called Variant
[2015-09-30T20:58Z] Varscan paired fix
[2015-09-30T20:58Z] Varscan paired fix
[2015-09-30T20:58Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:58Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:58Z] bgzip syn3-8_31030285_62213090-raw.snp.vcf
[2015-09-30T20:58Z] tabix index syn3-8_31030285_62213090-raw.snp.vcf.gz
[2015-09-30T20:58Z] bgzip syn3-8_31030285_62213090-raw.indel.vcf
[2015-09-30T20:58Z] tabix index syn3-8_31030285_62213090-raw.indel.vcf.gz
[2015-09-30T20:58Z] Combine variant files
[2015-09-30T20:58Z] INFO  21:58:13,516 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:13,518 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:58Z] INFO  21:58:13,518 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:58Z] INFO  21:58:13,518 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:58Z] INFO  21:58:13,522 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/8/tx/tmp33rw38/tx/tmp7dSx1o/syn3-8_31030285_62213090-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/8/tx/tmp33rw38/syn3-8_31030285_62213090-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/8/tx/tmp33rw38/syn3-8_31030285_62213090-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_31030285_62213090-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:58Z] INFO  21:58:13,527 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:58Z] INFO  21:58:13,527 HelpFormatter - Date/Time: 2015/09/30 21:58:13
[2015-09-30T20:58Z] INFO  21:58:13,527 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:13,527 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:13,597 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:58Z] INFO  21:58:13,731 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:58Z] INFO  21:58:13,828 IntervalUtils - Processing 902318 bp from intervals
[2015-09-30T20:58Z] WARN  21:58:13,829 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:58Z] WARN  21:58:13,829 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:58Z] INFO  21:58:13,881 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:58Z] INFO  21:58:13,884 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:58Z] INFO  21:58:13,884 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:58Z] INFO  21:58:13,885 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:58Z] INFO  21:58:13,885 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:58Z] INFO  21:58:14,674 ProgressMeter -            done       781.0     0.0 s      16.8 m       99.9%     0.0 s       0.0 s
[2015-09-30T20:58Z] INFO  21:58:14,674 ProgressMeter - Total runtime 0.79 secs, 0.01 min, 0.00 hours
[2015-09-30T20:58Z] bgzip syn3-8_31030285_62213090-raw.vcf
[2015-09-30T20:58Z] tabix index syn3-8_31030285_62213090-raw.vcf.gz
[2015-09-30T20:58Z] bgzip syn3-8_31030285_62213090-raw-rejectfix.vcf
[2015-09-30T20:58Z] tabix index syn3-8_31030285_62213090-raw-rejectfix.vcf.gz
[2015-09-30T20:58Z] GATK: VariantAnnotator
[2015-09-30T20:58Z] Varscan
[2015-09-30T20:58Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmpVOspb8/syn3-8_62288979_93648031-raw-normal.mpileup
[2015-09-30T20:58Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmpVOspb8/syn3-8_62288979_93648031-raw-tumor.mpileup
[2015-09-30T20:58Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:58Z] Min reads2:	2
[2015-09-30T20:58Z] Min strands2:	1
[2015-09-30T20:58Z] Min var freq:	0.1
[2015-09-30T20:58Z] Min freq for hom:	0.75
[2015-09-30T20:58Z] Normal purity:	1.0
[2015-09-30T20:58Z] Tumor purity:	1.0
[2015-09-30T20:58Z] Min avg qual:	15
[2015-09-30T20:58Z] P-value thresh:	0.98
[2015-09-30T20:58Z] Somatic p-value:	0.05
[2015-09-30T20:58Z] INFO  21:58:16,887 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:16,890 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:58Z] INFO  21:58:16,890 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:58Z] INFO  21:58:16,890 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:58Z] INFO  21:58:16,893 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/8/syn3-8_31030285_62213090-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/8/tx/tmpyzLCxF/syn3-8_31030285_62213090-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_31030285_62213090-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:58Z] INFO  21:58:16,899 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:58Z] INFO  21:58:16,899 HelpFormatter - Date/Time: 2015/09/30 21:58:16
[2015-09-30T20:58Z] INFO  21:58:16,899 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:16,899 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:16,994 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:58Z] INFO  21:58:17,072 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:58Z] INFO  21:58:17,080 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:58Z] INFO  21:58:17,109 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T20:58Z] INFO  21:58:17,441 IntervalUtils - Processing 782 bp from intervals
[2015-09-30T20:58Z] WARN  21:58:17,445 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:58Z] WARN  21:58:17,445 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:58Z] INFO  21:58:17,500 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:58Z] INFO  21:58:17,584 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:58Z] INFO  21:58:17,585 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:58Z] INFO  21:58:17,585 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:58Z] INFO  21:58:17,585 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:58Z] INFO  21:58:17,618 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:58Z] INFO  21:58:22,587 VariantAnnotator - Processed 651 loci.
[2015-09-30T20:58Z]
[2015-09-30T20:58Z] INFO  21:58:22,609 ProgressMeter -            done      2341.0     5.0 s      35.8 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:58Z] INFO  21:58:22,609 ProgressMeter - Total runtime 5.02 secs, 0.08 min, 0.00 hours
[2015-09-30T20:58Z] INFO  21:58:22,610 MicroScheduler - 2273 reads were filtered out during the traversal out of approximately 49197 total reads (4.62%)
[2015-09-30T20:58Z] INFO  21:58:22,610 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:58Z] INFO  21:58:22,610 MicroScheduler -   -> 2261 reads (4.60% of total) failing DuplicateReadFilter
[2015-09-30T20:58Z] INFO  21:58:22,610 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:58Z] INFO  21:58:22,611 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:58Z] INFO  21:58:22,611 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:58Z] INFO  21:58:22,611 MicroScheduler -   -> 12 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:58Z] INFO  21:58:23,529 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:58Z] Genotyping with varscan: ('8', 124975213, 146364022) 1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam
[2015-09-30T20:58Z] samtools mpileup
[2015-09-30T20:58Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:58Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:58Z] Varscan
[2015-09-30T20:58Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmpTwuJ6U/syn3-8_93896832_124968568-raw-normal.mpileup
[2015-09-30T20:58Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmpTwuJ6U/syn3-8_93896832_124968568-raw-tumor.mpileup
[2015-09-30T20:58Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:58Z] Min reads2:	2
[2015-09-30T20:58Z] Min strands2:	1
[2015-09-30T20:58Z] Min var freq:	0.1
[2015-09-30T20:58Z] Min freq for hom:	0.75
[2015-09-30T20:58Z] Normal purity:	1.0
[2015-09-30T20:58Z] Tumor purity:	1.0
[2015-09-30T20:58Z] Min avg qual:	15
[2015-09-30T20:58Z] P-value thresh:	0.98
[2015-09-30T20:58Z] Somatic p-value:	0.05
[2015-09-30T20:58Z] 813270 positions in tumor
[2015-09-30T20:58Z] 813257 positions shared in normal
[2015-09-30T20:58Z] 783006 had sufficient coverage for comparison
[2015-09-30T20:58Z] 782159 were called Reference
[2015-09-30T20:58Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:58Z] 51 were removed by the strand filter
[2015-09-30T20:58Z] 808 were called Germline
[2015-09-30T20:58Z] 1 were called LOH
[2015-09-30T20:58Z] 29 were called Somatic
[2015-09-30T20:58Z] 9 were called Unknown
[2015-09-30T20:58Z] 0 were called Variant
[2015-09-30T20:58Z] Varscan paired fix
[2015-09-30T20:58Z] Varscan paired fix
[2015-09-30T20:58Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:58Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:58Z] bgzip syn3-8_62288979_93648031-raw.snp.vcf
[2015-09-30T20:58Z] tabix index syn3-8_62288979_93648031-raw.snp.vcf.gz
[2015-09-30T20:58Z] bgzip syn3-8_62288979_93648031-raw.indel.vcf
[2015-09-30T20:58Z] tabix index syn3-8_62288979_93648031-raw.indel.vcf.gz
[2015-09-30T20:58Z] Combine variant files
[2015-09-30T20:58Z] INFO  21:58:54,347 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:54,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:58Z] INFO  21:58:54,350 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:58Z] INFO  21:58:54,350 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:58Z] INFO  21:58:54,353 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/8/tx/tmpVOspb8/tx/tmpUVqLJR/syn3-8_62288979_93648031-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/8/tx/tmpVOspb8/syn3-8_62288979_93648031-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/8/tx/tmpVOspb8/syn3-8_62288979_93648031-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_62288979_93648031-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:58Z] INFO  21:58:54,359 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:58Z] INFO  21:58:54,359 HelpFormatter - Date/Time: 2015/09/30 21:58:54
[2015-09-30T20:58Z] INFO  21:58:54,360 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:54,360 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:54,436 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:58Z] INFO  21:58:54,577 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:58Z] INFO  21:58:54,685 IntervalUtils - Processing 820076 bp from intervals
[2015-09-30T20:58Z] WARN  21:58:54,686 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:58Z] WARN  21:58:54,686 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:58Z] INFO  21:58:54,744 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:58Z] INFO  21:58:54,746 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:58Z] INFO  21:58:54,747 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:58Z] INFO  21:58:54,747 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:58Z] INFO  21:58:54,747 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:58Z] INFO  21:58:55,648 ProgressMeter -            done       972.0     0.0 s      15.4 m       99.9%     0.0 s       0.0 s
[2015-09-30T20:58Z] INFO  21:58:55,649 ProgressMeter - Total runtime 0.90 secs, 0.02 min, 0.00 hours
[2015-09-30T20:58Z] bgzip syn3-8_62288979_93648031-raw.vcf
[2015-09-30T20:58Z] tabix index syn3-8_62288979_93648031-raw.vcf.gz
[2015-09-30T20:58Z] bgzip syn3-8_62288979_93648031-raw-rejectfix.vcf
[2015-09-30T20:58Z] tabix index syn3-8_62288979_93648031-raw-rejectfix.vcf.gz
[2015-09-30T20:58Z] GATK: VariantAnnotator
[2015-09-30T20:58Z] INFO  21:58:57,906 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:57,908 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:58Z] INFO  21:58:57,908 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:58Z] INFO  21:58:57,908 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:58Z] INFO  21:58:57,912 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/8/syn3-8_62288979_93648031-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/8/tx/tmpiO5x_s/syn3-8_62288979_93648031-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_62288979_93648031-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:58Z] INFO  21:58:57,917 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:58Z] INFO  21:58:57,917 HelpFormatter - Date/Time: 2015/09/30 21:58:57
[2015-09-30T20:58Z] INFO  21:58:57,918 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:57,918 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:58Z] INFO  21:58:57,993 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:58Z] INFO  21:58:58,075 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:58Z] INFO  21:58:58,082 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:58Z] INFO  21:58:58,103 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:58Z] INFO  21:58:58,443 IntervalUtils - Processing 972 bp from intervals
[2015-09-30T20:58Z] WARN  21:58:58,447 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:58Z] WARN  21:58:58,447 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:58Z] INFO  21:58:58,500 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:58Z] INFO  21:58:58,589 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:58Z] INFO  21:58:58,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:58Z] INFO  21:58:58,589 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:58Z] INFO  21:58:58,590 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:58Z] INFO  21:58:58,674 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:59Z] samtools mpileup
[2015-09-30T20:59Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:59Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:59Z] INFO  21:59:03,805 VariantAnnotator - Processed 792 loci.
[2015-09-30T20:59Z]
[2015-09-30T20:59Z] INFO  21:59:03,839 ProgressMeter -            done      2601.0     5.0 s      33.6 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:59Z] INFO  21:59:03,839 ProgressMeter - Total runtime 5.25 secs, 0.09 min, 0.00 hours
[2015-09-30T20:59Z] INFO  21:59:03,840 MicroScheduler - 3583 reads were filtered out during the traversal out of approximately 79459 total reads (4.51%)
[2015-09-30T20:59Z] INFO  21:59:03,840 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:59Z] INFO  21:59:03,840 MicroScheduler -   -> 3568 reads (4.49% of total) failing DuplicateReadFilter
[2015-09-30T20:59Z] INFO  21:59:03,840 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:59Z] INFO  21:59:03,841 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:59Z] INFO  21:59:03,841 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:59Z] INFO  21:59:03,841 MicroScheduler -   -> 15 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T20:59Z] INFO  21:59:05,103 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:59Z] Genotyping with varscan: ('9', 0, 32405837) 1_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam
[2015-09-30T20:59Z] samtools mpileup
[2015-09-30T20:59Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:59Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:59Z] 1016555 positions in tumor
[2015-09-30T20:59Z] 1016546 positions shared in normal
[2015-09-30T20:59Z] 978465 had sufficient coverage for comparison
[2015-09-30T20:59Z] 977520 were called Reference
[2015-09-30T20:59Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T20:59Z] 39 were removed by the strand filter
[2015-09-30T20:59Z] 915 were called Germline
[2015-09-30T20:59Z] 5 were called LOH
[2015-09-30T20:59Z] 17 were called Somatic
[2015-09-30T20:59Z] 8 were called Unknown
[2015-09-30T20:59Z] 0 were called Variant
[2015-09-30T20:59Z] Varscan paired fix
[2015-09-30T20:59Z] Varscan paired fix
[2015-09-30T20:59Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T20:59Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T20:59Z] bgzip syn3-8_93896832_124968568-raw.snp.vcf
[2015-09-30T20:59Z] tabix index syn3-8_93896832_124968568-raw.snp.vcf.gz
[2015-09-30T20:59Z] bgzip syn3-8_93896832_124968568-raw.indel.vcf
[2015-09-30T20:59Z] tabix index syn3-8_93896832_124968568-raw.indel.vcf.gz
[2015-09-30T20:59Z] Combine variant files
[2015-09-30T20:59Z] INFO  21:59:16,880 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:59Z] INFO  21:59:16,882 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T20:59Z] INFO  21:59:16,882 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:59Z] INFO  21:59:16,882 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:59Z] INFO  21:59:16,886 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/8/tx/tmpTwuJ6U/tx/tmpCtkLDb/syn3-8_93896832_124968568-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/8/tx/tmpTwuJ6U/syn3-8_93896832_124968568-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/8/tx/tmpTwuJ6U/syn3-8_93896832_124968568-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_93896832_124968568-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T20:59Z] INFO  21:59:16,891 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:59Z] INFO  21:59:16,891 HelpFormatter - Date/Time: 2015/09/30 21:59:16
[2015-09-30T20:59Z] INFO  21:59:16,891 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:59Z] INFO  21:59:16,892 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T20:59Z] INFO  21:59:16,966 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:59Z] INFO  21:59:17,227 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T20:59Z] INFO  21:59:17,348 IntervalUtils - Processing 1023564 bp from intervals
[2015-09-30T20:59Z] WARN  21:59:17,349 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:59Z] WARN  21:59:17,349 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:59Z] INFO  21:59:17,406 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T20:59Z] INFO  21:59:17,409 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:59Z] INFO  21:59:17,409 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:59Z] INFO  21:59:17,410 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:59Z] INFO  21:59:17,410 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:59Z] INFO  21:59:18,590 ProgressMeter -            done      1073.0     1.0 s      18.3 m      100.0%     1.0 s       0.0 s
[2015-09-30T20:59Z] INFO  21:59:18,591 ProgressMeter - Total runtime 1.18 secs, 0.02 min, 0.00 hours
[2015-09-30T20:59Z] bgzip syn3-8_93896832_124968568-raw.vcf
[2015-09-30T20:59Z] tabix index syn3-8_93896832_124968568-raw.vcf.gz
[2015-09-30T20:59Z] bgzip syn3-8_93896832_124968568-raw-rejectfix.vcf
[2015-09-30T20:59Z] tabix index syn3-8_93896832_124968568-raw-rejectfix.vcf.gz
[2015-09-30T20:59Z] GATK: VariantAnnotator
[2015-09-30T20:59Z] INFO  21:59:21,991 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:59Z] INFO  21:59:21,993 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T20:59Z] INFO  21:59:21,993 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T20:59Z] INFO  21:59:21,993 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T20:59Z] INFO  21:59:21,997 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/8/syn3-8_93896832_124968568-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/8/tx/tmpgPsyIa/syn3-8_93896832_124968568-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_93896832_124968568-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T20:59Z] INFO  21:59:22,002 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T20:59Z] INFO  21:59:22,002 HelpFormatter - Date/Time: 2015/09/30 21:59:21
[2015-09-30T20:59Z] INFO  21:59:22,003 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:59Z] INFO  21:59:22,003 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T20:59Z] INFO  21:59:22,095 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T20:59Z] INFO  21:59:22,171 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T20:59Z] INFO  21:59:22,178 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T20:59Z] INFO  21:59:22,201 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T20:59Z] INFO  21:59:22,552 IntervalUtils - Processing 1073 bp from intervals
[2015-09-30T20:59Z] WARN  21:59:22,556 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:59Z] WARN  21:59:22,556 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T20:59Z] INFO  21:59:22,612 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T20:59Z] INFO  21:59:22,707 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T20:59Z] INFO  21:59:22,708 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T20:59Z] INFO  21:59:22,708 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T20:59Z] INFO  21:59:22,708 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T20:59Z] INFO  21:59:22,804 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T20:59Z] INFO  21:59:28,323 VariantAnnotator - Processed 899 loci.
[2015-09-30T20:59Z]
[2015-09-30T20:59Z] INFO  21:59:28,345 ProgressMeter -            done      3186.0     5.0 s      29.5 m       99.9%     5.0 s       0.0 s
[2015-09-30T20:59Z] INFO  21:59:28,345 ProgressMeter - Total runtime 5.64 secs, 0.09 min, 0.00 hours
[2015-09-30T20:59Z] INFO  21:59:28,345 MicroScheduler - 2642 reads were filtered out during the traversal out of approximately 63077 total reads (4.19%)
[2015-09-30T20:59Z] INFO  21:59:28,346 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T20:59Z] INFO  21:59:28,346 MicroScheduler -   -> 2633 reads (4.17% of total) failing DuplicateReadFilter
[2015-09-30T20:59Z] INFO  21:59:28,346 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T20:59Z] INFO  21:59:28,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T20:59Z] INFO  21:59:28,346 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T20:59Z] INFO  21:59:28,347 MicroScheduler -   -> 9 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T20:59Z] INFO  21:59:29,532 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T20:59Z] Genotyping with varscan: ('9', 32406980, 65488652) 1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam
[2015-09-30T20:59Z] samtools mpileup
[2015-09-30T20:59Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:59Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:59Z] samtools mpileup
[2015-09-30T20:59Z] [mpileup] 1 samples in 1 input files
[2015-09-30T20:59Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T20:59Z] Varscan
[2015-09-30T20:59Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmpcxqAWl/syn3-8_124975213_146364022-raw-normal.mpileup
[2015-09-30T20:59Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/8/tx/tmpcxqAWl/syn3-8_124975213_146364022-raw-tumor.mpileup
[2015-09-30T20:59Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:59Z] Min reads2:	2
[2015-09-30T20:59Z] Min strands2:	1
[2015-09-30T20:59Z] Min var freq:	0.1
[2015-09-30T20:59Z] Min freq for hom:	0.75
[2015-09-30T20:59Z] Normal purity:	1.0
[2015-09-30T20:59Z] Tumor purity:	1.0
[2015-09-30T20:59Z] Min avg qual:	15
[2015-09-30T20:59Z] P-value thresh:	0.98
[2015-09-30T20:59Z] Somatic p-value:	0.05
[2015-09-30T20:59Z] Varscan
[2015-09-30T20:59Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmpc2KQwl/syn3-9_0_32405837-raw-normal.mpileup
[2015-09-30T20:59Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmpc2KQwl/syn3-9_0_32405837-raw-tumor.mpileup
[2015-09-30T20:59Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T20:59Z] Min reads2:	2
[2015-09-30T20:59Z] Min strands2:	1
[2015-09-30T20:59Z] Min var freq:	0.1
[2015-09-30T20:59Z] Min freq for hom:	0.75
[2015-09-30T20:59Z] Normal purity:	1.0
[2015-09-30T20:59Z] Tumor purity:	1.0
[2015-09-30T20:59Z] Min avg qual:	15
[2015-09-30T20:59Z] P-value thresh:	0.98
[2015-09-30T20:59Z] Somatic p-value:	0.05
[2015-09-30T21:00Z] samtools mpileup
[2015-09-30T21:00Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:00Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:00Z] 946924 positions in tumor
[2015-09-30T21:00Z] 946918 positions shared in normal
[2015-09-30T21:00Z] 939000 had sufficient coverage for comparison
[2015-09-30T21:00Z] 937569 were called Reference
[2015-09-30T21:00Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:00Z] 53 were removed by the strand filter
[2015-09-30T21:00Z] 1403 were called Germline
[2015-09-30T21:00Z] 6 were called LOH
[2015-09-30T21:00Z] 16 were called Somatic
[2015-09-30T21:00Z] 6 were called Unknown
[2015-09-30T21:00Z] 0 were called Variant
[2015-09-30T21:00Z] Varscan paired fix
[2015-09-30T21:00Z] Varscan paired fix
[2015-09-30T21:00Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:00Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:00Z] bgzip syn3-8_124975213_146364022-raw.snp.vcf
[2015-09-30T21:00Z] tabix index syn3-8_124975213_146364022-raw.snp.vcf.gz
[2015-09-30T21:00Z] bgzip syn3-8_124975213_146364022-raw.indel.vcf
[2015-09-30T21:00Z] tabix index syn3-8_124975213_146364022-raw.indel.vcf.gz
[2015-09-30T21:00Z] Combine variant files
[2015-09-30T21:00Z] INFO  22:00:30,424 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:30,426 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:00Z] INFO  22:00:30,426 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:00Z] INFO  22:00:30,427 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:00Z] INFO  22:00:30,430 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/8/tx/tmpcxqAWl/tx/tmpXMfpcM/syn3-8_124975213_146364022-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/8/tx/tmpcxqAWl/syn3-8_124975213_146364022-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/8/tx/tmpcxqAWl/syn3-8_124975213_146364022-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_124975213_146364022-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:00Z] INFO  22:00:30,436 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:00Z] INFO  22:00:30,437 HelpFormatter - Date/Time: 2015/09/30 22:00:30
[2015-09-30T21:00Z] INFO  22:00:30,437 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:30,437 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:30,512 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:00Z] 855106 positions in tumor
[2015-09-30T21:00Z] 855098 positions shared in normal
[2015-09-30T21:00Z] 831884 had sufficient coverage for comparison
[2015-09-30T21:00Z] 830693 were called Reference
[2015-09-30T21:00Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:00Z] 77 were removed by the strand filter
[2015-09-30T21:00Z] 1143 were called Germline
[2015-09-30T21:00Z] 7 were called LOH
[2015-09-30T21:00Z] 27 were called Somatic
[2015-09-30T21:00Z] 14 were called Unknown
[2015-09-30T21:00Z] 0 were called Variant
[2015-09-30T21:00Z] Varscan paired fix
[2015-09-30T21:00Z] Varscan paired fix
[2015-09-30T21:00Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:00Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:00Z] bgzip syn3-9_0_32405837-raw.snp.vcf
[2015-09-30T21:00Z] tabix index syn3-9_0_32405837-raw.snp.vcf.gz
[2015-09-30T21:00Z] bgzip syn3-9_0_32405837-raw.indel.vcf
[2015-09-30T21:00Z] INFO  22:00:30,870 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:00Z] tabix index syn3-9_0_32405837-raw.indel.vcf.gz
[2015-09-30T21:00Z] INFO  22:00:30,983 IntervalUtils - Processing 951635 bp from intervals
[2015-09-30T21:00Z] WARN  22:00:30,984 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:00Z] WARN  22:00:30,984 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:00Z] Combine variant files
[2015-09-30T21:00Z] INFO  22:00:31,044 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:00Z] INFO  22:00:31,046 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:00Z] INFO  22:00:31,047 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:00Z] INFO  22:00:31,047 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:00Z] INFO  22:00:31,047 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:00Z] INFO  22:00:32,288 ProgressMeter -            done      1567.0     1.0 s      13.2 m       99.8%     1.0 s       0.0 s
[2015-09-30T21:00Z] INFO  22:00:32,288 ProgressMeter - Total runtime 1.24 secs, 0.02 min, 0.00 hours
[2015-09-30T21:00Z] bgzip syn3-8_124975213_146364022-raw.vcf
[2015-09-30T21:00Z] INFO  22:00:32,674 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:32,676 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:00Z] INFO  22:00:32,676 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:00Z] INFO  22:00:32,676 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:00Z] INFO  22:00:32,680 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/9/tx/tmpc2KQwl/tx/tmpkMSLKt/syn3-9_0_32405837-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/9/tx/tmpc2KQwl/syn3-9_0_32405837-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/9/tx/tmpc2KQwl/syn3-9_0_32405837-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_0_32405837-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:00Z] INFO  22:00:32,685 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:00Z] INFO  22:00:32,685 HelpFormatter - Date/Time: 2015/09/30 22:00:32
[2015-09-30T21:00Z] INFO  22:00:32,686 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:32,686 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:00Z] tabix index syn3-8_124975213_146364022-raw.vcf.gz
[2015-09-30T21:00Z] INFO  22:00:32,765 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:00Z] bgzip syn3-8_124975213_146364022-raw-rejectfix.vcf
[2015-09-30T21:00Z] tabix index syn3-8_124975213_146364022-raw-rejectfix.vcf.gz
[2015-09-30T21:00Z] GATK: VariantAnnotator
[2015-09-30T21:00Z] INFO  22:00:33,227 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:00Z] INFO  22:00:33,324 IntervalUtils - Processing 859116 bp from intervals
[2015-09-30T21:00Z] WARN  22:00:33,325 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:00Z] WARN  22:00:33,325 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:00Z] INFO  22:00:33,384 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:00Z] INFO  22:00:33,386 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:00Z] INFO  22:00:33,387 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:00Z] INFO  22:00:33,387 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:00Z] INFO  22:00:33,388 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:00Z] Varscan
[2015-09-30T21:00Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmp9wexMK/syn3-9_32406980_65488652-raw-normal.mpileup
[2015-09-30T21:00Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmp9wexMK/syn3-9_32406980_65488652-raw-tumor.mpileup
[2015-09-30T21:00Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:00Z] Min reads2:	2
[2015-09-30T21:00Z] Min strands2:	1
[2015-09-30T21:00Z] Min var freq:	0.1
[2015-09-30T21:00Z] Min freq for hom:	0.75
[2015-09-30T21:00Z] Normal purity:	1.0
[2015-09-30T21:00Z] Tumor purity:	1.0
[2015-09-30T21:00Z] Min avg qual:	15
[2015-09-30T21:00Z] P-value thresh:	0.98
[2015-09-30T21:00Z] Somatic p-value:	0.05
[2015-09-30T21:00Z] INFO  22:00:34,483 ProgressMeter -            done      1306.0     1.0 s      14.0 m       99.7%     1.0 s       0.0 s
[2015-09-30T21:00Z] INFO  22:00:34,484 ProgressMeter - Total runtime 1.10 secs, 0.02 min, 0.00 hours
[2015-09-30T21:00Z] bgzip syn3-9_0_32405837-raw.vcf
[2015-09-30T21:00Z] tabix index syn3-9_0_32405837-raw.vcf.gz
[2015-09-30T21:00Z] bgzip syn3-9_0_32405837-raw-rejectfix.vcf
[2015-09-30T21:00Z] tabix index syn3-9_0_32405837-raw-rejectfix.vcf.gz
[2015-09-30T21:00Z] GATK: VariantAnnotator
[2015-09-30T21:00Z] INFO  22:00:36,258 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:36,260 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:00Z] INFO  22:00:36,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:00Z] INFO  22:00:36,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:00Z] INFO  22:00:36,264 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/8/syn3-8_124975213_146364022-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/8/tx/tmpLpc4Ws/syn3-8_124975213_146364022-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/8/syn3-8_124975213_146364022-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:00Z] INFO  22:00:36,270 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:00Z] INFO  22:00:36,270 HelpFormatter - Date/Time: 2015/09/30 22:00:36
[2015-09-30T21:00Z] INFO  22:00:36,270 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:36,270 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:36,642 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:00Z] INFO  22:00:36,797 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:00Z] INFO  22:00:36,805 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:00Z] INFO  22:00:36,828 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:00Z] INFO  22:00:37,010 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:37,012 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:00Z] INFO  22:00:37,012 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:00Z] INFO  22:00:37,012 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:00Z] INFO  22:00:37,016 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/9/syn3-9_0_32405837-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/9/tx/tmp8dV7nC/syn3-9_0_32405837-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_0_32405837-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:00Z] INFO  22:00:37,021 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:00Z] INFO  22:00:37,022 HelpFormatter - Date/Time: 2015/09/30 22:00:37
[2015-09-30T21:00Z] INFO  22:00:37,022 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:37,022 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:00Z] INFO  22:00:37,111 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:00Z] INFO  22:00:37,187 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:00Z] INFO  22:00:37,195 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:00Z] INFO  22:00:37,205 IntervalUtils - Processing 1567 bp from intervals
[2015-09-30T21:00Z] WARN  22:00:37,210 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:00Z] WARN  22:00:37,210 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:00Z] INFO  22:00:37,217 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:00Z] INFO  22:00:37,269 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:00Z] INFO  22:00:37,374 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:00Z] INFO  22:00:37,375 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:00Z] INFO  22:00:37,375 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:00Z] INFO  22:00:37,376 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:00Z] INFO  22:00:37,553 IntervalUtils - Processing 1306 bp from intervals
[2015-09-30T21:00Z] WARN  22:00:37,557 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:00Z] WARN  22:00:37,557 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:00Z] INFO  22:00:37,612 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:00Z] INFO  22:00:37,704 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:00Z] INFO  22:00:37,709 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:00Z] INFO  22:00:37,710 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:00Z] INFO  22:00:37,710 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:00Z] INFO  22:00:37,710 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:00Z] INFO  22:00:37,800 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:00Z] INFO  22:00:43,557 VariantAnnotator - Processed 1104 loci.
[2015-09-30T21:00Z]
[2015-09-30T21:00Z] INFO  22:00:43,577 ProgressMeter -            done      5302.0     5.0 s      18.4 m       99.9%     5.0 s       0.0 s
[2015-09-30T21:00Z] INFO  22:00:43,577 ProgressMeter - Total runtime 5.87 secs, 0.10 min, 0.00 hours
[2015-09-30T21:00Z] INFO  22:00:43,577 MicroScheduler - 3427 reads were filtered out during the traversal out of approximately 79046 total reads (4.34%)
[2015-09-30T21:00Z] INFO  22:00:43,578 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:00Z] INFO  22:00:43,578 MicroScheduler -   -> 3404 reads (4.31% of total) failing DuplicateReadFilter
[2015-09-30T21:00Z] INFO  22:00:43,578 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:00Z] INFO  22:00:43,578 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:00Z] INFO  22:00:43,579 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:00Z] INFO  22:00:43,579 MicroScheduler -   -> 23 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:00Z] INFO  22:00:44,532 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:00Z] Genotyping with varscan: ('9', 65505265, 96581951) 1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam
[2015-09-30T21:00Z] samtools mpileup
[2015-09-30T21:00Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:00Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:00Z] INFO  22:00:45,956 VariantAnnotator - Processed 1374 loci.
[2015-09-30T21:00Z]
[2015-09-30T21:00Z] INFO  22:00:46,003 ProgressMeter -            done      9159.0     8.0 s      15.7 m       99.0%     8.0 s       0.0 s
[2015-09-30T21:00Z] INFO  22:00:46,003 ProgressMeter - Total runtime 8.63 secs, 0.14 min, 0.00 hours
[2015-09-30T21:00Z] INFO  22:00:46,003 MicroScheduler - 7568 reads were filtered out during the traversal out of approximately 138831 total reads (5.45%)
[2015-09-30T21:00Z] INFO  22:00:46,004 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:00Z] INFO  22:00:46,004 MicroScheduler -   -> 7546 reads (5.44% of total) failing DuplicateReadFilter
[2015-09-30T21:00Z] INFO  22:00:46,004 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:00Z] INFO  22:00:46,004 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:00Z] INFO  22:00:46,005 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:00Z] INFO  22:00:46,005 MicroScheduler -   -> 22 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:00Z] INFO  22:00:47,060 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:00Z] Genotyping with varscan: ('9', 96714155, 127734373) 1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam
[2015-09-30T21:00Z] samtools mpileup
[2015-09-30T21:00Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:00Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:01Z] 903667 positions in tumor
[2015-09-30T21:01Z] 903661 positions shared in normal
[2015-09-30T21:01Z] 885005 had sufficient coverage for comparison
[2015-09-30T21:01Z] 882840 were called Reference
[2015-09-30T21:01Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:01Z] 407 were removed by the strand filter
[2015-09-30T21:01Z] 2081 were called Germline
[2015-09-30T21:01Z] 7 were called LOH
[2015-09-30T21:01Z] 66 were called Somatic
[2015-09-30T21:01Z] 11 were called Unknown
[2015-09-30T21:01Z] 0 were called Variant
[2015-09-30T21:01Z] Varscan paired fix
[2015-09-30T21:01Z] Varscan paired fix
[2015-09-30T21:01Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:01Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:01Z] bgzip syn3-9_32406980_65488652-raw.snp.vcf
[2015-09-30T21:01Z] tabix index syn3-9_32406980_65488652-raw.snp.vcf.gz
[2015-09-30T21:01Z] bgzip syn3-9_32406980_65488652-raw.indel.vcf
[2015-09-30T21:01Z] tabix index syn3-9_32406980_65488652-raw.indel.vcf.gz
[2015-09-30T21:01Z] Combine variant files
[2015-09-30T21:01Z] INFO  22:01:15,388 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:01Z] INFO  22:01:15,390 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:01Z] INFO  22:01:15,390 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:01Z] INFO  22:01:15,390 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:01Z] INFO  22:01:15,393 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/9/tx/tmp9wexMK/tx/tmpolMhLQ/syn3-9_32406980_65488652-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/9/tx/tmp9wexMK/syn3-9_32406980_65488652-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/9/tx/tmp9wexMK/syn3-9_32406980_65488652-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_32406980_65488652-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:01Z] INFO  22:01:15,399 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:01Z] INFO  22:01:15,399 HelpFormatter - Date/Time: 2015/09/30 22:01:15
[2015-09-30T21:01Z] INFO  22:01:15,399 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:01Z] INFO  22:01:15,399 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:01Z] INFO  22:01:15,471 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:01Z] INFO  22:01:15,829 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:01Z] INFO  22:01:15,923 IntervalUtils - Processing 906990 bp from intervals
[2015-09-30T21:01Z] WARN  22:01:15,924 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:01Z] WARN  22:01:15,924 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:01Z] INFO  22:01:15,978 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:01Z] INFO  22:01:15,980 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:01Z] INFO  22:01:15,981 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:01Z] INFO  22:01:15,981 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:01Z] INFO  22:01:15,982 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:01Z] INFO  22:01:17,389 ProgressMeter -            done      1909.0     1.0 s      12.3 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:01Z] INFO  22:01:17,390 ProgressMeter - Total runtime 1.41 secs, 0.02 min, 0.00 hours
[2015-09-30T21:01Z] bgzip syn3-9_32406980_65488652-raw.vcf
[2015-09-30T21:01Z] tabix index syn3-9_32406980_65488652-raw.vcf.gz
[2015-09-30T21:01Z] bgzip syn3-9_32406980_65488652-raw-rejectfix.vcf
[2015-09-30T21:01Z] tabix index syn3-9_32406980_65488652-raw-rejectfix.vcf.gz
[2015-09-30T21:01Z] GATK: VariantAnnotator
[2015-09-30T21:01Z] INFO  22:01:19,782 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:01Z] INFO  22:01:19,784 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:01Z] INFO  22:01:19,784 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:01Z] INFO  22:01:19,785 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:01Z] INFO  22:01:19,788 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/9/syn3-9_32406980_65488652-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/9/tx/tmpnxkUBM/syn3-9_32406980_65488652-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_32406980_65488652-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:01Z] INFO  22:01:19,793 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:01Z] INFO  22:01:19,794 HelpFormatter - Date/Time: 2015/09/30 22:01:19
[2015-09-30T21:01Z] INFO  22:01:19,794 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:01Z] INFO  22:01:19,794 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:01Z] INFO  22:01:19,887 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:01Z] INFO  22:01:19,960 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:01Z] INFO  22:01:19,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:01Z] INFO  22:01:19,989 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:01Z] INFO  22:01:20,375 IntervalUtils - Processing 1909 bp from intervals
[2015-09-30T21:01Z] WARN  22:01:20,379 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:01Z] WARN  22:01:20,379 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:01Z] INFO  22:01:20,433 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:01Z] INFO  22:01:23,316 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:01Z] INFO  22:01:23,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:01Z] INFO  22:01:23,317 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:01Z] INFO  22:01:23,318 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:01Z] INFO  22:01:23,348 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:01Z] samtools mpileup
[2015-09-30T21:01Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:01Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:01Z] INFO  22:01:30,504 VariantAnnotator - Processed 1752 loci.
[2015-09-30T21:01Z]
[2015-09-30T21:01Z] INFO  22:01:30,524 ProgressMeter -            done     27015.0     7.0 s       4.4 m       99.9%     7.0 s       0.0 s
[2015-09-30T21:01Z] INFO  22:01:30,525 ProgressMeter - Total runtime 7.21 secs, 0.12 min, 0.00 hours
[2015-09-30T21:01Z] INFO  22:01:30,525 MicroScheduler - 5172 reads were filtered out during the traversal out of approximately 118420 total reads (4.37%)
[2015-09-30T21:01Z] INFO  22:01:30,525 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:01Z] INFO  22:01:30,525 MicroScheduler -   -> 5143 reads (4.34% of total) failing DuplicateReadFilter
[2015-09-30T21:01Z] INFO  22:01:30,526 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:01Z] INFO  22:01:30,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:01Z] INFO  22:01:30,526 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:01Z] INFO  22:01:30,526 MicroScheduler -   -> 29 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:01Z] INFO  22:01:31,460 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:01Z] Genotyping with varscan: ('9', 127737328, 141213431) 1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam
[2015-09-30T21:01Z] samtools mpileup
[2015-09-30T21:01Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:01Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:01Z] samtools mpileup
[2015-09-30T21:01Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:01Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:02Z] Varscan
[2015-09-30T21:02Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmpxgLC2y/syn3-9_65505265_96581951-raw-normal.mpileup
[2015-09-30T21:02Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmpxgLC2y/syn3-9_65505265_96581951-raw-tumor.mpileup
[2015-09-30T21:02Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:02Z] Min reads2:	2
[2015-09-30T21:02Z] Min strands2:	1
[2015-09-30T21:02Z] Min var freq:	0.1
[2015-09-30T21:02Z] Min freq for hom:	0.75
[2015-09-30T21:02Z] Normal purity:	1.0
[2015-09-30T21:02Z] Tumor purity:	1.0
[2015-09-30T21:02Z] Min avg qual:	15
[2015-09-30T21:02Z] P-value thresh:	0.98
[2015-09-30T21:02Z] Somatic p-value:	0.05
[2015-09-30T21:02Z] Varscan
[2015-09-30T21:02Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmpiB_7Dd/syn3-9_96714155_127734373-raw-normal.mpileup
[2015-09-30T21:02Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmpiB_7Dd/syn3-9_96714155_127734373-raw-tumor.mpileup
[2015-09-30T21:02Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:02Z] Min reads2:	2
[2015-09-30T21:02Z] Min strands2:	1
[2015-09-30T21:02Z] Min var freq:	0.1
[2015-09-30T21:02Z] Min freq for hom:	0.75
[2015-09-30T21:02Z] Normal purity:	1.0
[2015-09-30T21:02Z] Tumor purity:	1.0
[2015-09-30T21:02Z] Min avg qual:	15
[2015-09-30T21:02Z] P-value thresh:	0.98
[2015-09-30T21:02Z] Somatic p-value:	0.05
[2015-09-30T21:02Z] samtools mpileup
[2015-09-30T21:02Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:02Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:02Z] 1176387 positions in tumor
[2015-09-30T21:02Z] 1176378 positions shared in normal
[2015-09-30T21:02Z] 1141794 had sufficient coverage for comparison
[2015-09-30T21:02Z] 1138870 were called Reference
[2015-09-30T21:02Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:02Z] 471 were removed by the strand filter
[2015-09-30T21:02Z] 2781 were called Germline
[2015-09-30T21:02Z] 21 were called LOH
[2015-09-30T21:02Z] 102 were called Somatic
[2015-09-30T21:02Z] 20 were called Unknown
[2015-09-30T21:02Z] 0 were called Variant
[2015-09-30T21:02Z] Varscan paired fix
[2015-09-30T21:02Z] Varscan paired fix
[2015-09-30T21:02Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:02Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:02Z] bgzip syn3-9_65505265_96581951-raw.snp.vcf
[2015-09-30T21:02Z] tabix index syn3-9_65505265_96581951-raw.snp.vcf.gz
[2015-09-30T21:02Z] bgzip syn3-9_65505265_96581951-raw.indel.vcf
[2015-09-30T21:02Z] tabix index syn3-9_65505265_96581951-raw.indel.vcf.gz
[2015-09-30T21:02Z] Combine variant files
[2015-09-30T21:02Z] INFO  22:02:59,685 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:02Z] INFO  22:02:59,687 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:02Z] INFO  22:02:59,687 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:02Z] INFO  22:02:59,688 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:02Z] INFO  22:02:59,691 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/9/tx/tmpxgLC2y/tx/tmp52PIbN/syn3-9_65505265_96581951-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/9/tx/tmpxgLC2y/syn3-9_65505265_96581951-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/9/tx/tmpxgLC2y/syn3-9_65505265_96581951-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_65505265_96581951-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:02Z] INFO  22:02:59,696 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:02Z] INFO  22:02:59,697 HelpFormatter - Date/Time: 2015/09/30 22:02:59
[2015-09-30T21:02Z] INFO  22:02:59,697 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:02Z] INFO  22:02:59,697 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:02Z] INFO  22:02:59,776 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:02Z] INFO  22:02:59,916 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:03Z] INFO  22:03:00,036 IntervalUtils - Processing 1183943 bp from intervals
[2015-09-30T21:03Z] WARN  22:03:00,037 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:03Z] WARN  22:03:00,037 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:03Z] INFO  22:03:00,095 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:03Z] INFO  22:03:00,099 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:03Z] INFO  22:03:00,099 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:03Z] INFO  22:03:00,100 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:03Z] INFO  22:03:00,100 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:03Z] INFO  22:03:02,130 ProgressMeter -            done      2794.0     2.0 s      12.1 m      100.0%     2.0 s       0.0 s
[2015-09-30T21:03Z] INFO  22:03:02,130 ProgressMeter - Total runtime 2.03 secs, 0.03 min, 0.00 hours
[2015-09-30T21:03Z] bgzip syn3-9_65505265_96581951-raw.vcf
[2015-09-30T21:03Z] tabix index syn3-9_65505265_96581951-raw.vcf.gz
[2015-09-30T21:03Z] bgzip syn3-9_65505265_96581951-raw-rejectfix.vcf
[2015-09-30T21:03Z] tabix index syn3-9_65505265_96581951-raw-rejectfix.vcf.gz
[2015-09-30T21:03Z] GATK: VariantAnnotator
[2015-09-30T21:03Z] INFO  22:03:04,928 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:03Z] INFO  22:03:04,930 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:03Z] INFO  22:03:04,931 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:03Z] INFO  22:03:04,931 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:03Z] INFO  22:03:04,934 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/9/syn3-9_65505265_96581951-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/9/tx/tmp3nmjwy/syn3-9_65505265_96581951-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_65505265_96581951-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:03Z] INFO  22:03:04,940 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:03Z] INFO  22:03:04,940 HelpFormatter - Date/Time: 2015/09/30 22:03:04
[2015-09-30T21:03Z] INFO  22:03:04,940 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:03Z] INFO  22:03:04,940 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:03Z] INFO  22:03:05,006 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:03Z] INFO  22:03:05,082 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:03Z] INFO  22:03:05,089 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:03Z] INFO  22:03:05,112 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:03Z] INFO  22:03:05,588 IntervalUtils - Processing 2794 bp from intervals
[2015-09-30T21:03Z] WARN  22:03:05,646 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:03Z] WARN  22:03:05,646 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:03Z] INFO  22:03:05,703 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:03Z] INFO  22:03:05,812 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:03Z] INFO  22:03:05,812 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:03Z] INFO  22:03:05,812 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:03Z] INFO  22:03:05,813 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:03Z] INFO  22:03:05,845 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:03Z] INFO  22:03:17,547 VariantAnnotator - Processed 2438 loci.
[2015-09-30T21:03Z]
[2015-09-30T21:03Z] INFO  22:03:17,568 ProgressMeter -            done     35035.0    11.0 s       5.6 m      100.0%    11.0 s       0.0 s
[2015-09-30T21:03Z] INFO  22:03:17,568 ProgressMeter - Total runtime 11.76 secs, 0.20 min, 0.00 hours
[2015-09-30T21:03Z] INFO  22:03:17,568 MicroScheduler - 10918 reads were filtered out during the traversal out of approximately 213656 total reads (5.11%)
[2015-09-30T21:03Z] INFO  22:03:17,569 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:03Z] INFO  22:03:17,569 MicroScheduler -   -> 10811 reads (5.06% of total) failing DuplicateReadFilter
[2015-09-30T21:03Z] INFO  22:03:17,569 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:03Z] INFO  22:03:17,569 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:03Z] INFO  22:03:17,570 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:03Z] INFO  22:03:17,570 MicroScheduler -   -> 107 reads (0.05% of total) failing UnmappedReadFilter
[2015-09-30T21:03Z] INFO  22:03:18,735 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:03Z] Genotyping with varscan: ('10', 0, 31134673) 1_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam
[2015-09-30T21:03Z] samtools mpileup
[2015-09-30T21:03Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:03Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:03Z] 1667564 positions in tumor
[2015-09-30T21:03Z] 1667557 positions shared in normal
[2015-09-30T21:03Z] 1644395 had sufficient coverage for comparison
[2015-09-30T21:03Z] 1642593 were called Reference
[2015-09-30T21:03Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:03Z] 77 were removed by the strand filter
[2015-09-30T21:03Z] 1745 were called Germline
[2015-09-30T21:03Z] 5 were called LOH
[2015-09-30T21:03Z] 42 were called Somatic
[2015-09-30T21:03Z] 10 were called Unknown
[2015-09-30T21:03Z] 0 were called Variant
[2015-09-30T21:03Z] Varscan paired fix
[2015-09-30T21:03Z] Varscan paired fix
[2015-09-30T21:03Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:03Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:03Z] bgzip syn3-9_96714155_127734373-raw.snp.vcf
[2015-09-30T21:03Z] tabix index syn3-9_96714155_127734373-raw.snp.vcf.gz
[2015-09-30T21:03Z] samtools mpileup
[2015-09-30T21:03Z] bgzip syn3-9_96714155_127734373-raw.indel.vcf
[2015-09-30T21:03Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:03Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:03Z] tabix index syn3-9_96714155_127734373-raw.indel.vcf.gz
[2015-09-30T21:03Z] Combine variant files
[2015-09-30T21:03Z] INFO  22:03:59,913 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:03Z] INFO  22:03:59,915 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:03Z] INFO  22:03:59,916 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:03Z] INFO  22:03:59,916 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:03Z] INFO  22:03:59,919 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/9/tx/tmpiB_7Dd/tx/tmpCqdZND/syn3-9_96714155_127734373-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/9/tx/tmpiB_7Dd/syn3-9_96714155_127734373-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/9/tx/tmpiB_7Dd/syn3-9_96714155_127734373-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_96714155_127734373-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:03Z] INFO  22:03:59,925 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:03Z] INFO  22:03:59,925 HelpFormatter - Date/Time: 2015/09/30 22:03:59
[2015-09-30T21:03Z] INFO  22:03:59,925 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:03Z] INFO  22:03:59,925 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:04Z] INFO  22:04:00,000 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:04Z] INFO  22:04:00,146 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:04Z] INFO  22:04:00,322 IntervalUtils - Processing 1674397 bp from intervals
[2015-09-30T21:04Z] WARN  22:04:00,323 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:04Z] WARN  22:04:00,323 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:04Z] INFO  22:04:00,381 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:04Z] INFO  22:04:00,385 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:04Z] INFO  22:04:00,385 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:04Z] INFO  22:04:00,386 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:04Z] INFO  22:04:00,386 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:04Z] INFO  22:04:02,159 ProgressMeter -            done      2064.0     1.0 s      14.3 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:04Z] INFO  22:04:02,159 ProgressMeter - Total runtime 1.77 secs, 0.03 min, 0.00 hours
[2015-09-30T21:04Z] bgzip syn3-9_96714155_127734373-raw.vcf
[2015-09-30T21:04Z] tabix index syn3-9_96714155_127734373-raw.vcf.gz
[2015-09-30T21:04Z] bgzip syn3-9_96714155_127734373-raw-rejectfix.vcf
[2015-09-30T21:04Z] tabix index syn3-9_96714155_127734373-raw-rejectfix.vcf.gz
[2015-09-30T21:04Z] GATK: VariantAnnotator
[2015-09-30T21:04Z] INFO  22:04:04,705 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:04Z] INFO  22:04:04,707 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:04Z] INFO  22:04:04,707 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:04Z] INFO  22:04:04,708 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:04Z] INFO  22:04:04,711 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/9/syn3-9_96714155_127734373-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/9/tx/tmpRq96eo/syn3-9_96714155_127734373-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_96714155_127734373-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:04Z] INFO  22:04:04,716 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:04Z] INFO  22:04:04,717 HelpFormatter - Date/Time: 2015/09/30 22:04:04
[2015-09-30T21:04Z] INFO  22:04:04,717 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:04Z] INFO  22:04:04,717 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:04Z] INFO  22:04:04,809 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:04Z] INFO  22:04:04,885 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:04Z] INFO  22:04:04,893 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:04Z] INFO  22:04:04,915 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:04Z] INFO  22:04:05,281 IntervalUtils - Processing 2065 bp from intervals
[2015-09-30T21:04Z] WARN  22:04:05,285 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:04Z] WARN  22:04:05,285 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:04Z] INFO  22:04:05,341 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:04Z] INFO  22:04:05,565 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:04Z] INFO  22:04:05,566 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:04Z] INFO  22:04:05,566 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:04Z] INFO  22:04:05,566 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:04Z] INFO  22:04:05,599 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:04Z] INFO  22:04:14,830 VariantAnnotator - Processed 1720 loci.
[2015-09-30T21:04Z]
[2015-09-30T21:04Z] INFO  22:04:14,867 ProgressMeter -            done      7152.0     9.0 s      21.7 m      100.0%     9.0 s       0.0 s
[2015-09-30T21:04Z] INFO  22:04:14,867 ProgressMeter - Total runtime 9.30 secs, 0.16 min, 0.00 hours
[2015-09-30T21:04Z] INFO  22:04:14,867 MicroScheduler - 7077 reads were filtered out during the traversal out of approximately 147526 total reads (4.80%)
[2015-09-30T21:04Z] INFO  22:04:14,867 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:04Z] INFO  22:04:14,868 MicroScheduler -   -> 7056 reads (4.78% of total) failing DuplicateReadFilter
[2015-09-30T21:04Z] INFO  22:04:14,868 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:04Z] INFO  22:04:14,868 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:04Z] INFO  22:04:14,868 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:04Z] INFO  22:04:14,869 MicroScheduler -   -> 21 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T21:04Z] Varscan
[2015-09-30T21:04Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmpTKw9z9/syn3-9_127737328_141213431-raw-normal.mpileup
[2015-09-30T21:04Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/9/tx/tmpTKw9z9/syn3-9_127737328_141213431-raw-tumor.mpileup
[2015-09-30T21:04Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:04Z] Min reads2:	2
[2015-09-30T21:04Z] Min strands2:	1
[2015-09-30T21:04Z] Min var freq:	0.1
[2015-09-30T21:04Z] Min freq for hom:	0.75
[2015-09-30T21:04Z] Normal purity:	1.0
[2015-09-30T21:04Z] Tumor purity:	1.0
[2015-09-30T21:04Z] Min avg qual:	15
[2015-09-30T21:04Z] P-value thresh:	0.98
[2015-09-30T21:04Z] Somatic p-value:	0.05
[2015-09-30T21:04Z] INFO  22:04:15,838 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:04Z] Genotyping with varscan: ('10', 31137165, 62208748) 1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam
[2015-09-30T21:04Z] samtools mpileup
[2015-09-30T21:04Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:04Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:04Z] Varscan
[2015-09-30T21:04Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpMM3St3/syn3-10_0_31134673-raw-normal.mpileup
[2015-09-30T21:04Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpMM3St3/syn3-10_0_31134673-raw-tumor.mpileup
[2015-09-30T21:04Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:04Z] Min reads2:	2
[2015-09-30T21:04Z] Min strands2:	1
[2015-09-30T21:04Z] Min var freq:	0.1
[2015-09-30T21:04Z] Min freq for hom:	0.75
[2015-09-30T21:04Z] Normal purity:	1.0
[2015-09-30T21:04Z] Tumor purity:	1.0
[2015-09-30T21:04Z] Min avg qual:	15
[2015-09-30T21:04Z] P-value thresh:	0.98
[2015-09-30T21:04Z] Somatic p-value:	0.05
[2015-09-30T21:04Z] samtools mpileup
[2015-09-30T21:04Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:04Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:05Z] Varscan
[2015-09-30T21:05Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpdK7_oM/syn3-10_31137165_62208748-raw-normal.mpileup
[2015-09-30T21:05Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpdK7_oM/syn3-10_31137165_62208748-raw-tumor.mpileup
[2015-09-30T21:05Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:05Z] Min reads2:	2
[2015-09-30T21:05Z] Min strands2:	1
[2015-09-30T21:05Z] Min var freq:	0.1
[2015-09-30T21:05Z] Min freq for hom:	0.75
[2015-09-30T21:05Z] Normal purity:	1.0
[2015-09-30T21:05Z] Tumor purity:	1.0
[2015-09-30T21:05Z] Min avg qual:	15
[2015-09-30T21:05Z] P-value thresh:	0.98
[2015-09-30T21:05Z] Somatic p-value:	0.05
[2015-09-30T21:05Z] 1280772 positions in tumor
[2015-09-30T21:05Z] 1280760 positions shared in normal
[2015-09-30T21:05Z] 1252900 had sufficient coverage for comparison
[2015-09-30T21:05Z] 1250873 were called Reference
[2015-09-30T21:05Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:05Z] 98 were removed by the strand filter
[2015-09-30T21:05Z] 1956 were called Germline
[2015-09-30T21:05Z] 12 were called LOH
[2015-09-30T21:05Z] 47 were called Somatic
[2015-09-30T21:05Z] 12 were called Unknown
[2015-09-30T21:05Z] 0 were called Variant
[2015-09-30T21:05Z] Varscan paired fix
[2015-09-30T21:05Z] Varscan paired fix
[2015-09-30T21:05Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:05Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:05Z] bgzip syn3-10_0_31134673-raw.snp.vcf
[2015-09-30T21:05Z] tabix index syn3-10_0_31134673-raw.snp.vcf.gz
[2015-09-30T21:05Z] bgzip syn3-10_0_31134673-raw.indel.vcf
[2015-09-30T21:05Z] tabix index syn3-10_0_31134673-raw.indel.vcf.gz
[2015-09-30T21:05Z] Combine variant files
[2015-09-30T21:05Z] INFO  22:05:30,717 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:30,719 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:05Z] INFO  22:05:30,719 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:05Z] INFO  22:05:30,720 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:05Z] INFO  22:05:30,723 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/10/tx/tmpMM3St3/tx/tmpT6DUT9/syn3-10_0_31134673-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/10/tx/tmpMM3St3/syn3-10_0_31134673-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/10/tx/tmpMM3St3/syn3-10_0_31134673-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_0_31134673-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:05Z] INFO  22:05:30,729 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:05Z] INFO  22:05:30,729 HelpFormatter - Date/Time: 2015/09/30 22:05:30
[2015-09-30T21:05Z] INFO  22:05:30,730 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:30,730 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:30,808 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:05Z] INFO  22:05:30,953 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:05Z] INFO  22:05:31,070 IntervalUtils - Processing 1286154 bp from intervals
[2015-09-30T21:05Z] WARN  22:05:31,071 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:05Z] WARN  22:05:31,071 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:05Z] INFO  22:05:31,131 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:05Z] INFO  22:05:31,135 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:05Z] INFO  22:05:31,136 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:05Z] INFO  22:05:31,136 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:05Z] INFO  22:05:31,136 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:05Z] INFO  22:05:32,661 ProgressMeter -            done      2268.0     1.0 s      11.2 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:05Z] INFO  22:05:32,662 ProgressMeter - Total runtime 1.53 secs, 0.03 min, 0.00 hours
[2015-09-30T21:05Z] bgzip syn3-10_0_31134673-raw.vcf
[2015-09-30T21:05Z] tabix index syn3-10_0_31134673-raw.vcf.gz
[2015-09-30T21:05Z] bgzip syn3-10_0_31134673-raw-rejectfix.vcf
[2015-09-30T21:05Z] tabix index syn3-10_0_31134673-raw-rejectfix.vcf.gz
[2015-09-30T21:05Z] GATK: VariantAnnotator
[2015-09-30T21:05Z] 1763337 positions in tumor
[2015-09-30T21:05Z] 1763329 positions shared in normal
[2015-09-30T21:05Z] 1752886 had sufficient coverage for comparison
[2015-09-30T21:05Z] 1750317 were called Reference
[2015-09-30T21:05Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:05Z] 141 were removed by the strand filter
[2015-09-30T21:05Z] 2509 were called Germline
[2015-09-30T21:05Z] 3 were called LOH
[2015-09-30T21:05Z] 45 were called Somatic
[2015-09-30T21:05Z] 12 were called Unknown
[2015-09-30T21:05Z] 0 were called Variant
[2015-09-30T21:05Z] Varscan paired fix
[2015-09-30T21:05Z] Varscan paired fix
[2015-09-30T21:05Z] INFO  22:05:35,400 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:35,402 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:05Z] INFO  22:05:35,402 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:05Z] INFO  22:05:35,402 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:05Z] INFO  22:05:35,406 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/10/syn3-10_0_31134673-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/10/tx/tmpSbFLB6/syn3-10_0_31134673-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_0_31134673-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:05Z] INFO  22:05:35,412 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:05Z] INFO  22:05:35,412 HelpFormatter - Date/Time: 2015/09/30 22:05:35
[2015-09-30T21:05Z] INFO  22:05:35,412 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:35,412 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:35,509 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:05Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:05Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:05Z] bgzip syn3-9_127737328_141213431-raw.snp.vcf
[2015-09-30T21:05Z] tabix index syn3-9_127737328_141213431-raw.snp.vcf.gz
[2015-09-30T21:05Z] INFO  22:05:35,591 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:05Z] INFO  22:05:35,599 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:05Z] bgzip syn3-9_127737328_141213431-raw.indel.vcf
[2015-09-30T21:05Z] INFO  22:05:35,623 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:05Z] tabix index syn3-9_127737328_141213431-raw.indel.vcf.gz
[2015-09-30T21:05Z] Combine variant files
[2015-09-30T21:05Z] INFO  22:05:36,011 IntervalUtils - Processing 2282 bp from intervals
[2015-09-30T21:05Z] WARN  22:05:36,015 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:05Z] WARN  22:05:36,016 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:05Z] INFO  22:05:36,075 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:05Z] INFO  22:05:36,260 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:05Z] INFO  22:05:36,261 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:05Z] INFO  22:05:36,261 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:05Z] INFO  22:05:36,262 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:05Z] INFO  22:05:36,294 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:05Z] INFO  22:05:37,824 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:37,826 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:05Z] INFO  22:05:37,826 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:05Z] INFO  22:05:37,826 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:05Z] INFO  22:05:37,830 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/9/tx/tmpTKw9z9/tx/tmpwnIOes/syn3-9_127737328_141213431-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/9/tx/tmpTKw9z9/syn3-9_127737328_141213431-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/9/tx/tmpTKw9z9/syn3-9_127737328_141213431-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_127737328_141213431-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:05Z] INFO  22:05:37,836 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:05Z] INFO  22:05:37,836 HelpFormatter - Date/Time: 2015/09/30 22:05:37
[2015-09-30T21:05Z] INFO  22:05:37,836 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:37,836 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:38,174 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:05Z] INFO  22:05:38,546 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:05Z] INFO  22:05:38,692 IntervalUtils - Processing 1771848 bp from intervals
[2015-09-30T21:05Z] WARN  22:05:38,693 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:05Z] WARN  22:05:38,693 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:05Z] INFO  22:05:38,749 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:05Z] INFO  22:05:38,753 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:05Z] INFO  22:05:38,754 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:05Z] INFO  22:05:38,754 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:05Z] INFO  22:05:38,754 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:05Z] INFO  22:05:40,520 ProgressMeter -            done      2864.0     1.0 s      10.3 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:05Z] INFO  22:05:40,521 ProgressMeter - Total runtime 1.77 secs, 0.03 min, 0.00 hours
[2015-09-30T21:05Z] bgzip syn3-9_127737328_141213431-raw.vcf
[2015-09-30T21:05Z] tabix index syn3-9_127737328_141213431-raw.vcf.gz
[2015-09-30T21:05Z] bgzip syn3-9_127737328_141213431-raw-rejectfix.vcf
[2015-09-30T21:05Z] tabix index syn3-9_127737328_141213431-raw-rejectfix.vcf.gz
[2015-09-30T21:05Z] GATK: VariantAnnotator
[2015-09-30T21:05Z] INFO  22:05:43,234 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:43,236 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:05Z] INFO  22:05:43,237 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:05Z] INFO  22:05:43,237 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:05Z] INFO  22:05:43,240 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/9/syn3-9_127737328_141213431-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/9/tx/tmpAASTQj/syn3-9_127737328_141213431-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/9/syn3-9_127737328_141213431-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:05Z] INFO  22:05:43,246 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:05Z] INFO  22:05:43,246 HelpFormatter - Date/Time: 2015/09/30 22:05:43
[2015-09-30T21:05Z] INFO  22:05:43,246 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:43,247 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:05Z] INFO  22:05:43,342 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:05Z] INFO  22:05:43,419 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:05Z] INFO  22:05:43,427 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:05Z] INFO  22:05:43,450 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:05Z] INFO  22:05:43,952 IntervalUtils - Processing 2864 bp from intervals
[2015-09-30T21:05Z] WARN  22:05:43,956 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:05Z] WARN  22:05:43,956 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:05Z] INFO  22:05:44,014 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:05Z] INFO  22:05:44,199 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:05Z] INFO  22:05:44,199 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:05Z] INFO  22:05:44,200 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:05Z] INFO  22:05:44,200 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:05Z] INFO  22:05:44,256 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:05Z] INFO  22:05:45,421 VariantAnnotator - Processed 1921 loci.
[2015-09-30T21:05Z]
[2015-09-30T21:05Z] INFO  22:05:45,452 ProgressMeter -            done     10605.0     9.0 s      14.4 m      100.0%     9.0 s       0.0 s
[2015-09-30T21:05Z] INFO  22:05:45,452 ProgressMeter - Total runtime 9.19 secs, 0.15 min, 0.00 hours
[2015-09-30T21:05Z] INFO  22:05:45,452 MicroScheduler - 6607 reads were filtered out during the traversal out of approximately 144645 total reads (4.57%)
[2015-09-30T21:05Z] INFO  22:05:45,453 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:05Z] INFO  22:05:45,453 MicroScheduler -   -> 6581 reads (4.55% of total) failing DuplicateReadFilter
[2015-09-30T21:05Z] INFO  22:05:45,453 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:05Z] INFO  22:05:45,453 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:05Z] INFO  22:05:45,453 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:05Z] INFO  22:05:45,454 MicroScheduler -   -> 26 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:05Z] INFO  22:05:46,590 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:05Z] Genotyping with varscan: ('10', 62267938, 93388847) 1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam
[2015-09-30T21:05Z] samtools mpileup
[2015-09-30T21:05Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:05Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:05Z] INFO  22:05:58,466 VariantAnnotator - Processed 2420 loci.
[2015-09-30T21:05Z]
[2015-09-30T21:05Z] INFO  22:05:58,488 ProgressMeter -            done     22782.0    14.0 s      10.5 m      100.0%    14.0 s       0.0 s
[2015-09-30T21:05Z] INFO  22:05:58,488 ProgressMeter - Total runtime 14.29 secs, 0.24 min, 0.00 hours
[2015-09-30T21:05Z] INFO  22:05:58,489 MicroScheduler - 14018 reads were filtered out during the traversal out of approximately 252364 total reads (5.55%)
[2015-09-30T21:05Z] INFO  22:05:58,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:05Z] INFO  22:05:58,489 MicroScheduler -   -> 13947 reads (5.53% of total) failing DuplicateReadFilter
[2015-09-30T21:05Z] INFO  22:05:58,489 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:05Z] INFO  22:05:58,489 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:05Z] INFO  22:05:58,490 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:05Z] INFO  22:05:58,490 MicroScheduler -   -> 71 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:05Z] INFO  22:05:59,517 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:05Z] Genotyping with varscan: ('10', 93389481, 124436664) 1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam
[2015-09-30T21:05Z] samtools mpileup
[2015-09-30T21:06Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:06Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:06Z] 1114106 positions in tumor
[2015-09-30T21:06Z] 1114092 positions shared in normal
[2015-09-30T21:06Z] 1077771 had sufficient coverage for comparison
[2015-09-30T21:06Z] 1075603 were called Reference
[2015-09-30T21:06Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:06Z] 358 were removed by the strand filter
[2015-09-30T21:06Z] 2075 were called Germline
[2015-09-30T21:06Z] 11 were called LOH
[2015-09-30T21:06Z] 72 were called Somatic
[2015-09-30T21:06Z] 10 were called Unknown
[2015-09-30T21:06Z] 0 were called Variant
[2015-09-30T21:06Z] Varscan paired fix
[2015-09-30T21:06Z] Varscan paired fix
[2015-09-30T21:06Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:06Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:06Z] bgzip syn3-10_31137165_62208748-raw.snp.vcf
[2015-09-30T21:06Z] tabix index syn3-10_31137165_62208748-raw.snp.vcf.gz
[2015-09-30T21:06Z] bgzip syn3-10_31137165_62208748-raw.indel.vcf
[2015-09-30T21:06Z] tabix index syn3-10_31137165_62208748-raw.indel.vcf.gz
[2015-09-30T21:06Z] Combine variant files
[2015-09-30T21:06Z] INFO  22:06:17,148 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:06Z] INFO  22:06:17,150 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:06Z] INFO  22:06:17,150 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:06Z] INFO  22:06:17,151 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:06Z] INFO  22:06:17,154 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/10/tx/tmpdK7_oM/tx/tmprfMYFG/syn3-10_31137165_62208748-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/10/tx/tmpdK7_oM/syn3-10_31137165_62208748-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/10/tx/tmpdK7_oM/syn3-10_31137165_62208748-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_31137165_62208748-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:06Z] INFO  22:06:17,160 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:06Z] INFO  22:06:17,160 HelpFormatter - Date/Time: 2015/09/30 22:06:17
[2015-09-30T21:06Z] INFO  22:06:17,160 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:06Z] INFO  22:06:17,160 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:06Z] INFO  22:06:17,236 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:06Z] INFO  22:06:17,378 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:06Z] INFO  22:06:17,492 IntervalUtils - Processing 1121601 bp from intervals
[2015-09-30T21:06Z] WARN  22:06:17,493 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:06Z] WARN  22:06:17,493 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:06Z] INFO  22:06:17,550 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:06Z] INFO  22:06:17,554 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:06Z] INFO  22:06:17,554 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:06Z] INFO  22:06:17,554 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:06Z] INFO  22:06:17,555 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:06Z] INFO  22:06:18,950 ProgressMeter -            done      2031.0     1.0 s      11.5 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:06Z] INFO  22:06:18,951 ProgressMeter - Total runtime 1.40 secs, 0.02 min, 0.00 hours
[2015-09-30T21:06Z] bgzip syn3-10_31137165_62208748-raw.vcf
[2015-09-30T21:06Z] tabix index syn3-10_31137165_62208748-raw.vcf.gz
[2015-09-30T21:06Z] bgzip syn3-10_31137165_62208748-raw-rejectfix.vcf
[2015-09-30T21:06Z] tabix index syn3-10_31137165_62208748-raw-rejectfix.vcf.gz
[2015-09-30T21:06Z] GATK: VariantAnnotator
[2015-09-30T21:06Z] INFO  22:06:21,754 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:06Z] INFO  22:06:21,756 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:06Z] INFO  22:06:21,756 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:06Z] INFO  22:06:21,756 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:06Z] INFO  22:06:21,760 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/10/syn3-10_31137165_62208748-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/10/tx/tmpi_Qjuz/syn3-10_31137165_62208748-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_31137165_62208748-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:06Z] INFO  22:06:21,765 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:06Z] INFO  22:06:21,765 HelpFormatter - Date/Time: 2015/09/30 22:06:21
[2015-09-30T21:06Z] INFO  22:06:21,766 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:06Z] INFO  22:06:21,766 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:06Z] INFO  22:06:21,839 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:06Z] INFO  22:06:21,987 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:06Z] INFO  22:06:21,995 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:06Z] INFO  22:06:22,063 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2015-09-30T21:06Z] INFO  22:06:22,477 IntervalUtils - Processing 2031 bp from intervals
[2015-09-30T21:06Z] WARN  22:06:22,481 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:06Z] WARN  22:06:22,481 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:06Z] INFO  22:06:22,536 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:06Z] INFO  22:06:22,700 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:06Z] INFO  22:06:22,701 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:06Z] INFO  22:06:22,701 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:06Z] INFO  22:06:22,702 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:06Z] INFO  22:06:22,734 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:06Z] INFO  22:06:30,360 VariantAnnotator - Processed 1805 loci.
[2015-09-30T21:06Z]
[2015-09-30T21:06Z] INFO  22:06:30,398 ProgressMeter -            done     14064.0     7.0 s       9.1 m      100.0%     7.0 s       0.0 s
[2015-09-30T21:06Z] INFO  22:06:30,398 ProgressMeter - Total runtime 7.70 secs, 0.13 min, 0.00 hours
[2015-09-30T21:06Z] INFO  22:06:30,398 MicroScheduler - 5744 reads were filtered out during the traversal out of approximately 129438 total reads (4.44%)
[2015-09-30T21:06Z] INFO  22:06:30,398 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:06Z] INFO  22:06:30,399 MicroScheduler -   -> 5719 reads (4.42% of total) failing DuplicateReadFilter
[2015-09-30T21:06Z] INFO  22:06:30,399 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:06Z] INFO  22:06:30,399 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:06Z] INFO  22:06:30,399 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:06Z] INFO  22:06:30,399 MicroScheduler -   -> 25 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:06Z] INFO  22:06:31,303 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:06Z] Genotyping with varscan: ('10', 124438084, 135534747) 1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam
[2015-09-30T21:06Z] samtools mpileup
[2015-09-30T21:06Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:06Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:06Z] samtools mpileup
[2015-09-30T21:06Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:06Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:06Z] samtools mpileup
[2015-09-30T21:06Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:06Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:07Z] samtools mpileup
[2015-09-30T21:07Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:07Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:07Z] Varscan
[2015-09-30T21:07Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpn1fw1j/syn3-10_124438084_135534747-raw-normal.mpileup
[2015-09-30T21:07Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpn1fw1j/syn3-10_124438084_135534747-raw-tumor.mpileup
[2015-09-30T21:07Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:07Z] Min reads2:	2
[2015-09-30T21:07Z] Min strands2:	1
[2015-09-30T21:07Z] Min var freq:	0.1
[2015-09-30T21:07Z] Min freq for hom:	0.75
[2015-09-30T21:07Z] Normal purity:	1.0
[2015-09-30T21:07Z] Tumor purity:	1.0
[2015-09-30T21:07Z] Min avg qual:	15
[2015-09-30T21:07Z] P-value thresh:	0.98
[2015-09-30T21:07Z] Somatic p-value:	0.05
[2015-09-30T21:07Z] Varscan
[2015-09-30T21:07Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpO7JJic/syn3-10_62267938_93388847-raw-normal.mpileup
[2015-09-30T21:07Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpO7JJic/syn3-10_62267938_93388847-raw-tumor.mpileup
[2015-09-30T21:07Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:07Z] Min reads2:	2
[2015-09-30T21:07Z] Min strands2:	1
[2015-09-30T21:07Z] Min var freq:	0.1
[2015-09-30T21:07Z] Min freq for hom:	0.75
[2015-09-30T21:07Z] Normal purity:	1.0
[2015-09-30T21:07Z] Tumor purity:	1.0
[2015-09-30T21:07Z] Min avg qual:	15
[2015-09-30T21:07Z] P-value thresh:	0.98
[2015-09-30T21:07Z] Somatic p-value:	0.05
[2015-09-30T21:07Z] 575259 positions in tumor
[2015-09-30T21:07Z] 575255 positions shared in normal
[2015-09-30T21:07Z] 570433 had sufficient coverage for comparison
[2015-09-30T21:07Z] 569239 were called Reference
[2015-09-30T21:07Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:07Z] 138 were removed by the strand filter
[2015-09-30T21:07Z] 1174 were called Germline
[2015-09-30T21:07Z] 1 were called LOH
[2015-09-30T21:07Z] 13 were called Somatic
[2015-09-30T21:07Z] 6 were called Unknown
[2015-09-30T21:07Z] 0 were called Variant
[2015-09-30T21:07Z] Varscan paired fix
[2015-09-30T21:07Z] Varscan paired fix
[2015-09-30T21:07Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:07Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:07Z] bgzip syn3-10_124438084_135534747-raw.snp.vcf
[2015-09-30T21:07Z] tabix index syn3-10_124438084_135534747-raw.snp.vcf.gz
[2015-09-30T21:07Z] bgzip syn3-10_124438084_135534747-raw.indel.vcf
[2015-09-30T21:07Z] tabix index syn3-10_124438084_135534747-raw.indel.vcf.gz
[2015-09-30T21:07Z] Combine variant files
[2015-09-30T21:07Z] INFO  22:07:47,705 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:07Z] INFO  22:07:47,707 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:07Z] INFO  22:07:47,707 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:07Z] INFO  22:07:47,707 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:07Z] INFO  22:07:47,711 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/10/tx/tmpn1fw1j/tx/tmpQmlYN6/syn3-10_124438084_135534747-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/10/tx/tmpn1fw1j/syn3-10_124438084_135534747-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/10/tx/tmpn1fw1j/syn3-10_124438084_135534747-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_124438084_135534747-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:07Z] INFO  22:07:47,717 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:07Z] INFO  22:07:47,717 HelpFormatter - Date/Time: 2015/09/30 22:07:47
[2015-09-30T21:07Z] INFO  22:07:47,717 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:07Z] INFO  22:07:47,718 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:07Z] INFO  22:07:47,798 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:07Z] INFO  22:07:47,935 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:07Z] INFO  22:07:48,040 IntervalUtils - Processing 577156 bp from intervals
[2015-09-30T21:07Z] WARN  22:07:48,041 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:07Z] WARN  22:07:48,041 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:07Z] INFO  22:07:48,098 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:07Z] INFO  22:07:48,100 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:07Z] INFO  22:07:48,101 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:07Z] INFO  22:07:48,101 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:07Z] INFO  22:07:48,102 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:07Z] INFO  22:07:49,324 ProgressMeter -            done      1221.0     1.0 s      16.7 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:07Z] INFO  22:07:49,325 ProgressMeter - Total runtime 1.22 secs, 0.02 min, 0.00 hours
[2015-09-30T21:07Z] bgzip syn3-10_124438084_135534747-raw.vcf
[2015-09-30T21:07Z] tabix index syn3-10_124438084_135534747-raw.vcf.gz
[2015-09-30T21:07Z] bgzip syn3-10_124438084_135534747-raw-rejectfix.vcf
[2015-09-30T21:07Z] tabix index syn3-10_124438084_135534747-raw-rejectfix.vcf.gz
[2015-09-30T21:07Z] GATK: VariantAnnotator
[2015-09-30T21:07Z] INFO  22:07:51,737 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:07Z] INFO  22:07:51,739 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:07Z] INFO  22:07:51,739 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:07Z] INFO  22:07:51,739 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:07Z] INFO  22:07:51,743 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/10/syn3-10_124438084_135534747-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/10/tx/tmplA2jK7/syn3-10_124438084_135534747-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_124438084_135534747-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:07Z] INFO  22:07:51,748 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:07Z] INFO  22:07:51,749 HelpFormatter - Date/Time: 2015/09/30 22:07:51
[2015-09-30T21:07Z] INFO  22:07:51,749 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:07Z] INFO  22:07:51,749 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:07Z] INFO  22:07:51,938 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:07Z] INFO  22:07:52,015 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:07Z] INFO  22:07:52,022 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:07Z] INFO  22:07:52,045 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:07Z] INFO  22:07:52,717 IntervalUtils - Processing 1221 bp from intervals
[2015-09-30T21:07Z] WARN  22:07:52,722 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:07Z] WARN  22:07:52,722 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:07Z] INFO  22:07:52,784 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:07Z] INFO  22:07:52,865 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:07Z] INFO  22:07:52,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:07Z] INFO  22:07:52,866 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:07Z] INFO  22:07:52,866 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:07Z] INFO  22:07:52,960 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:07Z] INFO  22:07:59,223 VariantAnnotator - Processed 1054 loci.
[2015-09-30T21:07Z]
[2015-09-30T21:07Z] INFO  22:07:59,243 ProgressMeter -            done      8994.0     6.0 s      11.8 m       99.9%     6.0 s       0.0 s
[2015-09-30T21:07Z] INFO  22:07:59,243 ProgressMeter - Total runtime 6.38 secs, 0.11 min, 0.00 hours
[2015-09-30T21:07Z] INFO  22:07:59,244 MicroScheduler - 4969 reads were filtered out during the traversal out of approximately 91284 total reads (5.44%)
[2015-09-30T21:07Z] INFO  22:07:59,244 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:07Z] INFO  22:07:59,244 MicroScheduler -   -> 4948 reads (5.42% of total) failing DuplicateReadFilter
[2015-09-30T21:07Z] INFO  22:07:59,245 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:07Z] INFO  22:07:59,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:07Z] INFO  22:07:59,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:07Z] INFO  22:07:59,245 MicroScheduler -   -> 21 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:08Z] INFO  22:08:00,204 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:08Z] Genotyping with varscan: ('11', 0, 31082819) 1_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam
[2015-09-30T21:08Z] samtools mpileup
[2015-09-30T21:08Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:08Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:08Z] 1406431 positions in tumor
[2015-09-30T21:08Z] 1406423 positions shared in normal
[2015-09-30T21:08Z] 1383721 had sufficient coverage for comparison
[2015-09-30T21:08Z] 1381898 were called Reference
[2015-09-30T21:08Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:08Z] 99 were removed by the strand filter
[2015-09-30T21:08Z] 1778 were called Germline
[2015-09-30T21:08Z] 4 were called LOH
[2015-09-30T21:08Z] 29 were called Somatic
[2015-09-30T21:08Z] 12 were called Unknown
[2015-09-30T21:08Z] 0 were called Variant
[2015-09-30T21:08Z] Varscan paired fix
[2015-09-30T21:08Z] Varscan paired fix
[2015-09-30T21:08Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:08Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:08Z] bgzip syn3-10_62267938_93388847-raw.snp.vcf
[2015-09-30T21:08Z] tabix index syn3-10_62267938_93388847-raw.snp.vcf.gz
[2015-09-30T21:08Z] bgzip syn3-10_62267938_93388847-raw.indel.vcf
[2015-09-30T21:08Z] tabix index syn3-10_62267938_93388847-raw.indel.vcf.gz
[2015-09-30T21:08Z] Combine variant files
[2015-09-30T21:08Z] Varscan
[2015-09-30T21:08Z] INFO  22:08:33,980 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:08Z] INFO  22:08:33,982 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:08Z] INFO  22:08:33,983 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:08Z] INFO  22:08:33,983 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:08Z] INFO  22:08:33,986 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/10/tx/tmpO7JJic/tx/tmp0N7vlm/syn3-10_62267938_93388847-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/10/tx/tmpO7JJic/syn3-10_62267938_93388847-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/10/tx/tmpO7JJic/syn3-10_62267938_93388847-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_62267938_93388847-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:08Z] INFO  22:08:33,992 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:08Z] INFO  22:08:33,992 HelpFormatter - Date/Time: 2015/09/30 22:08:33
[2015-09-30T21:08Z] INFO  22:08:33,993 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:08Z] INFO  22:08:33,993 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:08Z] INFO  22:08:34,080 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:08Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpnyv7Dx/syn3-10_93389481_124436664-raw-normal.mpileup
[2015-09-30T21:08Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/10/tx/tmpnyv7Dx/syn3-10_93389481_124436664-raw-tumor.mpileup
[2015-09-30T21:08Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:08Z] Min reads2:	2
[2015-09-30T21:08Z] Min strands2:	1
[2015-09-30T21:08Z] Min var freq:	0.1
[2015-09-30T21:08Z] Min freq for hom:	0.75
[2015-09-30T21:08Z] Normal purity:	1.0
[2015-09-30T21:08Z] Tumor purity:	1.0
[2015-09-30T21:08Z] Min avg qual:	15
[2015-09-30T21:08Z] P-value thresh:	0.98
[2015-09-30T21:08Z] Somatic p-value:	0.05
[2015-09-30T21:08Z] INFO  22:08:34,229 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:08Z] INFO  22:08:34,354 IntervalUtils - Processing 1412566 bp from intervals
[2015-09-30T21:08Z] WARN  22:08:34,355 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:08Z] WARN  22:08:34,355 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:08Z] INFO  22:08:34,413 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:08Z] INFO  22:08:34,416 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:08Z] INFO  22:08:34,417 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:08Z] INFO  22:08:34,417 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:08Z] INFO  22:08:34,417 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:08Z] INFO  22:08:36,199 ProgressMeter -            done      2004.0     1.0 s      14.8 m       98.9%     1.0 s       0.0 s
[2015-09-30T21:08Z] INFO  22:08:36,200 ProgressMeter - Total runtime 1.78 secs, 0.03 min, 0.00 hours
[2015-09-30T21:08Z] bgzip syn3-10_62267938_93388847-raw.vcf
[2015-09-30T21:08Z] tabix index syn3-10_62267938_93388847-raw.vcf.gz
[2015-09-30T21:08Z] bgzip syn3-10_62267938_93388847-raw-rejectfix.vcf
[2015-09-30T21:08Z] tabix index syn3-10_62267938_93388847-raw-rejectfix.vcf.gz
[2015-09-30T21:08Z] GATK: VariantAnnotator
[2015-09-30T21:08Z] INFO  22:08:38,960 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:08Z] INFO  22:08:38,962 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:08Z] INFO  22:08:38,962 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:08Z] INFO  22:08:38,962 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:08Z] INFO  22:08:38,966 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/10/syn3-10_62267938_93388847-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/10/tx/tmpNZe280/syn3-10_62267938_93388847-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_62267938_93388847-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:08Z] INFO  22:08:38,976 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:08Z] INFO  22:08:38,976 HelpFormatter - Date/Time: 2015/09/30 22:08:38
[2015-09-30T21:08Z] INFO  22:08:38,976 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:08Z] INFO  22:08:38,977 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:08Z] INFO  22:08:39,340 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:08Z] INFO  22:08:39,416 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:08Z] INFO  22:08:39,423 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:08Z] INFO  22:08:39,445 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:08Z] INFO  22:08:39,881 IntervalUtils - Processing 2004 bp from intervals
[2015-09-30T21:08Z] WARN  22:08:39,885 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:08Z] WARN  22:08:39,885 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:08Z] INFO  22:08:39,939 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:08Z] INFO  22:08:40,105 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:08Z] INFO  22:08:40,105 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:08Z] INFO  22:08:40,106 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:08Z] INFO  22:08:40,106 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:08Z] INFO  22:08:40,138 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:08Z] INFO  22:08:49,122 VariantAnnotator - Processed 1717 loci.
[2015-09-30T21:08Z]
[2015-09-30T21:08Z] INFO  22:08:49,144 ProgressMeter -            done      7943.0     9.0 s      19.0 m       99.9%     9.0 s       0.0 s
[2015-09-30T21:08Z] INFO  22:08:49,144 ProgressMeter - Total runtime 9.04 secs, 0.15 min, 0.00 hours
[2015-09-30T21:08Z] INFO  22:08:49,144 MicroScheduler - 7123 reads were filtered out during the traversal out of approximately 148690 total reads (4.79%)
[2015-09-30T21:08Z] INFO  22:08:49,145 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:08Z] INFO  22:08:49,145 MicroScheduler -   -> 7081 reads (4.76% of total) failing DuplicateReadFilter
[2015-09-30T21:08Z] INFO  22:08:49,145 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:08Z] INFO  22:08:49,145 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:08Z] INFO  22:08:49,146 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:08Z] INFO  22:08:49,146 MicroScheduler -   -> 42 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:08Z] INFO  22:08:50,152 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:08Z] Genotyping with varscan: ('11', 31085657, 62105890) 1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam
[2015-09-30T21:08Z] samtools mpileup
[2015-09-30T21:08Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:08Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:09Z] samtools mpileup
[2015-09-30T21:09Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:09Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:09Z] samtools mpileup
[2015-09-30T21:09Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:09Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:09Z] 2049076 positions in tumor
[2015-09-30T21:09Z] 2049064 positions shared in normal
[2015-09-30T21:09Z] 2019944 had sufficient coverage for comparison
[2015-09-30T21:09Z] 2017563 were called Reference
[2015-09-30T21:09Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:09Z] 119 were removed by the strand filter
[2015-09-30T21:09Z] 2299 were called Germline
[2015-09-30T21:09Z] 6 were called LOH
[2015-09-30T21:09Z] 58 were called Somatic
[2015-09-30T21:09Z] 18 were called Unknown
[2015-09-30T21:09Z] 0 were called Variant
[2015-09-30T21:09Z] Varscan paired fix
[2015-09-30T21:09Z] Varscan paired fix
[2015-09-30T21:09Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:09Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:09Z] bgzip syn3-10_93389481_124436664-raw.snp.vcf
[2015-09-30T21:09Z] tabix index syn3-10_93389481_124436664-raw.snp.vcf.gz
[2015-09-30T21:09Z] bgzip syn3-10_93389481_124436664-raw.indel.vcf
[2015-09-30T21:09Z] tabix index syn3-10_93389481_124436664-raw.indel.vcf.gz
[2015-09-30T21:09Z] Combine variant files
[2015-09-30T21:09Z] INFO  22:09:57,082 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:09Z] INFO  22:09:57,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:09Z] INFO  22:09:57,084 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:09Z] INFO  22:09:57,085 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:09Z] INFO  22:09:57,088 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/10/tx/tmpnyv7Dx/tx/tmpV2Z9c9/syn3-10_93389481_124436664-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/10/tx/tmpnyv7Dx/syn3-10_93389481_124436664-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/10/tx/tmpnyv7Dx/syn3-10_93389481_124436664-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_93389481_124436664-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:09Z] INFO  22:09:57,093 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:09Z] INFO  22:09:57,093 HelpFormatter - Date/Time: 2015/09/30 22:09:57
[2015-09-30T21:09Z] INFO  22:09:57,094 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:09Z] INFO  22:09:57,094 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:09Z] INFO  22:09:57,166 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:09Z] INFO  22:09:57,519 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:09Z] INFO  22:09:57,661 IntervalUtils - Processing 2054965 bp from intervals
[2015-09-30T21:09Z] WARN  22:09:57,662 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:09Z] WARN  22:09:57,662 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:09Z] INFO  22:09:57,717 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:09Z] INFO  22:09:57,722 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:09Z] INFO  22:09:57,722 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:09Z] INFO  22:09:57,722 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:09Z] INFO  22:09:57,723 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:09Z] INFO  22:09:59,440 ProgressMeter -            done      2788.0     1.0 s      10.3 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:09Z] INFO  22:09:59,441 ProgressMeter - Total runtime 1.72 secs, 0.03 min, 0.00 hours
[2015-09-30T21:09Z] bgzip syn3-10_93389481_124436664-raw.vcf
[2015-09-30T21:09Z] tabix index syn3-10_93389481_124436664-raw.vcf.gz
[2015-09-30T21:10Z] bgzip syn3-10_93389481_124436664-raw-rejectfix.vcf
[2015-09-30T21:10Z] tabix index syn3-10_93389481_124436664-raw-rejectfix.vcf.gz
[2015-09-30T21:10Z] GATK: VariantAnnotator
[2015-09-30T21:10Z] INFO  22:10:02,196 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:10Z] INFO  22:10:02,198 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:10Z] INFO  22:10:02,198 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:10Z] INFO  22:10:02,198 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:10Z] INFO  22:10:02,202 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/10/syn3-10_93389481_124436664-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/10/tx/tmpQ9H4W5/syn3-10_93389481_124436664-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/10/syn3-10_93389481_124436664-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:10Z] INFO  22:10:02,207 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:10Z] INFO  22:10:02,207 HelpFormatter - Date/Time: 2015/09/30 22:10:02
[2015-09-30T21:10Z] INFO  22:10:02,207 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:10Z] INFO  22:10:02,208 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:10Z] INFO  22:10:04,129 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:10Z] INFO  22:10:04,219 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:10Z] INFO  22:10:04,226 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:10Z] INFO  22:10:04,248 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:10Z] INFO  22:10:05,858 IntervalUtils - Processing 2795 bp from intervals
[2015-09-30T21:10Z] WARN  22:10:05,862 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:10Z] WARN  22:10:05,863 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:10Z] INFO  22:10:05,916 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:10Z] INFO  22:10:06,119 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:10Z] INFO  22:10:06,119 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:10Z] INFO  22:10:06,119 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:10Z] INFO  22:10:06,120 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:10Z] INFO  22:10:06,151 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:10Z] INFO  22:10:17,904 VariantAnnotator - Processed 2250 loci.
[2015-09-30T21:10Z]
[2015-09-30T21:10Z] INFO  22:10:17,924 ProgressMeter -            done     12130.0    11.0 s      16.2 m      100.0%    11.0 s       0.0 s
[2015-09-30T21:10Z] INFO  22:10:17,924 ProgressMeter - Total runtime 11.81 secs, 0.20 min, 0.00 hours
[2015-09-30T21:10Z] INFO  22:10:17,925 MicroScheduler - 9200 reads were filtered out during the traversal out of approximately 190936 total reads (4.82%)
[2015-09-30T21:10Z] INFO  22:10:17,925 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:10Z] INFO  22:10:17,925 MicroScheduler -   -> 9148 reads (4.79% of total) failing DuplicateReadFilter
[2015-09-30T21:10Z] INFO  22:10:17,925 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:10Z] INFO  22:10:17,926 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:10Z] INFO  22:10:17,926 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:10Z] INFO  22:10:17,926 MicroScheduler -   -> 52 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:10Z] INFO  22:10:18,884 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:10Z] Genotyping with varscan: ('11', 62123540, 93141822) 1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam
[2015-09-30T21:10Z] samtools mpileup
[2015-09-30T21:10Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:10Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:10Z] Varscan
[2015-09-30T21:10Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmpezPOvM/syn3-11_0_31082819-raw-normal.mpileup
[2015-09-30T21:10Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmpezPOvM/syn3-11_0_31082819-raw-tumor.mpileup
[2015-09-30T21:10Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:10Z] Min reads2:	2
[2015-09-30T21:10Z] Min strands2:	1
[2015-09-30T21:10Z] Min var freq:	0.1
[2015-09-30T21:10Z] Min freq for hom:	0.75
[2015-09-30T21:10Z] Normal purity:	1.0
[2015-09-30T21:10Z] Tumor purity:	1.0
[2015-09-30T21:10Z] Min avg qual:	15
[2015-09-30T21:10Z] P-value thresh:	0.98
[2015-09-30T21:10Z] Somatic p-value:	0.05
[2015-09-30T21:10Z] Varscan
[2015-09-30T21:10Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmp2AgzQH/syn3-11_31085657_62105890-raw-normal.mpileup
[2015-09-30T21:10Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmp2AgzQH/syn3-11_31085657_62105890-raw-tumor.mpileup
[2015-09-30T21:10Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:10Z] Min reads2:	2
[2015-09-30T21:10Z] Min strands2:	1
[2015-09-30T21:10Z] Min var freq:	0.1
[2015-09-30T21:10Z] Min freq for hom:	0.75
[2015-09-30T21:10Z] Normal purity:	1.0
[2015-09-30T21:10Z] Tumor purity:	1.0
[2015-09-30T21:10Z] Min avg qual:	15
[2015-09-30T21:10Z] P-value thresh:	0.98
[2015-09-30T21:10Z] Somatic p-value:	0.05
[2015-09-30T21:11Z] 1945207 positions in tumor
[2015-09-30T21:11Z] 1945189 positions shared in normal
[2015-09-30T21:11Z] 1917422 had sufficient coverage for comparison
[2015-09-30T21:11Z] 1913850 were called Reference
[2015-09-30T21:11Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:11Z] 314 were removed by the strand filter
[2015-09-30T21:11Z] 3476 were called Germline
[2015-09-30T21:11Z] 9 were called LOH
[2015-09-30T21:11Z] 74 were called Somatic
[2015-09-30T21:11Z] 13 were called Unknown
[2015-09-30T21:11Z] 0 were called Variant
[2015-09-30T21:11Z] Varscan paired fix
[2015-09-30T21:11Z] Varscan paired fix
[2015-09-30T21:11Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:11Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:11Z] bgzip syn3-11_0_31082819-raw.snp.vcf
[2015-09-30T21:11Z] tabix index syn3-11_0_31082819-raw.snp.vcf.gz
[2015-09-30T21:11Z] bgzip syn3-11_0_31082819-raw.indel.vcf
[2015-09-30T21:11Z] tabix index syn3-11_0_31082819-raw.indel.vcf.gz
[2015-09-30T21:11Z] Combine variant files
[2015-09-30T21:11Z] INFO  22:11:44,637 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:11Z] INFO  22:11:44,639 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:11Z] INFO  22:11:44,639 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:11Z] INFO  22:11:44,639 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:11Z] INFO  22:11:44,643 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/11/tx/tmpezPOvM/tx/tmpv7EJWh/syn3-11_0_31082819-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/11/tx/tmpezPOvM/syn3-11_0_31082819-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/11/tx/tmpezPOvM/syn3-11_0_31082819-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_0_31082819-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:11Z] INFO  22:11:44,649 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:11Z] INFO  22:11:44,649 HelpFormatter - Date/Time: 2015/09/30 22:11:44
[2015-09-30T21:11Z] INFO  22:11:44,649 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:11Z] INFO  22:11:44,650 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:11Z] INFO  22:11:46,193 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:11Z] INFO  22:11:46,629 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:11Z] INFO  22:11:47,662 IntervalUtils - Processing 1954600 bp from intervals
[2015-09-30T21:11Z] WARN  22:11:47,663 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:11Z] WARN  22:11:47,663 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:11Z] INFO  22:11:47,721 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:11Z] INFO  22:11:47,725 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:11Z] INFO  22:11:47,725 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:11Z] INFO  22:11:47,725 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:11Z] INFO  22:11:47,726 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:11Z] INFO  22:11:49,838 ProgressMeter -            done      3741.0     2.0 s       9.4 m       99.9%     2.0 s       0.0 s
[2015-09-30T21:11Z] INFO  22:11:49,839 ProgressMeter - Total runtime 2.11 secs, 0.04 min, 0.00 hours
[2015-09-30T21:11Z] bgzip syn3-11_0_31082819-raw.vcf
[2015-09-30T21:11Z] tabix index syn3-11_0_31082819-raw.vcf.gz
[2015-09-30T21:11Z] bgzip syn3-11_0_31082819-raw-rejectfix.vcf
[2015-09-30T21:11Z] tabix index syn3-11_0_31082819-raw-rejectfix.vcf.gz
[2015-09-30T21:11Z] GATK: VariantAnnotator
[2015-09-30T21:11Z] 1555241 positions in tumor
[2015-09-30T21:11Z] 1555234 positions shared in normal
[2015-09-30T21:11Z] 1537483 had sufficient coverage for comparison
[2015-09-30T21:11Z] 1535341 were called Reference
[2015-09-30T21:11Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:11Z] 125 were removed by the strand filter
[2015-09-30T21:11Z] 2093 were called Germline
[2015-09-30T21:11Z] 9 were called LOH
[2015-09-30T21:11Z] 35 were called Somatic
[2015-09-30T21:11Z] 5 were called Unknown
[2015-09-30T21:11Z] 0 were called Variant
[2015-09-30T21:11Z] Varscan paired fix
[2015-09-30T21:11Z] Varscan paired fix
[2015-09-30T21:11Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:11Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:11Z] bgzip syn3-11_31085657_62105890-raw.snp.vcf
[2015-09-30T21:11Z] INFO  22:11:52,943 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:11Z] INFO  22:11:52,945 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:11Z] INFO  22:11:52,946 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:11Z] INFO  22:11:52,946 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:11Z] INFO  22:11:52,949 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/11/syn3-11_0_31082819-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/11/tx/tmppifAit/syn3-11_0_31082819-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_0_31082819-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:11Z] INFO  22:11:52,955 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:11Z] INFO  22:11:52,955 HelpFormatter - Date/Time: 2015/09/30 22:11:52
[2015-09-30T21:11Z] INFO  22:11:52,955 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:11Z] INFO  22:11:52,956 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:11Z] tabix index syn3-11_31085657_62105890-raw.snp.vcf.gz
[2015-09-30T21:11Z] INFO  22:11:53,049 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:11Z] bgzip syn3-11_31085657_62105890-raw.indel.vcf
[2015-09-30T21:11Z] tabix index syn3-11_31085657_62105890-raw.indel.vcf.gz
[2015-09-30T21:11Z] INFO  22:11:53,133 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:11Z] INFO  22:11:53,142 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:11Z] INFO  22:11:53,165 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:11Z] Combine variant files
[2015-09-30T21:11Z] INFO  22:11:53,646 IntervalUtils - Processing 3745 bp from intervals
[2015-09-30T21:11Z] WARN  22:11:53,650 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:11Z] WARN  22:11:53,651 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:11Z] INFO  22:11:53,933 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:11Z] INFO  22:11:54,086 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:11Z] INFO  22:11:54,087 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:11Z] INFO  22:11:54,087 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:11Z] INFO  22:11:54,087 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:11Z] INFO  22:11:54,119 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:11Z] INFO  22:11:55,311 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:11Z] INFO  22:11:55,313 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:11Z] INFO  22:11:55,313 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:11Z] INFO  22:11:55,313 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:11Z] INFO  22:11:55,317 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/11/tx/tmp2AgzQH/tx/tmpEkAT0j/syn3-11_31085657_62105890-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/11/tx/tmp2AgzQH/syn3-11_31085657_62105890-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/11/tx/tmp2AgzQH/syn3-11_31085657_62105890-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_31085657_62105890-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:11Z] INFO  22:11:55,322 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:11Z] INFO  22:11:55,322 HelpFormatter - Date/Time: 2015/09/30 22:11:55
[2015-09-30T21:11Z] INFO  22:11:55,323 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:11Z] INFO  22:11:55,323 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:11Z] INFO  22:11:55,404 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:11Z] INFO  22:11:55,539 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:11Z] INFO  22:11:55,662 IntervalUtils - Processing 1559957 bp from intervals
[2015-09-30T21:11Z] WARN  22:11:55,663 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:11Z] WARN  22:11:55,664 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:11Z] INFO  22:11:55,723 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:11Z] INFO  22:11:55,727 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:11Z] INFO  22:11:55,727 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:11Z] INFO  22:11:55,727 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:11Z] INFO  22:11:55,728 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:11Z] INFO  22:11:57,362 ProgressMeter -            done      2291.0     1.0 s      11.9 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:11Z] INFO  22:11:57,362 ProgressMeter - Total runtime 1.64 secs, 0.03 min, 0.00 hours
[2015-09-30T21:11Z] bgzip syn3-11_31085657_62105890-raw.vcf
[2015-09-30T21:11Z] tabix index syn3-11_31085657_62105890-raw.vcf.gz
[2015-09-30T21:11Z] bgzip syn3-11_31085657_62105890-raw-rejectfix.vcf
[2015-09-30T21:11Z] tabix index syn3-11_31085657_62105890-raw-rejectfix.vcf.gz
[2015-09-30T21:11Z] GATK: VariantAnnotator
[2015-09-30T21:12Z] INFO  22:12:00,336 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:12Z] INFO  22:12:00,338 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:12Z] INFO  22:12:00,338 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:12Z] INFO  22:12:00,338 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:12Z] INFO  22:12:00,342 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/11/syn3-11_31085657_62105890-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/11/tx/tmpIkLolF/syn3-11_31085657_62105890-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_31085657_62105890-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:12Z] INFO  22:12:00,347 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:12Z] INFO  22:12:00,347 HelpFormatter - Date/Time: 2015/09/30 22:12:00
[2015-09-30T21:12Z] INFO  22:12:00,348 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:12Z] INFO  22:12:00,348 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:12Z] INFO  22:12:00,767 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:12Z] INFO  22:12:00,843 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:12Z] INFO  22:12:00,851 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:12Z] INFO  22:12:00,873 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:12Z] INFO  22:12:01,287 IntervalUtils - Processing 2293 bp from intervals
[2015-09-30T21:12Z] WARN  22:12:01,291 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:12Z] WARN  22:12:01,291 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:12Z] INFO  22:12:01,347 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:12Z] INFO  22:12:01,528 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:12Z] INFO  22:12:01,528 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:12Z] INFO  22:12:01,529 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:12Z] INFO  22:12:01,529 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:12Z] INFO  22:12:01,562 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:12Z] samtools mpileup
[2015-09-30T21:12Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:12Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:12Z] INFO  22:12:09,335 VariantAnnotator - Processed 3251 loci.
[2015-09-30T21:12Z]
[2015-09-30T21:12Z] INFO  22:12:09,649 ProgressMeter -            done     31385.0    15.0 s       8.3 m      100.0%    15.0 s       0.0 s
[2015-09-30T21:12Z] INFO  22:12:09,650 ProgressMeter - Total runtime 15.56 secs, 0.26 min, 0.00 hours
[2015-09-30T21:12Z] INFO  22:12:09,650 MicroScheduler - 17408 reads were filtered out during the traversal out of approximately 305739 total reads (5.69%)
[2015-09-30T21:12Z] INFO  22:12:09,650 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:12Z] INFO  22:12:09,651 MicroScheduler -   -> 17265 reads (5.65% of total) failing DuplicateReadFilter
[2015-09-30T21:12Z] INFO  22:12:09,651 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:12Z] INFO  22:12:09,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:12Z] INFO  22:12:09,651 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:12Z] INFO  22:12:09,652 MicroScheduler -   -> 143 reads (0.05% of total) failing UnmappedReadFilter
[2015-09-30T21:12Z] INFO  22:12:10,708 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:12Z] Genotyping with varscan: ('11', 93147865, 124180877) 1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam
[2015-09-30T21:12Z] INFO  22:12:12,199 VariantAnnotator - Processed 2012 loci.
[2015-09-30T21:12Z]
[2015-09-30T21:12Z] INFO  22:12:12,306 ProgressMeter -            done     16554.0    10.0 s      10.9 m      100.0%    10.0 s       0.0 s
[2015-09-30T21:12Z] INFO  22:12:12,307 ProgressMeter - Total runtime 10.78 secs, 0.18 min, 0.00 hours
[2015-09-30T21:12Z] INFO  22:12:12,307 MicroScheduler - 7649 reads were filtered out during the traversal out of approximately 160574 total reads (4.76%)
[2015-09-30T21:12Z] INFO  22:12:12,307 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:12Z] INFO  22:12:12,307 MicroScheduler -   -> 7598 reads (4.73% of total) failing DuplicateReadFilter
[2015-09-30T21:12Z] INFO  22:12:12,308 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:12Z] INFO  22:12:12,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:12Z] INFO  22:12:12,308 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:12Z] INFO  22:12:12,308 MicroScheduler -   -> 51 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:12Z] INFO  22:12:13,259 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:12Z] Genotyping with varscan: ('11', 124188917, 135006516) 1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam
[2015-09-30T21:12Z] samtools mpileup
[2015-09-30T21:12Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:12Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:12Z] samtools mpileup
[2015-09-30T21:12Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:12Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:12Z] samtools mpileup
[2015-09-30T21:12Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:12Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:12Z] Varscan
[2015-09-30T21:12Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmpltEu9x/syn3-11_124188917_135006516-raw-normal.mpileup
[2015-09-30T21:12Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmpltEu9x/syn3-11_124188917_135006516-raw-tumor.mpileup
[2015-09-30T21:12Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:12Z] Min reads2:	2
[2015-09-30T21:12Z] Min strands2:	1
[2015-09-30T21:12Z] Min var freq:	0.1
[2015-09-30T21:12Z] Min freq for hom:	0.75
[2015-09-30T21:12Z] Normal purity:	1.0
[2015-09-30T21:12Z] Tumor purity:	1.0
[2015-09-30T21:12Z] Min avg qual:	15
[2015-09-30T21:12Z] P-value thresh:	0.98
[2015-09-30T21:12Z] Somatic p-value:	0.05
[2015-09-30T21:13Z] samtools mpileup
[2015-09-30T21:13Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:13Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:13Z] 489282 positions in tumor
[2015-09-30T21:13Z] 489281 positions shared in normal
[2015-09-30T21:13Z] 486124 had sufficient coverage for comparison
[2015-09-30T21:13Z] 485463 were called Reference
[2015-09-30T21:13Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:13Z] 25 were removed by the strand filter
[2015-09-30T21:13Z] 645 were called Germline
[2015-09-30T21:13Z] 2 were called LOH
[2015-09-30T21:13Z] 10 were called Somatic
[2015-09-30T21:13Z] 4 were called Unknown
[2015-09-30T21:13Z] 0 were called Variant
[2015-09-30T21:13Z] Varscan paired fix
[2015-09-30T21:13Z] Varscan paired fix
[2015-09-30T21:13Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:13Z] bgzip syn3-11_124188917_135006516-raw.snp.vcf
[2015-09-30T21:13Z] tabix index syn3-11_124188917_135006516-raw.snp.vcf.gz
[2015-09-30T21:13Z] bgzip syn3-11_124188917_135006516-raw.indel.vcf
[2015-09-30T21:13Z] tabix index syn3-11_124188917_135006516-raw.indel.vcf.gz
[2015-09-30T21:13Z] Combine variant files
[2015-09-30T21:13Z] INFO  22:13:16,162 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:13Z] INFO  22:13:16,164 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:13Z] INFO  22:13:16,164 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:13Z] INFO  22:13:16,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:13Z] INFO  22:13:16,168 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/11/tx/tmpltEu9x/tx/tmplqiLqk/syn3-11_124188917_135006516-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/11/tx/tmpltEu9x/syn3-11_124188917_135006516-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/11/tx/tmpltEu9x/syn3-11_124188917_135006516-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_124188917_135006516-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:13Z] INFO  22:13:16,174 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:13Z] INFO  22:13:16,174 HelpFormatter - Date/Time: 2015/09/30 22:13:16
[2015-09-30T21:13Z] INFO  22:13:16,174 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:13Z] INFO  22:13:16,175 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:13Z] INFO  22:13:16,249 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:13Z] INFO  22:13:16,640 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:13Z] INFO  22:13:16,741 IntervalUtils - Processing 489980 bp from intervals
[2015-09-30T21:13Z] WARN  22:13:16,742 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:13Z] WARN  22:13:16,742 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:13Z] INFO  22:13:16,801 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:13Z] INFO  22:13:16,803 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:13Z] INFO  22:13:16,803 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:13Z] INFO  22:13:16,803 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:13Z] INFO  22:13:16,804 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:13Z] INFO  22:13:17,663 ProgressMeter -            done       737.0     0.0 s      19.4 m       99.8%     0.0 s       0.0 s
[2015-09-30T21:13Z] INFO  22:13:17,664 ProgressMeter - Total runtime 0.86 secs, 0.01 min, 0.00 hours
[2015-09-30T21:13Z] bgzip syn3-11_124188917_135006516-raw.vcf
[2015-09-30T21:13Z] tabix index syn3-11_124188917_135006516-raw.vcf.gz
[2015-09-30T21:13Z] bgzip syn3-11_124188917_135006516-raw-rejectfix.vcf
[2015-09-30T21:13Z] tabix index syn3-11_124188917_135006516-raw-rejectfix.vcf.gz
[2015-09-30T21:13Z] GATK: VariantAnnotator
[2015-09-30T21:13Z] INFO  22:13:20,829 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:13Z] INFO  22:13:20,831 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:13Z] INFO  22:13:20,831 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:13Z] INFO  22:13:20,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:13Z] INFO  22:13:20,835 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/11/syn3-11_124188917_135006516-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/11/tx/tmpwxlNJH/syn3-11_124188917_135006516-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_124188917_135006516-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:13Z] INFO  22:13:20,840 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:13Z] INFO  22:13:20,840 HelpFormatter - Date/Time: 2015/09/30 22:13:20
[2015-09-30T21:13Z] INFO  22:13:20,841 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:13Z] INFO  22:13:20,841 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:13Z] INFO  22:13:20,934 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:13Z] INFO  22:13:21,011 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:13Z] INFO  22:13:21,019 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:13Z] INFO  22:13:21,042 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:13Z] INFO  22:13:21,391 IntervalUtils - Processing 737 bp from intervals
[2015-09-30T21:13Z] WARN  22:13:21,395 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:13Z] WARN  22:13:21,395 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:13Z] INFO  22:13:21,477 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:13Z] INFO  22:13:21,556 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:13Z] INFO  22:13:21,557 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:13Z] INFO  22:13:21,557 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:13Z] INFO  22:13:21,558 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:13Z] INFO  22:13:21,591 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:13Z] INFO  22:13:25,988 VariantAnnotator - Processed 633 loci.
[2015-09-30T21:13Z]
[2015-09-30T21:13Z] INFO  22:13:26,011 ProgressMeter -            done      3578.0     4.0 s      20.7 m       99.9%     4.0 s       0.0 s
[2015-09-30T21:13Z] INFO  22:13:26,011 ProgressMeter - Total runtime 4.45 secs, 0.07 min, 0.00 hours
[2015-09-30T21:13Z] INFO  22:13:26,011 MicroScheduler - 2755 reads were filtered out during the traversal out of approximately 54740 total reads (5.03%)
[2015-09-30T21:13Z] INFO  22:13:26,012 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:13Z] INFO  22:13:26,012 MicroScheduler -   -> 2736 reads (5.00% of total) failing DuplicateReadFilter
[2015-09-30T21:13Z] INFO  22:13:26,012 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:13Z] INFO  22:13:26,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:13Z] INFO  22:13:26,013 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:13Z] INFO  22:13:26,013 MicroScheduler -   -> 19 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:13Z] INFO  22:13:26,983 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:13Z] Genotyping with varscan: ('12', 0, 31107241) 1_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam
[2015-09-30T21:13Z] samtools mpileup
[2015-09-30T21:13Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:13Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:13Z] Varscan
[2015-09-30T21:13Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmpBd1a0D/syn3-11_62123540_93141822-raw-normal.mpileup
[2015-09-30T21:13Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmpBd1a0D/syn3-11_62123540_93141822-raw-tumor.mpileup
[2015-09-30T21:13Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:13Z] Min reads2:	2
[2015-09-30T21:13Z] Min strands2:	1
[2015-09-30T21:13Z] Min var freq:	0.1
[2015-09-30T21:13Z] Min freq for hom:	0.75
[2015-09-30T21:13Z] Normal purity:	1.0
[2015-09-30T21:13Z] Tumor purity:	1.0
[2015-09-30T21:13Z] Min avg qual:	15
[2015-09-30T21:13Z] P-value thresh:	0.98
[2015-09-30T21:13Z] Somatic p-value:	0.05
[2015-09-30T21:14Z] Varscan
[2015-09-30T21:14Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmpXgHoCp/syn3-11_93147865_124180877-raw-normal.mpileup
[2015-09-30T21:14Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/11/tx/tmpXgHoCp/syn3-11_93147865_124180877-raw-tumor.mpileup
[2015-09-30T21:14Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:14Z] Min reads2:	2
[2015-09-30T21:14Z] Min strands2:	1
[2015-09-30T21:14Z] Min var freq:	0.1
[2015-09-30T21:14Z] Min freq for hom:	0.75
[2015-09-30T21:14Z] Normal purity:	1.0
[2015-09-30T21:14Z] Tumor purity:	1.0
[2015-09-30T21:14Z] Min avg qual:	15
[2015-09-30T21:14Z] P-value thresh:	0.98
[2015-09-30T21:14Z] Somatic p-value:	0.05
[2015-09-30T21:14Z] samtools mpileup
[2015-09-30T21:14Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:14Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:15Z] 1641958 positions in tumor
[2015-09-30T21:15Z] 1641949 positions shared in normal
[2015-09-30T21:15Z] 1605690 had sufficient coverage for comparison
[2015-09-30T21:15Z] 1603746 were called Reference
[2015-09-30T21:15Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:15Z] 78 were removed by the strand filter
[2015-09-30T21:15Z] 1890 were called Germline
[2015-09-30T21:15Z] 6 were called LOH
[2015-09-30T21:15Z] 39 were called Somatic
[2015-09-30T21:15Z] 9 were called Unknown
[2015-09-30T21:15Z] 0 were called Variant
[2015-09-30T21:15Z] Varscan paired fix
[2015-09-30T21:15Z] Varscan paired fix
[2015-09-30T21:15Z] 2328503 positions in tumor
[2015-09-30T21:15Z] 2328493 positions shared in normal
[2015-09-30T21:15Z] 2302346 had sufficient coverage for comparison
[2015-09-30T21:15Z] 2299846 were called Reference
[2015-09-30T21:15Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:15Z] 142 were removed by the strand filter
[2015-09-30T21:15Z] 2421 were called Germline
[2015-09-30T21:15Z] 4 were called LOH
[2015-09-30T21:15Z] 50 were called Somatic
[2015-09-30T21:15Z] 25 were called Unknown
[2015-09-30T21:15Z] 0 were called Variant
[2015-09-30T21:15Z] Varscan paired fix
[2015-09-30T21:15Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:15Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:15Z] bgzip syn3-11_93147865_124180877-raw.snp.vcf
[2015-09-30T21:15Z] Varscan paired fix
[2015-09-30T21:15Z] tabix index syn3-11_93147865_124180877-raw.snp.vcf.gz
[2015-09-30T21:15Z] bgzip syn3-11_93147865_124180877-raw.indel.vcf
[2015-09-30T21:15Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:15Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:15Z] tabix index syn3-11_93147865_124180877-raw.indel.vcf.gz
[2015-09-30T21:15Z] bgzip syn3-11_62123540_93141822-raw.snp.vcf
[2015-09-30T21:15Z] tabix index syn3-11_62123540_93141822-raw.snp.vcf.gz
[2015-09-30T21:15Z] bgzip syn3-11_62123540_93141822-raw.indel.vcf
[2015-09-30T21:15Z] Combine variant files
[2015-09-30T21:15Z] tabix index syn3-11_62123540_93141822-raw.indel.vcf.gz
[2015-09-30T21:15Z] Combine variant files
[2015-09-30T21:15Z] INFO  22:15:20,143 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:20,145 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:15Z] INFO  22:15:20,145 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:15Z] INFO  22:15:20,145 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:15Z] INFO  22:15:20,149 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/11/tx/tmpXgHoCp/tx/tmpq5eVxw/syn3-11_93147865_124180877-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/11/tx/tmpXgHoCp/syn3-11_93147865_124180877-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/11/tx/tmpXgHoCp/syn3-11_93147865_124180877-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_93147865_124180877-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:15Z] INFO  22:15:20,155 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:15Z] INFO  22:15:20,155 HelpFormatter - Date/Time: 2015/09/30 22:15:20
[2015-09-30T21:15Z] INFO  22:15:20,155 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:20,155 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:20,233 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:15Z] INFO  22:15:20,329 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:20,331 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:15Z] INFO  22:15:20,331 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:15Z] INFO  22:15:20,331 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:15Z] INFO  22:15:20,335 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/11/tx/tmpBd1a0D/tx/tmpJ3wtdu/syn3-11_62123540_93141822-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/11/tx/tmpBd1a0D/syn3-11_62123540_93141822-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/11/tx/tmpBd1a0D/syn3-11_62123540_93141822-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_62123540_93141822-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:15Z] INFO  22:15:20,340 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:15Z] INFO  22:15:20,340 HelpFormatter - Date/Time: 2015/09/30 22:15:20
[2015-09-30T21:15Z] INFO  22:15:20,341 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:20,341 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:20,371 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:15Z] INFO  22:15:20,421 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:15Z] INFO  22:15:20,509 IntervalUtils - Processing 1648208 bp from intervals
[2015-09-30T21:15Z] WARN  22:15:20,510 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:15Z] WARN  22:15:20,510 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:15Z] INFO  22:15:20,569 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:15Z] INFO  22:15:20,573 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:15Z] INFO  22:15:20,573 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:15Z] INFO  22:15:20,574 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:15Z] INFO  22:15:20,574 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:15Z] INFO  22:15:20,713 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:15Z] INFO  22:15:20,859 IntervalUtils - Processing 2336441 bp from intervals
[2015-09-30T21:15Z] WARN  22:15:20,861 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:15Z] WARN  22:15:20,861 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:15Z] INFO  22:15:20,921 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:15Z] INFO  22:15:20,926 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:15Z] INFO  22:15:20,926 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:15Z] INFO  22:15:20,926 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:15Z] INFO  22:15:20,927 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:15Z] INFO  22:15:22,176 ProgressMeter -            done      2211.0     1.0 s      12.1 m       99.7%     1.0 s       0.0 s
[2015-09-30T21:15Z] INFO  22:15:22,177 ProgressMeter - Total runtime 1.60 secs, 0.03 min, 0.00 hours
[2015-09-30T21:15Z] bgzip syn3-11_93147865_124180877-raw.vcf
[2015-09-30T21:15Z] tabix index syn3-11_93147865_124180877-raw.vcf.gz
[2015-09-30T21:15Z] INFO  22:15:22,659 ProgressMeter -            done      2716.0     1.0 s      10.6 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:15Z] INFO  22:15:22,660 ProgressMeter - Total runtime 1.73 secs, 0.03 min, 0.00 hours
[2015-09-30T21:15Z] bgzip syn3-11_93147865_124180877-raw-rejectfix.vcf
[2015-09-30T21:15Z] bgzip syn3-11_62123540_93141822-raw.vcf
[2015-09-30T21:15Z] tabix index syn3-11_93147865_124180877-raw-rejectfix.vcf.gz
[2015-09-30T21:15Z] tabix index syn3-11_62123540_93141822-raw.vcf.gz
[2015-09-30T21:15Z] GATK: VariantAnnotator
[2015-09-30T21:15Z] bgzip syn3-11_62123540_93141822-raw-rejectfix.vcf
[2015-09-30T21:15Z] tabix index syn3-11_62123540_93141822-raw-rejectfix.vcf.gz
[2015-09-30T21:15Z] GATK: VariantAnnotator
[2015-09-30T21:15Z] INFO  22:15:25,367 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:25,369 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:15Z] INFO  22:15:25,369 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:15Z] INFO  22:15:25,369 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:15Z] INFO  22:15:25,373 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/11/syn3-11_93147865_124180877-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/11/tx/tmpOaXi0U/syn3-11_93147865_124180877-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_93147865_124180877-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:15Z] INFO  22:15:25,378 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:15Z] INFO  22:15:25,379 HelpFormatter - Date/Time: 2015/09/30 22:15:25
[2015-09-30T21:15Z] INFO  22:15:25,379 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:25,379 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:25,969 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:15Z] INFO  22:15:26,045 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:15Z] INFO  22:15:26,053 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:15Z] INFO  22:15:26,075 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:15Z] INFO  22:15:26,498 IntervalUtils - Processing 2211 bp from intervals
[2015-09-30T21:15Z] WARN  22:15:26,502 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:15Z] WARN  22:15:26,502 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:15Z] INFO  22:15:26,560 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:15Z] INFO  22:15:26,631 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:26,633 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:15Z] INFO  22:15:26,633 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:15Z] INFO  22:15:26,634 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:15Z] INFO  22:15:26,637 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/11/syn3-11_62123540_93141822-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/11/tx/tmpXsp27w/syn3-11_62123540_93141822-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/11/syn3-11_62123540_93141822-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:15Z] INFO  22:15:26,643 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:15Z] INFO  22:15:26,643 HelpFormatter - Date/Time: 2015/09/30 22:15:26
[2015-09-30T21:15Z] INFO  22:15:26,643 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:26,643 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:15Z] INFO  22:15:26,716 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:15Z] INFO  22:15:26,798 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:15Z] INFO  22:15:26,803 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:15Z] INFO  22:15:26,804 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:15Z] INFO  22:15:26,804 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:15Z] INFO  22:15:26,805 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:15Z] INFO  22:15:26,805 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:15Z] INFO  22:15:26,836 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T21:15Z] INFO  22:15:26,837 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:15Z] Varscan
[2015-09-30T21:15Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmpVtij51/syn3-12_0_31107241-raw-normal.mpileup
[2015-09-30T21:15Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmpVtij51/syn3-12_0_31107241-raw-tumor.mpileup
[2015-09-30T21:15Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:15Z] Min reads2:	2
[2015-09-30T21:15Z] Min strands2:	1
[2015-09-30T21:15Z] Min var freq:	0.1
[2015-09-30T21:15Z] Min freq for hom:	0.75
[2015-09-30T21:15Z] Normal purity:	1.0
[2015-09-30T21:15Z] Tumor purity:	1.0
[2015-09-30T21:15Z] Min avg qual:	15
[2015-09-30T21:15Z] P-value thresh:	0.98
[2015-09-30T21:15Z] Somatic p-value:	0.05
[2015-09-30T21:15Z] INFO  22:15:27,392 IntervalUtils - Processing 2722 bp from intervals
[2015-09-30T21:15Z] WARN  22:15:27,396 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:15Z] WARN  22:15:27,396 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:15Z] INFO  22:15:27,522 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:15Z] INFO  22:15:27,682 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:15Z] INFO  22:15:27,682 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:15Z] INFO  22:15:27,683 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:15Z] INFO  22:15:27,683 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:15Z] INFO  22:15:27,715 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:15Z] INFO  22:15:38,139 VariantAnnotator - Processed 1859 loci.
[2015-09-30T21:15Z]
[2015-09-30T21:15Z] INFO  22:15:38,170 ProgressMeter -            done      8710.0    11.0 s      21.7 m      100.0%    11.0 s       0.0 s
[2015-09-30T21:15Z] INFO  22:15:38,171 ProgressMeter - Total runtime 11.37 secs, 0.19 min, 0.00 hours
[2015-09-30T21:15Z] INFO  22:15:38,171 MicroScheduler - 7192 reads were filtered out during the traversal out of approximately 151297 total reads (4.75%)
[2015-09-30T21:15Z] INFO  22:15:38,171 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:15Z] INFO  22:15:38,172 MicroScheduler -   -> 7149 reads (4.73% of total) failing DuplicateReadFilter
[2015-09-30T21:15Z] INFO  22:15:38,172 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:15Z] INFO  22:15:38,172 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:15Z] INFO  22:15:38,172 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:15Z] INFO  22:15:38,172 MicroScheduler -   -> 43 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:15Z] INFO  22:15:39,114 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:15Z] Genotyping with varscan: ('12', 31116488, 62142833) 1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam
[2015-09-30T21:15Z] samtools mpileup
[2015-09-30T21:15Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:15Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:15Z] INFO  22:15:41,366 VariantAnnotator - Processed 2346 loci.
[2015-09-30T21:15Z]
[2015-09-30T21:15Z] INFO  22:15:41,389 ProgressMeter -            done     13532.0    13.0 s      16.9 m      100.0%    13.0 s       0.0 s
[2015-09-30T21:15Z] INFO  22:15:41,390 ProgressMeter - Total runtime 13.71 secs, 0.23 min, 0.00 hours
[2015-09-30T21:15Z] INFO  22:15:41,390 MicroScheduler - 11797 reads were filtered out during the traversal out of approximately 225409 total reads (5.23%)
[2015-09-30T21:15Z] INFO  22:15:41,390 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:15Z] INFO  22:15:41,390 MicroScheduler -   -> 11757 reads (5.22% of total) failing DuplicateReadFilter
[2015-09-30T21:15Z] INFO  22:15:41,391 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:15Z] INFO  22:15:41,391 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:15Z] INFO  22:15:41,391 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:15Z] INFO  22:15:41,391 MicroScheduler -   -> 40 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:15Z] INFO  22:15:42,325 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:15Z] Genotyping with varscan: ('12', 62147092, 93167456) 1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam
[2015-09-30T21:15Z] samtools mpileup
[2015-09-30T21:15Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:15Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:16Z] samtools mpileup
[2015-09-30T21:16Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:16Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:16Z] Varscan
[2015-09-30T21:16Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmpHxSMBx/syn3-12_62147092_93167456-raw-normal.mpileup
[2015-09-30T21:16Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmpHxSMBx/syn3-12_62147092_93167456-raw-tumor.mpileup
[2015-09-30T21:16Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:16Z] Min reads2:	2
[2015-09-30T21:16Z] Min strands2:	1
[2015-09-30T21:16Z] Min var freq:	0.1
[2015-09-30T21:16Z] Min freq for hom:	0.75
[2015-09-30T21:16Z] Normal purity:	1.0
[2015-09-30T21:16Z] Tumor purity:	1.0
[2015-09-30T21:16Z] Min avg qual:	15
[2015-09-30T21:16Z] P-value thresh:	0.98
[2015-09-30T21:16Z] Somatic p-value:	0.05
[2015-09-30T21:16Z] 1902848 positions in tumor
[2015-09-30T21:16Z] 1902837 positions shared in normal
[2015-09-30T21:16Z] 1857118 had sufficient coverage for comparison
[2015-09-30T21:16Z] 1853849 were called Reference
[2015-09-30T21:16Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:16Z] 225 were removed by the strand filter
[2015-09-30T21:16Z] 3178 were called Germline
[2015-09-30T21:16Z] 11 were called LOH
[2015-09-30T21:16Z] 60 were called Somatic
[2015-09-30T21:16Z] 20 were called Unknown
[2015-09-30T21:16Z] 0 were called Variant
[2015-09-30T21:16Z] Varscan paired fix
[2015-09-30T21:16Z] Varscan paired fix
[2015-09-30T21:16Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:16Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:16Z] bgzip syn3-12_0_31107241-raw.snp.vcf
[2015-09-30T21:16Z] tabix index syn3-12_0_31107241-raw.snp.vcf.gz
[2015-09-30T21:16Z] bgzip syn3-12_0_31107241-raw.indel.vcf
[2015-09-30T21:16Z] tabix index syn3-12_0_31107241-raw.indel.vcf.gz
[2015-09-30T21:16Z] Combine variant files
[2015-09-30T21:16Z] INFO  22:16:45,150 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:16Z] INFO  22:16:45,152 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:16Z] INFO  22:16:45,152 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:16Z] INFO  22:16:45,153 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:16Z] INFO  22:16:45,156 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/12/tx/tmpVtij51/tx/tmpAeBNYc/syn3-12_0_31107241-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/12/tx/tmpVtij51/syn3-12_0_31107241-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/12/tx/tmpVtij51/syn3-12_0_31107241-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_0_31107241-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:16Z] INFO  22:16:45,162 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:16Z] INFO  22:16:45,162 HelpFormatter - Date/Time: 2015/09/30 22:16:45
[2015-09-30T21:16Z] INFO  22:16:45,162 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:16Z] INFO  22:16:45,163 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:16Z] INFO  22:16:45,238 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:16Z] INFO  22:16:45,378 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:16Z] INFO  22:16:45,507 IntervalUtils - Processing 1912448 bp from intervals
[2015-09-30T21:16Z] WARN  22:16:45,508 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:16Z] WARN  22:16:45,508 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:16Z] INFO  22:16:45,567 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:16Z] INFO  22:16:45,571 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:16Z] INFO  22:16:45,571 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:16Z] INFO  22:16:45,572 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:16Z] INFO  22:16:45,572 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:16Z] INFO  22:16:47,462 ProgressMeter -            done      3575.0     1.0 s       8.8 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:16Z] INFO  22:16:47,462 ProgressMeter - Total runtime 1.89 secs, 0.03 min, 0.00 hours
[2015-09-30T21:16Z] bgzip syn3-12_0_31107241-raw.vcf
[2015-09-30T21:16Z] tabix index syn3-12_0_31107241-raw.vcf.gz
[2015-09-30T21:16Z] bgzip syn3-12_0_31107241-raw-rejectfix.vcf
[2015-09-30T21:16Z] tabix index syn3-12_0_31107241-raw-rejectfix.vcf.gz
[2015-09-30T21:16Z] GATK: VariantAnnotator
[2015-09-30T21:16Z] INFO  22:16:50,663 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:16Z] INFO  22:16:50,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:16Z] INFO  22:16:50,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:16Z] INFO  22:16:50,665 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:16Z] INFO  22:16:50,669 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/12/syn3-12_0_31107241-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/12/tx/tmpgjFHH3/syn3-12_0_31107241-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_0_31107241-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:16Z] INFO  22:16:50,674 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:16Z] INFO  22:16:50,675 HelpFormatter - Date/Time: 2015/09/30 22:16:50
[2015-09-30T21:16Z] INFO  22:16:50,675 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:16Z] INFO  22:16:50,675 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:16Z] INFO  22:16:50,774 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:16Z] INFO  22:16:50,887 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:16Z] INFO  22:16:50,895 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:16Z] INFO  22:16:50,925 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T21:16Z] INFO  22:16:51,404 IntervalUtils - Processing 3575 bp from intervals
[2015-09-30T21:16Z] WARN  22:16:51,409 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:16Z] WARN  22:16:51,473 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:16Z] INFO  22:16:51,529 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:16Z] INFO  22:16:51,663 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:16Z] INFO  22:16:51,663 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:16Z] INFO  22:16:51,664 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:16Z] INFO  22:16:51,664 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:16Z] INFO  22:16:51,695 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:17Z] samtools mpileup
[2015-09-30T21:17Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:17Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:17Z] INFO  22:17:05,077 VariantAnnotator - Processed 3031 loci.
[2015-09-30T21:17Z]
[2015-09-30T21:17Z] INFO  22:17:05,109 ProgressMeter -            done     23334.0    13.0 s       9.6 m      100.0%    13.0 s       0.0 s
[2015-09-30T21:17Z] INFO  22:17:05,109 ProgressMeter - Total runtime 13.45 secs, 0.22 min, 0.00 hours
[2015-09-30T21:17Z] INFO  22:17:05,109 MicroScheduler - 10658 reads were filtered out during the traversal out of approximately 230182 total reads (4.63%)
[2015-09-30T21:17Z] INFO  22:17:05,110 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:17Z] INFO  22:17:05,110 MicroScheduler -   -> 10596 reads (4.60% of total) failing DuplicateReadFilter
[2015-09-30T21:17Z] INFO  22:17:05,110 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:17Z] INFO  22:17:05,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:17Z] INFO  22:17:05,110 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:17Z] INFO  22:17:05,111 MicroScheduler -   -> 62 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:17Z] INFO  22:17:06,039 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:17Z] Genotyping with varscan: ('12', 93169109, 124189486) 1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam
[2015-09-30T21:17Z] samtools mpileup
[2015-09-30T21:17Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:17Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:17Z] 980588 positions in tumor
[2015-09-30T21:17Z] 980576 positions shared in normal
[2015-09-30T21:17Z] 925999 had sufficient coverage for comparison
[2015-09-30T21:17Z] 925043 were called Reference
[2015-09-30T21:17Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:17Z] 66 were removed by the strand filter
[2015-09-30T21:17Z] 903 were called Germline
[2015-09-30T21:17Z] 5 were called LOH
[2015-09-30T21:17Z] 32 were called Somatic
[2015-09-30T21:17Z] 16 were called Unknown
[2015-09-30T21:17Z] 0 were called Variant
[2015-09-30T21:17Z] Varscan paired fix
[2015-09-30T21:17Z] Varscan paired fix
[2015-09-30T21:17Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:17Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:17Z] bgzip syn3-12_62147092_93167456-raw.snp.vcf
[2015-09-30T21:17Z] tabix index syn3-12_62147092_93167456-raw.snp.vcf.gz
[2015-09-30T21:17Z] bgzip syn3-12_62147092_93167456-raw.indel.vcf
[2015-09-30T21:17Z] tabix index syn3-12_62147092_93167456-raw.indel.vcf.gz
[2015-09-30T21:17Z] Combine variant files
[2015-09-30T21:17Z] INFO  22:17:11,847 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:17Z] INFO  22:17:11,849 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:17Z] INFO  22:17:11,849 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:17Z] INFO  22:17:11,849 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:17Z] INFO  22:17:11,853 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/12/tx/tmpHxSMBx/tx/tmpL4yZBe/syn3-12_62147092_93167456-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/12/tx/tmpHxSMBx/syn3-12_62147092_93167456-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/12/tx/tmpHxSMBx/syn3-12_62147092_93167456-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_62147092_93167456-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:17Z] INFO  22:17:11,858 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:17Z] INFO  22:17:11,859 HelpFormatter - Date/Time: 2015/09/30 22:17:11
[2015-09-30T21:17Z] INFO  22:17:11,859 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:17Z] INFO  22:17:11,859 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:17Z] INFO  22:17:11,934 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:17Z] INFO  22:17:12,073 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:17Z] INFO  22:17:12,185 IntervalUtils - Processing 991077 bp from intervals
[2015-09-30T21:17Z] WARN  22:17:12,185 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:17Z] WARN  22:17:12,186 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:17Z] INFO  22:17:12,240 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:17Z] INFO  22:17:12,243 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:17Z] INFO  22:17:12,243 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:17Z] INFO  22:17:12,244 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:17Z] INFO  22:17:12,244 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:17Z] INFO  22:17:15,526 ProgressMeter -            done      1064.0     3.0 s      51.4 m      100.0%     3.0 s       0.0 s
[2015-09-30T21:17Z] INFO  22:17:15,526 ProgressMeter - Total runtime 3.28 secs, 0.05 min, 0.00 hours
[2015-09-30T21:17Z] bgzip syn3-12_62147092_93167456-raw.vcf
[2015-09-30T21:17Z] tabix index syn3-12_62147092_93167456-raw.vcf.gz
[2015-09-30T21:17Z] bgzip syn3-12_62147092_93167456-raw-rejectfix.vcf
[2015-09-30T21:17Z] tabix index syn3-12_62147092_93167456-raw-rejectfix.vcf.gz
[2015-09-30T21:17Z] GATK: VariantAnnotator
[2015-09-30T21:17Z] INFO  22:17:20,819 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:17Z] INFO  22:17:20,821 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:17Z] INFO  22:17:20,821 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:17Z] INFO  22:17:20,821 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:17Z] INFO  22:17:20,825 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/12/syn3-12_62147092_93167456-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/12/tx/tmpJwRMcY/syn3-12_62147092_93167456-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_62147092_93167456-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:17Z] INFO  22:17:20,831 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:17Z] INFO  22:17:20,831 HelpFormatter - Date/Time: 2015/09/30 22:17:20
[2015-09-30T21:17Z] INFO  22:17:20,831 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:17Z] INFO  22:17:20,831 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:17Z] INFO  22:17:20,924 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:17Z] INFO  22:17:21,179 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:17Z] INFO  22:17:21,187 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:17Z] INFO  22:17:21,210 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:17Z] INFO  22:17:21,539 IntervalUtils - Processing 1065 bp from intervals
[2015-09-30T21:17Z] WARN  22:17:21,544 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:17Z] WARN  22:17:21,544 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:17Z] INFO  22:17:21,599 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:17Z] INFO  22:17:21,706 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:17Z] INFO  22:17:21,707 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:17Z] INFO  22:17:21,707 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:17Z] INFO  22:17:21,707 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:17Z] INFO  22:17:21,739 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:17Z] INFO  22:17:26,543 VariantAnnotator - Processed 879 loci.
[2015-09-30T21:17Z]
[2015-09-30T21:17Z] INFO  22:17:26,564 ProgressMeter -            done      3048.0     4.0 s      26.6 m       99.9%     4.0 s       0.0 s
[2015-09-30T21:17Z] INFO  22:17:26,565 ProgressMeter - Total runtime 4.86 secs, 0.08 min, 0.00 hours
[2015-09-30T21:17Z] INFO  22:17:26,565 MicroScheduler - 2147 reads were filtered out during the traversal out of approximately 55615 total reads (3.86%)
[2015-09-30T21:17Z] INFO  22:17:26,565 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:17Z] INFO  22:17:26,565 MicroScheduler -   -> 2133 reads (3.84% of total) failing DuplicateReadFilter
[2015-09-30T21:17Z] INFO  22:17:26,566 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:17Z] INFO  22:17:26,566 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:17Z] INFO  22:17:26,566 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:17Z] INFO  22:17:26,566 MicroScheduler -   -> 14 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:17Z] INFO  22:17:27,647 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:17Z] Genotyping with varscan: ('12', 124191013, 133851895) 1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam
[2015-09-30T21:17Z] samtools mpileup
[2015-09-30T21:17Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:17Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:17Z] samtools mpileup
[2015-09-30T21:17Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:17Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:18Z] Varscan
[2015-09-30T21:18Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmp6dkQ3Z/syn3-12_124191013_133851895-raw-normal.mpileup
[2015-09-30T21:18Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmp6dkQ3Z/syn3-12_124191013_133851895-raw-tumor.mpileup
[2015-09-30T21:18Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:18Z] Min reads2:	2
[2015-09-30T21:18Z] Min strands2:	1
[2015-09-30T21:18Z] Min var freq:	0.1
[2015-09-30T21:18Z] Min freq for hom:	0.75
[2015-09-30T21:18Z] Normal purity:	1.0
[2015-09-30T21:18Z] Tumor purity:	1.0
[2015-09-30T21:18Z] Min avg qual:	15
[2015-09-30T21:18Z] P-value thresh:	0.98
[2015-09-30T21:18Z] Somatic p-value:	0.05
[2015-09-30T21:18Z] Varscan
[2015-09-30T21:18Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmpobtcrH/syn3-12_31116488_62142833-raw-normal.mpileup
[2015-09-30T21:18Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmpobtcrH/syn3-12_31116488_62142833-raw-tumor.mpileup
[2015-09-30T21:18Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:18Z] Min reads2:	2
[2015-09-30T21:18Z] Min strands2:	1
[2015-09-30T21:18Z] Min var freq:	0.1
[2015-09-30T21:18Z] Min freq for hom:	0.75
[2015-09-30T21:18Z] Normal purity:	1.0
[2015-09-30T21:18Z] Tumor purity:	1.0
[2015-09-30T21:18Z] Min avg qual:	15
[2015-09-30T21:18Z] P-value thresh:	0.98
[2015-09-30T21:18Z] Somatic p-value:	0.05
[2015-09-30T21:18Z] 484812 positions in tumor
[2015-09-30T21:18Z] 484808 positions shared in normal
[2015-09-30T21:18Z] 477662 had sufficient coverage for comparison
[2015-09-30T21:18Z] 476818 were called Reference
[2015-09-30T21:18Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:18Z] 62 were removed by the strand filter
[2015-09-30T21:18Z] 826 were called Germline
[2015-09-30T21:18Z] 2 were called LOH
[2015-09-30T21:18Z] 13 were called Somatic
[2015-09-30T21:18Z] 3 were called Unknown
[2015-09-30T21:18Z] 0 were called Variant
[2015-09-30T21:18Z] Varscan paired fix
[2015-09-30T21:18Z] Varscan paired fix
[2015-09-30T21:18Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:18Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:18Z] bgzip syn3-12_124191013_133851895-raw.snp.vcf
[2015-09-30T21:18Z] tabix index syn3-12_124191013_133851895-raw.snp.vcf.gz
[2015-09-30T21:18Z] bgzip syn3-12_124191013_133851895-raw.indel.vcf
[2015-09-30T21:18Z] tabix index syn3-12_124191013_133851895-raw.indel.vcf.gz
[2015-09-30T21:18Z] Combine variant files
[2015-09-30T21:18Z] INFO  22:18:33,611 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:18Z] INFO  22:18:33,613 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:18Z] INFO  22:18:33,613 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:18Z] INFO  22:18:33,614 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:18Z] INFO  22:18:33,617 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/12/tx/tmp6dkQ3Z/tx/tmp6sBvia/syn3-12_124191013_133851895-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/12/tx/tmp6dkQ3Z/syn3-12_124191013_133851895-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/12/tx/tmp6dkQ3Z/syn3-12_124191013_133851895-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_124191013_133851895-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:18Z] INFO  22:18:33,623 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:18Z] INFO  22:18:33,623 HelpFormatter - Date/Time: 2015/09/30 22:18:33
[2015-09-30T21:18Z] INFO  22:18:33,623 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:18Z] INFO  22:18:33,623 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:18Z] INFO  22:18:33,876 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:18Z] INFO  22:18:34,010 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:18Z] INFO  22:18:34,103 IntervalUtils - Processing 487679 bp from intervals
[2015-09-30T21:18Z] WARN  22:18:34,104 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:18Z] WARN  22:18:34,104 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:18Z] INFO  22:18:34,156 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:18Z] INFO  22:18:34,158 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:18Z] INFO  22:18:34,158 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:18Z] INFO  22:18:34,158 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:18Z] INFO  22:18:34,159 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:18Z] samtools mpileup
[2015-09-30T21:18Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:18Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:18Z] INFO  22:18:35,229 ProgressMeter -            done       944.0     1.0 s      18.9 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:18Z] INFO  22:18:35,229 ProgressMeter - Total runtime 1.07 secs, 0.02 min, 0.00 hours
[2015-09-30T21:18Z] bgzip syn3-12_124191013_133851895-raw.vcf
[2015-09-30T21:18Z] tabix index syn3-12_124191013_133851895-raw.vcf.gz
[2015-09-30T21:18Z] bgzip syn3-12_124191013_133851895-raw-rejectfix.vcf
[2015-09-30T21:18Z] tabix index syn3-12_124191013_133851895-raw-rejectfix.vcf.gz
[2015-09-30T21:18Z] GATK: VariantAnnotator
[2015-09-30T21:18Z] INFO  22:18:37,580 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:18Z] INFO  22:18:37,582 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:18Z] INFO  22:18:37,582 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:18Z] INFO  22:18:37,582 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:18Z] INFO  22:18:37,586 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/12/syn3-12_124191013_133851895-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/12/tx/tmp78UIag/syn3-12_124191013_133851895-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_124191013_133851895-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:18Z] INFO  22:18:37,591 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:18Z] INFO  22:18:37,591 HelpFormatter - Date/Time: 2015/09/30 22:18:37
[2015-09-30T21:18Z] INFO  22:18:37,591 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:18Z] INFO  22:18:37,592 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:18Z] INFO  22:18:37,684 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:18Z] INFO  22:18:37,761 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:18Z] INFO  22:18:37,768 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:18Z] INFO  22:18:37,790 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:18Z] INFO  22:18:38,143 IntervalUtils - Processing 944 bp from intervals
[2015-09-30T21:18Z] WARN  22:18:38,147 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:18Z] WARN  22:18:38,148 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:18Z] INFO  22:18:38,203 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:18Z] INFO  22:18:38,275 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:18Z] INFO  22:18:38,275 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:18Z] INFO  22:18:38,276 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:18Z] INFO  22:18:38,276 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:18Z] INFO  22:18:38,309 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:18Z] INFO  22:18:43,764 VariantAnnotator - Processed 780 loci.
[2015-09-30T21:18Z]
[2015-09-30T21:18Z] INFO  22:18:43,786 ProgressMeter -            done      4258.0     5.0 s      21.6 m       99.9%     5.0 s       0.0 s
[2015-09-30T21:18Z] INFO  22:18:43,786 ProgressMeter - Total runtime 5.51 secs, 0.09 min, 0.00 hours
[2015-09-30T21:18Z] INFO  22:18:43,786 MicroScheduler - 4050 reads were filtered out during the traversal out of approximately 74310 total reads (5.45%)
[2015-09-30T21:18Z] INFO  22:18:43,787 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:18Z] INFO  22:18:43,787 MicroScheduler -   -> 4035 reads (5.43% of total) failing DuplicateReadFilter
[2015-09-30T21:18Z] INFO  22:18:43,787 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:18Z] INFO  22:18:43,787 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:18Z] INFO  22:18:43,788 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:18Z] INFO  22:18:43,788 MicroScheduler -   -> 15 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:18Z] INFO  22:18:44,868 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:18Z] Genotyping with varscan: ('13', 0, 31036104) 1_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam
[2015-09-30T21:18Z] samtools mpileup
[2015-09-30T21:18Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:18Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:19Z] samtools mpileup
[2015-09-30T21:19Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:19Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:19Z] Varscan
[2015-09-30T21:19Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/13/tx/tmpCwHcAA/syn3-13_0_31036104-raw-normal.mpileup
[2015-09-30T21:19Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/13/tx/tmpCwHcAA/syn3-13_0_31036104-raw-tumor.mpileup
[2015-09-30T21:19Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:19Z] Min reads2:	2
[2015-09-30T21:19Z] Min strands2:	1
[2015-09-30T21:19Z] Min var freq:	0.1
[2015-09-30T21:19Z] Min freq for hom:	0.75
[2015-09-30T21:19Z] Normal purity:	1.0
[2015-09-30T21:19Z] Tumor purity:	1.0
[2015-09-30T21:19Z] Min avg qual:	15
[2015-09-30T21:19Z] P-value thresh:	0.98
[2015-09-30T21:19Z] Somatic p-value:	0.05
[2015-09-30T21:19Z] 575078 positions in tumor
[2015-09-30T21:19Z] 575070 positions shared in normal
[2015-09-30T21:19Z] 559878 had sufficient coverage for comparison
[2015-09-30T21:19Z] 558810 were called Reference
[2015-09-30T21:19Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:19Z] 90 were removed by the strand filter
[2015-09-30T21:19Z] 1045 were called Germline
[2015-09-30T21:19Z] 1 were called LOH
[2015-09-30T21:19Z] 17 were called Somatic
[2015-09-30T21:19Z] 5 were called Unknown
[2015-09-30T21:19Z] 0 were called Variant
[2015-09-30T21:19Z] Varscan paired fix
[2015-09-30T21:19Z] Varscan paired fix
[2015-09-30T21:19Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:19Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:19Z] bgzip syn3-13_0_31036104-raw.snp.vcf
[2015-09-30T21:19Z] tabix index syn3-13_0_31036104-raw.snp.vcf.gz
[2015-09-30T21:19Z] bgzip syn3-13_0_31036104-raw.indel.vcf
[2015-09-30T21:19Z] tabix index syn3-13_0_31036104-raw.indel.vcf.gz
[2015-09-30T21:19Z] Combine variant files
[2015-09-30T21:19Z] INFO  22:19:47,417 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:19Z] INFO  22:19:47,419 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:19Z] INFO  22:19:47,419 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:19Z] INFO  22:19:47,420 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:19Z] INFO  22:19:47,423 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/13/tx/tmpCwHcAA/tx/tmpHqkM6L/syn3-13_0_31036104-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/13/tx/tmpCwHcAA/syn3-13_0_31036104-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/13/tx/tmpCwHcAA/syn3-13_0_31036104-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/13/syn3-13_0_31036104-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:19Z] INFO  22:19:47,429 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:19Z] INFO  22:19:47,430 HelpFormatter - Date/Time: 2015/09/30 22:19:47
[2015-09-30T21:19Z] INFO  22:19:47,430 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:19Z] INFO  22:19:47,430 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:19Z] INFO  22:19:47,506 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:19Z] INFO  22:19:47,643 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:19Z] INFO  22:19:47,726 IntervalUtils - Processing 578686 bp from intervals
[2015-09-30T21:19Z] WARN  22:19:47,727 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:19Z] WARN  22:19:47,727 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:19Z] INFO  22:19:47,783 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:19Z] INFO  22:19:47,785 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:19Z] INFO  22:19:47,785 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:19Z] INFO  22:19:47,785 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:19Z] INFO  22:19:47,786 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:19Z] INFO  22:19:48,698 ProgressMeter -            done      1145.0     0.0 s      13.3 m       99.8%     0.0 s       0.0 s
[2015-09-30T21:19Z] INFO  22:19:48,698 ProgressMeter - Total runtime 0.91 secs, 0.02 min, 0.00 hours
[2015-09-30T21:19Z] bgzip syn3-13_0_31036104-raw.vcf
[2015-09-30T21:19Z] tabix index syn3-13_0_31036104-raw.vcf.gz
[2015-09-30T21:19Z] bgzip syn3-13_0_31036104-raw-rejectfix.vcf
[2015-09-30T21:19Z] tabix index syn3-13_0_31036104-raw-rejectfix.vcf.gz
[2015-09-30T21:19Z] GATK: VariantAnnotator
[2015-09-30T21:19Z] INFO  22:19:51,043 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:19Z] INFO  22:19:51,045 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:19Z] INFO  22:19:51,045 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:19Z] INFO  22:19:51,045 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:19Z] INFO  22:19:51,048 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/13/syn3-13_0_31036104-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/13/tx/tmpaN8pgm/syn3-13_0_31036104-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/13/syn3-13_0_31036104-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:19Z] INFO  22:19:51,053 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:19Z] INFO  22:19:51,054 HelpFormatter - Date/Time: 2015/09/30 22:19:51
[2015-09-30T21:19Z] INFO  22:19:51,054 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:19Z] INFO  22:19:51,054 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:19Z] INFO  22:19:51,119 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:19Z] INFO  22:19:51,192 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:19Z] INFO  22:19:51,199 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:19Z] INFO  22:19:51,221 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:19Z] INFO  22:19:51,518 IntervalUtils - Processing 1145 bp from intervals
[2015-09-30T21:19Z] WARN  22:19:51,522 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:19Z] WARN  22:19:51,522 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:19Z] INFO  22:19:51,576 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:19Z] INFO  22:19:51,676 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:19Z] INFO  22:19:51,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:19Z] INFO  22:19:51,677 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:19Z] INFO  22:19:51,677 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:19Z] INFO  22:19:51,965 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:19Z] INFO  22:19:56,819 VariantAnnotator - Processed 975 loci.
[2015-09-30T21:19Z]
[2015-09-30T21:19Z] INFO  22:19:56,837 ProgressMeter -            done      6313.0     5.0 s      13.6 m       99.8%     5.0 s       0.0 s
[2015-09-30T21:19Z] INFO  22:19:56,837 ProgressMeter - Total runtime 5.16 secs, 0.09 min, 0.00 hours
[2015-09-30T21:19Z] INFO  22:19:56,838 MicroScheduler - 2731 reads were filtered out during the traversal out of approximately 63335 total reads (4.31%)
[2015-09-30T21:19Z] INFO  22:19:56,838 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:19Z] INFO  22:19:56,838 MicroScheduler -   -> 2713 reads (4.28% of total) failing DuplicateReadFilter
[2015-09-30T21:19Z] INFO  22:19:56,839 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:19Z] INFO  22:19:56,839 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:19Z] INFO  22:19:56,839 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:19Z] INFO  22:19:56,839 MicroScheduler -   -> 18 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:19Z] INFO  22:19:57,778 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:19Z] Genotyping with varscan: ('13', 31036377, 62334609) 1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam
[2015-09-30T21:19Z] samtools mpileup
[2015-09-30T21:19Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:19Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:20Z] Varscan
[2015-09-30T21:20Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmpj5_HiD/syn3-12_93169109_124189486-raw-normal.mpileup
[2015-09-30T21:20Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/12/tx/tmpj5_HiD/syn3-12_93169109_124189486-raw-tumor.mpileup
[2015-09-30T21:20Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:20Z] Min reads2:	2
[2015-09-30T21:20Z] Min strands2:	1
[2015-09-30T21:20Z] Min var freq:	0.1
[2015-09-30T21:20Z] Min freq for hom:	0.75
[2015-09-30T21:20Z] Normal purity:	1.0
[2015-09-30T21:20Z] Tumor purity:	1.0
[2015-09-30T21:20Z] Min avg qual:	15
[2015-09-30T21:20Z] P-value thresh:	0.98
[2015-09-30T21:20Z] Somatic p-value:	0.05
[2015-09-30T21:20Z] 2212154 positions in tumor
[2015-09-30T21:20Z] 2212146 positions shared in normal
[2015-09-30T21:20Z] 2184838 had sufficient coverage for comparison
[2015-09-30T21:20Z] 2182357 were called Reference
[2015-09-30T21:20Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:20Z] 162 were removed by the strand filter
[2015-09-30T21:20Z] 2415 were called Germline
[2015-09-30T21:20Z] 9 were called LOH
[2015-09-30T21:20Z] 36 were called Somatic
[2015-09-30T21:20Z] 21 were called Unknown
[2015-09-30T21:20Z] 0 were called Variant
[2015-09-30T21:20Z] Varscan paired fix
[2015-09-30T21:20Z] Varscan paired fix
[2015-09-30T21:20Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:20Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:20Z] bgzip syn3-12_31116488_62142833-raw.snp.vcf
[2015-09-30T21:20Z] tabix index syn3-12_31116488_62142833-raw.snp.vcf.gz
[2015-09-30T21:20Z] bgzip syn3-12_31116488_62142833-raw.indel.vcf
[2015-09-30T21:20Z] tabix index syn3-12_31116488_62142833-raw.indel.vcf.gz
[2015-09-30T21:20Z] Combine variant files
[2015-09-30T21:20Z] INFO  22:20:07,218 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:20Z] INFO  22:20:07,220 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:20Z] INFO  22:20:07,220 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:20Z] INFO  22:20:07,220 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:20Z] INFO  22:20:07,224 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/12/tx/tmpobtcrH/tx/tmpMws6o4/syn3-12_31116488_62142833-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/12/tx/tmpobtcrH/syn3-12_31116488_62142833-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/12/tx/tmpobtcrH/syn3-12_31116488_62142833-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_31116488_62142833-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:20Z] INFO  22:20:07,229 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:20Z] INFO  22:20:07,229 HelpFormatter - Date/Time: 2015/09/30 22:20:07
[2015-09-30T21:20Z] INFO  22:20:07,230 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:20Z] INFO  22:20:07,230 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:20Z] INFO  22:20:07,305 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:20Z] INFO  22:20:07,431 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:20Z] INFO  22:20:07,560 IntervalUtils - Processing 2217019 bp from intervals
[2015-09-30T21:20Z] WARN  22:20:07,561 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:20Z] WARN  22:20:07,561 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:20Z] INFO  22:20:07,619 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:20Z] INFO  22:20:07,623 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:20Z] INFO  22:20:07,624 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:20Z] INFO  22:20:07,624 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:20Z] INFO  22:20:07,624 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:20Z] INFO  22:20:09,251 ProgressMeter -            done      2605.0     1.0 s      10.4 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:20Z] INFO  22:20:09,251 ProgressMeter - Total runtime 1.63 secs, 0.03 min, 0.00 hours
[2015-09-30T21:20Z] bgzip syn3-12_31116488_62142833-raw.vcf
[2015-09-30T21:20Z] tabix index syn3-12_31116488_62142833-raw.vcf.gz
[2015-09-30T21:20Z] bgzip syn3-12_31116488_62142833-raw-rejectfix.vcf
[2015-09-30T21:20Z] tabix index syn3-12_31116488_62142833-raw-rejectfix.vcf.gz
[2015-09-30T21:20Z] GATK: VariantAnnotator
[2015-09-30T21:20Z] INFO  22:20:12,152 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:20Z] INFO  22:20:12,154 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:20Z] INFO  22:20:12,154 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:20Z] INFO  22:20:12,154 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:20Z] INFO  22:20:12,158 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/12/syn3-12_31116488_62142833-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/12/tx/tmpNWjoHn/syn3-12_31116488_62142833-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_31116488_62142833-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:20Z] INFO  22:20:12,164 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:20Z] INFO  22:20:12,164 HelpFormatter - Date/Time: 2015/09/30 22:20:12
[2015-09-30T21:20Z] INFO  22:20:12,164 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:20Z] INFO  22:20:12,164 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:20Z] INFO  22:20:12,667 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:20Z] INFO  22:20:12,744 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:20Z] INFO  22:20:12,752 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:20Z] INFO  22:20:12,774 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:20Z] INFO  22:20:13,261 IntervalUtils - Processing 2609 bp from intervals
[2015-09-30T21:20Z] WARN  22:20:13,266 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:20Z] WARN  22:20:13,266 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:20Z] INFO  22:20:13,324 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:20Z] INFO  22:20:13,531 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:20Z] INFO  22:20:13,531 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:20Z] INFO  22:20:13,532 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:20Z] INFO  22:20:13,532 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:20Z] INFO  22:20:13,565 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:20Z] INFO  22:20:25,532 VariantAnnotator - Processed 2306 loci.
[2015-09-30T21:20Z]
[2015-09-30T21:20Z] INFO  22:20:25,551 ProgressMeter -            done     16356.0    12.0 s      12.2 m      100.0%    12.0 s       0.0 s
[2015-09-30T21:20Z] INFO  22:20:25,552 ProgressMeter - Total runtime 12.02 secs, 0.20 min, 0.00 hours
[2015-09-30T21:20Z] INFO  22:20:25,552 MicroScheduler - 9929 reads were filtered out during the traversal out of approximately 201648 total reads (4.92%)
[2015-09-30T21:20Z] INFO  22:20:25,552 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:20Z] INFO  22:20:25,553 MicroScheduler -   -> 9888 reads (4.90% of total) failing DuplicateReadFilter
[2015-09-30T21:20Z] INFO  22:20:25,553 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:20Z] INFO  22:20:25,553 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:20Z] INFO  22:20:25,553 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:20Z] INFO  22:20:25,553 MicroScheduler -   -> 41 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:20Z] INFO  22:20:26,490 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:20Z] Genotyping with varscan: ('13', 63745563, 94765401) 1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam
[2015-09-30T21:20Z] samtools mpileup
[2015-09-30T21:20Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:20Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:20Z] samtools mpileup
[2015-09-30T21:20Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:20Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:20Z] samtools mpileup
[2015-09-30T21:20Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:20Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:20Z] Varscan
[2015-09-30T21:20Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/13/tx/tmpT66Q0h/syn3-13_63745563_94765401-raw-normal.mpileup
[2015-09-30T21:20Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/13/tx/tmpT66Q0h/syn3-13_63745563_94765401-raw-tumor.mpileup
[2015-09-30T21:20Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:20Z] Min reads2:	2
[2015-09-30T21:20Z] Min strands2:	1
[2015-09-30T21:20Z] Min var freq:	0.1
[2015-09-30T21:20Z] Min freq for hom:	0.75
[2015-09-30T21:20Z] Normal purity:	1.0
[2015-09-30T21:20Z] Tumor purity:	1.0
[2015-09-30T21:20Z] Min avg qual:	15
[2015-09-30T21:20Z] P-value thresh:	0.98
[2015-09-30T21:20Z] Somatic p-value:	0.05
[2015-09-30T21:20Z] 323448 positions in tumor
[2015-09-30T21:20Z] 323447 positions shared in normal
[2015-09-30T21:20Z] 309745 had sufficient coverage for comparison
[2015-09-30T21:20Z] 309385 were called Reference
[2015-09-30T21:20Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:20Z] 22 were removed by the strand filter
[2015-09-30T21:20Z] 342 were called Germline
[2015-09-30T21:20Z] 0 were called LOH
[2015-09-30T21:20Z] 12 were called Somatic
[2015-09-30T21:20Z] 6 were called Unknown
[2015-09-30T21:20Z] 0 were called Variant
[2015-09-30T21:20Z] Varscan paired fix
[2015-09-30T21:20Z] Varscan paired fix
[2015-09-30T21:20Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:20Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:20Z] bgzip syn3-13_63745563_94765401-raw.snp.vcf
[2015-09-30T21:20Z] tabix index syn3-13_63745563_94765401-raw.snp.vcf.gz
[2015-09-30T21:20Z] bgzip syn3-13_63745563_94765401-raw.indel.vcf
[2015-09-30T21:20Z] tabix index syn3-13_63745563_94765401-raw.indel.vcf.gz
[2015-09-30T21:21Z] Combine variant files
[2015-09-30T21:21Z] INFO  22:21:03,399 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:03,401 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:21Z] INFO  22:21:03,401 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:21Z] INFO  22:21:03,401 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:21Z] INFO  22:21:03,405 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/13/tx/tmpT66Q0h/tx/tmpFundj6/syn3-13_63745563_94765401-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/13/tx/tmpT66Q0h/syn3-13_63745563_94765401-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/13/tx/tmpT66Q0h/syn3-13_63745563_94765401-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/13/syn3-13_63745563_94765401-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:21Z] INFO  22:21:03,411 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:21Z] INFO  22:21:03,412 HelpFormatter - Date/Time: 2015/09/30 22:21:03
[2015-09-30T21:21Z] INFO  22:21:03,412 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:03,412 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:03,487 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:21Z] INFO  22:21:03,632 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:21Z] INFO  22:21:03,720 IntervalUtils - Processing 325612 bp from intervals
[2015-09-30T21:21Z] WARN  22:21:03,721 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] WARN  22:21:03,721 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] INFO  22:21:03,778 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:21Z] INFO  22:21:03,779 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:21Z] INFO  22:21:03,780 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:21Z] INFO  22:21:03,780 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:21Z] INFO  22:21:03,781 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:21Z] Varscan
[2015-09-30T21:21Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/13/tx/tmpJWcfQX/syn3-13_31036377_62334609-raw-normal.mpileup
[2015-09-30T21:21Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/13/tx/tmpJWcfQX/syn3-13_31036377_62334609-raw-tumor.mpileup
[2015-09-30T21:21Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:21Z] Min reads2:	2
[2015-09-30T21:21Z] Min strands2:	1
[2015-09-30T21:21Z] Min var freq:	0.1
[2015-09-30T21:21Z] Min freq for hom:	0.75
[2015-09-30T21:21Z] Normal purity:	1.0
[2015-09-30T21:21Z] Tumor purity:	1.0
[2015-09-30T21:21Z] Min avg qual:	15
[2015-09-30T21:21Z] P-value thresh:	0.98
[2015-09-30T21:21Z] Somatic p-value:	0.05
[2015-09-30T21:21Z] INFO  22:21:05,547 ProgressMeter -            done       440.0     1.0 s      66.9 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:21Z] INFO  22:21:05,548 ProgressMeter - Total runtime 1.77 secs, 0.03 min, 0.00 hours
[2015-09-30T21:21Z] bgzip syn3-13_63745563_94765401-raw.vcf
[2015-09-30T21:21Z] tabix index syn3-13_63745563_94765401-raw.vcf.gz
[2015-09-30T21:21Z] bgzip syn3-13_63745563_94765401-raw-rejectfix.vcf
[2015-09-30T21:21Z] tabix index syn3-13_63745563_94765401-raw-rejectfix.vcf.gz
[2015-09-30T21:21Z] GATK: VariantAnnotator
[2015-09-30T21:21Z] INFO  22:21:08,211 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:08,213 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:21Z] INFO  22:21:08,213 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:21Z] INFO  22:21:08,213 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:21Z] INFO  22:21:08,217 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/13/syn3-13_63745563_94765401-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/13/tx/tmpAi5PY9/syn3-13_63745563_94765401-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/13/syn3-13_63745563_94765401-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:21Z] INFO  22:21:08,222 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:21Z] INFO  22:21:08,223 HelpFormatter - Date/Time: 2015/09/30 22:21:08
[2015-09-30T21:21Z] INFO  22:21:08,251 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:08,251 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:08,317 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:21Z] INFO  22:21:08,395 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:21Z] INFO  22:21:08,403 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:21Z] INFO  22:21:08,426 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:21Z] INFO  22:21:08,718 IntervalUtils - Processing 440 bp from intervals
[2015-09-30T21:21Z] WARN  22:21:08,722 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] WARN  22:21:08,722 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] INFO  22:21:08,779 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:21Z] INFO  22:21:08,869 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:21Z] INFO  22:21:08,870 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:21Z] INFO  22:21:08,870 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:21Z] INFO  22:21:08,870 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:21Z] INFO  22:21:08,903 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:21Z] INFO  22:21:11,577 VariantAnnotator - Processed 334 loci.
[2015-09-30T21:21Z]
[2015-09-30T21:21Z] INFO  22:21:11,787 ProgressMeter -            done      1086.0     2.0 s      44.7 m       99.8%     2.0 s       0.0 s
[2015-09-30T21:21Z] INFO  22:21:11,788 ProgressMeter - Total runtime 2.92 secs, 0.05 min, 0.00 hours
[2015-09-30T21:21Z] INFO  22:21:11,788 MicroScheduler - 865 reads were filtered out during the traversal out of approximately 21048 total reads (4.11%)
[2015-09-30T21:21Z] INFO  22:21:11,788 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:21Z] INFO  22:21:11,788 MicroScheduler -   -> 861 reads (4.09% of total) failing DuplicateReadFilter
[2015-09-30T21:21Z] INFO  22:21:11,789 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:21Z] INFO  22:21:11,789 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:21Z] INFO  22:21:11,789 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:21Z] INFO  22:21:11,790 MicroScheduler -   -> 4 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:21Z] INFO  22:21:12,841 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:21Z] Genotyping with varscan: ('13', 94938309, 115169878) 1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam
[2015-09-30T21:21Z] samtools mpileup
[2015-09-30T21:21Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:21Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:21Z] 2254719 positions in tumor
[2015-09-30T21:21Z] 2254710 positions shared in normal
[2015-09-30T21:21Z] 2218285 had sufficient coverage for comparison
[2015-09-30T21:21Z] 2215910 were called Reference
[2015-09-30T21:21Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:21Z] 116 were removed by the strand filter
[2015-09-30T21:21Z] 2292 were called Germline
[2015-09-30T21:21Z] 2 were called LOH
[2015-09-30T21:21Z] 58 were called Somatic
[2015-09-30T21:21Z] 23 were called Unknown
[2015-09-30T21:21Z] 0 were called Variant
[2015-09-30T21:21Z] Varscan paired fix
[2015-09-30T21:21Z] Varscan paired fix
[2015-09-30T21:21Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:21Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:21Z] bgzip syn3-12_93169109_124189486-raw.snp.vcf
[2015-09-30T21:21Z] tabix index syn3-12_93169109_124189486-raw.snp.vcf.gz
[2015-09-30T21:21Z] bgzip syn3-12_93169109_124189486-raw.indel.vcf
[2015-09-30T21:21Z] tabix index syn3-12_93169109_124189486-raw.indel.vcf.gz
[2015-09-30T21:21Z] Combine variant files
[2015-09-30T21:21Z] INFO  22:21:36,222 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:36,224 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:21Z] INFO  22:21:36,225 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:21Z] INFO  22:21:36,225 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:21Z] INFO  22:21:36,228 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/12/tx/tmpj5_HiD/tx/tmpUTkhox/syn3-12_93169109_124189486-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/12/tx/tmpj5_HiD/syn3-12_93169109_124189486-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/12/tx/tmpj5_HiD/syn3-12_93169109_124189486-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_93169109_124189486-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:21Z] INFO  22:21:36,234 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:21Z] INFO  22:21:36,235 HelpFormatter - Date/Time: 2015/09/30 22:21:36
[2015-09-30T21:21Z] INFO  22:21:36,235 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:36,235 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:36,314 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:21Z] INFO  22:21:36,455 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:21Z] INFO  22:21:36,612 IntervalUtils - Processing 2264179 bp from intervals
[2015-09-30T21:21Z] WARN  22:21:36,614 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] WARN  22:21:36,614 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] INFO  22:21:36,671 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:21Z] INFO  22:21:36,676 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:21Z] INFO  22:21:36,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:21Z] INFO  22:21:36,677 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:21Z] INFO  22:21:36,677 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:21Z] INFO  22:21:38,636 ProgressMeter -            done      2639.0     1.0 s      12.4 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:21Z] INFO  22:21:38,637 ProgressMeter - Total runtime 1.96 secs, 0.03 min, 0.00 hours
[2015-09-30T21:21Z] bgzip syn3-12_93169109_124189486-raw.vcf
[2015-09-30T21:21Z] tabix index syn3-12_93169109_124189486-raw.vcf.gz
[2015-09-30T21:21Z] bgzip syn3-12_93169109_124189486-raw-rejectfix.vcf
[2015-09-30T21:21Z] tabix index syn3-12_93169109_124189486-raw-rejectfix.vcf.gz
[2015-09-30T21:21Z] GATK: VariantAnnotator
[2015-09-30T21:21Z] INFO  22:21:41,791 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:41,793 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:21Z] INFO  22:21:41,793 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:21Z] INFO  22:21:41,793 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:21Z] INFO  22:21:41,797 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/12/syn3-12_93169109_124189486-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/12/tx/tmp4ji3c2/syn3-12_93169109_124189486-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/12/syn3-12_93169109_124189486-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:21Z] INFO  22:21:41,803 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:21Z] INFO  22:21:41,804 HelpFormatter - Date/Time: 2015/09/30 22:21:41
[2015-09-30T21:21Z] INFO  22:21:41,804 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:41,804 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:42,258 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:21Z] INFO  22:21:42,402 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:21Z] INFO  22:21:42,410 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:21Z] INFO  22:21:42,727 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.32
[2015-09-30T21:21Z] samtools mpileup
[2015-09-30T21:21Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:21Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:21Z] INFO  22:21:43,408 IntervalUtils - Processing 2640 bp from intervals
[2015-09-30T21:21Z] WARN  22:21:43,412 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] WARN  22:21:43,412 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] INFO  22:21:43,469 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:21Z] INFO  22:21:43,703 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:21Z] INFO  22:21:43,703 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:21Z] INFO  22:21:43,704 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:21Z] INFO  22:21:43,704 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:21Z] INFO  22:21:43,736 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:21Z] 1115994 positions in tumor
[2015-09-30T21:21Z] 1115980 positions shared in normal
[2015-09-30T21:21Z] 1077801 had sufficient coverage for comparison
[2015-09-30T21:21Z] 1076529 were called Reference
[2015-09-30T21:21Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:21Z] 54 were removed by the strand filter
[2015-09-30T21:21Z] 1238 were called Germline
[2015-09-30T21:21Z] 2 were called LOH
[2015-09-30T21:21Z] 20 were called Somatic
[2015-09-30T21:21Z] 12 were called Unknown
[2015-09-30T21:21Z] 0 were called Variant
[2015-09-30T21:21Z] Varscan paired fix
[2015-09-30T21:21Z] Varscan paired fix
[2015-09-30T21:21Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:21Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:21Z] bgzip syn3-13_31036377_62334609-raw.snp.vcf
[2015-09-30T21:21Z] tabix index syn3-13_31036377_62334609-raw.snp.vcf.gz
[2015-09-30T21:21Z] bgzip syn3-13_31036377_62334609-raw.indel.vcf
[2015-09-30T21:21Z] tabix index syn3-13_31036377_62334609-raw.indel.vcf.gz
[2015-09-30T21:21Z] Combine variant files
[2015-09-30T21:21Z] INFO  22:21:48,330 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:48,333 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:21Z] INFO  22:21:48,333 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:21Z] INFO  22:21:48,333 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:21Z] INFO  22:21:48,336 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/13/tx/tmpJWcfQX/tx/tmpHhv1kJ/syn3-13_31036377_62334609-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/13/tx/tmpJWcfQX/syn3-13_31036377_62334609-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/13/tx/tmpJWcfQX/syn3-13_31036377_62334609-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/13/syn3-13_31036377_62334609-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:21Z] INFO  22:21:48,342 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:21Z] INFO  22:21:48,342 HelpFormatter - Date/Time: 2015/09/30 22:21:48
[2015-09-30T21:21Z] INFO  22:21:48,342 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:48,343 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:48,419 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:21Z] INFO  22:21:48,743 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:21Z] INFO  22:21:48,855 IntervalUtils - Processing 1124551 bp from intervals
[2015-09-30T21:21Z] WARN  22:21:48,856 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] WARN  22:21:48,856 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] INFO  22:21:48,912 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:21Z] INFO  22:21:48,916 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:21Z] INFO  22:21:48,916 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:21Z] INFO  22:21:48,916 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:21Z] INFO  22:21:48,917 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:21Z] INFO  22:21:50,073 ProgressMeter -            done      1443.0     1.0 s      13.4 m       99.6%     1.0 s       0.0 s
[2015-09-30T21:21Z] INFO  22:21:50,074 ProgressMeter - Total runtime 1.16 secs, 0.02 min, 0.00 hours
[2015-09-30T21:21Z] bgzip syn3-13_31036377_62334609-raw.vcf
[2015-09-30T21:21Z] tabix index syn3-13_31036377_62334609-raw.vcf.gz
[2015-09-30T21:21Z] bgzip syn3-13_31036377_62334609-raw-rejectfix.vcf
[2015-09-30T21:21Z] tabix index syn3-13_31036377_62334609-raw-rejectfix.vcf.gz
[2015-09-30T21:21Z] GATK: VariantAnnotator
[2015-09-30T21:21Z] INFO  22:21:52,402 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:52,404 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:21Z] INFO  22:21:52,404 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:21Z] INFO  22:21:52,404 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:21Z] INFO  22:21:52,408 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/13/syn3-13_31036377_62334609-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/13/tx/tmpzbpwZP/syn3-13_31036377_62334609-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/13/syn3-13_31036377_62334609-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:21Z] INFO  22:21:52,413 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:21Z] INFO  22:21:52,413 HelpFormatter - Date/Time: 2015/09/30 22:21:52
[2015-09-30T21:21Z] INFO  22:21:52,414 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:52,414 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:21Z] INFO  22:21:52,509 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:21Z] INFO  22:21:52,585 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:21Z] INFO  22:21:52,592 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:21Z] INFO  22:21:52,614 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:21Z] INFO  22:21:53,043 IntervalUtils - Processing 1443 bp from intervals
[2015-09-30T21:21Z] WARN  22:21:53,047 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] WARN  22:21:53,047 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:21Z] INFO  22:21:53,103 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:21Z] INFO  22:21:53,220 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:21Z] INFO  22:21:53,220 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:21Z] INFO  22:21:53,221 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:21Z] INFO  22:21:53,221 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:21Z] INFO  22:21:53,321 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:21Z] INFO  22:21:55,700 VariantAnnotator - Processed 2243 loci.
[2015-09-30T21:21Z]
[2015-09-30T21:21Z] INFO  22:21:55,721 ProgressMeter -            done     10216.0    12.0 s      19.6 m      100.0%    12.0 s       0.0 s
[2015-09-30T21:21Z] INFO  22:21:55,721 ProgressMeter - Total runtime 12.02 secs, 0.20 min, 0.00 hours
[2015-09-30T21:21Z] INFO  22:21:55,721 MicroScheduler - 9170 reads were filtered out during the traversal out of approximately 191499 total reads (4.79%)
[2015-09-30T21:21Z] INFO  22:21:55,722 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:21Z] INFO  22:21:55,722 MicroScheduler -   -> 9124 reads (4.76% of total) failing DuplicateReadFilter
[2015-09-30T21:21Z] INFO  22:21:55,722 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:21Z] INFO  22:21:55,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:21Z] INFO  22:21:55,723 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:21Z] INFO  22:21:55,723 MicroScheduler -   -> 46 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:21Z] INFO  22:21:56,788 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:21Z] Genotyping with varscan: ('14', 0, 31050569) 1_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam
[2015-09-30T21:21Z] samtools mpileup
[2015-09-30T21:21Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:21Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:21Z] INFO  22:21:59,535 VariantAnnotator - Processed 1209 loci.
[2015-09-30T21:21Z]
[2015-09-30T21:21Z] INFO  22:21:59,555 ProgressMeter -            done      4896.0     6.0 s      21.6 m       99.9%     6.0 s       0.0 s
[2015-09-30T21:21Z] INFO  22:21:59,556 ProgressMeter - Total runtime 6.34 secs, 0.11 min, 0.00 hours
[2015-09-30T21:21Z] INFO  22:21:59,556 MicroScheduler - 3539 reads were filtered out during the traversal out of approximately 85831 total reads (4.12%)
[2015-09-30T21:21Z] INFO  22:21:59,556 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:21Z] INFO  22:21:59,556 MicroScheduler -   -> 3520 reads (4.10% of total) failing DuplicateReadFilter
[2015-09-30T21:21Z] INFO  22:21:59,557 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:21Z] INFO  22:21:59,557 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:21Z] INFO  22:21:59,557 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:21Z] INFO  22:21:59,557 MicroScheduler -   -> 19 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:22Z] INFO  22:22:00,490 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:22Z] Genotyping with varscan: ('14', 31055710, 62162825) 1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam
[2015-09-30T21:22Z] samtools mpileup
[2015-09-30T21:22Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:22Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:22Z] Varscan
[2015-09-30T21:22Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/13/tx/tmpzEBqQc/syn3-13_94938309_115169878-raw-normal.mpileup
[2015-09-30T21:22Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/13/tx/tmpzEBqQc/syn3-13_94938309_115169878-raw-tumor.mpileup
[2015-09-30T21:22Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:22Z] Min reads2:	2
[2015-09-30T21:22Z] Min strands2:	1
[2015-09-30T21:22Z] Min var freq:	0.1
[2015-09-30T21:22Z] Min freq for hom:	0.75
[2015-09-30T21:22Z] Normal purity:	1.0
[2015-09-30T21:22Z] Tumor purity:	1.0
[2015-09-30T21:22Z] Min avg qual:	15
[2015-09-30T21:22Z] P-value thresh:	0.98
[2015-09-30T21:22Z] Somatic p-value:	0.05
[2015-09-30T21:22Z] samtools mpileup
[2015-09-30T21:22Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:22Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:22Z] samtools mpileup
[2015-09-30T21:22Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:22Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:22Z] 824477 positions in tumor
[2015-09-30T21:22Z] 824474 positions shared in normal
[2015-09-30T21:22Z] 808715 had sufficient coverage for comparison
[2015-09-30T21:22Z] 807384 were called Reference
[2015-09-30T21:22Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:22Z] 55 were removed by the strand filter
[2015-09-30T21:22Z] 1306 were called Germline
[2015-09-30T21:22Z] 1 were called LOH
[2015-09-30T21:22Z] 20 were called Somatic
[2015-09-30T21:22Z] 4 were called Unknown
[2015-09-30T21:22Z] 0 were called Variant
[2015-09-30T21:22Z] Varscan paired fix
[2015-09-30T21:22Z] Varscan paired fix
[2015-09-30T21:22Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:22Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:22Z] bgzip syn3-13_94938309_115169878-raw.snp.vcf
[2015-09-30T21:22Z] tabix index syn3-13_94938309_115169878-raw.snp.vcf.gz
[2015-09-30T21:22Z] bgzip syn3-13_94938309_115169878-raw.indel.vcf
[2015-09-30T21:22Z] tabix index syn3-13_94938309_115169878-raw.indel.vcf.gz
[2015-09-30T21:22Z] Combine variant files
[2015-09-30T21:22Z] INFO  22:22:49,018 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:22Z] INFO  22:22:49,020 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:22Z] INFO  22:22:49,020 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:22Z] INFO  22:22:49,020 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:22Z] INFO  22:22:49,024 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/13/tx/tmpzEBqQc/tx/tmpJ3G94I/syn3-13_94938309_115169878-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/13/tx/tmpzEBqQc/syn3-13_94938309_115169878-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/13/tx/tmpzEBqQc/syn3-13_94938309_115169878-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/13/syn3-13_94938309_115169878-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:22Z] INFO  22:22:49,034 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:22Z] INFO  22:22:49,034 HelpFormatter - Date/Time: 2015/09/30 22:22:49
[2015-09-30T21:22Z] INFO  22:22:49,034 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:22Z] INFO  22:22:49,034 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:22Z] INFO  22:22:49,112 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:22Z] INFO  22:22:49,471 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:22Z] INFO  22:22:49,584 IntervalUtils - Processing 830267 bp from intervals
[2015-09-30T21:22Z] WARN  22:22:49,585 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:22Z] WARN  22:22:49,586 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:22Z] INFO  22:22:49,642 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:22Z] INFO  22:22:49,644 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:22Z] INFO  22:22:49,645 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:22Z] INFO  22:22:49,645 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:22Z] INFO  22:22:49,645 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:22Z] INFO  22:22:50,886 ProgressMeter -            done      1482.0     1.0 s      14.0 m       99.4%     1.0 s       0.0 s
[2015-09-30T21:22Z] INFO  22:22:50,887 ProgressMeter - Total runtime 1.24 secs, 0.02 min, 0.00 hours
[2015-09-30T21:22Z] bgzip syn3-13_94938309_115169878-raw.vcf
[2015-09-30T21:22Z] tabix index syn3-13_94938309_115169878-raw.vcf.gz
[2015-09-30T21:22Z] bgzip syn3-13_94938309_115169878-raw-rejectfix.vcf
[2015-09-30T21:22Z] tabix index syn3-13_94938309_115169878-raw-rejectfix.vcf.gz
[2015-09-30T21:22Z] GATK: VariantAnnotator
[2015-09-30T21:22Z] INFO  22:22:53,318 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:22Z] INFO  22:22:53,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:22Z] INFO  22:22:53,320 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:22Z] INFO  22:22:53,321 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:22Z] INFO  22:22:53,324 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/13/syn3-13_94938309_115169878-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/13/tx/tmpCyqe7C/syn3-13_94938309_115169878-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/13/syn3-13_94938309_115169878-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:22Z] INFO  22:22:53,330 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:22Z] INFO  22:22:53,330 HelpFormatter - Date/Time: 2015/09/30 22:22:53
[2015-09-30T21:22Z] INFO  22:22:53,330 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:22Z] INFO  22:22:53,330 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:22Z] INFO  22:22:53,424 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:22Z] INFO  22:22:53,500 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:22Z] INFO  22:22:53,508 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:22Z] INFO  22:22:53,530 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:22Z] INFO  22:22:53,901 IntervalUtils - Processing 1486 bp from intervals
[2015-09-30T21:22Z] WARN  22:22:53,906 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:22Z] WARN  22:22:53,906 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:22Z] INFO  22:22:53,963 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:22Z] INFO  22:22:54,063 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:22Z] INFO  22:22:54,063 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:22Z] INFO  22:22:54,064 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:22Z] INFO  22:22:54,064 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:22Z] INFO  22:22:54,161 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:23Z] INFO  22:23:00,724 VariantAnnotator - Processed 1273 loci.
[2015-09-30T21:23Z]
[2015-09-30T21:23Z] INFO  22:23:00,744 ProgressMeter -            done      8671.0     6.0 s      12.8 m       99.9%     6.0 s       0.0 s
[2015-09-30T21:23Z] INFO  22:23:00,744 ProgressMeter - Total runtime 6.68 secs, 0.11 min, 0.00 hours
[2015-09-30T21:23Z] INFO  22:23:00,745 MicroScheduler - 5413 reads were filtered out during the traversal out of approximately 107550 total reads (5.03%)
[2015-09-30T21:23Z] INFO  22:23:00,745 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:23Z] INFO  22:23:00,745 MicroScheduler -   -> 5394 reads (5.02% of total) failing DuplicateReadFilter
[2015-09-30T21:23Z] INFO  22:23:00,745 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:23Z] INFO  22:23:00,746 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:23Z] INFO  22:23:00,746 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:23Z] INFO  22:23:00,746 MicroScheduler -   -> 19 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:23Z] INFO  22:23:01,902 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:23Z] Genotyping with varscan: ('14', 62186823, 93262365) 1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam
[2015-09-30T21:23Z] samtools mpileup
[2015-09-30T21:23Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:23Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:23Z] Varscan
[2015-09-30T21:23Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/14/tx/tmp8iql9o/syn3-14_0_31050569-raw-normal.mpileup
[2015-09-30T21:23Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/14/tx/tmp8iql9o/syn3-14_0_31050569-raw-tumor.mpileup
[2015-09-30T21:23Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:23Z] Min reads2:	2
[2015-09-30T21:23Z] Min strands2:	1
[2015-09-30T21:23Z] Min var freq:	0.1
[2015-09-30T21:23Z] Min freq for hom:	0.75
[2015-09-30T21:23Z] Normal purity:	1.0
[2015-09-30T21:23Z] Tumor purity:	1.0
[2015-09-30T21:23Z] Min avg qual:	15
[2015-09-30T21:23Z] P-value thresh:	0.98
[2015-09-30T21:23Z] Somatic p-value:	0.05
[2015-09-30T21:23Z] Varscan
[2015-09-30T21:23Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/14/tx/tmppjXoJ7/syn3-14_31055710_62162825-raw-normal.mpileup
[2015-09-30T21:23Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/14/tx/tmppjXoJ7/syn3-14_31055710_62162825-raw-tumor.mpileup
[2015-09-30T21:23Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:23Z] Min reads2:	2
[2015-09-30T21:23Z] Min strands2:	1
[2015-09-30T21:23Z] Min var freq:	0.1
[2015-09-30T21:23Z] Min freq for hom:	0.75
[2015-09-30T21:23Z] Normal purity:	1.0
[2015-09-30T21:23Z] Tumor purity:	1.0
[2015-09-30T21:23Z] Min avg qual:	15
[2015-09-30T21:23Z] P-value thresh:	0.98
[2015-09-30T21:23Z] Somatic p-value:	0.05
[2015-09-30T21:23Z] 838707 positions in tumor
[2015-09-30T21:23Z] 838705 positions shared in normal
[2015-09-30T21:23Z] 830407 had sufficient coverage for comparison
[2015-09-30T21:23Z] 829051 were called Reference
[2015-09-30T21:23Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:23Z] 91 were removed by the strand filter
[2015-09-30T21:23Z] 1321 were called Germline
[2015-09-30T21:23Z] 4 were called LOH
[2015-09-30T21:23Z] 25 were called Somatic
[2015-09-30T21:23Z] 6 were called Unknown
[2015-09-30T21:23Z] 0 were called Variant
[2015-09-30T21:23Z] Varscan paired fix
[2015-09-30T21:23Z] Varscan paired fix
[2015-09-30T21:23Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:23Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:23Z] bgzip syn3-14_0_31050569-raw.snp.vcf
[2015-09-30T21:23Z] tabix index syn3-14_0_31050569-raw.snp.vcf.gz
[2015-09-30T21:23Z] bgzip syn3-14_0_31050569-raw.indel.vcf
[2015-09-30T21:23Z] tabix index syn3-14_0_31050569-raw.indel.vcf.gz
[2015-09-30T21:23Z] Combine variant files
[2015-09-30T21:23Z] INFO  22:23:45,399 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:23Z] INFO  22:23:45,401 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:23Z] INFO  22:23:45,401 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:23Z] INFO  22:23:45,401 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:23Z] INFO  22:23:45,405 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/14/tx/tmp8iql9o/tx/tmpnTX0v5/syn3-14_0_31050569-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/14/tx/tmp8iql9o/syn3-14_0_31050569-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/14/tx/tmp8iql9o/syn3-14_0_31050569-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/14/syn3-14_0_31050569-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:23Z] INFO  22:23:45,410 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:23Z] INFO  22:23:45,410 HelpFormatter - Date/Time: 2015/09/30 22:23:45
[2015-09-30T21:23Z] INFO  22:23:45,411 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:23Z] INFO  22:23:45,411 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:23Z] INFO  22:23:45,701 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:23Z] INFO  22:23:45,843 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:23Z] INFO  22:23:45,925 IntervalUtils - Processing 839940 bp from intervals
[2015-09-30T21:23Z] WARN  22:23:45,926 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:23Z] WARN  22:23:45,926 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:23Z] INFO  22:23:45,985 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:23Z] INFO  22:23:45,987 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:23Z] INFO  22:23:45,988 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:23Z] INFO  22:23:45,988 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:23Z] INFO  22:23:45,988 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:23Z] INFO  22:23:47,105 ProgressMeter -            done      1417.0     1.0 s      13.1 m       99.6%     1.0 s       0.0 s
[2015-09-30T21:23Z] INFO  22:23:47,106 ProgressMeter - Total runtime 1.12 secs, 0.02 min, 0.00 hours
[2015-09-30T21:23Z] bgzip syn3-14_0_31050569-raw.vcf
[2015-09-30T21:23Z] tabix index syn3-14_0_31050569-raw.vcf.gz
[2015-09-30T21:23Z] bgzip syn3-14_0_31050569-raw-rejectfix.vcf
[2015-09-30T21:23Z] tabix index syn3-14_0_31050569-raw-rejectfix.vcf.gz
[2015-09-30T21:23Z] GATK: VariantAnnotator
[2015-09-30T21:23Z] INFO  22:23:49,498 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:23Z] INFO  22:23:49,500 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:23Z] INFO  22:23:49,500 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:23Z] INFO  22:23:49,500 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:23Z] INFO  22:23:49,504 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/14/syn3-14_0_31050569-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/14/tx/tmpdEIRks/syn3-14_0_31050569-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/14/syn3-14_0_31050569-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:23Z] INFO  22:23:49,509 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:23Z] INFO  22:23:49,509 HelpFormatter - Date/Time: 2015/09/30 22:23:49
[2015-09-30T21:23Z] INFO  22:23:49,510 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:23Z] INFO  22:23:49,510 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:23Z] INFO  22:23:49,598 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:23Z] INFO  22:23:49,671 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:23Z] INFO  22:23:49,679 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:23Z] INFO  22:23:49,701 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:23Z] INFO  22:23:50,071 IntervalUtils - Processing 1417 bp from intervals
[2015-09-30T21:23Z] WARN  22:23:50,075 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:23Z] WARN  22:23:50,075 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:23Z] INFO  22:23:50,129 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:23Z] INFO  22:23:50,200 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:23Z] INFO  22:23:50,200 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:23Z] INFO  22:23:50,201 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:23Z] INFO  22:23:50,201 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:23Z] INFO  22:23:50,288 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:23Z] 1226836 positions in tumor
[2015-09-30T21:23Z] 1226825 positions shared in normal
[2015-09-30T21:23Z] 1179937 had sufficient coverage for comparison
[2015-09-30T21:23Z] 1178567 were called Reference
[2015-09-30T21:23Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:23Z] 75 were removed by the strand filter
[2015-09-30T21:23Z] 1331 were called Germline
[2015-09-30T21:23Z] 3 were called LOH
[2015-09-30T21:23Z] 27 were called Somatic
[2015-09-30T21:23Z] 9 were called Unknown
[2015-09-30T21:23Z] 0 were called Variant
[2015-09-30T21:23Z] Varscan paired fix
[2015-09-30T21:23Z] Varscan paired fix
[2015-09-30T21:23Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:23Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:23Z] bgzip syn3-14_31055710_62162825-raw.snp.vcf
[2015-09-30T21:23Z] tabix index syn3-14_31055710_62162825-raw.snp.vcf.gz
[2015-09-30T21:23Z] bgzip syn3-14_31055710_62162825-raw.indel.vcf
[2015-09-30T21:23Z] tabix index syn3-14_31055710_62162825-raw.indel.vcf.gz
[2015-09-30T21:23Z] Combine variant files
[2015-09-30T21:23Z] INFO  22:23:57,661 VariantAnnotator - Processed 1260 loci.
[2015-09-30T21:23Z]
[2015-09-30T21:23Z] INFO  22:23:57,680 ProgressMeter -            done      8774.0     7.0 s      14.2 m       99.9%     7.0 s       0.0 s
[2015-09-30T21:23Z] INFO  22:23:57,680 ProgressMeter - Total runtime 7.48 secs, 0.12 min, 0.00 hours
[2015-09-30T21:23Z] INFO  22:23:57,681 MicroScheduler - 5516 reads were filtered out during the traversal out of approximately 113868 total reads (4.84%)
[2015-09-30T21:23Z] INFO  22:23:57,681 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:23Z] INFO  22:23:57,681 MicroScheduler -   -> 5494 reads (4.82% of total) failing DuplicateReadFilter
[2015-09-30T21:23Z] INFO  22:23:57,681 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:23Z] INFO  22:23:57,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:23Z] INFO  22:23:57,682 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:23Z] INFO  22:23:57,682 MicroScheduler -   -> 22 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:23Z] INFO  22:23:58,596 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:23Z] INFO  22:23:58,597 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:23Z] INFO  22:23:58,598 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:23Z] INFO  22:23:58,598 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:23Z] INFO  22:23:58,601 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/14/tx/tmppjXoJ7/tx/tmp7OxXy1/syn3-14_31055710_62162825-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/14/tx/tmppjXoJ7/syn3-14_31055710_62162825-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/14/tx/tmppjXoJ7/syn3-14_31055710_62162825-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/14/syn3-14_31055710_62162825-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:23Z] INFO  22:23:58,606 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:23Z] INFO  22:23:58,606 HelpFormatter - Date/Time: 2015/09/30 22:23:58
[2015-09-30T21:23Z] INFO  22:23:58,606 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:23Z] INFO  22:23:58,607 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:23Z] INFO  22:23:58,614 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:23Z] Genotyping with varscan: ('14', 93263525, 107349540) 1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam
[2015-09-30T21:23Z] INFO  22:23:58,683 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:23Z] INFO  22:23:58,824 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:23Z] samtools mpileup
[2015-09-30T21:23Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:23Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:23Z] INFO  22:23:58,938 IntervalUtils - Processing 1235919 bp from intervals
[2015-09-30T21:23Z] WARN  22:23:58,939 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:23Z] WARN  22:23:58,939 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:23Z] INFO  22:23:58,995 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:23Z] INFO  22:23:58,998 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:23Z] INFO  22:23:58,999 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:23Z] INFO  22:23:58,999 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:23Z] INFO  22:23:58,999 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:23Z] samtools mpileup
[2015-09-30T21:23Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:23Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:24Z] INFO  22:24:00,243 ProgressMeter -            done      1564.0     1.0 s      13.3 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:24Z] INFO  22:24:00,244 ProgressMeter - Total runtime 1.25 secs, 0.02 min, 0.00 hours
[2015-09-30T21:24Z] bgzip syn3-14_31055710_62162825-raw.vcf
[2015-09-30T21:24Z] tabix index syn3-14_31055710_62162825-raw.vcf.gz
[2015-09-30T21:24Z] bgzip syn3-14_31055710_62162825-raw-rejectfix.vcf
[2015-09-30T21:24Z] tabix index syn3-14_31055710_62162825-raw-rejectfix.vcf.gz
[2015-09-30T21:24Z] GATK: VariantAnnotator
[2015-09-30T21:24Z] INFO  22:24:02,683 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:24Z] INFO  22:24:02,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:24Z] INFO  22:24:02,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:24Z] INFO  22:24:02,685 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:24Z] INFO  22:24:02,688 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/14/syn3-14_31055710_62162825-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/14/tx/tmpWUoH0y/syn3-14_31055710_62162825-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/14/syn3-14_31055710_62162825-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:24Z] INFO  22:24:02,694 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:24Z] INFO  22:24:02,694 HelpFormatter - Date/Time: 2015/09/30 22:24:02
[2015-09-30T21:24Z] INFO  22:24:02,694 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:24Z] INFO  22:24:02,694 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:24Z] INFO  22:24:02,790 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:24Z] INFO  22:24:02,865 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:24Z] INFO  22:24:02,872 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:24Z] INFO  22:24:02,895 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:24Z] INFO  22:24:03,262 IntervalUtils - Processing 1564 bp from intervals
[2015-09-30T21:24Z] WARN  22:24:03,266 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:24Z] WARN  22:24:03,266 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:24Z] INFO  22:24:03,322 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:24Z] INFO  22:24:03,422 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:24Z] INFO  22:24:03,422 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:24Z] INFO  22:24:03,423 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:24Z] INFO  22:24:03,423 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:24Z] INFO  22:24:03,522 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:24Z] INFO  22:24:09,799 VariantAnnotator - Processed 1288 loci.
[2015-09-30T21:24Z]
[2015-09-30T21:24Z] INFO  22:24:09,819 ProgressMeter -            done      4915.0     6.0 s      21.7 m       99.9%     6.0 s       0.0 s
[2015-09-30T21:24Z] INFO  22:24:09,819 ProgressMeter - Total runtime 6.40 secs, 0.11 min, 0.00 hours
[2015-09-30T21:24Z] INFO  22:24:09,819 MicroScheduler - 3707 reads were filtered out during the traversal out of approximately 87069 total reads (4.26%)
[2015-09-30T21:24Z] INFO  22:24:09,820 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:24Z] INFO  22:24:09,820 MicroScheduler -   -> 3689 reads (4.24% of total) failing DuplicateReadFilter
[2015-09-30T21:24Z] INFO  22:24:09,820 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:24Z] INFO  22:24:09,820 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:24Z] INFO  22:24:09,821 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:24Z] INFO  22:24:09,821 MicroScheduler -   -> 18 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:24Z] INFO  22:24:10,957 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:24Z] Genotyping with varscan: ('15', 0, 31041107) 1_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam
[2015-09-30T21:24Z] samtools mpileup
[2015-09-30T21:24Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:24Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:24Z] samtools mpileup
[2015-09-30T21:24Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:24Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:24Z] samtools mpileup
[2015-09-30T21:24Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:24Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:24Z] Varscan
[2015-09-30T21:24Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/14/tx/tmpfZnuzs/syn3-14_62186823_93262365-raw-normal.mpileup
[2015-09-30T21:24Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/14/tx/tmpfZnuzs/syn3-14_62186823_93262365-raw-tumor.mpileup
[2015-09-30T21:24Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:24Z] Min reads2:	2
[2015-09-30T21:24Z] Min strands2:	1
[2015-09-30T21:24Z] Min var freq:	0.1
[2015-09-30T21:24Z] Min freq for hom:	0.75
[2015-09-30T21:24Z] Normal purity:	1.0
[2015-09-30T21:24Z] Tumor purity:	1.0
[2015-09-30T21:24Z] Min avg qual:	15
[2015-09-30T21:24Z] P-value thresh:	0.98
[2015-09-30T21:24Z] Somatic p-value:	0.05
[2015-09-30T21:25Z] Varscan
[2015-09-30T21:25Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/15/tx/tmpgreUwu/syn3-15_0_31041107-raw-normal.mpileup
[2015-09-30T21:25Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/15/tx/tmpgreUwu/syn3-15_0_31041107-raw-tumor.mpileup
[2015-09-30T21:25Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:25Z] Min reads2:	2
[2015-09-30T21:25Z] Min strands2:	1
[2015-09-30T21:25Z] Min var freq:	0.1
[2015-09-30T21:25Z] Min freq for hom:	0.75
[2015-09-30T21:25Z] Normal purity:	1.0
[2015-09-30T21:25Z] Tumor purity:	1.0
[2015-09-30T21:25Z] Min avg qual:	15
[2015-09-30T21:25Z] P-value thresh:	0.98
[2015-09-30T21:25Z] Somatic p-value:	0.05
[2015-09-30T21:25Z] Varscan
[2015-09-30T21:25Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/14/tx/tmpuWJW9U/syn3-14_93263525_107349540-raw-normal.mpileup
[2015-09-30T21:25Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/14/tx/tmpuWJW9U/syn3-14_93263525_107349540-raw-tumor.mpileup
[2015-09-30T21:25Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:25Z] Min reads2:	2
[2015-09-30T21:25Z] Min strands2:	1
[2015-09-30T21:25Z] Min var freq:	0.1
[2015-09-30T21:25Z] Min freq for hom:	0.75
[2015-09-30T21:25Z] Normal purity:	1.0
[2015-09-30T21:25Z] Tumor purity:	1.0
[2015-09-30T21:25Z] Min avg qual:	15
[2015-09-30T21:25Z] P-value thresh:	0.98
[2015-09-30T21:25Z] Somatic p-value:	0.05
[2015-09-30T21:25Z] 654987 positions in tumor
[2015-09-30T21:25Z] 654978 positions shared in normal
[2015-09-30T21:25Z] 641018 had sufficient coverage for comparison
[2015-09-30T21:25Z] 639291 were called Reference
[2015-09-30T21:25Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:25Z] 319 were removed by the strand filter
[2015-09-30T21:25Z] 1661 were called Germline
[2015-09-30T21:25Z] 6 were called LOH
[2015-09-30T21:25Z] 56 were called Somatic
[2015-09-30T21:25Z] 4 were called Unknown
[2015-09-30T21:25Z] 0 were called Variant
[2015-09-30T21:25Z] Varscan paired fix
[2015-09-30T21:25Z] Varscan paired fix
[2015-09-30T21:25Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:25Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:25Z] bgzip syn3-15_0_31041107-raw.snp.vcf
[2015-09-30T21:25Z] tabix index syn3-15_0_31041107-raw.snp.vcf.gz
[2015-09-30T21:25Z] bgzip syn3-15_0_31041107-raw.indel.vcf
[2015-09-30T21:25Z] tabix index syn3-15_0_31041107-raw.indel.vcf.gz
[2015-09-30T21:25Z] Combine variant files
[2015-09-30T21:25Z] INFO  22:25:33,013 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:25Z] INFO  22:25:33,015 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:25Z] INFO  22:25:33,015 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:25Z] INFO  22:25:33,015 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:25Z] INFO  22:25:33,019 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/15/tx/tmpgreUwu/tx/tmpI5Qx3J/syn3-15_0_31041107-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/15/tx/tmpgreUwu/syn3-15_0_31041107-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/15/tx/tmpgreUwu/syn3-15_0_31041107-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/15/syn3-15_0_31041107-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:25Z] INFO  22:25:33,024 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:25Z] INFO  22:25:33,024 HelpFormatter - Date/Time: 2015/09/30 22:25:33
[2015-09-30T21:25Z] INFO  22:25:33,025 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:25Z] INFO  22:25:33,025 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:25Z] INFO  22:25:33,103 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:25Z] INFO  22:25:33,490 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:25Z] INFO  22:25:33,576 IntervalUtils - Processing 659213 bp from intervals
[2015-09-30T21:25Z] WARN  22:25:33,577 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:25Z] WARN  22:25:33,577 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:25Z] INFO  22:25:33,635 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:25Z] INFO  22:25:33,637 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:25Z] INFO  22:25:33,638 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:25Z] INFO  22:25:33,638 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:25Z] INFO  22:25:33,638 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:25Z] INFO  22:25:34,670 ProgressMeter -            done      1536.0     1.0 s      11.2 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:25Z] INFO  22:25:34,671 ProgressMeter - Total runtime 1.03 secs, 0.02 min, 0.00 hours
[2015-09-30T21:25Z] bgzip syn3-15_0_31041107-raw.vcf
[2015-09-30T21:25Z] tabix index syn3-15_0_31041107-raw.vcf.gz
[2015-09-30T21:25Z] bgzip syn3-15_0_31041107-raw-rejectfix.vcf
[2015-09-30T21:25Z] tabix index syn3-15_0_31041107-raw-rejectfix.vcf.gz
[2015-09-30T21:25Z] GATK: VariantAnnotator
[2015-09-30T21:25Z] INFO  22:25:37,627 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:25Z] INFO  22:25:37,629 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:25Z] INFO  22:25:37,629 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:25Z] INFO  22:25:37,629 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:25Z] INFO  22:25:37,633 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/15/syn3-15_0_31041107-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/15/tx/tmpTBZ8Kn/syn3-15_0_31041107-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/15/syn3-15_0_31041107-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:25Z] INFO  22:25:37,639 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:25Z] INFO  22:25:37,639 HelpFormatter - Date/Time: 2015/09/30 22:25:37
[2015-09-30T21:25Z] INFO  22:25:37,639 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:25Z] INFO  22:25:37,639 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:25Z] INFO  22:25:37,734 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:25Z] INFO  22:25:37,812 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:25Z] INFO  22:25:37,820 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:25Z] INFO  22:25:37,842 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:25Z] INFO  22:25:38,257 IntervalUtils - Processing 1536 bp from intervals
[2015-09-30T21:25Z] WARN  22:25:38,261 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:25Z] WARN  22:25:38,261 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:25Z] INFO  22:25:38,319 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:25Z] INFO  22:25:38,391 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:25Z] INFO  22:25:38,391 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:25Z] INFO  22:25:38,391 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:25Z] INFO  22:25:38,392 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:25Z] INFO  22:25:38,492 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:25Z] INFO  22:25:45,440 VariantAnnotator - Processed 1406 loci.
[2015-09-30T21:25Z]
[2015-09-30T21:25Z] INFO  22:25:45,470 ProgressMeter -            done     11259.0     7.0 s      10.5 m       99.9%     7.0 s       0.0 s
[2015-09-30T21:25Z] INFO  22:25:45,470 ProgressMeter - Total runtime 7.08 secs, 0.12 min, 0.00 hours
[2015-09-30T21:25Z] INFO  22:25:45,471 MicroScheduler - 5547 reads were filtered out during the traversal out of approximately 131129 total reads (4.23%)
[2015-09-30T21:25Z] INFO  22:25:45,471 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:25Z] INFO  22:25:45,471 MicroScheduler -   -> 5528 reads (4.22% of total) failing DuplicateReadFilter
[2015-09-30T21:25Z] INFO  22:25:45,471 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:25Z] INFO  22:25:45,472 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:25Z] INFO  22:25:45,472 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:25Z] INFO  22:25:45,472 MicroScheduler -   -> 19 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T21:25Z] INFO  22:25:46,394 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:25Z] Genotyping with varscan: ('15', 31042312, 62147370) 1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam
[2015-09-30T21:25Z] samtools mpileup
[2015-09-30T21:25Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:25Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:25Z] 1552808 positions in tumor
[2015-09-30T21:25Z] 1552804 positions shared in normal
[2015-09-30T21:25Z] 1526832 had sufficient coverage for comparison
[2015-09-30T21:25Z] 1525146 were called Reference
[2015-09-30T21:25Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:25Z] 73 were removed by the strand filter
[2015-09-30T21:25Z] 1624 were called Germline
[2015-09-30T21:25Z] 7 were called LOH
[2015-09-30T21:25Z] 38 were called Somatic
[2015-09-30T21:25Z] 17 were called Unknown
[2015-09-30T21:25Z] 0 were called Variant
[2015-09-30T21:25Z] Varscan paired fix
[2015-09-30T21:25Z] Varscan paired fix
[2015-09-30T21:25Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:25Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:25Z] bgzip syn3-14_62186823_93262365-raw.snp.vcf
[2015-09-30T21:25Z] tabix index syn3-14_62186823_93262365-raw.snp.vcf.gz
[2015-09-30T21:25Z] bgzip syn3-14_62186823_93262365-raw.indel.vcf
[2015-09-30T21:25Z] tabix index syn3-14_62186823_93262365-raw.indel.vcf.gz
[2015-09-30T21:25Z] Combine variant files
[2015-09-30T21:26Z] INFO  22:26:01,006 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:01,008 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:26Z] INFO  22:26:01,008 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:26Z] INFO  22:26:01,008 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:26Z] INFO  22:26:01,012 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/14/tx/tmpfZnuzs/tx/tmpCYCEIE/syn3-14_62186823_93262365-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/14/tx/tmpfZnuzs/syn3-14_62186823_93262365-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/14/tx/tmpfZnuzs/syn3-14_62186823_93262365-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/14/syn3-14_62186823_93262365-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:26Z] INFO  22:26:01,017 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:26Z] INFO  22:26:01,017 HelpFormatter - Date/Time: 2015/09/30 22:26:01
[2015-09-30T21:26Z] INFO  22:26:01,018 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:01,018 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:01,090 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:26Z] INFO  22:26:01,281 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:26Z] INFO  22:26:01,407 IntervalUtils - Processing 1557127 bp from intervals
[2015-09-30T21:26Z] WARN  22:26:01,408 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:26Z] WARN  22:26:01,408 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:26Z] INFO  22:26:01,463 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:26Z] INFO  22:26:01,467 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:26Z] INFO  22:26:01,467 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:26Z] INFO  22:26:01,468 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:26Z] INFO  22:26:01,468 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:26Z] INFO  22:26:02,853 ProgressMeter -            done      1979.0     1.0 s      11.7 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:26Z] INFO  22:26:02,853 ProgressMeter - Total runtime 1.39 secs, 0.02 min, 0.00 hours
[2015-09-30T21:26Z] bgzip syn3-14_62186823_93262365-raw.vcf
[2015-09-30T21:26Z] tabix index syn3-14_62186823_93262365-raw.vcf.gz
[2015-09-30T21:26Z] bgzip syn3-14_62186823_93262365-raw-rejectfix.vcf
[2015-09-30T21:26Z] tabix index syn3-14_62186823_93262365-raw-rejectfix.vcf.gz
[2015-09-30T21:26Z] 1006356 positions in tumor
[2015-09-30T21:26Z] 1006347 positions shared in normal
[2015-09-30T21:26Z] 993690 had sufficient coverage for comparison
[2015-09-30T21:26Z] 991582 were called Reference
[2015-09-30T21:26Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:26Z] 217 were removed by the strand filter
[2015-09-30T21:26Z] 2061 were called Germline
[2015-09-30T21:26Z] 7 were called LOH
[2015-09-30T21:26Z] 31 were called Somatic
[2015-09-30T21:26Z] 9 were called Unknown
[2015-09-30T21:26Z] 0 were called Variant
[2015-09-30T21:26Z] Varscan paired fix
[2015-09-30T21:26Z] GATK: VariantAnnotator
[2015-09-30T21:26Z] Varscan paired fix
[2015-09-30T21:26Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:26Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:26Z] bgzip syn3-14_93263525_107349540-raw.snp.vcf
[2015-09-30T21:26Z] tabix index syn3-14_93263525_107349540-raw.snp.vcf.gz
[2015-09-30T21:26Z] bgzip syn3-14_93263525_107349540-raw.indel.vcf
[2015-09-30T21:26Z] tabix index syn3-14_93263525_107349540-raw.indel.vcf.gz
[2015-09-30T21:26Z] Combine variant files
[2015-09-30T21:26Z] INFO  22:26:05,610 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:05,612 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:26Z] INFO  22:26:05,612 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:26Z] INFO  22:26:05,612 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:26Z] INFO  22:26:05,615 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/14/syn3-14_62186823_93262365-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/14/tx/tmpKfQm70/syn3-14_62186823_93262365-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/14/syn3-14_62186823_93262365-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:26Z] INFO  22:26:05,621 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:26Z] INFO  22:26:05,621 HelpFormatter - Date/Time: 2015/09/30 22:26:05
[2015-09-30T21:26Z] INFO  22:26:05,621 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:05,622 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:05,985 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:26Z] INFO  22:26:06,060 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:26Z] INFO  22:26:06,068 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:26Z] INFO  22:26:06,090 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:26Z] INFO  22:26:06,495 IntervalUtils - Processing 1993 bp from intervals
[2015-09-30T21:26Z] WARN  22:26:06,500 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:26Z] WARN  22:26:06,500 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:26Z] INFO  22:26:06,557 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:26Z] INFO  22:26:06,615 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:06,617 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:26Z] INFO  22:26:06,617 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:26Z] INFO  22:26:06,618 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:26Z] INFO  22:26:06,621 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/14/tx/tmpuWJW9U/tx/tmpwaUzzg/syn3-14_93263525_107349540-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/14/tx/tmpuWJW9U/syn3-14_93263525_107349540-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/14/tx/tmpuWJW9U/syn3-14_93263525_107349540-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/14/syn3-14_93263525_107349540-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:26Z] INFO  22:26:06,626 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:26Z] INFO  22:26:06,627 HelpFormatter - Date/Time: 2015/09/30 22:26:06
[2015-09-30T21:26Z] INFO  22:26:06,627 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:06,627 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:06,700 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:26Z] INFO  22:26:06,739 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:26Z] INFO  22:26:06,739 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:26Z] INFO  22:26:06,740 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:26Z] INFO  22:26:06,740 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:26Z] INFO  22:26:06,772 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:26Z] INFO  22:26:06,846 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:26Z] INFO  22:26:06,954 IntervalUtils - Processing 1055285 bp from intervals
[2015-09-30T21:26Z] WARN  22:26:06,955 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:26Z] WARN  22:26:06,956 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:26Z] INFO  22:26:07,009 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:26Z] INFO  22:26:07,012 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:26Z] INFO  22:26:07,012 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:26Z] INFO  22:26:07,012 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:26Z] INFO  22:26:07,013 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:26Z] INFO  22:26:09,435 ProgressMeter -            done      2131.0     2.0 s      18.9 m      100.0%     2.0 s       0.0 s
[2015-09-30T21:26Z] INFO  22:26:09,436 ProgressMeter - Total runtime 2.42 secs, 0.04 min, 0.00 hours
[2015-09-30T21:26Z] bgzip syn3-14_93263525_107349540-raw.vcf
[2015-09-30T21:26Z] tabix index syn3-14_93263525_107349540-raw.vcf.gz
[2015-09-30T21:26Z] bgzip syn3-14_93263525_107349540-raw-rejectfix.vcf
[2015-09-30T21:26Z] tabix index syn3-14_93263525_107349540-raw-rejectfix.vcf.gz
[2015-09-30T21:26Z] GATK: VariantAnnotator
[2015-09-30T21:26Z] INFO  22:26:12,048 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:12,050 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:26Z] INFO  22:26:12,051 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:26Z] INFO  22:26:12,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:26Z] INFO  22:26:12,054 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/14/syn3-14_93263525_107349540-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/14/tx/tmpItpAGr/syn3-14_93263525_107349540-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/14/syn3-14_93263525_107349540-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:26Z] INFO  22:26:12,060 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:26Z] INFO  22:26:12,060 HelpFormatter - Date/Time: 2015/09/30 22:26:12
[2015-09-30T21:26Z] INFO  22:26:12,060 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:12,061 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:26Z] INFO  22:26:12,157 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:26Z] INFO  22:26:12,233 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:26Z] INFO  22:26:12,241 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:26Z] INFO  22:26:12,263 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:26Z] INFO  22:26:12,697 IntervalUtils - Processing 2136 bp from intervals
[2015-09-30T21:26Z] WARN  22:26:12,701 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:26Z] WARN  22:26:12,701 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:26Z] INFO  22:26:12,757 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:26Z] INFO  22:26:12,918 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:26Z] INFO  22:26:12,918 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:26Z] INFO  22:26:12,919 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:26Z] INFO  22:26:12,919 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:26Z] INFO  22:26:12,952 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:26Z] INFO  22:26:17,639 VariantAnnotator - Processed 1603 loci.
[2015-09-30T21:26Z]
[2015-09-30T21:26Z] INFO  22:26:17,661 ProgressMeter -            done      6673.0    10.0 s      27.3 m       99.9%    10.0 s       0.0 s
[2015-09-30T21:26Z] INFO  22:26:17,661 ProgressMeter - Total runtime 10.92 secs, 0.18 min, 0.00 hours
[2015-09-30T21:26Z] INFO  22:26:17,662 MicroScheduler - 6371 reads were filtered out during the traversal out of approximately 134779 total reads (4.73%)
[2015-09-30T21:26Z] INFO  22:26:17,662 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:26Z] INFO  22:26:17,662 MicroScheduler -   -> 6337 reads (4.70% of total) failing DuplicateReadFilter
[2015-09-30T21:26Z] INFO  22:26:17,662 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:26Z] INFO  22:26:17,663 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:26Z] INFO  22:26:17,663 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:26Z] INFO  22:26:17,663 MicroScheduler -   -> 34 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:26Z] INFO  22:26:18,620 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:26Z] Genotyping with varscan: ('15', 62148224, 93170844) 1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam
[2015-09-30T21:26Z] samtools mpileup
[2015-09-30T21:26Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:26Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:26Z] INFO  22:26:21,892 VariantAnnotator - Processed 1885 loci.
[2015-09-30T21:26Z]
[2015-09-30T21:26Z] INFO  22:26:21,913 ProgressMeter -            done     18996.0     8.0 s       7.9 m      100.0%     8.0 s       0.0 s
[2015-09-30T21:26Z] INFO  22:26:21,914 ProgressMeter - Total runtime 9.00 secs, 0.15 min, 0.00 hours
[2015-09-30T21:26Z] INFO  22:26:21,914 MicroScheduler - 7976 reads were filtered out during the traversal out of approximately 147182 total reads (5.42%)
[2015-09-30T21:26Z] INFO  22:26:21,914 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:26Z] INFO  22:26:21,914 MicroScheduler -   -> 7942 reads (5.40% of total) failing DuplicateReadFilter
[2015-09-30T21:26Z] INFO  22:26:21,915 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:26Z] INFO  22:26:21,915 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:26Z] INFO  22:26:21,915 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:26Z] INFO  22:26:21,915 MicroScheduler -   -> 34 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:26Z] INFO  22:26:22,932 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:26Z] Genotyping with varscan: ('15', 93173163, 102531392) 1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam
[2015-09-30T21:26Z] samtools mpileup
[2015-09-30T21:26Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:26Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:26Z] samtools mpileup
[2015-09-30T21:26Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:26Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:26Z] Varscan
[2015-09-30T21:26Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/15/tx/tmpwcxGpt/syn3-15_93173163_102531392-raw-normal.mpileup
[2015-09-30T21:26Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/15/tx/tmpwcxGpt/syn3-15_93173163_102531392-raw-tumor.mpileup
[2015-09-30T21:26Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:26Z] Min reads2:	2
[2015-09-30T21:26Z] Min strands2:	1
[2015-09-30T21:26Z] Min var freq:	0.1
[2015-09-30T21:26Z] Min freq for hom:	0.75
[2015-09-30T21:26Z] Normal purity:	1.0
[2015-09-30T21:26Z] Tumor purity:	1.0
[2015-09-30T21:26Z] Min avg qual:	15
[2015-09-30T21:26Z] P-value thresh:	0.98
[2015-09-30T21:26Z] Somatic p-value:	0.05
[2015-09-30T21:27Z] samtools mpileup
[2015-09-30T21:27Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:27Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:27Z] 299771 positions in tumor
[2015-09-30T21:27Z] 299769 positions shared in normal
[2015-09-30T21:27Z] 294273 had sufficient coverage for comparison
[2015-09-30T21:27Z] 293594 were called Reference
[2015-09-30T21:27Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:27Z] 42 were removed by the strand filter
[2015-09-30T21:27Z] 662 were called Germline
[2015-09-30T21:27Z] 4 were called LOH
[2015-09-30T21:27Z] 9 were called Somatic
[2015-09-30T21:27Z] 4 were called Unknown
[2015-09-30T21:27Z] 0 were called Variant
[2015-09-30T21:27Z] Varscan paired fix
[2015-09-30T21:27Z] Varscan paired fix
[2015-09-30T21:27Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:27Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:27Z] bgzip syn3-15_93173163_102531392-raw.snp.vcf
[2015-09-30T21:27Z] tabix index syn3-15_93173163_102531392-raw.snp.vcf.gz
[2015-09-30T21:27Z] bgzip syn3-15_93173163_102531392-raw.indel.vcf
[2015-09-30T21:27Z] tabix index syn3-15_93173163_102531392-raw.indel.vcf.gz
[2015-09-30T21:27Z] Combine variant files
[2015-09-30T21:27Z] INFO  22:27:11,216 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:27Z] INFO  22:27:11,218 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:27Z] INFO  22:27:11,219 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:27Z] INFO  22:27:11,219 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:27Z] INFO  22:27:11,222 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/15/tx/tmpwcxGpt/tx/tmpUN7B5I/syn3-15_93173163_102531392-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/15/tx/tmpwcxGpt/syn3-15_93173163_102531392-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/15/tx/tmpwcxGpt/syn3-15_93173163_102531392-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/15/syn3-15_93173163_102531392-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:27Z] INFO  22:27:11,228 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:27Z] INFO  22:27:11,228 HelpFormatter - Date/Time: 2015/09/30 22:27:11
[2015-09-30T21:27Z] INFO  22:27:11,228 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:27Z] INFO  22:27:11,229 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:27Z] INFO  22:27:11,301 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:27Z] INFO  22:27:11,426 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:27Z] INFO  22:27:11,509 IntervalUtils - Processing 301747 bp from intervals
[2015-09-30T21:27Z] WARN  22:27:11,510 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:27Z] WARN  22:27:11,510 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:27Z] INFO  22:27:11,564 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:27Z] INFO  22:27:11,565 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:27Z] INFO  22:27:11,566 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:27Z] INFO  22:27:11,566 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:27Z] INFO  22:27:11,566 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:27Z] INFO  22:27:12,189 ProgressMeter -            done       729.0     0.0 s      14.2 m       99.6%     0.0 s       0.0 s
[2015-09-30T21:27Z] INFO  22:27:12,190 ProgressMeter - Total runtime 0.62 secs, 0.01 min, 0.00 hours
[2015-09-30T21:27Z] bgzip syn3-15_93173163_102531392-raw.vcf
[2015-09-30T21:27Z] tabix index syn3-15_93173163_102531392-raw.vcf.gz
[2015-09-30T21:27Z] bgzip syn3-15_93173163_102531392-raw-rejectfix.vcf
[2015-09-30T21:27Z] tabix index syn3-15_93173163_102531392-raw-rejectfix.vcf.gz
[2015-09-30T21:27Z] GATK: VariantAnnotator
[2015-09-30T21:27Z] INFO  22:27:14,719 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:27Z] INFO  22:27:14,721 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:27Z] INFO  22:27:14,721 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:27Z] INFO  22:27:14,722 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:27Z] INFO  22:27:14,725 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/15/syn3-15_93173163_102531392-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/15/tx/tmp89Kurp/syn3-15_93173163_102531392-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/15/syn3-15_93173163_102531392-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:27Z] INFO  22:27:14,730 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:27Z] INFO  22:27:14,731 HelpFormatter - Date/Time: 2015/09/30 22:27:14
[2015-09-30T21:27Z] INFO  22:27:14,731 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:27Z] INFO  22:27:14,731 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:27Z] INFO  22:27:14,826 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:27Z] INFO  22:27:14,900 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:27Z] INFO  22:27:14,907 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:27Z] INFO  22:27:14,928 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:27Z] INFO  22:27:15,218 IntervalUtils - Processing 729 bp from intervals
[2015-09-30T21:27Z] WARN  22:27:15,222 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:27Z] WARN  22:27:15,222 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:27Z] INFO  22:27:15,276 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:27Z] INFO  22:27:15,331 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:27Z] INFO  22:27:15,331 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:27Z] INFO  22:27:15,331 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:27Z] INFO  22:27:15,332 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:27Z] INFO  22:27:15,363 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:27Z] INFO  22:27:19,435 VariantAnnotator - Processed 633 loci.
[2015-09-30T21:27Z]
[2015-09-30T21:27Z] INFO  22:27:19,456 ProgressMeter -            done      5147.0     4.0 s      13.4 m       99.9%     4.0 s       0.0 s
[2015-09-30T21:27Z] INFO  22:27:19,456 ProgressMeter - Total runtime 4.13 secs, 0.07 min, 0.00 hours
[2015-09-30T21:27Z] INFO  22:27:19,457 MicroScheduler - 2855 reads were filtered out during the traversal out of approximately 57320 total reads (4.98%)
[2015-09-30T21:27Z] INFO  22:27:19,457 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:27Z] INFO  22:27:19,457 MicroScheduler -   -> 2843 reads (4.96% of total) failing DuplicateReadFilter
[2015-09-30T21:27Z] INFO  22:27:19,457 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:27Z] INFO  22:27:19,458 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:27Z] INFO  22:27:19,458 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:27Z] INFO  22:27:19,458 MicroScheduler -   -> 12 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:27Z] INFO  22:27:20,411 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:27Z] Genotyping with varscan: ('16', 0, 31021934) 1_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam
[2015-09-30T21:27Z] samtools mpileup
[2015-09-30T21:27Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:27Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:27Z] samtools mpileup
[2015-09-30T21:27Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:27Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:28Z] Varscan
[2015-09-30T21:28Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/15/tx/tmp0dZfYI/syn3-15_31042312_62147370-raw-normal.mpileup
[2015-09-30T21:28Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/15/tx/tmp0dZfYI/syn3-15_31042312_62147370-raw-tumor.mpileup
[2015-09-30T21:28Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:28Z] Min reads2:	2
[2015-09-30T21:28Z] Min strands2:	1
[2015-09-30T21:28Z] Min var freq:	0.1
[2015-09-30T21:28Z] Min freq for hom:	0.75
[2015-09-30T21:28Z] Normal purity:	1.0
[2015-09-30T21:28Z] Tumor purity:	1.0
[2015-09-30T21:28Z] Min avg qual:	15
[2015-09-30T21:28Z] P-value thresh:	0.98
[2015-09-30T21:28Z] Somatic p-value:	0.05
[2015-09-30T21:29Z] samtools mpileup
[2015-09-30T21:29Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:29Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:29Z] Varscan
[2015-09-30T21:29Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/15/tx/tmpGop_5u/syn3-15_62148224_93170844-raw-normal.mpileup
[2015-09-30T21:29Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/15/tx/tmpGop_5u/syn3-15_62148224_93170844-raw-tumor.mpileup
[2015-09-30T21:29Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:29Z] Min reads2:	2
[2015-09-30T21:29Z] Min strands2:	1
[2015-09-30T21:29Z] Min var freq:	0.1
[2015-09-30T21:29Z] Min freq for hom:	0.75
[2015-09-30T21:29Z] Normal purity:	1.0
[2015-09-30T21:29Z] Tumor purity:	1.0
[2015-09-30T21:29Z] Min avg qual:	15
[2015-09-30T21:29Z] P-value thresh:	0.98
[2015-09-30T21:29Z] Somatic p-value:	0.05
[2015-09-30T21:29Z] 2227881 positions in tumor
[2015-09-30T21:29Z] 2227864 positions shared in normal
[2015-09-30T21:29Z] 2183288 had sufficient coverage for comparison
[2015-09-30T21:29Z] 2180530 were called Reference
[2015-09-30T21:29Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:29Z] 161 were removed by the strand filter
[2015-09-30T21:29Z] 2670 were called Germline
[2015-09-30T21:29Z] 6 were called LOH
[2015-09-30T21:29Z] 64 were called Somatic
[2015-09-30T21:29Z] 18 were called Unknown
[2015-09-30T21:29Z] 0 were called Variant
[2015-09-30T21:29Z] Varscan paired fix
[2015-09-30T21:29Z] Varscan paired fix
[2015-09-30T21:29Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:29Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:29Z] bgzip syn3-15_31042312_62147370-raw.snp.vcf
[2015-09-30T21:29Z] tabix index syn3-15_31042312_62147370-raw.snp.vcf.gz
[2015-09-30T21:29Z] bgzip syn3-15_31042312_62147370-raw.indel.vcf
[2015-09-30T21:29Z] tabix index syn3-15_31042312_62147370-raw.indel.vcf.gz
[2015-09-30T21:29Z] Combine variant files
[2015-09-30T21:29Z] INFO  22:29:57,452 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:29Z] INFO  22:29:57,454 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:29Z] INFO  22:29:57,454 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:29Z] INFO  22:29:57,454 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:29Z] INFO  22:29:57,457 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/15/tx/tmp0dZfYI/tx/tmpGBpeGX/syn3-15_31042312_62147370-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/15/tx/tmp0dZfYI/syn3-15_31042312_62147370-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/15/tx/tmp0dZfYI/syn3-15_31042312_62147370-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/15/syn3-15_31042312_62147370-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:29Z] INFO  22:29:57,464 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:29Z] INFO  22:29:57,464 HelpFormatter - Date/Time: 2015/09/30 22:29:57
[2015-09-30T21:29Z] INFO  22:29:57,464 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:29Z] INFO  22:29:57,464 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:29Z] INFO  22:29:57,543 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:29Z] INFO  22:29:57,819 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:29Z] INFO  22:29:57,963 IntervalUtils - Processing 2237327 bp from intervals
[2015-09-30T21:29Z] WARN  22:29:57,965 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:29Z] WARN  22:29:57,965 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:29Z] INFO  22:29:58,025 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:29Z] INFO  22:29:58,030 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:29Z] INFO  22:29:58,030 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:29Z] INFO  22:29:58,031 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:29Z] INFO  22:29:58,031 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:29Z] INFO  22:29:59,859 ProgressMeter -            done      2987.0     1.0 s      10.2 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:29Z] INFO  22:29:59,860 ProgressMeter - Total runtime 1.83 secs, 0.03 min, 0.00 hours
[2015-09-30T21:30Z] bgzip syn3-15_31042312_62147370-raw.vcf
[2015-09-30T21:30Z] tabix index syn3-15_31042312_62147370-raw.vcf.gz
[2015-09-30T21:30Z] bgzip syn3-15_31042312_62147370-raw-rejectfix.vcf
[2015-09-30T21:30Z] tabix index syn3-15_31042312_62147370-raw-rejectfix.vcf.gz
[2015-09-30T21:30Z] GATK: VariantAnnotator
[2015-09-30T21:30Z] INFO  22:30:02,670 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:30Z] INFO  22:30:02,672 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:30Z] INFO  22:30:02,672 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:30Z] INFO  22:30:02,672 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:30Z] INFO  22:30:02,676 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/15/syn3-15_31042312_62147370-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/15/tx/tmpfbqRc5/syn3-15_31042312_62147370-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/15/syn3-15_31042312_62147370-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:30Z] INFO  22:30:02,681 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:30Z] INFO  22:30:02,681 HelpFormatter - Date/Time: 2015/09/30 22:30:02
[2015-09-30T21:30Z] INFO  22:30:02,682 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:30Z] INFO  22:30:02,682 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:30Z] INFO  22:30:02,773 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:30Z] INFO  22:30:02,851 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:30Z] INFO  22:30:02,858 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:30Z] INFO  22:30:02,881 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:30Z] INFO  22:30:03,326 IntervalUtils - Processing 2987 bp from intervals
[2015-09-30T21:30Z] WARN  22:30:03,330 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:30Z] WARN  22:30:03,330 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:30Z] INFO  22:30:03,387 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:30Z] INFO  22:30:03,593 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:30Z] INFO  22:30:03,593 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:30Z] INFO  22:30:03,593 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:30Z] INFO  22:30:03,594 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:30Z] INFO  22:30:03,626 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:30Z] INFO  22:30:16,380 VariantAnnotator - Processed 2584 loci.
[2015-09-30T21:30Z]
[2015-09-30T21:30Z] INFO  22:30:16,400 ProgressMeter -            done     15343.0    12.0 s      13.9 m      100.0%    12.0 s       0.0 s
[2015-09-30T21:30Z] INFO  22:30:16,401 ProgressMeter - Total runtime 12.81 secs, 0.21 min, 0.00 hours
[2015-09-30T21:30Z] INFO  22:30:16,401 MicroScheduler - 9339 reads were filtered out during the traversal out of approximately 208380 total reads (4.48%)
[2015-09-30T21:30Z] INFO  22:30:16,401 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:30Z] INFO  22:30:16,402 MicroScheduler -   -> 9283 reads (4.45% of total) failing DuplicateReadFilter
[2015-09-30T21:30Z] INFO  22:30:16,402 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:30Z] INFO  22:30:16,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:30Z] INFO  22:30:16,402 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:30Z] INFO  22:30:16,402 MicroScheduler -   -> 56 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:30Z] INFO  22:30:17,344 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:30Z] Genotyping with varscan: ('16', 31044089, 62860191) 1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam
[2015-09-30T21:30Z] samtools mpileup
[2015-09-30T21:30Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:30Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:31Z] samtools mpileup
[2015-09-30T21:31Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:31Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:31Z] 2364926 positions in tumor
[2015-09-30T21:31Z] 2364918 positions shared in normal
[2015-09-30T21:31Z] 2330102 had sufficient coverage for comparison
[2015-09-30T21:31Z] 2327214 were called Reference
[2015-09-30T21:31Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:31Z] 195 were removed by the strand filter
[2015-09-30T21:31Z] 2801 were called Germline
[2015-09-30T21:31Z] 9 were called LOH
[2015-09-30T21:31Z] 67 were called Somatic
[2015-09-30T21:31Z] 11 were called Unknown
[2015-09-30T21:31Z] 0 were called Variant
[2015-09-30T21:31Z] Varscan paired fix
[2015-09-30T21:31Z] Varscan paired fix
[2015-09-30T21:31Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:31Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:31Z] bgzip syn3-15_62148224_93170844-raw.snp.vcf
[2015-09-30T21:31Z] tabix index syn3-15_62148224_93170844-raw.snp.vcf.gz
[2015-09-30T21:31Z] bgzip syn3-15_62148224_93170844-raw.indel.vcf
[2015-09-30T21:31Z] tabix index syn3-15_62148224_93170844-raw.indel.vcf.gz
[2015-09-30T21:31Z] Combine variant files
[2015-09-30T21:31Z] INFO  22:31:10,083 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:31Z] INFO  22:31:10,085 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:31Z] INFO  22:31:10,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:31Z] INFO  22:31:10,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:31Z] INFO  22:31:10,089 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/15/tx/tmpGop_5u/tx/tmpW8MJOR/syn3-15_62148224_93170844-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/15/tx/tmpGop_5u/syn3-15_62148224_93170844-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/15/tx/tmpGop_5u/syn3-15_62148224_93170844-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/15/syn3-15_62148224_93170844-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:31Z] INFO  22:31:10,094 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:31Z] INFO  22:31:10,095 HelpFormatter - Date/Time: 2015/09/30 22:31:10
[2015-09-30T21:31Z] INFO  22:31:10,095 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:31Z] INFO  22:31:10,095 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:31Z] INFO  22:31:10,166 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:31Z] INFO  22:31:10,361 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:31Z] INFO  22:31:10,503 IntervalUtils - Processing 2371101 bp from intervals
[2015-09-30T21:31Z] WARN  22:31:10,504 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:31Z] WARN  22:31:10,505 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:31Z] INFO  22:31:10,558 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:31Z] INFO  22:31:10,563 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:31Z] INFO  22:31:10,563 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:31Z] INFO  22:31:10,564 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:31Z] INFO  22:31:10,564 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:31Z] INFO  22:31:12,408 ProgressMeter -            done      3111.0     1.0 s       9.9 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:31Z] INFO  22:31:12,409 ProgressMeter - Total runtime 1.85 secs, 0.03 min, 0.00 hours
[2015-09-30T21:31Z] bgzip syn3-15_62148224_93170844-raw.vcf
[2015-09-30T21:31Z] tabix index syn3-15_62148224_93170844-raw.vcf.gz
[2015-09-30T21:31Z] bgzip syn3-15_62148224_93170844-raw-rejectfix.vcf
[2015-09-30T21:31Z] tabix index syn3-15_62148224_93170844-raw-rejectfix.vcf.gz
[2015-09-30T21:31Z] GATK: VariantAnnotator
[2015-09-30T21:31Z] INFO  22:31:15,025 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:31Z] INFO  22:31:15,027 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:31Z] INFO  22:31:15,027 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:31Z] INFO  22:31:15,027 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:31Z] INFO  22:31:15,031 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/15/syn3-15_62148224_93170844-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/15/tx/tmpcBGFOS/syn3-15_62148224_93170844-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/15/syn3-15_62148224_93170844-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:31Z] INFO  22:31:15,036 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:31Z] INFO  22:31:15,036 HelpFormatter - Date/Time: 2015/09/30 22:31:15
[2015-09-30T21:31Z] INFO  22:31:15,036 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:31Z] INFO  22:31:15,037 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:31Z] INFO  22:31:15,396 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:31Z] INFO  22:31:15,472 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:31Z] INFO  22:31:15,480 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:31Z] INFO  22:31:15,502 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:31Z] INFO  22:31:15,919 IntervalUtils - Processing 3111 bp from intervals
[2015-09-30T21:31Z] WARN  22:31:15,923 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:31Z] WARN  22:31:15,924 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:31Z] INFO  22:31:16,044 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:31Z] INFO  22:31:16,218 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:31Z] INFO  22:31:16,218 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:31Z] INFO  22:31:16,219 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:31Z] INFO  22:31:16,219 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:31Z] INFO  22:31:16,251 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:31Z] Varscan
[2015-09-30T21:31Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/16/tx/tmpQU5Zuq/syn3-16_0_31021934-raw-normal.mpileup
[2015-09-30T21:31Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/16/tx/tmpQU5Zuq/syn3-16_0_31021934-raw-tumor.mpileup
[2015-09-30T21:31Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:31Z] Min reads2:	2
[2015-09-30T21:31Z] Min strands2:	1
[2015-09-30T21:31Z] Min var freq:	0.1
[2015-09-30T21:31Z] Min freq for hom:	0.75
[2015-09-30T21:31Z] Normal purity:	1.0
[2015-09-30T21:31Z] Tumor purity:	1.0
[2015-09-30T21:31Z] Min avg qual:	15
[2015-09-30T21:31Z] P-value thresh:	0.98
[2015-09-30T21:31Z] Somatic p-value:	0.05
[2015-09-30T21:31Z] INFO  22:31:30,799 VariantAnnotator - Processed 2685 loci.
[2015-09-30T21:31Z]
[2015-09-30T21:31Z] INFO  22:31:32,973 ProgressMeter -            done     15001.0    16.0 s      18.6 m      100.0%    16.0 s       0.0 s
[2015-09-30T21:31Z] INFO  22:31:32,973 ProgressMeter - Total runtime 16.75 secs, 0.28 min, 0.00 hours
[2015-09-30T21:31Z] INFO  22:31:32,973 MicroScheduler - 12540 reads were filtered out during the traversal out of approximately 254276 total reads (4.93%)
[2015-09-30T21:31Z] INFO  22:31:32,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:31Z] INFO  22:31:32,974 MicroScheduler -   -> 12446 reads (4.89% of total) failing DuplicateReadFilter
[2015-09-30T21:31Z] INFO  22:31:32,974 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:31Z] INFO  22:31:32,974 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:31Z] INFO  22:31:32,975 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:31Z] INFO  22:31:32,975 MicroScheduler -   -> 94 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T21:31Z] INFO  22:31:33,904 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:31Z] Genotyping with varscan: ('16', 64294277, 90354753) 1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam
[2015-09-30T21:31Z] samtools mpileup
[2015-09-30T21:31Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:31Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:31Z] Varscan
[2015-09-30T21:31Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/16/tx/tmpNchSeN/syn3-16_31044089_62860191-raw-normal.mpileup
[2015-09-30T21:31Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/16/tx/tmpNchSeN/syn3-16_31044089_62860191-raw-tumor.mpileup
[2015-09-30T21:31Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:31Z] Min reads2:	2
[2015-09-30T21:31Z] Min strands2:	1
[2015-09-30T21:31Z] Min var freq:	0.1
[2015-09-30T21:31Z] Min freq for hom:	0.75
[2015-09-30T21:31Z] Normal purity:	1.0
[2015-09-30T21:31Z] Tumor purity:	1.0
[2015-09-30T21:31Z] Min avg qual:	15
[2015-09-30T21:31Z] P-value thresh:	0.98
[2015-09-30T21:31Z] Somatic p-value:	0.05
[2015-09-30T21:32Z] 1106481 positions in tumor
[2015-09-30T21:32Z] 1106477 positions shared in normal
[2015-09-30T21:32Z] 1091970 had sufficient coverage for comparison
[2015-09-30T21:32Z] 1090010 were called Reference
[2015-09-30T21:32Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:32Z] 207 were removed by the strand filter
[2015-09-30T21:32Z] 1909 were called Germline
[2015-09-30T21:32Z] 5 were called LOH
[2015-09-30T21:32Z] 34 were called Somatic
[2015-09-30T21:32Z] 12 were called Unknown
[2015-09-30T21:32Z] 0 were called Variant
[2015-09-30T21:32Z] Varscan paired fix
[2015-09-30T21:32Z] Varscan paired fix
[2015-09-30T21:32Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:32Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:32Z] bgzip syn3-16_31044089_62860191-raw.snp.vcf
[2015-09-30T21:32Z] tabix index syn3-16_31044089_62860191-raw.snp.vcf.gz
[2015-09-30T21:32Z] bgzip syn3-16_31044089_62860191-raw.indel.vcf
[2015-09-30T21:32Z] tabix index syn3-16_31044089_62860191-raw.indel.vcf.gz
[2015-09-30T21:32Z] Combine variant files
[2015-09-30T21:32Z] INFO  22:32:36,163 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:32Z] INFO  22:32:36,165 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:32Z] INFO  22:32:36,165 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:32Z] INFO  22:32:36,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:32Z] INFO  22:32:36,169 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/16/tx/tmpNchSeN/tx/tmpUTWziP/syn3-16_31044089_62860191-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/16/tx/tmpNchSeN/syn3-16_31044089_62860191-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/16/tx/tmpNchSeN/syn3-16_31044089_62860191-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/16/syn3-16_31044089_62860191-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:32Z] INFO  22:32:36,175 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:32Z] INFO  22:32:36,175 HelpFormatter - Date/Time: 2015/09/30 22:32:36
[2015-09-30T21:32Z] INFO  22:32:36,175 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:32Z] INFO  22:32:36,176 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:32Z] INFO  22:32:36,252 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:32Z] INFO  22:32:36,390 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:32Z] INFO  22:32:36,499 IntervalUtils - Processing 1115296 bp from intervals
[2015-09-30T21:32Z] WARN  22:32:36,499 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:32Z] WARN  22:32:36,500 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:32Z] INFO  22:32:36,557 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:32Z] INFO  22:32:36,560 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:32Z] INFO  22:32:36,561 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:32Z] INFO  22:32:36,561 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:32Z] INFO  22:32:36,561 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:32Z] INFO  22:32:38,007 ProgressMeter -            done      1991.0     1.0 s      12.1 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:32Z] INFO  22:32:38,008 ProgressMeter - Total runtime 1.45 secs, 0.02 min, 0.00 hours
[2015-09-30T21:32Z] bgzip syn3-16_31044089_62860191-raw.vcf
[2015-09-30T21:32Z] tabix index syn3-16_31044089_62860191-raw.vcf.gz
[2015-09-30T21:32Z] bgzip syn3-16_31044089_62860191-raw-rejectfix.vcf
[2015-09-30T21:32Z] tabix index syn3-16_31044089_62860191-raw-rejectfix.vcf.gz
[2015-09-30T21:32Z] GATK: VariantAnnotator
[2015-09-30T21:32Z] INFO  22:32:40,842 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:32Z] INFO  22:32:40,844 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:32Z] INFO  22:32:40,845 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:32Z] INFO  22:32:40,845 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:32Z] INFO  22:32:40,848 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/16/syn3-16_31044089_62860191-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/16/tx/tmpBYW_qs/syn3-16_31044089_62860191-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/16/syn3-16_31044089_62860191-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:32Z] INFO  22:32:40,854 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:32Z] INFO  22:32:40,854 HelpFormatter - Date/Time: 2015/09/30 22:32:40
[2015-09-30T21:32Z] INFO  22:32:40,854 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:32Z] INFO  22:32:40,855 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:32Z] INFO  22:32:40,930 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:32Z] INFO  22:32:41,015 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:32Z] INFO  22:32:41,023 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:32Z] INFO  22:32:41,046 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:32Z] INFO  22:32:41,424 IntervalUtils - Processing 1991 bp from intervals
[2015-09-30T21:32Z] WARN  22:32:41,429 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:32Z] WARN  22:32:41,429 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:32Z] INFO  22:32:41,485 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:32Z] INFO  22:32:41,650 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:32Z] INFO  22:32:41,650 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:32Z] INFO  22:32:41,651 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:32Z] INFO  22:32:41,651 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:32Z] INFO  22:32:41,683 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:32Z] INFO  22:32:51,725 VariantAnnotator - Processed 1746 loci.
[2015-09-30T21:32Z]
[2015-09-30T21:32Z] INFO  22:32:51,746 ProgressMeter -            done     15172.0    10.0 s      11.1 m       99.9%    10.0 s       0.0 s
[2015-09-30T21:32Z] INFO  22:32:51,746 ProgressMeter - Total runtime 10.10 secs, 0.17 min, 0.00 hours
[2015-09-30T21:32Z] INFO  22:32:51,746 MicroScheduler - 8380 reads were filtered out during the traversal out of approximately 161765 total reads (5.18%)
[2015-09-30T21:32Z] INFO  22:32:51,747 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:32Z] INFO  22:32:51,747 MicroScheduler -   -> 8305 reads (5.13% of total) failing DuplicateReadFilter
[2015-09-30T21:32Z] INFO  22:32:51,747 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:32Z] INFO  22:32:51,747 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:32Z] INFO  22:32:51,748 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:32Z] INFO  22:32:51,748 MicroScheduler -   -> 75 reads (0.05% of total) failing UnmappedReadFilter
[2015-09-30T21:32Z] INFO  22:32:52,664 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:32Z] Genotyping with varscan: ('17', 0, 31039439) 1_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam
[2015-09-30T21:32Z] samtools mpileup
[2015-09-30T21:32Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:32Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:32Z] samtools mpileup
[2015-09-30T21:32Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:32Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:33Z] 3087617 positions in tumor
[2015-09-30T21:33Z] 3087596 positions shared in normal
[2015-09-30T21:33Z] 3066477 had sufficient coverage for comparison
[2015-09-30T21:33Z] 3062431 were called Reference
[2015-09-30T21:33Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:33Z] 299 were removed by the strand filter
[2015-09-30T21:33Z] 3889 were called Germline
[2015-09-30T21:33Z] 11 were called LOH
[2015-09-30T21:33Z] 121 were called Somatic
[2015-09-30T21:33Z] 25 were called Unknown
[2015-09-30T21:33Z] 0 were called Variant
[2015-09-30T21:33Z] Varscan paired fix
[2015-09-30T21:33Z] Varscan paired fix
[2015-09-30T21:33Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:33Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:33Z] bgzip syn3-16_0_31021934-raw.snp.vcf
[2015-09-30T21:33Z] tabix index syn3-16_0_31021934-raw.snp.vcf.gz
[2015-09-30T21:33Z] bgzip syn3-16_0_31021934-raw.indel.vcf
[2015-09-30T21:33Z] tabix index syn3-16_0_31021934-raw.indel.vcf.gz
[2015-09-30T21:33Z] Combine variant files
[2015-09-30T21:33Z] INFO  22:33:39,687 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:33Z] INFO  22:33:39,689 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:33Z] INFO  22:33:39,689 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:33Z] INFO  22:33:39,690 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:33Z] INFO  22:33:39,693 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/16/tx/tmpQU5Zuq/tx/tmpbcbvTI/syn3-16_0_31021934-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/16/tx/tmpQU5Zuq/syn3-16_0_31021934-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/16/tx/tmpQU5Zuq/syn3-16_0_31021934-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/16/syn3-16_0_31021934-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:33Z] INFO  22:33:39,698 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:33Z] INFO  22:33:39,699 HelpFormatter - Date/Time: 2015/09/30 22:33:39
[2015-09-30T21:33Z] INFO  22:33:39,699 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:33Z] INFO  22:33:39,699 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:33Z] INFO  22:33:39,774 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:33Z] INFO  22:33:39,913 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:33Z] INFO  22:33:40,067 IntervalUtils - Processing 3098080 bp from intervals
[2015-09-30T21:33Z] WARN  22:33:40,068 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:33Z] WARN  22:33:40,068 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:33Z] INFO  22:33:40,127 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:33Z] INFO  22:33:40,133 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:33Z] INFO  22:33:40,134 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:33Z] INFO  22:33:40,134 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:33Z] INFO  22:33:40,134 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:33Z] INFO  22:33:42,727 ProgressMeter -            done      4326.0     2.0 s      10.0 m      100.0%     2.0 s       0.0 s
[2015-09-30T21:33Z] INFO  22:33:42,727 ProgressMeter - Total runtime 2.59 secs, 0.04 min, 0.00 hours
[2015-09-30T21:33Z] bgzip syn3-16_0_31021934-raw.vcf
[2015-09-30T21:33Z] tabix index syn3-16_0_31021934-raw.vcf.gz
[2015-09-30T21:33Z] bgzip syn3-16_0_31021934-raw-rejectfix.vcf
[2015-09-30T21:33Z] tabix index syn3-16_0_31021934-raw-rejectfix.vcf.gz
[2015-09-30T21:33Z] GATK: VariantAnnotator
[2015-09-30T21:33Z] INFO  22:33:45,766 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:33Z] INFO  22:33:45,768 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:33Z] INFO  22:33:45,768 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:33Z] INFO  22:33:45,769 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:33Z] INFO  22:33:45,772 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/16/syn3-16_0_31021934-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/16/tx/tmpeqti0a/syn3-16_0_31021934-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/16/syn3-16_0_31021934-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:33Z] INFO  22:33:45,777 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:33Z] INFO  22:33:45,778 HelpFormatter - Date/Time: 2015/09/30 22:33:45
[2015-09-30T21:33Z] INFO  22:33:45,778 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:33Z] INFO  22:33:45,778 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:33Z] INFO  22:33:45,870 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:33Z] INFO  22:33:45,945 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:33Z] INFO  22:33:45,953 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:33Z] INFO  22:33:45,988 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T21:33Z] INFO  22:33:46,544 IntervalUtils - Processing 4329 bp from intervals
[2015-09-30T21:33Z] WARN  22:33:46,548 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:33Z] WARN  22:33:46,548 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:33Z] INFO  22:33:46,604 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:33Z] INFO  22:33:46,752 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:33Z] INFO  22:33:46,752 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:33Z] INFO  22:33:46,753 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:33Z] INFO  22:33:46,753 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:33Z] INFO  22:33:46,784 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:34Z] INFO  22:34:08,352 VariantAnnotator - Processed 3729 loci.
[2015-09-30T21:34Z]
[2015-09-30T21:34Z] INFO  22:34:08,372 ProgressMeter -            done     27714.0    21.0 s      13.0 m      100.0%    21.0 s       0.0 s
[2015-09-30T21:34Z] INFO  22:34:08,372 ProgressMeter - Total runtime 21.62 secs, 0.36 min, 0.01 hours
[2015-09-30T21:34Z] INFO  22:34:08,372 MicroScheduler - 19741 reads were filtered out during the traversal out of approximately 376626 total reads (5.24%)
[2015-09-30T21:34Z] INFO  22:34:08,372 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:34Z] INFO  22:34:08,373 MicroScheduler -   -> 19661 reads (5.22% of total) failing DuplicateReadFilter
[2015-09-30T21:34Z] INFO  22:34:08,373 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:34Z] INFO  22:34:08,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:34Z] INFO  22:34:08,373 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:34Z] INFO  22:34:08,373 MicroScheduler -   -> 80 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:34Z] INFO  22:34:09,317 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:34Z] Genotyping with varscan: ('17', 31047756, 62076645) 1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam
[2015-09-30T21:34Z] samtools mpileup
[2015-09-30T21:34Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:34Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:34Z] Varscan
[2015-09-30T21:34Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/16/tx/tmpzVddBQ/syn3-16_64294277_90354753-raw-normal.mpileup
[2015-09-30T21:34Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/16/tx/tmpzVddBQ/syn3-16_64294277_90354753-raw-tumor.mpileup
[2015-09-30T21:34Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:34Z] Min reads2:	2
[2015-09-30T21:34Z] Min strands2:	1
[2015-09-30T21:34Z] Min var freq:	0.1
[2015-09-30T21:34Z] Min freq for hom:	0.75
[2015-09-30T21:34Z] Normal purity:	1.0
[2015-09-30T21:34Z] Tumor purity:	1.0
[2015-09-30T21:34Z] Min avg qual:	15
[2015-09-30T21:34Z] P-value thresh:	0.98
[2015-09-30T21:34Z] Somatic p-value:	0.05
[2015-09-30T21:34Z] samtools mpileup
[2015-09-30T21:34Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:34Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:35Z] 1889358 positions in tumor
[2015-09-30T21:35Z] 1889350 positions shared in normal
[2015-09-30T21:35Z] 1874731 had sufficient coverage for comparison
[2015-09-30T21:35Z] 1871923 were called Reference
[2015-09-30T21:35Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:35Z] 149 were removed by the strand filter
[2015-09-30T21:35Z] 2744 were called Germline
[2015-09-30T21:35Z] 5 were called LOH
[2015-09-30T21:35Z] 43 were called Somatic
[2015-09-30T21:35Z] 16 were called Unknown
[2015-09-30T21:35Z] 0 were called Variant
[2015-09-30T21:35Z] Varscan paired fix
[2015-09-30T21:35Z] Varscan paired fix
[2015-09-30T21:35Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:35Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:35Z] bgzip syn3-16_64294277_90354753-raw.snp.vcf
[2015-09-30T21:35Z] tabix index syn3-16_64294277_90354753-raw.snp.vcf.gz
[2015-09-30T21:35Z] bgzip syn3-16_64294277_90354753-raw.indel.vcf
[2015-09-30T21:35Z] tabix index syn3-16_64294277_90354753-raw.indel.vcf.gz
[2015-09-30T21:35Z] Combine variant files
[2015-09-30T21:35Z] INFO  22:35:39,962 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:35Z] INFO  22:35:39,965 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:35Z] INFO  22:35:39,965 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:35Z] INFO  22:35:39,965 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:35Z] INFO  22:35:39,968 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/16/tx/tmpzVddBQ/tx/tmpsbQPRq/syn3-16_64294277_90354753-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/16/tx/tmpzVddBQ/syn3-16_64294277_90354753-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/16/tx/tmpzVddBQ/syn3-16_64294277_90354753-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/16/syn3-16_64294277_90354753-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:35Z] INFO  22:35:39,974 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:35Z] INFO  22:35:39,974 HelpFormatter - Date/Time: 2015/09/30 22:35:39
[2015-09-30T21:35Z] INFO  22:35:39,974 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:35Z] INFO  22:35:39,975 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:35Z] INFO  22:35:40,054 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:35Z] INFO  22:35:40,197 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:35Z] INFO  22:35:40,338 IntervalUtils - Processing 1897108 bp from intervals
[2015-09-30T21:35Z] WARN  22:35:40,340 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:35Z] WARN  22:35:40,340 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:35Z] INFO  22:35:40,399 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:35Z] INFO  22:35:40,403 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:35Z] INFO  22:35:40,403 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:35Z] INFO  22:35:40,404 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:35Z] INFO  22:35:40,404 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:35Z] INFO  22:35:42,197 ProgressMeter -            done      3113.0     1.0 s       9.6 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:35Z] INFO  22:35:42,198 ProgressMeter - Total runtime 1.79 secs, 0.03 min, 0.00 hours
[2015-09-30T21:35Z] bgzip syn3-16_64294277_90354753-raw.vcf
[2015-09-30T21:35Z] tabix index syn3-16_64294277_90354753-raw.vcf.gz
[2015-09-30T21:35Z] bgzip syn3-16_64294277_90354753-raw-rejectfix.vcf
[2015-09-30T21:35Z] tabix index syn3-16_64294277_90354753-raw-rejectfix.vcf.gz
[2015-09-30T21:35Z] GATK: VariantAnnotator
[2015-09-30T21:35Z] INFO  22:35:44,912 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:35Z] INFO  22:35:44,914 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:35Z] INFO  22:35:44,915 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:35Z] INFO  22:35:44,915 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:35Z] INFO  22:35:44,919 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/16/syn3-16_64294277_90354753-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/16/tx/tmpvme_Za/syn3-16_64294277_90354753-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/16/syn3-16_64294277_90354753-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:35Z] INFO  22:35:44,925 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:35Z] INFO  22:35:44,925 HelpFormatter - Date/Time: 2015/09/30 22:35:44
[2015-09-30T21:35Z] INFO  22:35:44,925 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:35Z] INFO  22:35:44,926 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:35Z] INFO  22:35:45,001 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:35Z] INFO  22:35:45,080 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:35Z] INFO  22:35:45,087 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:35Z] INFO  22:35:45,119 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T21:35Z] INFO  22:35:45,651 IntervalUtils - Processing 3113 bp from intervals
[2015-09-30T21:35Z] WARN  22:35:45,655 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:35Z] WARN  22:35:45,656 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:35Z] INFO  22:35:45,711 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:35Z] INFO  22:35:45,860 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:35Z] INFO  22:35:45,860 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:35Z] INFO  22:35:45,860 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:35Z] INFO  22:35:45,861 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:35Z] INFO  22:35:45,893 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:35Z] INFO  22:35:59,854 VariantAnnotator - Processed 2645 loci.
[2015-09-30T21:35Z]
[2015-09-30T21:35Z] INFO  22:35:59,884 ProgressMeter -            done     19307.0    14.0 s      12.1 m      100.0%    14.0 s       0.0 s
[2015-09-30T21:35Z] INFO  22:35:59,884 ProgressMeter - Total runtime 14.02 secs, 0.23 min, 0.00 hours
[2015-09-30T21:35Z] INFO  22:35:59,884 MicroScheduler - 12831 reads were filtered out during the traversal out of approximately 250706 total reads (5.12%)
[2015-09-30T21:35Z] INFO  22:35:59,884 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:35Z] INFO  22:35:59,885 MicroScheduler -   -> 12777 reads (5.10% of total) failing DuplicateReadFilter
[2015-09-30T21:35Z] INFO  22:35:59,885 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:35Z] INFO  22:35:59,885 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:35Z] INFO  22:35:59,885 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:35Z] INFO  22:35:59,885 MicroScheduler -   -> 54 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:36Z] INFO  22:36:01,060 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:36Z] Genotyping with varscan: ('17', 62078196, 81195210) 1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam
[2015-09-30T21:36Z] samtools mpileup
[2015-09-30T21:36Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:36Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:36Z] samtools mpileup
[2015-09-30T21:36Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:36Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:36Z] Varscan
[2015-09-30T21:36Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/17/tx/tmpE0SJyD/syn3-17_0_31039439-raw-normal.mpileup
[2015-09-30T21:36Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/17/tx/tmpE0SJyD/syn3-17_0_31039439-raw-tumor.mpileup
[2015-09-30T21:36Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:36Z] Min reads2:	2
[2015-09-30T21:36Z] Min strands2:	1
[2015-09-30T21:36Z] Min var freq:	0.1
[2015-09-30T21:36Z] Min freq for hom:	0.75
[2015-09-30T21:36Z] Normal purity:	1.0
[2015-09-30T21:36Z] Tumor purity:	1.0
[2015-09-30T21:36Z] Min avg qual:	15
[2015-09-30T21:36Z] P-value thresh:	0.98
[2015-09-30T21:36Z] Somatic p-value:	0.05
[2015-09-30T21:37Z] samtools mpileup
[2015-09-30T21:37Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:37Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:38Z] Varscan
[2015-09-30T21:38Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/17/tx/tmpTQ9vRx/syn3-17_31047756_62076645-raw-normal.mpileup
[2015-09-30T21:38Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/17/tx/tmpTQ9vRx/syn3-17_31047756_62076645-raw-tumor.mpileup
[2015-09-30T21:38Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:38Z] Min reads2:	2
[2015-09-30T21:38Z] Min strands2:	1
[2015-09-30T21:38Z] Min var freq:	0.1
[2015-09-30T21:38Z] Min freq for hom:	0.75
[2015-09-30T21:38Z] Normal purity:	1.0
[2015-09-30T21:38Z] Tumor purity:	1.0
[2015-09-30T21:38Z] Min avg qual:	15
[2015-09-30T21:38Z] P-value thresh:	0.98
[2015-09-30T21:38Z] Somatic p-value:	0.05
[2015-09-30T21:38Z] Varscan
[2015-09-30T21:38Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/17/tx/tmp3Ct3nC/syn3-17_62078196_81195210-raw-normal.mpileup
[2015-09-30T21:38Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/17/tx/tmp3Ct3nC/syn3-17_62078196_81195210-raw-tumor.mpileup
[2015-09-30T21:38Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:38Z] Min reads2:	2
[2015-09-30T21:38Z] Min strands2:	1
[2015-09-30T21:38Z] Min var freq:	0.1
[2015-09-30T21:38Z] Min freq for hom:	0.75
[2015-09-30T21:38Z] Normal purity:	1.0
[2015-09-30T21:38Z] Tumor purity:	1.0
[2015-09-30T21:38Z] Min avg qual:	15
[2015-09-30T21:38Z] P-value thresh:	0.98
[2015-09-30T21:38Z] Somatic p-value:	0.05
[2015-09-30T21:38Z] 3028391 positions in tumor
[2015-09-30T21:38Z] 3028382 positions shared in normal
[2015-09-30T21:38Z] 2999093 had sufficient coverage for comparison
[2015-09-30T21:38Z] 2994742 were called Reference
[2015-09-30T21:38Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:38Z] 277 were removed by the strand filter
[2015-09-30T21:38Z] 4230 were called Germline
[2015-09-30T21:38Z] 16 were called LOH
[2015-09-30T21:38Z] 77 were called Somatic
[2015-09-30T21:38Z] 28 were called Unknown
[2015-09-30T21:38Z] 0 were called Variant
[2015-09-30T21:38Z] Varscan paired fix
[2015-09-30T21:38Z] Varscan paired fix
[2015-09-30T21:38Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:38Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:38Z] bgzip syn3-17_0_31039439-raw.snp.vcf
[2015-09-30T21:38Z] tabix index syn3-17_0_31039439-raw.snp.vcf.gz
[2015-09-30T21:38Z] bgzip syn3-17_0_31039439-raw.indel.vcf
[2015-09-30T21:38Z] tabix index syn3-17_0_31039439-raw.indel.vcf.gz
[2015-09-30T21:38Z] Combine variant files
[2015-09-30T21:38Z] INFO  22:38:48,927 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:38Z] INFO  22:38:48,930 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:38Z] INFO  22:38:48,930 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:38Z] INFO  22:38:48,930 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:38Z] INFO  22:38:48,933 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/17/tx/tmpE0SJyD/tx/tmpvXSjwc/syn3-17_0_31039439-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/17/tx/tmpE0SJyD/syn3-17_0_31039439-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/17/tx/tmpE0SJyD/syn3-17_0_31039439-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/17/syn3-17_0_31039439-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:38Z] INFO  22:38:48,943 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:38Z] INFO  22:38:48,943 HelpFormatter - Date/Time: 2015/09/30 22:38:48
[2015-09-30T21:38Z] INFO  22:38:48,943 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:38Z] INFO  22:38:48,943 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:38Z] INFO  22:38:49,020 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:38Z] INFO  22:38:49,413 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:38Z] INFO  22:38:49,561 IntervalUtils - Processing 3037033 bp from intervals
[2015-09-30T21:38Z] WARN  22:38:49,562 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:38Z] WARN  22:38:49,563 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:38Z] INFO  22:38:49,618 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:38Z] INFO  22:38:49,623 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:38Z] INFO  22:38:49,624 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:38Z] INFO  22:38:49,624 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:38Z] INFO  22:38:49,625 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:38Z] INFO  22:38:52,034 ProgressMeter -            done      4806.0     2.0 s       8.4 m      100.0%     2.0 s       0.0 s
[2015-09-30T21:38Z] INFO  22:38:52,035 ProgressMeter - Total runtime 2.41 secs, 0.04 min, 0.00 hours
[2015-09-30T21:38Z] bgzip syn3-17_0_31039439-raw.vcf
[2015-09-30T21:38Z] tabix index syn3-17_0_31039439-raw.vcf.gz
[2015-09-30T21:38Z] bgzip syn3-17_0_31039439-raw-rejectfix.vcf
[2015-09-30T21:38Z] tabix index syn3-17_0_31039439-raw-rejectfix.vcf.gz
[2015-09-30T21:38Z] GATK: VariantAnnotator
[2015-09-30T21:38Z] INFO  22:38:55,204 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:38Z] INFO  22:38:55,206 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:38Z] INFO  22:38:55,206 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:38Z] INFO  22:38:55,206 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:38Z] INFO  22:38:55,209 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/17/syn3-17_0_31039439-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/17/tx/tmpTvizK9/syn3-17_0_31039439-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/17/syn3-17_0_31039439-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:38Z] INFO  22:38:55,215 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:38Z] INFO  22:38:55,215 HelpFormatter - Date/Time: 2015/09/30 22:38:55
[2015-09-30T21:38Z] INFO  22:38:55,215 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:38Z] INFO  22:38:55,215 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:38Z] INFO  22:38:55,308 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:38Z] INFO  22:38:55,383 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:38Z] INFO  22:38:55,390 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:38Z] INFO  22:38:55,428 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T21:38Z] INFO  22:38:55,987 IntervalUtils - Processing 4828 bp from intervals
[2015-09-30T21:38Z] WARN  22:38:55,991 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:38Z] WARN  22:38:55,991 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:38Z] INFO  22:38:56,044 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:38Z] INFO  22:38:56,188 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:38Z] INFO  22:38:56,189 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:38Z] INFO  22:38:56,189 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:38Z] INFO  22:38:56,189 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:38Z] INFO  22:38:56,220 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:39Z] INFO  22:39:17,170 VariantAnnotator - Processed 4057 loci.
[2015-09-30T21:39Z]
[2015-09-30T21:39Z] INFO  22:39:17,192 ProgressMeter -            done     53956.0    21.0 s       6.5 m      100.0%    21.0 s       0.0 s
[2015-09-30T21:39Z] INFO  22:39:17,193 ProgressMeter - Total runtime 21.00 secs, 0.35 min, 0.01 hours
[2015-09-30T21:39Z] INFO  22:39:17,193 MicroScheduler - 19847 reads were filtered out during the traversal out of approximately 375253 total reads (5.29%)
[2015-09-30T21:39Z] INFO  22:39:17,193 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:39Z] INFO  22:39:17,194 MicroScheduler -   -> 19724 reads (5.26% of total) failing DuplicateReadFilter
[2015-09-30T21:39Z] INFO  22:39:17,194 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:39Z] INFO  22:39:17,194 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:39Z] INFO  22:39:17,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:39Z] INFO  22:39:17,194 MicroScheduler -   -> 123 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:39Z] INFO  22:39:18,174 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:39Z] Genotyping with varscan: ('18', 0, 31142016) 1_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam
[2015-09-30T21:39Z] samtools mpileup
[2015-09-30T21:39Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:39Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:39Z] samtools mpileup
[2015-09-30T21:39Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:39Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:40Z] 1869743 positions in tumor
[2015-09-30T21:40Z] 1869729 positions shared in normal
[2015-09-30T21:40Z] 1849836 had sufficient coverage for comparison
[2015-09-30T21:40Z] 1847040 were called Reference
[2015-09-30T21:40Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:40Z] 104 were removed by the strand filter
[2015-09-30T21:40Z] 2732 were called Germline
[2015-09-30T21:40Z] 8 were called LOH
[2015-09-30T21:40Z] 45 were called Somatic
[2015-09-30T21:40Z] 11 were called Unknown
[2015-09-30T21:40Z] 0 were called Variant
[2015-09-30T21:40Z] Varscan paired fix
[2015-09-30T21:40Z] Varscan paired fix
[2015-09-30T21:40Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:40Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:40Z] bgzip syn3-17_62078196_81195210-raw.snp.vcf
[2015-09-30T21:40Z] tabix index syn3-17_62078196_81195210-raw.snp.vcf.gz
[2015-09-30T21:40Z] bgzip syn3-17_62078196_81195210-raw.indel.vcf
[2015-09-30T21:40Z] tabix index syn3-17_62078196_81195210-raw.indel.vcf.gz
[2015-09-30T21:40Z] Combine variant files
[2015-09-30T21:40Z] INFO  22:40:08,470 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:40Z] INFO  22:40:08,472 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:40Z] INFO  22:40:08,473 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:40Z] INFO  22:40:08,473 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:40Z] INFO  22:40:08,476 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/17/tx/tmp3Ct3nC/tx/tmp2kmEDU/syn3-17_62078196_81195210-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/17/tx/tmp3Ct3nC/syn3-17_62078196_81195210-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/17/tx/tmp3Ct3nC/syn3-17_62078196_81195210-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/17/syn3-17_62078196_81195210-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:40Z] INFO  22:40:08,482 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:40Z] INFO  22:40:08,482 HelpFormatter - Date/Time: 2015/09/30 22:40:08
[2015-09-30T21:40Z] INFO  22:40:08,483 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:40Z] INFO  22:40:08,483 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:40Z] INFO  22:40:08,560 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:40Z] INFO  22:40:08,702 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:40Z] INFO  22:40:08,832 IntervalUtils - Processing 1876990 bp from intervals
[2015-09-30T21:40Z] WARN  22:40:08,833 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:40Z] WARN  22:40:08,833 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:40Z] INFO  22:40:08,889 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:40Z] INFO  22:40:08,894 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:40Z] INFO  22:40:08,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:40Z] INFO  22:40:08,894 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:40Z] INFO  22:40:08,895 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:40Z] INFO  22:40:10,949 ProgressMeter -            done      3071.0     2.0 s      11.1 m       99.8%     2.0 s       0.0 s
[2015-09-30T21:40Z] INFO  22:40:10,949 ProgressMeter - Total runtime 2.06 secs, 0.03 min, 0.00 hours
[2015-09-30T21:40Z] bgzip syn3-17_62078196_81195210-raw.vcf
[2015-09-30T21:40Z] tabix index syn3-17_62078196_81195210-raw.vcf.gz
[2015-09-30T21:40Z] bgzip syn3-17_62078196_81195210-raw-rejectfix.vcf
[2015-09-30T21:40Z] tabix index syn3-17_62078196_81195210-raw-rejectfix.vcf.gz
[2015-09-30T21:40Z] GATK: VariantAnnotator
[2015-09-30T21:40Z] INFO  22:40:13,600 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:40Z] INFO  22:40:13,602 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:40Z] INFO  22:40:13,602 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:40Z] INFO  22:40:13,602 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:40Z] INFO  22:40:13,606 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/17/syn3-17_62078196_81195210-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/17/tx/tmpPUQ_Mr/syn3-17_62078196_81195210-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/17/syn3-17_62078196_81195210-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:40Z] INFO  22:40:13,611 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:40Z] INFO  22:40:13,611 HelpFormatter - Date/Time: 2015/09/30 22:40:13
[2015-09-30T21:40Z] INFO  22:40:13,612 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:40Z] INFO  22:40:13,612 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:40Z] INFO  22:40:13,698 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:40Z] INFO  22:40:13,771 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:40Z] INFO  22:40:13,778 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:40Z] INFO  22:40:13,800 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:40Z] INFO  22:40:14,228 IntervalUtils - Processing 3104 bp from intervals
[2015-09-30T21:40Z] WARN  22:40:14,232 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:40Z] WARN  22:40:14,232 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:40Z] INFO  22:40:14,606 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:40Z] INFO  22:40:14,744 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:40Z] INFO  22:40:14,744 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:40Z] INFO  22:40:14,745 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:40Z] INFO  22:40:14,745 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:40Z] INFO  22:40:14,776 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:40Z] Varscan
[2015-09-30T21:40Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/18/tx/tmphT1dgx/syn3-18_0_31142016-raw-normal.mpileup
[2015-09-30T21:40Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/18/tx/tmphT1dgx/syn3-18_0_31142016-raw-tumor.mpileup
[2015-09-30T21:40Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:40Z] Min reads2:	2
[2015-09-30T21:40Z] Min strands2:	1
[2015-09-30T21:40Z] Min var freq:	0.1
[2015-09-30T21:40Z] Min freq for hom:	0.75
[2015-09-30T21:40Z] Normal purity:	1.0
[2015-09-30T21:40Z] Tumor purity:	1.0
[2015-09-30T21:40Z] Min avg qual:	15
[2015-09-30T21:40Z] P-value thresh:	0.98
[2015-09-30T21:40Z] Somatic p-value:	0.05
[2015-09-30T21:40Z] INFO  22:40:29,101 VariantAnnotator - Processed 2686 loci.
[2015-09-30T21:40Z]
[2015-09-30T21:40Z] INFO  22:40:29,812 ProgressMeter -            done     20066.0    15.0 s      12.5 m      100.0%    15.0 s       0.0 s
[2015-09-30T21:40Z] INFO  22:40:29,812 ProgressMeter - Total runtime 15.07 secs, 0.25 min, 0.00 hours
[2015-09-30T21:40Z] INFO  22:40:29,813 MicroScheduler - 14716 reads were filtered out during the traversal out of approximately 271150 total reads (5.43%)
[2015-09-30T21:40Z] INFO  22:40:29,813 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:40Z] INFO  22:40:29,813 MicroScheduler -   -> 14648 reads (5.40% of total) failing DuplicateReadFilter
[2015-09-30T21:40Z] INFO  22:40:29,814 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:40Z] INFO  22:40:29,814 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:40Z] INFO  22:40:29,814 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:40Z] INFO  22:40:29,814 MicroScheduler -   -> 68 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:40Z] INFO  22:40:30,778 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:40Z] Genotyping with varscan: ('18', 31158315, 63430522) 1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam
[2015-09-30T21:40Z] samtools mpileup
[2015-09-30T21:40Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:40Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:40Z] 3211274 positions in tumor
[2015-09-30T21:40Z] 3211261 positions shared in normal
[2015-09-30T21:40Z] 3176092 had sufficient coverage for comparison
[2015-09-30T21:40Z] 3172347 were called Reference
[2015-09-30T21:40Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:40Z] 316 were removed by the strand filter
[2015-09-30T21:40Z] 3608 were called Germline
[2015-09-30T21:40Z] 13 were called LOH
[2015-09-30T21:40Z] 103 were called Somatic
[2015-09-30T21:40Z] 21 were called Unknown
[2015-09-30T21:40Z] 0 were called Variant
[2015-09-30T21:40Z] Varscan paired fix
[2015-09-30T21:40Z] Varscan paired fix
[2015-09-30T21:40Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:40Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:40Z] bgzip syn3-17_31047756_62076645-raw.snp.vcf
[2015-09-30T21:40Z] tabix index syn3-17_31047756_62076645-raw.snp.vcf.gz
[2015-09-30T21:40Z] bgzip syn3-17_31047756_62076645-raw.indel.vcf
[2015-09-30T21:40Z] tabix index syn3-17_31047756_62076645-raw.indel.vcf.gz
[2015-09-30T21:40Z] Combine variant files
[2015-09-30T21:40Z] INFO  22:40:54,990 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:40Z] INFO  22:40:54,992 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:40Z] INFO  22:40:54,992 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:40Z] INFO  22:40:54,992 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:40Z] INFO  22:40:54,996 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/17/tx/tmpTQ9vRx/tx/tmpbGywm4/syn3-17_31047756_62076645-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/17/tx/tmpTQ9vRx/syn3-17_31047756_62076645-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/17/tx/tmpTQ9vRx/syn3-17_31047756_62076645-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/17/syn3-17_31047756_62076645-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:40Z] INFO  22:40:55,001 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:40Z] INFO  22:40:55,001 HelpFormatter - Date/Time: 2015/09/30 22:40:54
[2015-09-30T21:40Z] INFO  22:40:55,001 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:40Z] INFO  22:40:55,001 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:40Z] INFO  22:40:55,072 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:40Z] INFO  22:40:55,320 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:40Z] INFO  22:40:55,474 IntervalUtils - Processing 3219528 bp from intervals
[2015-09-30T21:40Z] WARN  22:40:55,476 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:40Z] WARN  22:40:55,476 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:40Z] INFO  22:40:55,531 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:40Z] INFO  22:40:55,537 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:40Z] INFO  22:40:55,537 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:40Z] INFO  22:40:55,537 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:40Z] INFO  22:40:55,538 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:40Z] INFO  22:40:57,748 ProgressMeter -            done      3975.0     2.0 s       9.3 m      100.0%     2.0 s       0.0 s
[2015-09-30T21:40Z] INFO  22:40:57,749 ProgressMeter - Total runtime 2.21 secs, 0.04 min, 0.00 hours
[2015-09-30T21:40Z] bgzip syn3-17_31047756_62076645-raw.vcf
[2015-09-30T21:40Z] tabix index syn3-17_31047756_62076645-raw.vcf.gz
[2015-09-30T21:40Z] bgzip syn3-17_31047756_62076645-raw-rejectfix.vcf
[2015-09-30T21:40Z] tabix index syn3-17_31047756_62076645-raw-rejectfix.vcf.gz
[2015-09-30T21:40Z] GATK: VariantAnnotator
[2015-09-30T21:41Z] INFO  22:41:01,717 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:01,719 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:41Z] INFO  22:41:01,720 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:41Z] INFO  22:41:01,720 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:41Z] INFO  22:41:01,723 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/17/syn3-17_31047756_62076645-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/17/tx/tmpSTX6zj/syn3-17_31047756_62076645-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/17/syn3-17_31047756_62076645-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:41Z] INFO  22:41:01,729 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:41Z] INFO  22:41:01,729 HelpFormatter - Date/Time: 2015/09/30 22:41:01
[2015-09-30T21:41Z] INFO  22:41:01,730 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:01,730 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:01,866 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:41Z] INFO  22:41:01,942 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:41Z] INFO  22:41:01,949 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:41Z] INFO  22:41:01,987 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T21:41Z] INFO  22:41:02,525 IntervalUtils - Processing 3979 bp from intervals
[2015-09-30T21:41Z] WARN  22:41:02,530 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:41Z] WARN  22:41:02,530 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:41Z] INFO  22:41:02,584 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:41Z] INFO  22:41:02,735 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:41Z] INFO  22:41:02,735 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:41Z] INFO  22:41:02,736 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:41Z] INFO  22:41:02,736 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:41Z] INFO  22:41:02,767 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:41Z] samtools mpileup
[2015-09-30T21:41Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:41Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:41Z] 1140402 positions in tumor
[2015-09-30T21:41Z] 1140394 positions shared in normal
[2015-09-30T21:41Z] 1108345 had sufficient coverage for comparison
[2015-09-30T21:41Z] 1106629 were called Reference
[2015-09-30T21:41Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:41Z] 115 were removed by the strand filter
[2015-09-30T21:41Z] 1670 were called Germline
[2015-09-30T21:41Z] 8 were called LOH
[2015-09-30T21:41Z] 28 were called Somatic
[2015-09-30T21:41Z] 10 were called Unknown
[2015-09-30T21:41Z] 0 were called Variant
[2015-09-30T21:41Z] Varscan paired fix
[2015-09-30T21:41Z] Varscan paired fix
[2015-09-30T21:41Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:41Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:41Z] bgzip syn3-18_0_31142016-raw.snp.vcf
[2015-09-30T21:41Z] tabix index syn3-18_0_31142016-raw.snp.vcf.gz
[2015-09-30T21:41Z] bgzip syn3-18_0_31142016-raw.indel.vcf
[2015-09-30T21:41Z] tabix index syn3-18_0_31142016-raw.indel.vcf.gz
[2015-09-30T21:41Z] Combine variant files
[2015-09-30T21:41Z] INFO  22:41:10,304 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:10,306 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:41Z] INFO  22:41:10,307 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:41Z] INFO  22:41:10,307 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:41Z] INFO  22:41:10,310 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/18/tx/tmphT1dgx/tx/tmpaKFJek/syn3-18_0_31142016-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/18/tx/tmphT1dgx/syn3-18_0_31142016-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/18/tx/tmphT1dgx/syn3-18_0_31142016-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/18/syn3-18_0_31142016-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:41Z] INFO  22:41:10,316 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:41Z] INFO  22:41:10,317 HelpFormatter - Date/Time: 2015/09/30 22:41:10
[2015-09-30T21:41Z] INFO  22:41:10,317 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:10,317 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:10,394 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:41Z] INFO  22:41:10,540 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:41Z] INFO  22:41:10,645 IntervalUtils - Processing 1147892 bp from intervals
[2015-09-30T21:41Z] WARN  22:41:10,646 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:41Z] WARN  22:41:10,646 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:41Z] INFO  22:41:10,702 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:41Z] INFO  22:41:10,706 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:41Z] INFO  22:41:10,706 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:41Z] INFO  22:41:10,707 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:41Z] INFO  22:41:10,707 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:41Z] INFO  22:41:11,992 ProgressMeter -            done      1832.0     1.0 s      11.7 m       99.8%     1.0 s       0.0 s
[2015-09-30T21:41Z] INFO  22:41:11,992 ProgressMeter - Total runtime 1.29 secs, 0.02 min, 0.00 hours
[2015-09-30T21:41Z] bgzip syn3-18_0_31142016-raw.vcf
[2015-09-30T21:41Z] tabix index syn3-18_0_31142016-raw.vcf.gz
[2015-09-30T21:41Z] bgzip syn3-18_0_31142016-raw-rejectfix.vcf
[2015-09-30T21:41Z] tabix index syn3-18_0_31142016-raw-rejectfix.vcf.gz
[2015-09-30T21:41Z] GATK: VariantAnnotator
[2015-09-30T21:41Z] INFO  22:41:14,475 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:14,477 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:41Z] INFO  22:41:14,477 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:41Z] INFO  22:41:14,477 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:41Z] INFO  22:41:14,481 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/18/syn3-18_0_31142016-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/18/tx/tmpDghFxB/syn3-18_0_31142016-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/18/syn3-18_0_31142016-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:41Z] INFO  22:41:14,486 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:41Z] INFO  22:41:14,487 HelpFormatter - Date/Time: 2015/09/30 22:41:14
[2015-09-30T21:41Z] INFO  22:41:14,487 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:14,487 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:14,581 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:41Z] INFO  22:41:14,659 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:41Z] INFO  22:41:14,666 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:41Z] INFO  22:41:14,689 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:41Z] INFO  22:41:15,063 IntervalUtils - Processing 1832 bp from intervals
[2015-09-30T21:41Z] WARN  22:41:15,067 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:41Z] WARN  22:41:15,068 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:41Z] INFO  22:41:15,124 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:41Z] INFO  22:41:15,229 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:41Z] INFO  22:41:15,230 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:41Z] INFO  22:41:15,230 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:41Z] INFO  22:41:15,230 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:41Z] INFO  22:41:15,329 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:41Z] INFO  22:41:21,367 VariantAnnotator - Processed 3413 loci.
[2015-09-30T21:41Z]
[2015-09-30T21:41Z] INFO  22:41:21,390 ProgressMeter -            done     20553.0    18.0 s      15.1 m      100.0%    18.0 s       0.0 s
[2015-09-30T21:41Z] INFO  22:41:21,390 ProgressMeter - Total runtime 18.65 secs, 0.31 min, 0.01 hours
[2015-09-30T21:41Z] INFO  22:41:21,390 MicroScheduler - 17358 reads were filtered out during the traversal out of approximately 325334 total reads (5.34%)
[2015-09-30T21:41Z] INFO  22:41:21,391 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:41Z] INFO  22:41:21,391 MicroScheduler -   -> 17251 reads (5.30% of total) failing DuplicateReadFilter
[2015-09-30T21:41Z] INFO  22:41:21,391 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:41Z] INFO  22:41:21,391 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:41Z] INFO  22:41:21,392 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:41Z] INFO  22:41:21,392 MicroScheduler -   -> 107 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:41Z] INFO  22:41:22,331 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:41Z] Genotyping with varscan: ('18', 63476668, 78077248) 1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam
[2015-09-30T21:41Z] samtools mpileup
[2015-09-30T21:41Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:41Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:41Z] INFO  22:41:23,215 VariantAnnotator - Processed 1592 loci.
[2015-09-30T21:41Z]
[2015-09-30T21:41Z] INFO  22:41:23,235 ProgressMeter -            done     10284.0     8.0 s      13.0 m       99.9%     8.0 s       0.0 s
[2015-09-30T21:41Z] INFO  22:41:23,235 ProgressMeter - Total runtime 8.01 secs, 0.13 min, 0.00 hours
[2015-09-30T21:41Z] INFO  22:41:23,235 MicroScheduler - 4748 reads were filtered out during the traversal out of approximately 106710 total reads (4.45%)
[2015-09-30T21:41Z] INFO  22:41:23,236 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:41Z] INFO  22:41:23,236 MicroScheduler -   -> 4719 reads (4.42% of total) failing DuplicateReadFilter
[2015-09-30T21:41Z] INFO  22:41:23,236 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:41Z] INFO  22:41:23,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:41Z] INFO  22:41:23,237 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:41Z] INFO  22:41:23,237 MicroScheduler -   -> 29 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:41Z] INFO  22:41:24,164 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:41Z] Genotyping with varscan: ('19', 0, 31026185) 1_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam
[2015-09-30T21:41Z] samtools mpileup
[2015-09-30T21:41Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:41Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:41Z] samtools mpileup
[2015-09-30T21:41Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:41Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:41Z] Varscan
[2015-09-30T21:41Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/18/tx/tmpZ3XQYh/syn3-18_31158315_63430522-raw-normal.mpileup
[2015-09-30T21:41Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/18/tx/tmpZ3XQYh/syn3-18_31158315_63430522-raw-tumor.mpileup
[2015-09-30T21:41Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:41Z] Min reads2:	2
[2015-09-30T21:41Z] Min strands2:	1
[2015-09-30T21:41Z] Min var freq:	0.1
[2015-09-30T21:41Z] Min freq for hom:	0.75
[2015-09-30T21:41Z] Normal purity:	1.0
[2015-09-30T21:41Z] Tumor purity:	1.0
[2015-09-30T21:41Z] Min avg qual:	15
[2015-09-30T21:41Z] P-value thresh:	0.98
[2015-09-30T21:41Z] Somatic p-value:	0.05
[2015-09-30T21:41Z] Varscan
[2015-09-30T21:41Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/18/tx/tmpVzlGzZ/syn3-18_63476668_78077248-raw-normal.mpileup
[2015-09-30T21:41Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/18/tx/tmpVzlGzZ/syn3-18_63476668_78077248-raw-tumor.mpileup
[2015-09-30T21:41Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:41Z] Min reads2:	2
[2015-09-30T21:41Z] Min strands2:	1
[2015-09-30T21:41Z] Min var freq:	0.1
[2015-09-30T21:41Z] Min freq for hom:	0.75
[2015-09-30T21:41Z] Normal purity:	1.0
[2015-09-30T21:41Z] Tumor purity:	1.0
[2015-09-30T21:41Z] Min avg qual:	15
[2015-09-30T21:41Z] P-value thresh:	0.98
[2015-09-30T21:41Z] Somatic p-value:	0.05
[2015-09-30T21:41Z] 277590 positions in tumor
[2015-09-30T21:41Z] 277586 positions shared in normal
[2015-09-30T21:41Z] 270269 had sufficient coverage for comparison
[2015-09-30T21:41Z] 269857 were called Reference
[2015-09-30T21:41Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:41Z] 37 were removed by the strand filter
[2015-09-30T21:41Z] 394 were called Germline
[2015-09-30T21:41Z] 2 were called LOH
[2015-09-30T21:41Z] 10 were called Somatic
[2015-09-30T21:41Z] 6 were called Unknown
[2015-09-30T21:41Z] 0 were called Variant
[2015-09-30T21:41Z] Varscan paired fix
[2015-09-30T21:41Z] Varscan paired fix
[2015-09-30T21:41Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:41Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:41Z] bgzip syn3-18_63476668_78077248-raw.snp.vcf
[2015-09-30T21:41Z] tabix index syn3-18_63476668_78077248-raw.snp.vcf.gz
[2015-09-30T21:41Z] bgzip syn3-18_63476668_78077248-raw.indel.vcf
[2015-09-30T21:41Z] tabix index syn3-18_63476668_78077248-raw.indel.vcf.gz
[2015-09-30T21:41Z] Combine variant files
[2015-09-30T21:41Z] INFO  22:41:58,450 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:58,452 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:41Z] INFO  22:41:58,452 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:41Z] INFO  22:41:58,452 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:41Z] INFO  22:41:58,456 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/18/tx/tmpVzlGzZ/tx/tmpL5woQH/syn3-18_63476668_78077248-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/18/tx/tmpVzlGzZ/syn3-18_63476668_78077248-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/18/tx/tmpVzlGzZ/syn3-18_63476668_78077248-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/18/syn3-18_63476668_78077248-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:41Z] INFO  22:41:58,461 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:41Z] INFO  22:41:58,462 HelpFormatter - Date/Time: 2015/09/30 22:41:58
[2015-09-30T21:41Z] INFO  22:41:58,462 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:58,462 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:41Z] INFO  22:41:58,811 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:41Z] INFO  22:41:59,312 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:41Z] INFO  22:41:59,394 IntervalUtils - Processing 280150 bp from intervals
[2015-09-30T21:41Z] WARN  22:41:59,394 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:41Z] WARN  22:41:59,395 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:41Z] INFO  22:41:59,449 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:41Z] INFO  22:41:59,451 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:41Z] INFO  22:41:59,451 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:41Z] INFO  22:41:59,451 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:41Z] INFO  22:41:59,452 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:41Z] INFO  22:41:59,967 ProgressMeter -            done       438.0     0.0 s      19.6 m       99.6%     0.0 s       0.0 s
[2015-09-30T21:41Z] INFO  22:41:59,968 ProgressMeter - Total runtime 0.52 secs, 0.01 min, 0.00 hours
[2015-09-30T21:42Z] bgzip syn3-18_63476668_78077248-raw.vcf
[2015-09-30T21:42Z] tabix index syn3-18_63476668_78077248-raw.vcf.gz
[2015-09-30T21:42Z] bgzip syn3-18_63476668_78077248-raw-rejectfix.vcf
[2015-09-30T21:42Z] tabix index syn3-18_63476668_78077248-raw-rejectfix.vcf.gz
[2015-09-30T21:42Z] GATK: VariantAnnotator
[2015-09-30T21:42Z] INFO  22:42:02,130 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:42Z] INFO  22:42:02,132 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:42Z] INFO  22:42:02,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:42Z] INFO  22:42:02,132 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:42Z] INFO  22:42:02,136 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/18/syn3-18_63476668_78077248-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/18/tx/tmpLJykJJ/syn3-18_63476668_78077248-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/18/syn3-18_63476668_78077248-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:42Z] INFO  22:42:02,141 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:42Z] INFO  22:42:02,141 HelpFormatter - Date/Time: 2015/09/30 22:42:02
[2015-09-30T21:42Z] INFO  22:42:02,141 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:42Z] INFO  22:42:02,142 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:42Z] INFO  22:42:02,234 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:42Z] INFO  22:42:02,308 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:42Z] INFO  22:42:02,315 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:42Z] INFO  22:42:02,337 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:42Z] INFO  22:42:02,601 IntervalUtils - Processing 438 bp from intervals
[2015-09-30T21:42Z] WARN  22:42:02,605 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:42Z] WARN  22:42:02,605 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:42Z] INFO  22:42:02,659 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:42Z] INFO  22:42:02,714 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:42Z] INFO  22:42:02,715 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:42Z] INFO  22:42:02,715 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:42Z] INFO  22:42:02,716 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:42Z] INFO  22:42:02,747 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:42Z] INFO  22:42:05,598 VariantAnnotator - Processed 372 loci.
[2015-09-30T21:42Z]
[2015-09-30T21:42Z] INFO  22:42:05,618 ProgressMeter -            done      1603.0     2.0 s      30.2 m       99.8%     2.0 s       0.0 s
[2015-09-30T21:42Z] INFO  22:42:05,618 ProgressMeter - Total runtime 2.90 secs, 0.05 min, 0.00 hours
[2015-09-30T21:42Z] INFO  22:42:05,619 MicroScheduler - 1532 reads were filtered out during the traversal out of approximately 30444 total reads (5.03%)
[2015-09-30T21:42Z] INFO  22:42:05,619 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:42Z] INFO  22:42:05,619 MicroScheduler -   -> 1525 reads (5.01% of total) failing DuplicateReadFilter
[2015-09-30T21:42Z] INFO  22:42:05,619 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:42Z] INFO  22:42:05,620 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:42Z] INFO  22:42:05,620 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:42Z] INFO  22:42:05,620 MicroScheduler -   -> 7 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:42Z] INFO  22:42:06,558 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:42Z] Genotyping with varscan: ('19', 31038548, 59128983) 1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam
[2015-09-30T21:42Z] samtools mpileup
[2015-09-30T21:42Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:42Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:42Z] 951365 positions in tumor
[2015-09-30T21:42Z] 951358 positions shared in normal
[2015-09-30T21:42Z] 933628 had sufficient coverage for comparison
[2015-09-30T21:42Z] 932444 were called Reference
[2015-09-30T21:42Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:42Z] 43 were removed by the strand filter
[2015-09-30T21:42Z] 1149 were called Germline
[2015-09-30T21:42Z] 1 were called LOH
[2015-09-30T21:42Z] 25 were called Somatic
[2015-09-30T21:42Z] 9 were called Unknown
[2015-09-30T21:42Z] 0 were called Variant
[2015-09-30T21:42Z] Varscan paired fix
[2015-09-30T21:42Z] Varscan paired fix
[2015-09-30T21:42Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:42Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:42Z] bgzip syn3-18_31158315_63430522-raw.snp.vcf
[2015-09-30T21:42Z] tabix index syn3-18_31158315_63430522-raw.snp.vcf.gz
[2015-09-30T21:42Z] bgzip syn3-18_31158315_63430522-raw.indel.vcf
[2015-09-30T21:42Z] tabix index syn3-18_31158315_63430522-raw.indel.vcf.gz
[2015-09-30T21:42Z] Combine variant files
[2015-09-30T21:42Z] INFO  22:42:20,084 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:42Z] INFO  22:42:20,086 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:42Z] INFO  22:42:20,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:42Z] INFO  22:42:20,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:42Z] INFO  22:42:20,090 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/18/tx/tmpZ3XQYh/tx/tmpYdhu_b/syn3-18_31158315_63430522-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/18/tx/tmpZ3XQYh/syn3-18_31158315_63430522-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/18/tx/tmpZ3XQYh/syn3-18_31158315_63430522-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/18/syn3-18_31158315_63430522-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:42Z] INFO  22:42:20,095 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:42Z] INFO  22:42:20,095 HelpFormatter - Date/Time: 2015/09/30 22:42:20
[2015-09-30T21:42Z] INFO  22:42:20,096 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:42Z] INFO  22:42:20,096 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:42Z] INFO  22:42:20,169 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:42Z] INFO  22:42:20,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:42Z] INFO  22:42:20,560 IntervalUtils - Processing 955835 bp from intervals
[2015-09-30T21:42Z] WARN  22:42:20,561 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:42Z] WARN  22:42:20,561 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:42Z] INFO  22:42:20,616 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:42Z] INFO  22:42:20,619 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:42Z] INFO  22:42:20,619 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:42Z] INFO  22:42:20,619 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:42Z] INFO  22:42:20,620 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:42Z] INFO  22:42:21,683 ProgressMeter -            done      1313.0     1.0 s      13.5 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:42Z] INFO  22:42:21,683 ProgressMeter - Total runtime 1.06 secs, 0.02 min, 0.00 hours
[2015-09-30T21:42Z] bgzip syn3-18_31158315_63430522-raw.vcf
[2015-09-30T21:42Z] tabix index syn3-18_31158315_63430522-raw.vcf.gz
[2015-09-30T21:42Z] bgzip syn3-18_31158315_63430522-raw-rejectfix.vcf
[2015-09-30T21:42Z] tabix index syn3-18_31158315_63430522-raw-rejectfix.vcf.gz
[2015-09-30T21:42Z] GATK: VariantAnnotator
[2015-09-30T21:42Z] INFO  22:42:24,062 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:42Z] INFO  22:42:24,064 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:42Z] INFO  22:42:24,064 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:42Z] INFO  22:42:24,064 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:42Z] INFO  22:42:24,068 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/18/syn3-18_31158315_63430522-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/18/tx/tmpqxu7zd/syn3-18_31158315_63430522-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/18/syn3-18_31158315_63430522-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:42Z] INFO  22:42:24,073 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:42Z] INFO  22:42:24,073 HelpFormatter - Date/Time: 2015/09/30 22:42:24
[2015-09-30T21:42Z] INFO  22:42:24,073 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:42Z] INFO  22:42:24,073 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:42Z] INFO  22:42:24,164 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:42Z] INFO  22:42:24,235 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:42Z] INFO  22:42:24,242 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:42Z] INFO  22:42:24,263 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:42Z] INFO  22:42:24,581 IntervalUtils - Processing 1313 bp from intervals
[2015-09-30T21:42Z] WARN  22:42:24,585 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:42Z] WARN  22:42:24,585 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:42Z] INFO  22:42:24,637 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:42Z] INFO  22:42:24,770 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:42Z] INFO  22:42:24,771 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:42Z] INFO  22:42:24,771 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:42Z] INFO  22:42:24,771 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:42Z] INFO  22:42:25,070 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:42Z] INFO  22:42:31,224 VariantAnnotator - Processed 1134 loci.
[2015-09-30T21:42Z]
[2015-09-30T21:42Z] INFO  22:42:31,254 ProgressMeter -            done      5241.0     6.0 s      20.6 m       99.9%     6.0 s       0.0 s
[2015-09-30T21:42Z] INFO  22:42:31,255 ProgressMeter - Total runtime 6.48 secs, 0.11 min, 0.00 hours
[2015-09-30T21:42Z] INFO  22:42:31,255 MicroScheduler - 4049 reads were filtered out during the traversal out of approximately 89634 total reads (4.52%)
[2015-09-30T21:42Z] INFO  22:42:31,255 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:42Z] INFO  22:42:31,256 MicroScheduler -   -> 4026 reads (4.49% of total) failing DuplicateReadFilter
[2015-09-30T21:42Z] INFO  22:42:31,256 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:42Z] INFO  22:42:31,256 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:42Z] INFO  22:42:31,256 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:42Z] INFO  22:42:31,256 MicroScheduler -   -> 23 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:42Z] INFO  22:42:32,207 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:42Z] Genotyping with varscan: ('20', 0, 31018105) 1_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam
[2015-09-30T21:42Z] samtools mpileup
[2015-09-30T21:42Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:42Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:43Z] samtools mpileup
[2015-09-30T21:43Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:43Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:43Z] samtools mpileup
[2015-09-30T21:43Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:43Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:44Z] Varscan
[2015-09-30T21:44Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/20/tx/tmpym1Dsw/syn3-20_0_31018105-raw-normal.mpileup
[2015-09-30T21:44Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/20/tx/tmpym1Dsw/syn3-20_0_31018105-raw-tumor.mpileup
[2015-09-30T21:44Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:44Z] Min reads2:	2
[2015-09-30T21:44Z] Min strands2:	1
[2015-09-30T21:44Z] Min var freq:	0.1
[2015-09-30T21:44Z] Min freq for hom:	0.75
[2015-09-30T21:44Z] Normal purity:	1.0
[2015-09-30T21:44Z] Tumor purity:	1.0
[2015-09-30T21:44Z] Min avg qual:	15
[2015-09-30T21:44Z] P-value thresh:	0.98
[2015-09-30T21:44Z] Somatic p-value:	0.05
[2015-09-30T21:44Z] samtools mpileup
[2015-09-30T21:44Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:44Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:45Z] 1291496 positions in tumor
[2015-09-30T21:45Z] 1291491 positions shared in normal
[2015-09-30T21:45Z] 1273882 had sufficient coverage for comparison
[2015-09-30T21:45Z] 1271180 were called Reference
[2015-09-30T21:45Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:45Z] 328 were removed by the strand filter
[2015-09-30T21:45Z] 2626 were called Germline
[2015-09-30T21:45Z] 6 were called LOH
[2015-09-30T21:45Z] 49 were called Somatic
[2015-09-30T21:45Z] 21 were called Unknown
[2015-09-30T21:45Z] 0 were called Variant
[2015-09-30T21:45Z] Varscan paired fix
[2015-09-30T21:45Z] Varscan paired fix
[2015-09-30T21:45Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:45Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:45Z] bgzip syn3-20_0_31018105-raw.snp.vcf
[2015-09-30T21:45Z] tabix index syn3-20_0_31018105-raw.snp.vcf.gz
[2015-09-30T21:45Z] bgzip syn3-20_0_31018105-raw.indel.vcf
[2015-09-30T21:45Z] tabix index syn3-20_0_31018105-raw.indel.vcf.gz
[2015-09-30T21:45Z] Combine variant files
[2015-09-30T21:45Z] INFO  22:45:04,649 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:45Z] INFO  22:45:04,651 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:45Z] INFO  22:45:04,652 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:45Z] INFO  22:45:04,652 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:45Z] INFO  22:45:04,655 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/20/tx/tmpym1Dsw/tx/tmpegSgjZ/syn3-20_0_31018105-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/20/tx/tmpym1Dsw/syn3-20_0_31018105-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/20/tx/tmpym1Dsw/syn3-20_0_31018105-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/20/syn3-20_0_31018105-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:45Z] INFO  22:45:04,661 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:45Z] INFO  22:45:04,662 HelpFormatter - Date/Time: 2015/09/30 22:45:04
[2015-09-30T21:45Z] INFO  22:45:04,662 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:45Z] INFO  22:45:04,662 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:45Z] INFO  22:45:04,741 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:45Z] INFO  22:45:04,883 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:45Z] INFO  22:45:04,994 IntervalUtils - Processing 1298771 bp from intervals
[2015-09-30T21:45Z] WARN  22:45:04,995 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:45Z] WARN  22:45:04,995 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:45Z] INFO  22:45:05,053 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:45Z] INFO  22:45:05,056 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:45Z] INFO  22:45:05,057 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:45Z] INFO  22:45:05,057 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:45Z] INFO  22:45:05,057 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:45Z] INFO  22:45:06,735 ProgressMeter -            done      2799.0     1.0 s      10.0 m       99.7%     1.0 s       0.0 s
[2015-09-30T21:45Z] INFO  22:45:06,736 ProgressMeter - Total runtime 1.68 secs, 0.03 min, 0.00 hours
[2015-09-30T21:45Z] bgzip syn3-20_0_31018105-raw.vcf
[2015-09-30T21:45Z] tabix index syn3-20_0_31018105-raw.vcf.gz
[2015-09-30T21:45Z] bgzip syn3-20_0_31018105-raw-rejectfix.vcf
[2015-09-30T21:45Z] tabix index syn3-20_0_31018105-raw-rejectfix.vcf.gz
[2015-09-30T21:45Z] GATK: VariantAnnotator
[2015-09-30T21:45Z] INFO  22:45:09,748 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:45Z] INFO  22:45:09,750 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:45Z] INFO  22:45:09,750 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:45Z] INFO  22:45:09,750 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:45Z] INFO  22:45:09,754 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/20/syn3-20_0_31018105-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/20/tx/tmpl1EN7N/syn3-20_0_31018105-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/20/syn3-20_0_31018105-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:45Z] INFO  22:45:09,759 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:45Z] INFO  22:45:09,759 HelpFormatter - Date/Time: 2015/09/30 22:45:09
[2015-09-30T21:45Z] INFO  22:45:09,760 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:45Z] INFO  22:45:09,760 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:45Z] INFO  22:45:09,852 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:45Z] INFO  22:45:09,928 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:45Z] INFO  22:45:09,935 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:45Z] INFO  22:45:09,958 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:45Z] INFO  22:45:10,382 IntervalUtils - Processing 2801 bp from intervals
[2015-09-30T21:45Z] WARN  22:45:10,386 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:45Z] WARN  22:45:10,386 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:45Z] INFO  22:45:10,442 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:45Z] INFO  22:45:10,615 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:45Z] INFO  22:45:10,616 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:45Z] INFO  22:45:10,616 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:45Z] INFO  22:45:10,617 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:45Z] INFO  22:45:10,649 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:45Z] INFO  22:45:22,406 VariantAnnotator - Processed 2360 loci.
[2015-09-30T21:45Z]
[2015-09-30T21:45Z] INFO  22:45:22,424 ProgressMeter -            done     41990.0    11.0 s       4.7 m      100.0%    11.0 s       0.0 s
[2015-09-30T21:45Z] INFO  22:45:22,424 ProgressMeter - Total runtime 11.81 secs, 0.20 min, 0.00 hours
[2015-09-30T21:45Z] INFO  22:45:22,424 MicroScheduler - 10012 reads were filtered out during the traversal out of approximately 194002 total reads (5.16%)
[2015-09-30T21:45Z] INFO  22:45:22,424 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:45Z] INFO  22:45:22,425 MicroScheduler -   -> 9943 reads (5.13% of total) failing DuplicateReadFilter
[2015-09-30T21:45Z] INFO  22:45:22,425 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:45Z] INFO  22:45:22,425 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:45Z] INFO  22:45:22,425 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:45Z] INFO  22:45:22,426 MicroScheduler -   -> 69 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T21:45Z] INFO  22:45:23,445 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:45Z] Genotyping with varscan: ('20', 31018873, 62038916) 1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam
[2015-09-30T21:45Z] samtools mpileup
[2015-09-30T21:45Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:45Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:45Z] Varscan
[2015-09-30T21:45Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/19/tx/tmptauWvR/syn3-19_0_31026185-raw-normal.mpileup
[2015-09-30T21:45Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/19/tx/tmptauWvR/syn3-19_0_31026185-raw-tumor.mpileup
[2015-09-30T21:45Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:45Z] Min reads2:	2
[2015-09-30T21:45Z] Min strands2:	1
[2015-09-30T21:45Z] Min var freq:	0.1
[2015-09-30T21:45Z] Min freq for hom:	0.75
[2015-09-30T21:45Z] Normal purity:	1.0
[2015-09-30T21:45Z] Tumor purity:	1.0
[2015-09-30T21:45Z] Min avg qual:	15
[2015-09-30T21:45Z] P-value thresh:	0.98
[2015-09-30T21:45Z] Somatic p-value:	0.05
[2015-09-30T21:47Z] samtools mpileup
[2015-09-30T21:47Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:47Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:47Z] Varscan
[2015-09-30T21:47Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/19/tx/tmpMnjblI/syn3-19_31038548_59128983-raw-normal.mpileup
[2015-09-30T21:47Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/19/tx/tmpMnjblI/syn3-19_31038548_59128983-raw-tumor.mpileup
[2015-09-30T21:47Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:47Z] Min reads2:	2
[2015-09-30T21:47Z] Min strands2:	1
[2015-09-30T21:47Z] Min var freq:	0.1
[2015-09-30T21:47Z] Min freq for hom:	0.75
[2015-09-30T21:47Z] Normal purity:	1.0
[2015-09-30T21:47Z] Tumor purity:	1.0
[2015-09-30T21:47Z] Min avg qual:	15
[2015-09-30T21:47Z] P-value thresh:	0.98
[2015-09-30T21:47Z] Somatic p-value:	0.05
[2015-09-30T21:48Z] 3540416 positions in tumor
[2015-09-30T21:48Z] 3540398 positions shared in normal
[2015-09-30T21:48Z] 3516579 had sufficient coverage for comparison
[2015-09-30T21:48Z] 3510783 were called Reference
[2015-09-30T21:48Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:48Z] 554 were removed by the strand filter
[2015-09-30T21:48Z] 5574 were called Germline
[2015-09-30T21:48Z] 19 were called LOH
[2015-09-30T21:48Z] 162 were called Somatic
[2015-09-30T21:48Z] 41 were called Unknown
[2015-09-30T21:48Z] 0 were called Variant
[2015-09-30T21:48Z] Varscan paired fix
[2015-09-30T21:48Z] Varscan paired fix
[2015-09-30T21:48Z] Varscan
[2015-09-30T21:48Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/20/tx/tmp3w9hCh/syn3-20_31018873_62038916-raw-normal.mpileup
[2015-09-30T21:48Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/20/tx/tmp3w9hCh/syn3-20_31018873_62038916-raw-tumor.mpileup
[2015-09-30T21:48Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:48Z] Min reads2:	2
[2015-09-30T21:48Z] Min strands2:	1
[2015-09-30T21:48Z] Min var freq:	0.1
[2015-09-30T21:48Z] Min freq for hom:	0.75
[2015-09-30T21:48Z] Normal purity:	1.0
[2015-09-30T21:48Z] Tumor purity:	1.0
[2015-09-30T21:48Z] Min avg qual:	15
[2015-09-30T21:48Z] P-value thresh:	0.98
[2015-09-30T21:48Z] Somatic p-value:	0.05
[2015-09-30T21:48Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:48Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:48Z] bgzip syn3-19_0_31026185-raw.snp.vcf
[2015-09-30T21:48Z] tabix index syn3-19_0_31026185-raw.snp.vcf.gz
[2015-09-30T21:48Z] bgzip syn3-19_0_31026185-raw.indel.vcf
[2015-09-30T21:48Z] tabix index syn3-19_0_31026185-raw.indel.vcf.gz
[2015-09-30T21:48Z] Combine variant files
[2015-09-30T21:48Z] INFO  22:48:41,223 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:48Z] INFO  22:48:41,225 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:48Z] INFO  22:48:41,225 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:48Z] INFO  22:48:41,226 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:48Z] INFO  22:48:41,229 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/19/tx/tmptauWvR/tx/tmpvk0urn/syn3-19_0_31026185-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/19/tx/tmptauWvR/syn3-19_0_31026185-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/19/tx/tmptauWvR/syn3-19_0_31026185-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/19/syn3-19_0_31026185-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:48Z] INFO  22:48:41,235 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:48Z] INFO  22:48:41,236 HelpFormatter - Date/Time: 2015/09/30 22:48:41
[2015-09-30T21:48Z] INFO  22:48:41,236 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:48Z] INFO  22:48:41,236 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:48Z] INFO  22:48:41,315 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:48Z] INFO  22:48:41,453 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:48Z] INFO  22:48:41,615 IntervalUtils - Processing 3555807 bp from intervals
[2015-09-30T21:48Z] WARN  22:48:41,616 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:48Z] WARN  22:48:41,617 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:48Z] INFO  22:48:41,732 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:48Z] INFO  22:48:41,739 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:48Z] INFO  22:48:41,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:48Z] INFO  22:48:41,740 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:48Z] INFO  22:48:41,740 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:48Z] INFO  22:48:44,408 ProgressMeter -            done      6126.0     2.0 s       7.3 m      100.0%     2.0 s       0.0 s
[2015-09-30T21:48Z] INFO  22:48:44,408 ProgressMeter - Total runtime 2.67 secs, 0.04 min, 0.00 hours
[2015-09-30T21:48Z] bgzip syn3-19_0_31026185-raw.vcf
[2015-09-30T21:48Z] tabix index syn3-19_0_31026185-raw.vcf.gz
[2015-09-30T21:48Z] bgzip syn3-19_0_31026185-raw-rejectfix.vcf
[2015-09-30T21:48Z] tabix index syn3-19_0_31026185-raw-rejectfix.vcf.gz
[2015-09-30T21:48Z] GATK: VariantAnnotator
[2015-09-30T21:48Z] INFO  22:48:47,581 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:48Z] INFO  22:48:47,583 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:48Z] INFO  22:48:47,584 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:48Z] INFO  22:48:47,584 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:48Z] INFO  22:48:47,587 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/19/syn3-19_0_31026185-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/19/tx/tmptDgfvY/syn3-19_0_31026185-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/19/syn3-19_0_31026185-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:48Z] INFO  22:48:47,593 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:48Z] INFO  22:48:47,593 HelpFormatter - Date/Time: 2015/09/30 22:48:47
[2015-09-30T21:48Z] INFO  22:48:47,593 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:48Z] INFO  22:48:47,594 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:48Z] INFO  22:48:48,017 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:48Z] INFO  22:48:48,095 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:48Z] INFO  22:48:48,103 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:48Z] INFO  22:48:48,135 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T21:48Z] INFO  22:48:48,748 IntervalUtils - Processing 6132 bp from intervals
[2015-09-30T21:48Z] WARN  22:48:48,753 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:48Z] WARN  22:48:48,753 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:48Z] INFO  22:48:48,812 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:48Z] INFO  22:48:48,979 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:48Z] INFO  22:48:48,980 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:48Z] INFO  22:48:48,980 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:48Z] INFO  22:48:48,981 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:48Z] INFO  22:48:49,012 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:49Z] INFO  22:49:16,183 VariantAnnotator - Processed 5214 loci.
[2015-09-30T21:49Z]
[2015-09-30T21:49Z] INFO  22:49:16,224 ProgressMeter -            done     44418.0    27.0 s      10.2 m      100.0%    27.0 s       0.0 s
[2015-09-30T21:49Z] INFO  22:49:16,224 ProgressMeter - Total runtime 27.24 secs, 0.45 min, 0.01 hours
[2015-09-30T21:49Z] INFO  22:49:16,224 MicroScheduler - 29636 reads were filtered out during the traversal out of approximately 516781 total reads (5.73%)
[2015-09-30T21:49Z] INFO  22:49:16,225 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:49Z] INFO  22:49:16,225 MicroScheduler -   -> 29504 reads (5.71% of total) failing DuplicateReadFilter
[2015-09-30T21:49Z] INFO  22:49:16,225 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:49Z] INFO  22:49:16,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:49Z] INFO  22:49:16,225 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:49Z] INFO  22:49:16,226 MicroScheduler -   -> 132 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:49Z] INFO  22:49:17,171 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:49Z] Genotyping with varscan: ('20', 62039427, 63025520) 1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam
[2015-09-30T21:49Z] samtools mpileup
[2015-09-30T21:49Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:49Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:49Z] samtools mpileup
[2015-09-30T21:49Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:49Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:49Z] Varscan
[2015-09-30T21:49Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/20/tx/tmp_0uLJJ/syn3-20_62039427_63025520-raw-normal.mpileup
[2015-09-30T21:49Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/20/tx/tmp_0uLJJ/syn3-20_62039427_63025520-raw-tumor.mpileup
[2015-09-30T21:49Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:49Z] Min reads2:	2
[2015-09-30T21:49Z] Min strands2:	1
[2015-09-30T21:49Z] Min var freq:	0.1
[2015-09-30T21:49Z] Min freq for hom:	0.75
[2015-09-30T21:49Z] Normal purity:	1.0
[2015-09-30T21:49Z] Tumor purity:	1.0
[2015-09-30T21:49Z] Min avg qual:	15
[2015-09-30T21:49Z] P-value thresh:	0.98
[2015-09-30T21:49Z] Somatic p-value:	0.05
[2015-09-30T21:49Z] 179762 positions in tumor
[2015-09-30T21:49Z] 179761 positions shared in normal
[2015-09-30T21:49Z] 178555 had sufficient coverage for comparison
[2015-09-30T21:49Z] 178234 were called Reference
[2015-09-30T21:49Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:49Z] 25 were removed by the strand filter
[2015-09-30T21:49Z] 312 were called Germline
[2015-09-30T21:49Z] 2 were called LOH
[2015-09-30T21:49Z] 7 were called Somatic
[2015-09-30T21:49Z] 0 were called Unknown
[2015-09-30T21:49Z] 0 were called Variant
[2015-09-30T21:49Z] Varscan paired fix
[2015-09-30T21:49Z] Varscan paired fix
[2015-09-30T21:49Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:49Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:49Z] bgzip syn3-20_62039427_63025520-raw.snp.vcf
[2015-09-30T21:49Z] tabix index syn3-20_62039427_63025520-raw.snp.vcf.gz
[2015-09-30T21:49Z] bgzip syn3-20_62039427_63025520-raw.indel.vcf
[2015-09-30T21:49Z] tabix index syn3-20_62039427_63025520-raw.indel.vcf.gz
[2015-09-30T21:49Z] Combine variant files
[2015-09-30T21:49Z] INFO  22:49:50,235 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:49Z] INFO  22:49:50,237 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:49Z] INFO  22:49:50,237 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:49Z] INFO  22:49:50,238 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:49Z] INFO  22:49:50,241 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/20/tx/tmp_0uLJJ/tx/tmphEByF0/syn3-20_62039427_63025520-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/20/tx/tmp_0uLJJ/syn3-20_62039427_63025520-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/20/tx/tmp_0uLJJ/syn3-20_62039427_63025520-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/20/syn3-20_62039427_63025520-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:49Z] INFO  22:49:50,247 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:49Z] INFO  22:49:50,247 HelpFormatter - Date/Time: 2015/09/30 22:49:50
[2015-09-30T21:49Z] INFO  22:49:50,247 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:49Z] INFO  22:49:50,247 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:49Z] INFO  22:49:50,325 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:49Z] INFO  22:49:50,638 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:49Z] INFO  22:49:50,712 IntervalUtils - Processing 181131 bp from intervals
[2015-09-30T21:49Z] WARN  22:49:50,712 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:49Z] WARN  22:49:50,713 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:49Z] INFO  22:49:50,801 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:49Z] INFO  22:49:50,802 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:49Z] INFO  22:49:50,802 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:49Z] INFO  22:49:50,803 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:49Z] INFO  22:49:50,803 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:49Z] INFO  22:49:51,250 ProgressMeter -            done       315.0     0.0 s      23.7 m       99.9%     0.0 s       0.0 s
[2015-09-30T21:49Z] INFO  22:49:51,251 ProgressMeter - Total runtime 0.45 secs, 0.01 min, 0.00 hours
[2015-09-30T21:49Z] bgzip syn3-20_62039427_63025520-raw.vcf
[2015-09-30T21:49Z] tabix index syn3-20_62039427_63025520-raw.vcf.gz
[2015-09-30T21:49Z] bgzip syn3-20_62039427_63025520-raw-rejectfix.vcf
[2015-09-30T21:49Z] tabix index syn3-20_62039427_63025520-raw-rejectfix.vcf.gz
[2015-09-30T21:49Z] GATK: VariantAnnotator
[2015-09-30T21:49Z] INFO  22:49:53,418 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:49Z] INFO  22:49:53,420 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:49Z] INFO  22:49:53,420 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:49Z] INFO  22:49:53,421 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:49Z] INFO  22:49:53,424 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/20/syn3-20_62039427_63025520-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/20/tx/tmpZURAyq/syn3-20_62039427_63025520-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/20/syn3-20_62039427_63025520-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:49Z] INFO  22:49:53,430 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:49Z] INFO  22:49:53,430 HelpFormatter - Date/Time: 2015/09/30 22:49:53
[2015-09-30T21:49Z] INFO  22:49:53,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:49Z] INFO  22:49:53,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:49Z] INFO  22:49:53,525 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:49Z] INFO  22:49:53,603 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:49Z] INFO  22:49:53,610 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:49Z] INFO  22:49:53,633 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:49Z] INFO  22:49:53,906 IntervalUtils - Processing 315 bp from intervals
[2015-09-30T21:49Z] WARN  22:49:53,910 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:49Z] WARN  22:49:53,910 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:49Z] INFO  22:49:53,968 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:49Z] INFO  22:49:54,007 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:49Z] INFO  22:49:54,007 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:49Z] INFO  22:49:54,007 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:49Z] INFO  22:49:54,008 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:49Z] INFO  22:49:54,041 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:49Z] INFO  22:49:56,992 VariantAnnotator - Processed 296 loci.
[2015-09-30T21:49Z]
[2015-09-30T21:49Z] INFO  22:49:57,011 ProgressMeter -            done      2158.0     3.0 s      23.2 m       99.7%     3.0 s       0.0 s
[2015-09-30T21:49Z] INFO  22:49:57,012 ProgressMeter - Total runtime 3.00 secs, 0.05 min, 0.00 hours
[2015-09-30T21:49Z] INFO  22:49:57,012 MicroScheduler - 1950 reads were filtered out during the traversal out of approximately 33227 total reads (5.87%)
[2015-09-30T21:49Z] INFO  22:49:57,012 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:49Z] INFO  22:49:57,012 MicroScheduler -   -> 1946 reads (5.86% of total) failing DuplicateReadFilter
[2015-09-30T21:49Z] INFO  22:49:57,013 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:49Z] INFO  22:49:57,013 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:49Z] INFO  22:49:57,013 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:49Z] INFO  22:49:57,013 MicroScheduler -   -> 4 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T21:49Z] INFO  22:49:57,949 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:49Z] Genotyping with varscan: ('21', 0, 31023863) 1_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam
[2015-09-30T21:49Z] samtools mpileup
[2015-09-30T21:49Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:49Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:50Z] samtools mpileup
[2015-09-30T21:50Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:50Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:50Z] 2212028 positions in tumor
[2015-09-30T21:50Z] 2212020 positions shared in normal
[2015-09-30T21:50Z] 2191859 had sufficient coverage for comparison
[2015-09-30T21:50Z] 2189348 were called Reference
[2015-09-30T21:50Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:50Z] 99 were removed by the strand filter
[2015-09-30T21:50Z] 2432 were called Germline
[2015-09-30T21:50Z] 6 were called LOH
[2015-09-30T21:50Z] 57 were called Somatic
[2015-09-30T21:50Z] 16 were called Unknown
[2015-09-30T21:50Z] 0 were called Variant
[2015-09-30T21:50Z] Varscan paired fix
[2015-09-30T21:50Z] Varscan paired fix
[2015-09-30T21:50Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:50Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:50Z] bgzip syn3-20_31018873_62038916-raw.snp.vcf
[2015-09-30T21:50Z] tabix index syn3-20_31018873_62038916-raw.snp.vcf.gz
[2015-09-30T21:50Z] bgzip syn3-20_31018873_62038916-raw.indel.vcf
[2015-09-30T21:50Z] tabix index syn3-20_31018873_62038916-raw.indel.vcf.gz
[2015-09-30T21:50Z] Combine variant files
[2015-09-30T21:50Z] INFO  22:50:12,130 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:12,132 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:50Z] INFO  22:50:12,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:50Z] INFO  22:50:12,133 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:50Z] INFO  22:50:12,136 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/20/tx/tmp3w9hCh/tx/tmpuFl3jm/syn3-20_31018873_62038916-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/20/tx/tmp3w9hCh/syn3-20_31018873_62038916-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/20/tx/tmp3w9hCh/syn3-20_31018873_62038916-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/20/syn3-20_31018873_62038916-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:50Z] INFO  22:50:12,142 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:50Z] INFO  22:50:12,142 HelpFormatter - Date/Time: 2015/09/30 22:50:12
[2015-09-30T21:50Z] INFO  22:50:12,142 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:12,142 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:12,221 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:50Z] INFO  22:50:12,358 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:50Z] INFO  22:50:12,498 IntervalUtils - Processing 2222004 bp from intervals
[2015-09-30T21:50Z] WARN  22:50:12,500 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] WARN  22:50:12,500 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] INFO  22:50:12,557 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:50Z] INFO  22:50:12,564 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:50Z] INFO  22:50:12,564 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:50Z] INFO  22:50:12,564 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:50Z] INFO  22:50:12,565 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:50Z] INFO  22:50:14,317 ProgressMeter -            done      2981.0     1.0 s       9.8 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:50Z] INFO  22:50:14,317 ProgressMeter - Total runtime 1.75 secs, 0.03 min, 0.00 hours
[2015-09-30T21:50Z] bgzip syn3-20_31018873_62038916-raw.vcf
[2015-09-30T21:50Z] tabix index syn3-20_31018873_62038916-raw.vcf.gz
[2015-09-30T21:50Z] bgzip syn3-20_31018873_62038916-raw-rejectfix.vcf
[2015-09-30T21:50Z] tabix index syn3-20_31018873_62038916-raw-rejectfix.vcf.gz
[2015-09-30T21:50Z] GATK: VariantAnnotator
[2015-09-30T21:50Z] INFO  22:50:17,144 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:17,146 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:50Z] INFO  22:50:17,146 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:50Z] INFO  22:50:17,146 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:50Z] INFO  22:50:17,150 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/20/syn3-20_31018873_62038916-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/20/tx/tmpAfveIv/syn3-20_31018873_62038916-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/20/syn3-20_31018873_62038916-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:50Z] INFO  22:50:17,155 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:50Z] INFO  22:50:17,155 HelpFormatter - Date/Time: 2015/09/30 22:50:17
[2015-09-30T21:50Z] INFO  22:50:17,183 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:17,183 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:17,249 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:50Z] INFO  22:50:17,327 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:50Z] INFO  22:50:17,335 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:50Z] INFO  22:50:17,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T21:50Z] INFO  22:50:17,789 IntervalUtils - Processing 2985 bp from intervals
[2015-09-30T21:50Z] WARN  22:50:17,793 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] WARN  22:50:17,793 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] INFO  22:50:17,850 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:50Z] INFO  22:50:18,050 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:50Z] INFO  22:50:18,051 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:50Z] INFO  22:50:18,051 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:50Z] INFO  22:50:18,051 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:50Z] INFO  22:50:18,084 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:50Z] Varscan
[2015-09-30T21:50Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/21/tx/tmprYGCA9/syn3-21_0_31023863-raw-normal.mpileup
[2015-09-30T21:50Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/21/tx/tmprYGCA9/syn3-21_0_31023863-raw-tumor.mpileup
[2015-09-30T21:50Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:50Z] Min reads2:	2
[2015-09-30T21:50Z] Min strands2:	1
[2015-09-30T21:50Z] Min var freq:	0.1
[2015-09-30T21:50Z] Min freq for hom:	0.75
[2015-09-30T21:50Z] Normal purity:	1.0
[2015-09-30T21:50Z] Tumor purity:	1.0
[2015-09-30T21:50Z] Min avg qual:	15
[2015-09-30T21:50Z] P-value thresh:	0.98
[2015-09-30T21:50Z] Somatic p-value:	0.05
[2015-09-30T21:50Z] 4111463 positions in tumor
[2015-09-30T21:50Z] 4111445 positions shared in normal
[2015-09-30T21:50Z] 4089283 had sufficient coverage for comparison
[2015-09-30T21:50Z] 4082950 were called Reference
[2015-09-30T21:50Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:50Z] 444 were removed by the strand filter
[2015-09-30T21:50Z] 6164 were called Germline
[2015-09-30T21:50Z] 15 were called LOH
[2015-09-30T21:50Z] 129 were called Somatic
[2015-09-30T21:50Z] 25 were called Unknown
[2015-09-30T21:50Z] 0 were called Variant
[2015-09-30T21:50Z] Varscan paired fix
[2015-09-30T21:50Z] INFO  22:50:32,467 VariantAnnotator - Processed 2401 loci.
[2015-09-30T21:50Z]
[2015-09-30T21:50Z] INFO  22:50:33,057 ProgressMeter -            done     14297.0    15.0 s      17.5 m      100.0%    15.0 s       0.0 s
[2015-09-30T21:50Z] INFO  22:50:33,057 ProgressMeter - Total runtime 15.01 secs, 0.25 min, 0.00 hours
[2015-09-30T21:50Z] INFO  22:50:33,057 MicroScheduler - 12551 reads were filtered out during the traversal out of approximately 239408 total reads (5.24%)
[2015-09-30T21:50Z] INFO  22:50:33,058 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:50Z] INFO  22:50:33,058 MicroScheduler -   -> 12495 reads (5.22% of total) failing DuplicateReadFilter
[2015-09-30T21:50Z] INFO  22:50:33,058 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:50Z] INFO  22:50:33,058 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:50Z] INFO  22:50:33,058 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:50Z] INFO  22:50:33,059 MicroScheduler -   -> 56 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:50Z] Varscan paired fix
[2015-09-30T21:50Z] INFO  22:50:34,009 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:50Z] 349570 positions in tumor
[2015-09-30T21:50Z] 349567 positions shared in normal
[2015-09-30T21:50Z] 333027 had sufficient coverage for comparison
[2015-09-30T21:50Z] 332163 were called Reference
[2015-09-30T21:50Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:50Z] 123 were removed by the strand filter
[2015-09-30T21:50Z] 819 were called Germline
[2015-09-30T21:50Z] 4 were called LOH
[2015-09-30T21:50Z] 34 were called Somatic
[2015-09-30T21:50Z] 7 were called Unknown
[2015-09-30T21:50Z] 0 were called Variant
[2015-09-30T21:50Z] Varscan paired fix
[2015-09-30T21:50Z] Varscan paired fix
[2015-09-30T21:50Z] Genotyping with varscan: ('21', 31026814, 48129895) 1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam
[2015-09-30T21:50Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:50Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:50Z] bgzip syn3-19_31038548_59128983-raw.snp.vcf
[2015-09-30T21:50Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:50Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:50Z] bgzip syn3-21_0_31023863-raw.snp.vcf
[2015-09-30T21:50Z] tabix index syn3-21_0_31023863-raw.snp.vcf.gz
[2015-09-30T21:50Z] tabix index syn3-19_31038548_59128983-raw.snp.vcf.gz
[2015-09-30T21:50Z] bgzip syn3-21_0_31023863-raw.indel.vcf
[2015-09-30T21:50Z] bgzip syn3-19_31038548_59128983-raw.indel.vcf
[2015-09-30T21:50Z] tabix index syn3-21_0_31023863-raw.indel.vcf.gz
[2015-09-30T21:50Z] tabix index syn3-19_31038548_59128983-raw.indel.vcf.gz
[2015-09-30T21:50Z] samtools mpileup
[2015-09-30T21:50Z] Combine variant files
[2015-09-30T21:50Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:50Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:50Z] Combine variant files
[2015-09-30T21:50Z] INFO  22:50:37,863 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:37,865 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:50Z] INFO  22:50:37,865 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:50Z] INFO  22:50:37,866 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:50Z] INFO  22:50:37,869 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/19/tx/tmpMnjblI/tx/tmpMggRPe/syn3-19_31038548_59128983-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/19/tx/tmpMnjblI/syn3-19_31038548_59128983-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/19/tx/tmpMnjblI/syn3-19_31038548_59128983-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/19/syn3-19_31038548_59128983-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:50Z] INFO  22:50:37,875 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:50Z] INFO  22:50:37,875 HelpFormatter - Date/Time: 2015/09/30 22:50:37
[2015-09-30T21:50Z] INFO  22:50:37,876 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:37,876 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:37,914 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:37,916 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:50Z] INFO  22:50:37,917 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:50Z] INFO  22:50:37,917 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:50Z] INFO  22:50:37,920 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/21/tx/tmprYGCA9/tx/tmp9OFfmM/syn3-21_0_31023863-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/21/tx/tmprYGCA9/syn3-21_0_31023863-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/21/tx/tmprYGCA9/syn3-21_0_31023863-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/21/syn3-21_0_31023863-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:50Z] INFO  22:50:37,926 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:50Z] INFO  22:50:37,926 HelpFormatter - Date/Time: 2015/09/30 22:50:37
[2015-09-30T21:50Z] INFO  22:50:37,926 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:37,926 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:37,952 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:50Z] INFO  22:50:38,002 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:50Z] INFO  22:50:38,364 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:50Z] INFO  22:50:38,403 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:50Z] INFO  22:50:38,480 IntervalUtils - Processing 352675 bp from intervals
[2015-09-30T21:50Z] WARN  22:50:38,481 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] WARN  22:50:38,481 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] INFO  22:50:38,538 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:50Z] INFO  22:50:38,540 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:50Z] INFO  22:50:38,540 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:50Z] INFO  22:50:38,540 IntervalUtils - Processing 4122500 bp from intervals
[2015-09-30T21:50Z] INFO  22:50:38,541 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:50Z] INFO  22:50:38,541 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:50Z] WARN  22:50:38,542 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] WARN  22:50:38,542 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] INFO  22:50:38,601 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:50Z] INFO  22:50:38,608 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:50Z] INFO  22:50:38,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:50Z] INFO  22:50:38,608 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:50Z] INFO  22:50:38,609 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:50Z] INFO  22:50:39,250 ProgressMeter -            done       821.0     0.0 s      14.4 m       99.5%     0.0 s       0.0 s
[2015-09-30T21:50Z] INFO  22:50:39,250 ProgressMeter - Total runtime 0.71 secs, 0.01 min, 0.00 hours
[2015-09-30T21:50Z] bgzip syn3-21_0_31023863-raw.vcf
[2015-09-30T21:50Z] tabix index syn3-21_0_31023863-raw.vcf.gz
[2015-09-30T21:50Z] bgzip syn3-21_0_31023863-raw-rejectfix.vcf
[2015-09-30T21:50Z] tabix index syn3-21_0_31023863-raw-rejectfix.vcf.gz
[2015-09-30T21:50Z] GATK: VariantAnnotator
[2015-09-30T21:50Z] INFO  22:50:41,211 ProgressMeter -            done      6921.0     2.0 s       6.3 m      100.0%     2.0 s       0.0 s
[2015-09-30T21:50Z] INFO  22:50:41,212 ProgressMeter - Total runtime 2.60 secs, 0.04 min, 0.00 hours
[2015-09-30T21:50Z] bgzip syn3-19_31038548_59128983-raw.vcf
[2015-09-30T21:50Z] tabix index syn3-19_31038548_59128983-raw.vcf.gz
[2015-09-30T21:50Z] INFO  22:50:41,796 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:41,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:50Z] INFO  22:50:41,798 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:50Z] INFO  22:50:41,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:50Z] INFO  22:50:41,802 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/21/syn3-21_0_31023863-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/21/tx/tmpv4HMIR/syn3-21_0_31023863-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/21/syn3-21_0_31023863-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:50Z] INFO  22:50:41,807 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:50Z] INFO  22:50:41,808 HelpFormatter - Date/Time: 2015/09/30 22:50:41
[2015-09-30T21:50Z] INFO  22:50:41,808 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:41,808 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:42,431 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:50Z] INFO  22:50:42,505 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:50Z] INFO  22:50:42,512 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:50Z] INFO  22:50:42,534 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:50Z] bgzip syn3-19_31038548_59128983-raw-rejectfix.vcf
[2015-09-30T21:50Z] tabix index syn3-19_31038548_59128983-raw-rejectfix.vcf.gz
[2015-09-30T21:50Z] GATK: VariantAnnotator
[2015-09-30T21:50Z] INFO  22:50:42,870 IntervalUtils - Processing 824 bp from intervals
[2015-09-30T21:50Z] WARN  22:50:42,874 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] WARN  22:50:42,874 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] INFO  22:50:42,931 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:50Z] INFO  22:50:42,996 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:50Z] INFO  22:50:42,996 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:50Z] INFO  22:50:42,996 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:50Z] INFO  22:50:42,997 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:50Z] INFO  22:50:43,029 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:50Z] INFO  22:50:44,629 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:44,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:50Z] INFO  22:50:44,631 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:50Z] INFO  22:50:44,631 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:50Z] INFO  22:50:44,635 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/19/syn3-19_31038548_59128983-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/19/tx/tmpMHhG_d/syn3-19_31038548_59128983-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/19/syn3-19_31038548_59128983-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:50Z] INFO  22:50:44,640 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:50Z] INFO  22:50:44,641 HelpFormatter - Date/Time: 2015/09/30 22:50:44
[2015-09-30T21:50Z] INFO  22:50:44,641 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:44,641 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:50Z] INFO  22:50:44,735 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:50Z] INFO  22:50:44,812 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:50Z] INFO  22:50:44,820 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:50Z] INFO  22:50:44,857 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T21:50Z] INFO  22:50:45,487 IntervalUtils - Processing 6924 bp from intervals
[2015-09-30T21:50Z] WARN  22:50:45,491 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] WARN  22:50:45,492 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:50Z] INFO  22:50:45,550 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:50Z] INFO  22:50:45,743 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:50Z] INFO  22:50:45,743 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:50Z] INFO  22:50:45,744 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:50Z] INFO  22:50:45,744 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:50Z] INFO  22:50:45,776 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:50Z] INFO  22:50:47,542 VariantAnnotator - Processed 734 loci.
[2015-09-30T21:50Z]
[2015-09-30T21:50Z] INFO  22:50:47,578 ProgressMeter -            done      4960.0     4.0 s      15.4 m       99.9%     4.0 s       0.0 s
[2015-09-30T21:50Z] INFO  22:50:47,578 ProgressMeter - Total runtime 4.58 secs, 0.08 min, 0.00 hours
[2015-09-30T21:50Z] INFO  22:50:47,579 MicroScheduler - 4353 reads were filtered out during the traversal out of approximately 66802 total reads (6.52%)
[2015-09-30T21:50Z] INFO  22:50:47,579 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:50Z] INFO  22:50:47,579 MicroScheduler -   -> 4333 reads (6.49% of total) failing DuplicateReadFilter
[2015-09-30T21:50Z] INFO  22:50:47,580 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:50Z] INFO  22:50:47,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:50Z] INFO  22:50:47,580 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:50Z] INFO  22:50:47,580 MicroScheduler -   -> 20 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:50Z] INFO  22:50:48,500 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:50Z] Genotyping with varscan: ('22', 0, 31019358) 1_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam
[2015-09-30T21:50Z] samtools mpileup
[2015-09-30T21:50Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:50Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:51Z] INFO  22:51:13,906 VariantAnnotator - Processed 5871 loci.
[2015-09-30T21:51Z]
[2015-09-30T21:51Z] INFO  22:51:13,928 ProgressMeter -            done     48369.0    28.0 s       9.7 m      100.0%    28.0 s       0.0 s
[2015-09-30T21:51Z] INFO  22:51:13,928 ProgressMeter - Total runtime 28.19 secs, 0.47 min, 0.01 hours
[2015-09-30T21:51Z] INFO  22:51:13,928 MicroScheduler - 28200 reads were filtered out during the traversal out of approximately 540355 total reads (5.22%)
[2015-09-30T21:51Z] INFO  22:51:13,929 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:51Z] INFO  22:51:13,929 MicroScheduler -   -> 28060 reads (5.19% of total) failing DuplicateReadFilter
[2015-09-30T21:51Z] INFO  22:51:13,929 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:51Z] INFO  22:51:13,929 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:51Z] INFO  22:51:13,930 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:51Z] INFO  22:51:13,930 MicroScheduler -   -> 140 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:51Z] INFO  22:51:14,904 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:51Z] Genotyping with varscan: ('22', 31022170, 51304566) 1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam
[2015-09-30T21:51Z] samtools mpileup
[2015-09-30T21:51Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:51Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:51Z] samtools mpileup
[2015-09-30T21:51Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:51Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:51Z] samtools mpileup
[2015-09-30T21:51Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:51Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:52Z] Varscan
[2015-09-30T21:52Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/21/tx/tmpBF2XnS/syn3-21_31026814_48129895-raw-normal.mpileup
[2015-09-30T21:52Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/21/tx/tmpBF2XnS/syn3-21_31026814_48129895-raw-tumor.mpileup
[2015-09-30T21:52Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:52Z] Min reads2:	2
[2015-09-30T21:52Z] Min strands2:	1
[2015-09-30T21:52Z] Min var freq:	0.1
[2015-09-30T21:52Z] Min freq for hom:	0.75
[2015-09-30T21:52Z] Normal purity:	1.0
[2015-09-30T21:52Z] Tumor purity:	1.0
[2015-09-30T21:52Z] Min avg qual:	15
[2015-09-30T21:52Z] P-value thresh:	0.98
[2015-09-30T21:52Z] Somatic p-value:	0.05
[2015-09-30T21:52Z] samtools mpileup
[2015-09-30T21:52Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:52Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:53Z] Varscan
[2015-09-30T21:53Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/22/tx/tmpcx0Y_h/syn3-22_0_31019358-raw-normal.mpileup
[2015-09-30T21:53Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/22/tx/tmpcx0Y_h/syn3-22_0_31019358-raw-tumor.mpileup
[2015-09-30T21:53Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:53Z] Min reads2:	2
[2015-09-30T21:53Z] Min strands2:	1
[2015-09-30T21:53Z] Min var freq:	0.1
[2015-09-30T21:53Z] Min freq for hom:	0.75
[2015-09-30T21:53Z] Normal purity:	1.0
[2015-09-30T21:53Z] Tumor purity:	1.0
[2015-09-30T21:53Z] Min avg qual:	15
[2015-09-30T21:53Z] P-value thresh:	0.98
[2015-09-30T21:53Z] Somatic p-value:	0.05
[2015-09-30T21:53Z] 1322887 positions in tumor
[2015-09-30T21:53Z] 1322879 positions shared in normal
[2015-09-30T21:53Z] 1310113 had sufficient coverage for comparison
[2015-09-30T21:53Z] 1307748 were called Reference
[2015-09-30T21:53Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:53Z] 165 were removed by the strand filter
[2015-09-30T21:53Z] 2298 were called Germline
[2015-09-30T21:53Z] 9 were called LOH
[2015-09-30T21:53Z] 40 were called Somatic
[2015-09-30T21:53Z] 18 were called Unknown
[2015-09-30T21:53Z] 0 were called Variant
[2015-09-30T21:53Z] Varscan paired fix
[2015-09-30T21:53Z] Varscan paired fix
[2015-09-30T21:53Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:53Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:53Z] bgzip syn3-21_31026814_48129895-raw.snp.vcf
[2015-09-30T21:53Z] tabix index syn3-21_31026814_48129895-raw.snp.vcf.gz
[2015-09-30T21:53Z] bgzip syn3-21_31026814_48129895-raw.indel.vcf
[2015-09-30T21:53Z] tabix index syn3-21_31026814_48129895-raw.indel.vcf.gz
[2015-09-30T21:53Z] Combine variant files
[2015-09-30T21:53Z] INFO  22:53:17,304 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:53Z] INFO  22:53:17,306 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:53Z] INFO  22:53:17,306 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:53Z] INFO  22:53:17,306 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:53Z] INFO  22:53:17,309 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/21/tx/tmpBF2XnS/tx/tmpejFJMe/syn3-21_31026814_48129895-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/21/tx/tmpBF2XnS/syn3-21_31026814_48129895-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/21/tx/tmpBF2XnS/syn3-21_31026814_48129895-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/21/syn3-21_31026814_48129895-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:53Z] INFO  22:53:17,316 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:53Z] INFO  22:53:17,316 HelpFormatter - Date/Time: 2015/09/30 22:53:17
[2015-09-30T21:53Z] INFO  22:53:17,316 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:53Z] INFO  22:53:17,317 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:53Z] INFO  22:53:17,392 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:53Z] INFO  22:53:17,529 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:53Z] INFO  22:53:17,644 IntervalUtils - Processing 1326168 bp from intervals
[2015-09-30T21:53Z] WARN  22:53:17,645 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:53Z] WARN  22:53:17,645 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:53Z] INFO  22:53:17,703 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:53Z] INFO  22:53:17,706 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:53Z] INFO  22:53:17,706 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:53Z] INFO  22:53:17,707 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:53Z] INFO  22:53:17,707 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:53Z] INFO  22:53:19,370 ProgressMeter -            done      2597.0     1.0 s      10.7 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:53Z] INFO  22:53:19,370 ProgressMeter - Total runtime 1.66 secs, 0.03 min, 0.00 hours
[2015-09-30T21:53Z] bgzip syn3-21_31026814_48129895-raw.vcf
[2015-09-30T21:53Z] tabix index syn3-21_31026814_48129895-raw.vcf.gz
[2015-09-30T21:53Z] bgzip syn3-21_31026814_48129895-raw-rejectfix.vcf
[2015-09-30T21:53Z] tabix index syn3-21_31026814_48129895-raw-rejectfix.vcf.gz
[2015-09-30T21:53Z] GATK: VariantAnnotator
[2015-09-30T21:53Z] INFO  22:53:22,523 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:53Z] INFO  22:53:22,525 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:53Z] INFO  22:53:22,525 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:53Z] INFO  22:53:22,525 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:53Z] INFO  22:53:22,529 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/21/syn3-21_31026814_48129895-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/21/tx/tmpeWKdNe/syn3-21_31026814_48129895-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/21/syn3-21_31026814_48129895-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:53Z] INFO  22:53:22,534 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:53Z] INFO  22:53:22,535 HelpFormatter - Date/Time: 2015/09/30 22:53:22
[2015-09-30T21:53Z] INFO  22:53:22,535 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:53Z] INFO  22:53:22,535 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:53Z] INFO  22:53:22,630 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:53Z] INFO  22:53:22,709 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:53Z] INFO  22:53:22,716 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:53Z] INFO  22:53:22,739 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:53Z] INFO  22:53:23,223 IntervalUtils - Processing 2597 bp from intervals
[2015-09-30T21:53Z] WARN  22:53:23,227 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:53Z] WARN  22:53:23,227 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:53Z] INFO  22:53:23,285 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:53Z] INFO  22:53:23,461 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:53Z] INFO  22:53:23,461 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:53Z] INFO  22:53:23,462 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:53Z] INFO  22:53:23,462 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:53Z] INFO  22:53:23,495 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:53Z] INFO  22:53:35,401 VariantAnnotator - Processed 2186 loci.
[2015-09-30T21:53Z]
[2015-09-30T21:53Z] INFO  22:53:35,473 ProgressMeter -            done     18761.0    12.0 s      10.7 m      100.0%    12.0 s       0.0 s
[2015-09-30T21:53Z] INFO  22:53:35,473 ProgressMeter - Total runtime 12.01 secs, 0.20 min, 0.00 hours
[2015-09-30T21:53Z] INFO  22:53:35,473 MicroScheduler - 10518 reads were filtered out during the traversal out of approximately 202753 total reads (5.19%)
[2015-09-30T21:53Z] INFO  22:53:35,473 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:53Z] INFO  22:53:35,474 MicroScheduler -   -> 10476 reads (5.17% of total) failing DuplicateReadFilter
[2015-09-30T21:53Z] INFO  22:53:35,474 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:53Z] INFO  22:53:35,474 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:53Z] INFO  22:53:35,474 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:53Z] INFO  22:53:35,475 MicroScheduler -   -> 42 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:53Z] INFO  22:53:36,411 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:53Z] Genotyping with varscan: ('X', 0, 31090302) 1_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam
[2015-09-30T21:53Z] samtools mpileup
[2015-09-30T21:53Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:53Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:53Z] Varscan
[2015-09-30T21:53Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/22/tx/tmp1ul3wC/syn3-22_31022170_51304566-raw-normal.mpileup
[2015-09-30T21:53Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/22/tx/tmp1ul3wC/syn3-22_31022170_51304566-raw-tumor.mpileup
[2015-09-30T21:53Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:53Z] Min reads2:	2
[2015-09-30T21:53Z] Min strands2:	1
[2015-09-30T21:53Z] Min var freq:	0.1
[2015-09-30T21:53Z] Min freq for hom:	0.75
[2015-09-30T21:53Z] Normal purity:	1.0
[2015-09-30T21:53Z] Tumor purity:	1.0
[2015-09-30T21:53Z] Min avg qual:	15
[2015-09-30T21:53Z] P-value thresh:	0.98
[2015-09-30T21:53Z] Somatic p-value:	0.05
[2015-09-30T21:54Z] samtools mpileup
[2015-09-30T21:54Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:54Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:54Z] 1529243 positions in tumor
[2015-09-30T21:54Z] 1529234 positions shared in normal
[2015-09-30T21:54Z] 1514535 had sufficient coverage for comparison
[2015-09-30T21:54Z] 1511000 were called Reference
[2015-09-30T21:54Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:54Z] 477 were removed by the strand filter
[2015-09-30T21:54Z] 3435 were called Germline
[2015-09-30T21:54Z] 11 were called LOH
[2015-09-30T21:54Z] 73 were called Somatic
[2015-09-30T21:54Z] 16 were called Unknown
[2015-09-30T21:54Z] 0 were called Variant
[2015-09-30T21:54Z] Varscan paired fix
[2015-09-30T21:54Z] Varscan paired fix
[2015-09-30T21:54Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:54Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:54Z] bgzip syn3-22_0_31019358-raw.snp.vcf
[2015-09-30T21:54Z] tabix index syn3-22_0_31019358-raw.snp.vcf.gz
[2015-09-30T21:54Z] bgzip syn3-22_0_31019358-raw.indel.vcf
[2015-09-30T21:54Z] tabix index syn3-22_0_31019358-raw.indel.vcf.gz
[2015-09-30T21:54Z] Combine variant files
[2015-09-30T21:54Z] INFO  22:54:15,074 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:54Z] INFO  22:54:15,076 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:54Z] INFO  22:54:15,077 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:54Z] INFO  22:54:15,077 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:54Z] INFO  22:54:15,080 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/22/tx/tmpcx0Y_h/tx/tmpZDR9G6/syn3-22_0_31019358-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/22/tx/tmpcx0Y_h/syn3-22_0_31019358-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/22/tx/tmpcx0Y_h/syn3-22_0_31019358-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/22/syn3-22_0_31019358-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:54Z] INFO  22:54:15,086 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:54Z] INFO  22:54:15,086 HelpFormatter - Date/Time: 2015/09/30 22:54:15
[2015-09-30T21:54Z] INFO  22:54:15,086 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:54Z] INFO  22:54:15,087 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:54Z] INFO  22:54:15,163 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:54Z] INFO  22:54:15,304 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:54Z] INFO  22:54:15,419 IntervalUtils - Processing 1534650 bp from intervals
[2015-09-30T21:54Z] WARN  22:54:15,420 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:54Z] WARN  22:54:15,421 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:54Z] INFO  22:54:15,477 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:54Z] INFO  22:54:15,481 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:54Z] INFO  22:54:15,481 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:54Z] INFO  22:54:15,482 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:54Z] INFO  22:54:15,482 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:54Z] INFO  22:54:17,381 ProgressMeter -            done      3503.0     1.0 s       9.0 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:54Z] INFO  22:54:17,382 ProgressMeter - Total runtime 1.90 secs, 0.03 min, 0.00 hours
[2015-09-30T21:54Z] bgzip syn3-22_0_31019358-raw.vcf
[2015-09-30T21:54Z] tabix index syn3-22_0_31019358-raw.vcf.gz
[2015-09-30T21:54Z] bgzip syn3-22_0_31019358-raw-rejectfix.vcf
[2015-09-30T21:54Z] tabix index syn3-22_0_31019358-raw-rejectfix.vcf.gz
[2015-09-30T21:54Z] GATK: VariantAnnotator
[2015-09-30T21:54Z] INFO  22:54:20,242 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:54Z] INFO  22:54:20,244 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:54Z] INFO  22:54:20,244 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:54Z] INFO  22:54:20,244 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:54Z] INFO  22:54:20,248 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/22/syn3-22_0_31019358-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/22/tx/tmpBzlPz7/syn3-22_0_31019358-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/22/syn3-22_0_31019358-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:54Z] INFO  22:54:20,253 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:54Z] INFO  22:54:20,254 HelpFormatter - Date/Time: 2015/09/30 22:54:20
[2015-09-30T21:54Z] INFO  22:54:20,254 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:54Z] INFO  22:54:20,254 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:54Z] INFO  22:54:20,345 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:54Z] INFO  22:54:20,590 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:54Z] INFO  22:54:20,598 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:54Z] INFO  22:54:20,659 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T21:54Z] INFO  22:54:21,105 IntervalUtils - Processing 3506 bp from intervals
[2015-09-30T21:54Z] WARN  22:54:21,161 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:54Z] WARN  22:54:21,161 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:54Z] INFO  22:54:21,218 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:54Z] INFO  22:54:21,347 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:54Z] INFO  22:54:21,347 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:54Z] INFO  22:54:21,348 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:54Z] INFO  22:54:21,348 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:54Z] INFO  22:54:21,381 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:54Z] INFO  22:54:37,413 VariantAnnotator - Processed 3048 loci.
[2015-09-30T21:54Z]
[2015-09-30T21:54Z] INFO  22:54:37,433 ProgressMeter -            done     27005.0    16.0 s       9.9 m       99.9%    16.0 s       0.0 s
[2015-09-30T21:54Z] INFO  22:54:37,433 ProgressMeter - Total runtime 16.09 secs, 0.27 min, 0.00 hours
[2015-09-30T21:54Z] INFO  22:54:37,433 MicroScheduler - 15416 reads were filtered out during the traversal out of approximately 301160 total reads (5.12%)
[2015-09-30T21:54Z] INFO  22:54:37,434 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:54Z] INFO  22:54:37,434 MicroScheduler -   -> 15338 reads (5.09% of total) failing DuplicateReadFilter
[2015-09-30T21:54Z] INFO  22:54:37,434 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:54Z] INFO  22:54:37,434 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:54Z] INFO  22:54:37,434 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:54Z] INFO  22:54:37,435 MicroScheduler -   -> 78 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:54Z] INFO  22:54:38,416 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:54Z] Genotyping with varscan: ('X', 31132529, 62519711) 1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam
[2015-09-30T21:54Z] samtools mpileup
[2015-09-30T21:54Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:54Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:54Z] Varscan
[2015-09-30T21:54Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmpnDPnLW/syn3-X_0_31090302-raw-normal.mpileup
[2015-09-30T21:54Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmpnDPnLW/syn3-X_0_31090302-raw-tumor.mpileup
[2015-09-30T21:54Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:54Z] Min reads2:	2
[2015-09-30T21:54Z] Min strands2:	1
[2015-09-30T21:54Z] Min var freq:	0.1
[2015-09-30T21:54Z] Min freq for hom:	0.75
[2015-09-30T21:54Z] Normal purity:	1.0
[2015-09-30T21:54Z] Tumor purity:	1.0
[2015-09-30T21:54Z] Min avg qual:	15
[2015-09-30T21:54Z] P-value thresh:	0.98
[2015-09-30T21:54Z] Somatic p-value:	0.05
[2015-09-30T21:55Z] 1847789 positions in tumor
[2015-09-30T21:55Z] 1847782 positions shared in normal
[2015-09-30T21:55Z] 1834556 had sufficient coverage for comparison
[2015-09-30T21:55Z] 1831934 were called Reference
[2015-09-30T21:55Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:55Z] 133 were removed by the strand filter
[2015-09-30T21:55Z] 2555 were called Germline
[2015-09-30T21:55Z] 2 were called LOH
[2015-09-30T21:55Z] 51 were called Somatic
[2015-09-30T21:55Z] 14 were called Unknown
[2015-09-30T21:55Z] 0 were called Variant
[2015-09-30T21:55Z] Varscan paired fix
[2015-09-30T21:55Z] Varscan paired fix
[2015-09-30T21:55Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:55Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:55Z] bgzip syn3-22_31022170_51304566-raw.snp.vcf
[2015-09-30T21:55Z] tabix index syn3-22_31022170_51304566-raw.snp.vcf.gz
[2015-09-30T21:55Z] bgzip syn3-22_31022170_51304566-raw.indel.vcf
[2015-09-30T21:55Z] tabix index syn3-22_31022170_51304566-raw.indel.vcf.gz
[2015-09-30T21:55Z] Combine variant files
[2015-09-30T21:55Z] INFO  22:55:22,266 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:22,268 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:55Z] INFO  22:55:22,268 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:55Z] INFO  22:55:22,268 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:55Z] INFO  22:55:22,272 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/22/tx/tmp1ul3wC/tx/tmpguCaNv/syn3-22_31022170_51304566-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/22/tx/tmp1ul3wC/syn3-22_31022170_51304566-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/22/tx/tmp1ul3wC/syn3-22_31022170_51304566-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/22/syn3-22_31022170_51304566-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:55Z] INFO  22:55:22,277 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:55Z] INFO  22:55:22,277 HelpFormatter - Date/Time: 2015/09/30 22:55:22
[2015-09-30T21:55Z] INFO  22:55:22,278 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:22,278 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:22,354 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:55Z] INFO  22:55:22,493 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:55Z] INFO  22:55:22,622 IntervalUtils - Processing 1855729 bp from intervals
[2015-09-30T21:55Z] WARN  22:55:22,623 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:55Z] WARN  22:55:22,623 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:55Z] INFO  22:55:22,681 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:55Z] INFO  22:55:22,685 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:55Z] INFO  22:55:22,685 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:55Z] INFO  22:55:22,685 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:55Z] INFO  22:55:22,686 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:55Z] INFO  22:55:24,390 ProgressMeter -            done      2888.0     1.0 s       9.8 m      100.0%     1.0 s       0.0 s
[2015-09-30T21:55Z] INFO  22:55:24,390 ProgressMeter - Total runtime 1.70 secs, 0.03 min, 0.00 hours
[2015-09-30T21:55Z] bgzip syn3-22_31022170_51304566-raw.vcf
[2015-09-30T21:55Z] tabix index syn3-22_31022170_51304566-raw.vcf.gz
[2015-09-30T21:55Z] samtools mpileup
[2015-09-30T21:55Z] 989310 positions in tumor
[2015-09-30T21:55Z] 989304 positions shared in normal
[2015-09-30T21:55Z] 976302 had sufficient coverage for comparison
[2015-09-30T21:55Z] 975317 were called Reference
[2015-09-30T21:55Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:55Z] 105 were removed by the strand filter
[2015-09-30T21:55Z] 931 were called Germline
[2015-09-30T21:55Z] 4 were called LOH
[2015-09-30T21:55Z] 34 were called Somatic
[2015-09-30T21:55Z] 16 were called Unknown
[2015-09-30T21:55Z] 0 were called Variant
[2015-09-30T21:55Z] bgzip syn3-22_31022170_51304566-raw-rejectfix.vcf
[2015-09-30T21:55Z] Varscan paired fix
[2015-09-30T21:55Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:55Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:55Z] Varscan paired fix
[2015-09-30T21:55Z] tabix index syn3-22_31022170_51304566-raw-rejectfix.vcf.gz
[2015-09-30T21:55Z] GATK: VariantAnnotator
[2015-09-30T21:55Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:55Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:55Z] bgzip syn3-X_0_31090302-raw.snp.vcf
[2015-09-30T21:55Z] tabix index syn3-X_0_31090302-raw.snp.vcf.gz
[2015-09-30T21:55Z] bgzip syn3-X_0_31090302-raw.indel.vcf
[2015-09-30T21:55Z] tabix index syn3-X_0_31090302-raw.indel.vcf.gz
[2015-09-30T21:55Z] Combine variant files
[2015-09-30T21:55Z] INFO  22:55:27,154 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:27,156 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:55Z] INFO  22:55:27,157 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:55Z] INFO  22:55:27,157 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:55Z] INFO  22:55:27,160 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/22/syn3-22_31022170_51304566-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/22/tx/tmpMaW051/syn3-22_31022170_51304566-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/22/syn3-22_31022170_51304566-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:55Z] INFO  22:55:27,166 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:55Z] INFO  22:55:27,166 HelpFormatter - Date/Time: 2015/09/30 22:55:27
[2015-09-30T21:55Z] INFO  22:55:27,166 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:27,166 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:27,517 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:55Z] INFO  22:55:27,595 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:55Z] INFO  22:55:27,603 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:55Z] INFO  22:55:27,626 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:55Z] INFO  22:55:27,883 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:27,886 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:55Z] INFO  22:55:27,886 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:55Z] INFO  22:55:27,886 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:55Z] INFO  22:55:27,889 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/X/tx/tmpnDPnLW/tx/tmphubIWl/syn3-X_0_31090302-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/X/tx/tmpnDPnLW/syn3-X_0_31090302-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/X/tx/tmpnDPnLW/syn3-X_0_31090302-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_0_31090302-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:55Z] INFO  22:55:27,895 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:55Z] INFO  22:55:27,895 HelpFormatter - Date/Time: 2015/09/30 22:55:27
[2015-09-30T21:55Z] INFO  22:55:27,895 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:27,896 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:27,973 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:55Z] INFO  22:55:28,102 IntervalUtils - Processing 2906 bp from intervals
[2015-09-30T21:55Z] WARN  22:55:28,107 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:55Z] WARN  22:55:28,107 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:55Z] INFO  22:55:28,121 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:55Z] INFO  22:55:28,165 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:55Z] INFO  22:55:28,219 IntervalUtils - Processing 993323 bp from intervals
[2015-09-30T21:55Z] WARN  22:55:28,220 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:55Z] WARN  22:55:28,220 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:55Z] INFO  22:55:28,276 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:55Z] INFO  22:55:28,279 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:55Z] INFO  22:55:28,279 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:55Z] INFO  22:55:28,280 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:55Z] INFO  22:55:28,280 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:55Z] INFO  22:55:28,365 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:55Z] INFO  22:55:28,365 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:55Z] INFO  22:55:28,366 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:55Z] INFO  22:55:28,366 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:55Z] INFO  22:55:28,399 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:55Z] INFO  22:55:29,256 ProgressMeter -            done      1074.0     0.0 s      15.1 m       99.9%     0.0 s       0.0 s
[2015-09-30T21:55Z] INFO  22:55:29,257 ProgressMeter - Total runtime 0.98 secs, 0.02 min, 0.00 hours
[2015-09-30T21:55Z] bgzip syn3-X_0_31090302-raw.vcf
[2015-09-30T21:55Z] tabix index syn3-X_0_31090302-raw.vcf.gz
[2015-09-30T21:55Z] bgzip syn3-X_0_31090302-raw-rejectfix.vcf
[2015-09-30T21:55Z] tabix index syn3-X_0_31090302-raw-rejectfix.vcf.gz
[2015-09-30T21:55Z] GATK: VariantAnnotator
[2015-09-30T21:55Z] INFO  22:55:31,725 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:31,728 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:55Z] INFO  22:55:31,728 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:55Z] INFO  22:55:31,728 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:55Z] INFO  22:55:31,732 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/X/syn3-X_0_31090302-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/X/tx/tmpBMqHZF/syn3-X_0_31090302-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_0_31090302-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:55Z] INFO  22:55:31,739 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:55Z] INFO  22:55:31,739 HelpFormatter - Date/Time: 2015/09/30 22:55:31
[2015-09-30T21:55Z] INFO  22:55:31,739 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:31,742 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:55Z] INFO  22:55:32,174 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:55Z] INFO  22:55:32,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:55Z] INFO  22:55:32,295 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:55Z] INFO  22:55:32,494 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.20
[2015-09-30T21:55Z] INFO  22:55:33,337 IntervalUtils - Processing 1074 bp from intervals
[2015-09-30T21:55Z] WARN  22:55:33,341 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:55Z] WARN  22:55:33,341 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:55Z] INFO  22:55:33,398 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:55Z] INFO  22:55:34,094 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:55Z] INFO  22:55:34,095 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:55Z] INFO  22:55:34,095 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:55Z] INFO  22:55:34,096 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:55Z] INFO  22:55:34,128 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:55Z] INFO  22:55:39,337 VariantAnnotator - Processed 873 loci.
[2015-09-30T21:55Z]
[2015-09-30T21:55Z] INFO  22:55:39,358 ProgressMeter -            done      4719.0     5.0 s      18.6 m       99.9%     5.0 s       0.0 s
[2015-09-30T21:55Z] INFO  22:55:39,358 ProgressMeter - Total runtime 5.26 secs, 0.09 min, 0.00 hours
[2015-09-30T21:55Z] INFO  22:55:39,359 MicroScheduler - 3420 reads were filtered out during the traversal out of approximately 71492 total reads (4.78%)
[2015-09-30T21:55Z] INFO  22:55:39,359 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:55Z] INFO  22:55:39,359 MicroScheduler -   -> 3407 reads (4.77% of total) failing DuplicateReadFilter
[2015-09-30T21:55Z] INFO  22:55:39,359 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:55Z] INFO  22:55:39,360 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:55Z] INFO  22:55:39,360 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:55Z] INFO  22:55:39,360 MicroScheduler -   -> 13 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:55Z] INFO  22:55:40,299 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:55Z] Genotyping with varscan: ('X', 62568928, 94148729) 1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam
[2015-09-30T21:55Z] samtools mpileup
[2015-09-30T21:55Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:55Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:55Z] INFO  22:55:44,840 VariantAnnotator - Processed 2477 loci.
[2015-09-30T21:55Z]
[2015-09-30T21:55Z] INFO  22:55:44,859 ProgressMeter -            done     15889.0    16.0 s      17.3 m      100.0%    16.0 s       0.0 s
[2015-09-30T21:55Z] INFO  22:55:44,860 ProgressMeter - Total runtime 16.49 secs, 0.27 min, 0.00 hours
[2015-09-30T21:55Z] INFO  22:55:44,860 MicroScheduler - 13430 reads were filtered out during the traversal out of approximately 250555 total reads (5.36%)
[2015-09-30T21:55Z] INFO  22:55:44,860 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:55Z] INFO  22:55:44,860 MicroScheduler -   -> 13384 reads (5.34% of total) failing DuplicateReadFilter
[2015-09-30T21:55Z] INFO  22:55:44,861 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:55Z] INFO  22:55:44,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:55Z] INFO  22:55:44,861 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:55Z] INFO  22:55:44,861 MicroScheduler -   -> 46 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:55Z] INFO  22:55:46,043 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:55Z] Genotyping with varscan: ('X', 94317773, 125687021) 1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam
[2015-09-30T21:55Z] samtools mpileup
[2015-09-30T21:55Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:55Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:56Z] samtools mpileup
[2015-09-30T21:56Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:56Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:56Z] Varscan
[2015-09-30T21:56Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmp7WNNWx/syn3-X_31132529_62519711-raw-normal.mpileup
[2015-09-30T21:56Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmp7WNNWx/syn3-X_31132529_62519711-raw-tumor.mpileup
[2015-09-30T21:56Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:56Z] Min reads2:	2
[2015-09-30T21:56Z] Min strands2:	1
[2015-09-30T21:56Z] Min var freq:	0.1
[2015-09-30T21:56Z] Min freq for hom:	0.75
[2015-09-30T21:56Z] Normal purity:	1.0
[2015-09-30T21:56Z] Tumor purity:	1.0
[2015-09-30T21:56Z] Min avg qual:	15
[2015-09-30T21:56Z] P-value thresh:	0.98
[2015-09-30T21:56Z] Somatic p-value:	0.05
[2015-09-30T21:56Z] samtools mpileup
[2015-09-30T21:56Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:56Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:56Z] Varscan
[2015-09-30T21:56Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmptDtn2a/syn3-X_62568928_94148729-raw-normal.mpileup
[2015-09-30T21:56Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmptDtn2a/syn3-X_62568928_94148729-raw-tumor.mpileup
[2015-09-30T21:56Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:56Z] Min reads2:	2
[2015-09-30T21:56Z] Min strands2:	1
[2015-09-30T21:56Z] Min var freq:	0.1
[2015-09-30T21:56Z] Min freq for hom:	0.75
[2015-09-30T21:56Z] Normal purity:	1.0
[2015-09-30T21:56Z] Tumor purity:	1.0
[2015-09-30T21:56Z] Min avg qual:	15
[2015-09-30T21:56Z] P-value thresh:	0.98
[2015-09-30T21:56Z] Somatic p-value:	0.05
[2015-09-30T21:56Z] Varscan
[2015-09-30T21:56Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmp7F0bO2/syn3-X_94317773_125687021-raw-normal.mpileup
[2015-09-30T21:56Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmp7F0bO2/syn3-X_94317773_125687021-raw-tumor.mpileup
[2015-09-30T21:56Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:56Z] Min reads2:	2
[2015-09-30T21:56Z] Min strands2:	1
[2015-09-30T21:56Z] Min var freq:	0.1
[2015-09-30T21:56Z] Min freq for hom:	0.75
[2015-09-30T21:56Z] Normal purity:	1.0
[2015-09-30T21:56Z] Tumor purity:	1.0
[2015-09-30T21:56Z] Min avg qual:	15
[2015-09-30T21:56Z] P-value thresh:	0.98
[2015-09-30T21:56Z] Somatic p-value:	0.05
[2015-09-30T21:57Z] 1298445 positions in tumor
[2015-09-30T21:57Z] 1298441 positions shared in normal
[2015-09-30T21:57Z] 1276751 had sufficient coverage for comparison
[2015-09-30T21:57Z] 1275726 were called Reference
[2015-09-30T21:57Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:57Z] 141 were removed by the strand filter
[2015-09-30T21:57Z] 958 were called Germline
[2015-09-30T21:57Z] 3 were called LOH
[2015-09-30T21:57Z] 46 were called Somatic
[2015-09-30T21:57Z] 18 were called Unknown
[2015-09-30T21:57Z] 0 were called Variant
[2015-09-30T21:57Z] Varscan paired fix
[2015-09-30T21:57Z] Varscan paired fix
[2015-09-30T21:57Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:57Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:57Z] bgzip syn3-X_31132529_62519711-raw.snp.vcf
[2015-09-30T21:57Z] tabix index syn3-X_31132529_62519711-raw.snp.vcf.gz
[2015-09-30T21:57Z] bgzip syn3-X_31132529_62519711-raw.indel.vcf
[2015-09-30T21:57Z] tabix index syn3-X_31132529_62519711-raw.indel.vcf.gz
[2015-09-30T21:57Z] Combine variant files
[2015-09-30T21:57Z] INFO  22:57:06,018 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:06,020 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:57Z] INFO  22:57:06,020 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:57Z] INFO  22:57:06,020 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:57Z] INFO  22:57:06,023 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/X/tx/tmp7WNNWx/tx/tmp73555W/syn3-X_31132529_62519711-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/X/tx/tmp7WNNWx/syn3-X_31132529_62519711-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/X/tx/tmp7WNNWx/syn3-X_31132529_62519711-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_31132529_62519711-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:57Z] INFO  22:57:06,030 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:57Z] INFO  22:57:06,031 HelpFormatter - Date/Time: 2015/09/30 22:57:06
[2015-09-30T21:57Z] INFO  22:57:06,031 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:06,031 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:06,112 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:57Z] INFO  22:57:06,382 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:57Z] INFO  22:57:06,495 IntervalUtils - Processing 1301828 bp from intervals
[2015-09-30T21:57Z] WARN  22:57:06,496 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] WARN  22:57:06,496 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] INFO  22:57:06,555 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:06,559 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:06,559 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:57Z] INFO  22:57:06,559 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:57Z] INFO  22:57:06,560 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:57Z] INFO  22:57:07,624 ProgressMeter -            done      1015.0     1.0 s      17.5 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:57Z] INFO  22:57:07,625 ProgressMeter - Total runtime 1.07 secs, 0.02 min, 0.00 hours
[2015-09-30T21:57Z] bgzip syn3-X_31132529_62519711-raw.vcf
[2015-09-30T21:57Z] tabix index syn3-X_31132529_62519711-raw.vcf.gz
[2015-09-30T21:57Z] bgzip syn3-X_31132529_62519711-raw-rejectfix.vcf
[2015-09-30T21:57Z] tabix index syn3-X_31132529_62519711-raw-rejectfix.vcf.gz
[2015-09-30T21:57Z] GATK: VariantAnnotator
[2015-09-30T21:57Z] 826358 positions in tumor
[2015-09-30T21:57Z] 826356 positions shared in normal
[2015-09-30T21:57Z] 809469 had sufficient coverage for comparison
[2015-09-30T21:57Z] 809019 were called Reference
[2015-09-30T21:57Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:57Z] 38 were removed by the strand filter
[2015-09-30T21:57Z] 426 were called Germline
[2015-09-30T21:57Z] 1 were called LOH
[2015-09-30T21:57Z] 16 were called Somatic
[2015-09-30T21:57Z] 7 were called Unknown
[2015-09-30T21:57Z] 0 were called Variant
[2015-09-30T21:57Z] Varscan paired fix
[2015-09-30T21:57Z] Varscan paired fix
[2015-09-30T21:57Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:57Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:57Z] bgzip syn3-X_62568928_94148729-raw.snp.vcf
[2015-09-30T21:57Z] tabix index syn3-X_62568928_94148729-raw.snp.vcf.gz
[2015-09-30T21:57Z] bgzip syn3-X_62568928_94148729-raw.indel.vcf
[2015-09-30T21:57Z] tabix index syn3-X_62568928_94148729-raw.indel.vcf.gz
[2015-09-30T21:57Z] Combine variant files
[2015-09-30T21:57Z] INFO  22:57:10,126 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:10,128 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:57Z] INFO  22:57:10,128 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:57Z] INFO  22:57:10,128 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:57Z] INFO  22:57:10,132 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/X/syn3-X_31132529_62519711-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/X/tx/tmpK8jxsQ/syn3-X_31132529_62519711-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_31132529_62519711-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:57Z] INFO  22:57:10,137 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:57Z] INFO  22:57:10,137 HelpFormatter - Date/Time: 2015/09/30 22:57:10
[2015-09-30T21:57Z] INFO  22:57:10,138 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:10,138 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:10,233 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:57Z] INFO  22:57:10,311 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:57Z] INFO  22:57:10,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:57Z] INFO  22:57:10,341 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:57Z] INFO  22:57:10,705 IntervalUtils - Processing 1015 bp from intervals
[2015-09-30T21:57Z] WARN  22:57:10,709 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] WARN  22:57:10,709 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] INFO  22:57:10,768 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:57Z] INFO  22:57:10,856 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:10,857 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:57Z] INFO  22:57:10,857 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:57Z] INFO  22:57:10,858 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:57Z] INFO  22:57:10,890 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:57Z] INFO  22:57:11,149 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:11,151 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:57Z] INFO  22:57:11,152 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:57Z] INFO  22:57:11,152 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:57Z] INFO  22:57:11,155 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/X/tx/tmptDtn2a/tx/tmp41y6pK/syn3-X_62568928_94148729-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/X/tx/tmptDtn2a/syn3-X_62568928_94148729-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/X/tx/tmptDtn2a/syn3-X_62568928_94148729-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_62568928_94148729-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:57Z] INFO  22:57:11,161 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:57Z] INFO  22:57:11,161 HelpFormatter - Date/Time: 2015/09/30 22:57:11
[2015-09-30T21:57Z] INFO  22:57:11,162 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:11,162 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:11,242 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:57Z] INFO  22:57:11,381 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:57Z] INFO  22:57:11,488 IntervalUtils - Processing 829325 bp from intervals
[2015-09-30T21:57Z] WARN  22:57:11,489 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] WARN  22:57:11,489 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] INFO  22:57:11,549 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:11,551 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:11,552 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:57Z] INFO  22:57:11,552 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:57Z] INFO  22:57:11,553 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:57Z] INFO  22:57:12,464 ProgressMeter -            done       513.0     0.0 s      29.6 m       99.5%     0.0 s       0.0 s
[2015-09-30T21:57Z] INFO  22:57:12,464 ProgressMeter - Total runtime 0.91 secs, 0.02 min, 0.00 hours
[2015-09-30T21:57Z] bgzip syn3-X_62568928_94148729-raw.vcf
[2015-09-30T21:57Z] tabix index syn3-X_62568928_94148729-raw.vcf.gz
[2015-09-30T21:57Z] bgzip syn3-X_62568928_94148729-raw-rejectfix.vcf
[2015-09-30T21:57Z] tabix index syn3-X_62568928_94148729-raw-rejectfix.vcf.gz
[2015-09-30T21:57Z] GATK: VariantAnnotator
[2015-09-30T21:57Z] INFO  22:57:14,647 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:14,649 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:57Z] INFO  22:57:14,649 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:57Z] INFO  22:57:14,650 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:57Z] INFO  22:57:14,653 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/X/syn3-X_62568928_94148729-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/X/tx/tmpa2ads4/syn3-X_62568928_94148729-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_62568928_94148729-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:57Z] INFO  22:57:14,659 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:57Z] INFO  22:57:14,659 HelpFormatter - Date/Time: 2015/09/30 22:57:14
[2015-09-30T21:57Z] INFO  22:57:14,659 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:14,659 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:14,757 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:57Z] INFO  22:57:14,835 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:57Z] INFO  22:57:14,843 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:57Z] INFO  22:57:14,866 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:57Z] INFO  22:57:15,168 IntervalUtils - Processing 513 bp from intervals
[2015-09-30T21:57Z] WARN  22:57:15,173 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] WARN  22:57:15,173 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] INFO  22:57:15,232 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:57Z] INFO  22:57:15,315 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:15,315 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:57Z] INFO  22:57:15,316 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:57Z] INFO  22:57:15,316 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:57Z] INFO  22:57:15,350 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:57Z] INFO  22:57:16,802 VariantAnnotator - Processed 871 loci.
[2015-09-30T21:57Z]
[2015-09-30T21:57Z] INFO  22:57:16,825 ProgressMeter -            done      4804.0     5.0 s      20.7 m       99.9%     5.0 s       0.0 s
[2015-09-30T21:57Z] INFO  22:57:16,826 ProgressMeter - Total runtime 5.97 secs, 0.10 min, 0.00 hours
[2015-09-30T21:57Z] INFO  22:57:16,826 MicroScheduler - 2815 reads were filtered out during the traversal out of approximately 72434 total reads (3.89%)
[2015-09-30T21:57Z] INFO  22:57:16,826 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:57Z] INFO  22:57:16,827 MicroScheduler -   -> 2801 reads (3.87% of total) failing DuplicateReadFilter
[2015-09-30T21:57Z] INFO  22:57:16,827 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:57Z] INFO  22:57:16,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:57Z] INFO  22:57:16,827 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:57Z] INFO  22:57:16,828 MicroScheduler -   -> 14 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:57Z] INFO  22:57:17,779 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:57Z] Genotyping with varscan: ('X', 125953527, 155270560) 1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam
[2015-09-30T21:57Z] samtools mpileup
[2015-09-30T21:57Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:57Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:57Z] INFO  22:57:18,943 VariantAnnotator - Processed 408 loci.
[2015-09-30T21:57Z]
[2015-09-30T21:57Z] INFO  22:57:18,975 ProgressMeter -            done      1152.0     3.0 s      52.9 m       99.8%     3.0 s       0.0 s
[2015-09-30T21:57Z] INFO  22:57:18,976 ProgressMeter - Total runtime 3.66 secs, 0.06 min, 0.00 hours
[2015-09-30T21:57Z] INFO  22:57:18,976 MicroScheduler - 1362 reads were filtered out during the traversal out of approximately 31357 total reads (4.34%)
[2015-09-30T21:57Z] INFO  22:57:18,977 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:57Z] INFO  22:57:18,977 MicroScheduler -   -> 1354 reads (4.32% of total) failing DuplicateReadFilter
[2015-09-30T21:57Z] INFO  22:57:18,977 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:57Z] INFO  22:57:18,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:57Z] INFO  22:57:18,978 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:57Z] INFO  22:57:18,978 MicroScheduler -   -> 8 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:57Z] INFO  22:57:19,901 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:57Z] Genotyping with varscan: ('Y', 0, 28716339) 1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam
[2015-09-30T21:57Z] samtools mpileup
[2015-09-30T21:57Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:57Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:57Z] samtools mpileup
[2015-09-30T21:57Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:57Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:57Z] Varscan
[2015-09-30T21:57Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/Y/tx/tmpmH9pud/syn3-Y_0_28716339-raw-normal.mpileup
[2015-09-30T21:57Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/Y/tx/tmpmH9pud/syn3-Y_0_28716339-raw-tumor.mpileup
[2015-09-30T21:57Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:57Z] Min reads2:	2
[2015-09-30T21:57Z] Min strands2:	1
[2015-09-30T21:57Z] Min var freq:	0.1
[2015-09-30T21:57Z] Min freq for hom:	0.75
[2015-09-30T21:57Z] Normal purity:	1.0
[2015-09-30T21:57Z] Tumor purity:	1.0
[2015-09-30T21:57Z] Min avg qual:	15
[2015-09-30T21:57Z] P-value thresh:	0.98
[2015-09-30T21:57Z] Somatic p-value:	0.05
[2015-09-30T21:57Z] 23445 positions in tumor
[2015-09-30T21:57Z] 23423 positions shared in normal
[2015-09-30T21:57Z] 12238 had sufficient coverage for comparison
[2015-09-30T21:57Z] 11787 were called Reference
[2015-09-30T21:57Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:57Z] 43 were removed by the strand filter
[2015-09-30T21:57Z] 443 were called Germline
[2015-09-30T21:57Z] 3 were called LOH
[2015-09-30T21:57Z] 3 were called Somatic
[2015-09-30T21:57Z] 2 were called Unknown
[2015-09-30T21:57Z] 0 were called Variant
[2015-09-30T21:57Z] Varscan paired fix
[2015-09-30T21:57Z] Varscan paired fix
[2015-09-30T21:57Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:57Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:57Z] bgzip syn3-Y_0_28716339-raw.snp.vcf
[2015-09-30T21:57Z] tabix index syn3-Y_0_28716339-raw.snp.vcf.gz
[2015-09-30T21:57Z] bgzip syn3-Y_0_28716339-raw.indel.vcf
[2015-09-30T21:57Z] tabix index syn3-Y_0_28716339-raw.indel.vcf.gz
[2015-09-30T21:57Z] Combine variant files
[2015-09-30T21:57Z] INFO  22:57:28,166 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:28,168 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:57Z] INFO  22:57:28,168 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:57Z] INFO  22:57:28,168 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:57Z] INFO  22:57:28,172 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/Y/tx/tmpmH9pud/tx/tmpVDZ15g/syn3-Y_0_28716339-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/Y/tx/tmpmH9pud/syn3-Y_0_28716339-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/Y/tx/tmpmH9pud/syn3-Y_0_28716339-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/Y/syn3-Y_0_28716339-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:57Z] INFO  22:57:28,177 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:57Z] INFO  22:57:28,178 HelpFormatter - Date/Time: 2015/09/30 22:57:28
[2015-09-30T21:57Z] INFO  22:57:28,178 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:28,178 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:28,257 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:57Z] INFO  22:57:28,398 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:57Z] INFO  22:57:28,479 IntervalUtils - Processing 568521 bp from intervals
[2015-09-30T21:57Z] WARN  22:57:28,480 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] WARN  22:57:28,480 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] INFO  22:57:28,539 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:28,541 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:28,541 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:57Z] INFO  22:57:28,542 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:57Z] INFO  22:57:28,542 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:57Z] INFO  22:57:29,279 ProgressMeter -            done       427.0     0.0 s      28.8 m       98.9%     0.0 s       0.0 s
[2015-09-30T21:57Z] INFO  22:57:29,280 ProgressMeter - Total runtime 0.74 secs, 0.01 min, 0.00 hours
[2015-09-30T21:57Z] bgzip syn3-Y_0_28716339-raw.vcf
[2015-09-30T21:57Z] tabix index syn3-Y_0_28716339-raw.vcf.gz
[2015-09-30T21:57Z] bgzip syn3-Y_0_28716339-raw-rejectfix.vcf
[2015-09-30T21:57Z] tabix index syn3-Y_0_28716339-raw-rejectfix.vcf.gz
[2015-09-30T21:57Z] GATK: VariantAnnotator
[2015-09-30T21:57Z] INFO  22:57:31,433 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:31,435 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:57Z] INFO  22:57:31,435 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:57Z] INFO  22:57:31,435 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:57Z] INFO  22:57:31,439 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/Y/syn3-Y_0_28716339-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/Y/tx/tmpZt8tji/syn3-Y_0_28716339-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/Y/syn3-Y_0_28716339-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/Y/1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/Y/2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:57Z] INFO  22:57:31,444 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:57Z] INFO  22:57:31,445 HelpFormatter - Date/Time: 2015/09/30 22:57:31
[2015-09-30T21:57Z] INFO  22:57:31,445 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:31,445 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:31,519 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:57Z] INFO  22:57:31,610 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:57Z] INFO  22:57:31,618 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:57Z] INFO  22:57:31,640 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:57Z] INFO  22:57:31,895 IntervalUtils - Processing 427 bp from intervals
[2015-09-30T21:57Z] WARN  22:57:31,899 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] WARN  22:57:31,899 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] INFO  22:57:31,955 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:57Z] INFO  22:57:31,997 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:31,997 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:57Z] INFO  22:57:31,998 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:57Z] INFO  22:57:31,998 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:57Z] INFO  22:57:32,030 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:57Z] INFO  22:57:34,821 VariantAnnotator - Processed 407 loci.
[2015-09-30T21:57Z]
[2015-09-30T21:57Z] INFO  22:57:34,839 ProgressMeter -            done     13140.0     2.0 s       3.6 m       99.8%     2.0 s       0.0 s
[2015-09-30T21:57Z] INFO  22:57:34,839 ProgressMeter - Total runtime 2.84 secs, 0.05 min, 0.00 hours
[2015-09-30T21:57Z] INFO  22:57:34,839 MicroScheduler - 1132 reads were filtered out during the traversal out of approximately 13600 total reads (8.32%)
[2015-09-30T21:57Z] INFO  22:57:34,840 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:57Z] INFO  22:57:34,840 MicroScheduler -   -> 1080 reads (7.94% of total) failing DuplicateReadFilter
[2015-09-30T21:57Z] INFO  22:57:34,840 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:57Z] INFO  22:57:34,841 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:57Z] INFO  22:57:34,841 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:57Z] INFO  22:57:34,841 MicroScheduler -   -> 52 reads (0.38% of total) failing UnmappedReadFilter
[2015-09-30T21:57Z] INFO  22:57:35,780 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:57Z] MuTect: MuTect
[2015-09-30T21:57Z] INFO  22:57:44,102 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/1/syn3-1_0_31187470-raw-mutect-regions.bed to be BED
[2015-09-30T21:57Z] INFO  22:57:44,157 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:44,157 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T21:57Z] INFO  22:57:44,157 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:57Z] INFO  22:57:44,157 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:57Z] INFO  22:57:44,161 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/1/syn3-1_0_31187470-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/1/tx/tmpGA_Y4f/syn3-1_0_31187470-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T21:57Z] INFO  22:57:44,161 HelpFormatter - Date/Time: 2015/09/30 22:57:44
[2015-09-30T21:57Z] INFO  22:57:44,161 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:44,161 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:44,188 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T21:57Z] INFO  22:57:44,221 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T21:57Z] INFO  22:57:44,274 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:57Z] INFO  22:57:44,322 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T21:57Z] INFO  22:57:44,329 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:57Z] INFO  22:57:44,393 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T21:57Z] INFO  22:57:44,416 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T21:57Z] INFO  22:57:44,590 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T21:57Z] 1152791 positions in tumor
[2015-09-30T21:57Z] 1152784 positions shared in normal
[2015-09-30T21:57Z] 1131322 had sufficient coverage for comparison
[2015-09-30T21:57Z] 1130652 were called Reference
[2015-09-30T21:57Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:57Z] 60 were removed by the strand filter
[2015-09-30T21:57Z] 634 were called Germline
[2015-09-30T21:57Z] 1 were called LOH
[2015-09-30T21:57Z] 28 were called Somatic
[2015-09-30T21:57Z] 7 were called Unknown
[2015-09-30T21:57Z] 0 were called Variant
[2015-09-30T21:57Z] Varscan paired fix
[2015-09-30T21:57Z] Varscan paired fix
[2015-09-30T21:57Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:57Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:57Z] bgzip syn3-X_94317773_125687021-raw.snp.vcf
[2015-09-30T21:57Z] INFO  22:57:44,899 IntervalUtils - Processing 3069806 bp from intervals
[2015-09-30T21:57Z] INFO  22:57:44,903 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] INFO  22:57:44,904 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] tabix index syn3-X_94317773_125687021-raw.snp.vcf.gz
[2015-09-30T21:57Z] INFO  22:57:44,959 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:57Z] bgzip syn3-X_94317773_125687021-raw.indel.vcf
[2015-09-30T21:57Z] tabix index syn3-X_94317773_125687021-raw.indel.vcf.gz
[2015-09-30T21:57Z] INFO  22:57:45,137 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:45,137 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:57Z] INFO  22:57:45,137 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T21:57Z] INFO  22:57:45,138 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T21:57Z] Combine variant files
[2015-09-30T21:57Z] INFO  22:57:47,178 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:47,180 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:57Z] INFO  22:57:47,180 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:57Z] INFO  22:57:47,180 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:57Z] INFO  22:57:47,184 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/X/tx/tmp7F0bO2/tx/tmptrzxij/syn3-X_94317773_125687021-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/X/tx/tmp7F0bO2/syn3-X_94317773_125687021-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/X/tx/tmp7F0bO2/syn3-X_94317773_125687021-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_94317773_125687021-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:57Z] INFO  22:57:47,189 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:57Z] INFO  22:57:47,189 HelpFormatter - Date/Time: 2015/09/30 22:57:47
[2015-09-30T21:57Z] INFO  22:57:47,190 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:47,190 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:47,268 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:57Z] INFO  22:57:47,412 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:57Z] INFO  22:57:47,531 IntervalUtils - Processing 1156902 bp from intervals
[2015-09-30T21:57Z] WARN  22:57:47,532 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] WARN  22:57:47,532 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] INFO  22:57:47,589 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:47,592 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:47,593 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:57Z] INFO  22:57:47,593 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:57Z] INFO  22:57:47,594 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:57Z] INFO  22:57:47,733 MuTect - [MUTECT] Processed 1000056 reads in 2544 ms
[2015-09-30T21:57Z] INFO  22:57:48,505 ProgressMeter -            done       767.0     0.0 s      19.8 m       98.2%     0.0 s       0.0 s
[2015-09-30T21:57Z] INFO  22:57:48,505 ProgressMeter - Total runtime 0.91 secs, 0.02 min, 0.00 hours
[2015-09-30T21:57Z] bgzip syn3-X_94317773_125687021-raw.vcf
[2015-09-30T21:57Z] INFO  22:57:48,650 MuTect - [MUTECT] Processed 2000131 reads in 917 ms
[2015-09-30T21:57Z] tabix index syn3-X_94317773_125687021-raw.vcf.gz
[2015-09-30T21:57Z] bgzip syn3-X_94317773_125687021-raw-rejectfix.vcf
[2015-09-30T21:57Z] tabix index syn3-X_94317773_125687021-raw-rejectfix.vcf.gz
[2015-09-30T21:57Z] GATK: VariantAnnotator
[2015-09-30T21:57Z] INFO  22:57:49,301 MuTect - [MUTECT] Processed 3002172 reads in 650 ms
[2015-09-30T21:57Z] INFO  22:57:49,935 MuTect - [MUTECT] Processed 4002250 reads in 635 ms
[2015-09-30T21:57Z] INFO  22:57:50,789 MuTect - [MUTECT] Processed 5002335 reads in 854 ms
[2015-09-30T21:57Z] INFO  22:57:50,965 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:50,967 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:57Z] INFO  22:57:50,967 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:57Z] INFO  22:57:50,967 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:57Z] INFO  22:57:50,971 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/X/syn3-X_94317773_125687021-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/X/tx/tmpGmoFXi/syn3-X_94317773_125687021-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_94317773_125687021-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:57Z] INFO  22:57:50,977 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:57Z] INFO  22:57:50,977 HelpFormatter - Date/Time: 2015/09/30 22:57:50
[2015-09-30T21:57Z] INFO  22:57:50,977 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:50,977 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:57Z] INFO  22:57:51,074 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:57Z] INFO  22:57:51,150 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:57Z] INFO  22:57:51,157 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:57Z] INFO  22:57:51,179 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:57Z] INFO  22:57:51,480 IntervalUtils - Processing 767 bp from intervals
[2015-09-30T21:57Z] WARN  22:57:51,484 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] WARN  22:57:51,484 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:57Z] INFO  22:57:51,539 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:57Z] INFO  22:57:51,617 MuTect - [MUTECT] Processed 6002396 reads in 828 ms
[2015-09-30T21:57Z] INFO  22:57:51,638 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:57Z] INFO  22:57:51,638 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:57Z] INFO  22:57:51,639 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:57Z] INFO  22:57:51,639 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:57Z] INFO  22:57:51,672 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:57Z] INFO  22:57:51,689 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T21:57Z] INFO  22:57:52,328 MuTect - [MUTECT] Processed 7002431 reads in 711 ms
[2015-09-30T21:57Z] INFO  22:57:53,055 MuTect - [MUTECT] Processed 8002493 reads in 727 ms
[2015-09-30T21:57Z] INFO  22:57:53,786 MuTect - [MUTECT] Processed 9002590 reads in 731 ms
[2015-09-30T21:57Z] INFO  22:57:53,963 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T21:57Z] INFO  22:57:54,523 MuTect - [MUTECT] Processed 10002676 reads in 737 ms
[2015-09-30T21:57Z] INFO  22:57:55,241 MuTect - [MUTECT] Processed 11002732 reads in 718 ms
[2015-09-30T21:57Z] INFO  22:57:56,013 MuTect - [MUTECT] Processed 12002808 reads in 772 ms
[2015-09-30T21:57Z] INFO  22:57:56,219 VariantAnnotator - Processed 607 loci.
[2015-09-30T21:57Z]
[2015-09-30T21:57Z] INFO  22:57:56,244 ProgressMeter -            done      1750.0     4.0 s      43.9 m       99.5%     4.0 s       0.0 s
[2015-09-30T21:57Z] INFO  22:57:56,244 ProgressMeter - Total runtime 4.61 secs, 0.08 min, 0.00 hours
[2015-09-30T21:57Z] INFO  22:57:56,245 MicroScheduler - 2128 reads were filtered out during the traversal out of approximately 47767 total reads (4.45%)
[2015-09-30T21:57Z] INFO  22:57:56,245 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:57Z] INFO  22:57:56,245 MicroScheduler -   -> 2115 reads (4.43% of total) failing DuplicateReadFilter
[2015-09-30T21:57Z] INFO  22:57:56,245 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:57Z] INFO  22:57:56,246 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:57Z] INFO  22:57:56,246 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:57Z] INFO  22:57:56,246 MicroScheduler -   -> 13 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T21:57Z] INFO  22:57:56,262 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T21:57Z] INFO  22:57:56,743 MuTect - [MUTECT] Processed 13002919 reads in 729 ms
[2015-09-30T21:57Z] INFO  22:57:57,185 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:57Z] INFO  22:57:57,524 MuTect - [MUTECT] Processed 14002980 reads in 782 ms
[2015-09-30T21:57Z] INFO  22:57:58,277 MuTect - [MUTECT] Processed 15003096 reads in 753 ms
[2015-09-30T21:57Z] INFO  22:57:58,480 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T21:57Z] INFO  22:57:58,953 MuTect - [MUTECT] Processed 16003162 reads in 676 ms
[2015-09-30T21:57Z] MuTect: MuTect
[2015-09-30T21:57Z] INFO  22:57:59,594 MuTect - [MUTECT] Processed 17003207 reads in 640 ms
[2015-09-30T21:58Z] INFO  22:58:00,224 MuTect - [MUTECT] Processed 18003244 reads in 631 ms
[2015-09-30T21:58Z] INFO  22:58:00,814 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:01,113 MuTect - [MUTECT] Processed 19003285 reads in 889 ms
[2015-09-30T21:58Z] INFO  22:58:01,318 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/1/syn3-1_31187762_62229084-raw-mutect-regions.bed to be BED
[2015-09-30T21:58Z] INFO  22:58:01,370 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:58Z] INFO  22:58:01,370 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T21:58Z] INFO  22:58:01,370 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:58Z] INFO  22:58:01,370 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:58Z] INFO  22:58:01,374 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/1/syn3-1_31187762_62229084-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/1/tx/tmpyIkTlX/syn3-1_31187762_62229084-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T21:58Z] INFO  22:58:01,374 HelpFormatter - Date/Time: 2015/09/30 22:58:01
[2015-09-30T21:58Z] INFO  22:58:01,374 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:58Z] INFO  22:58:01,374 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:58Z] INFO  22:58:01,400 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T21:58Z] INFO  22:58:01,404 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T21:58Z] INFO  22:58:01,456 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:58Z] INFO  22:58:01,502 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T21:58Z] INFO  22:58:01,508 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:58Z] INFO  22:58:01,565 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T21:58Z] INFO  22:58:01,624 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T21:58Z] INFO  22:58:01,804 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T21:58Z] INFO  22:58:01,835 MuTect - [MUTECT] Processed 20003318 reads in 722 ms
[2015-09-30T21:58Z] INFO  22:58:01,931 IntervalUtils - Processing 2356624 bp from intervals
[2015-09-30T21:58Z] INFO  22:58:01,935 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:58Z] INFO  22:58:01,936 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:58Z] INFO  22:58:02,114 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:58Z] INFO  22:58:02,284 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:58Z] INFO  22:58:02,285 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:58Z] INFO  22:58:02,285 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T21:58Z] INFO  22:58:02,286 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T21:58Z] INFO  22:58:02,489 MuTect - [MUTECT] Processed 21003458 reads in 654 ms
[2015-09-30T21:58Z] INFO  22:58:03,125 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:03,170 MuTect - [MUTECT] Processed 22003485 reads in 681 ms
[2015-09-30T21:58Z] INFO  22:58:03,848 MuTect - [MUTECT] Processed 23003627 reads in 678 ms
[2015-09-30T21:58Z] samtools mpileup
[2015-09-30T21:58Z] [mpileup] 1 samples in 1 input files
[2015-09-30T21:58Z] <mpileup> Set max per-file depth to 8000
[2015-09-30T21:58Z] INFO  22:58:04,587 MuTect - [MUTECT] Processed 24003666 reads in 739 ms
[2015-09-30T21:58Z] INFO  22:58:04,842 MuTect - [MUTECT] Processed 1000041 reads in 2510 ms
[2015-09-30T21:58Z] INFO  22:58:05,265 MuTect - [MUTECT] Processed 25003670 reads in 678 ms
[2015-09-30T21:58Z] INFO  22:58:05,467 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:05,578 MuTect - [MUTECT] Processed 2000131 reads in 736 ms
[2015-09-30T21:58Z] INFO  22:58:05,929 MuTect - [MUTECT] Processed 26003699 reads in 664 ms
[2015-09-30T21:58Z] INFO  22:58:06,343 MuTect - [MUTECT] Processed 3000148 reads in 765 ms
[2015-09-30T21:58Z] INFO  22:58:06,575 MuTect - [MUTECT] Processed 27003800 reads in 646 ms
[2015-09-30T21:58Z] INFO  22:58:06,710 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:07,089 MuTect - [MUTECT] Processed 4000217 reads in 746 ms
[2015-09-30T21:58Z] INFO  22:58:07,219 MuTect - [MUTECT] Processed 28003877 reads in 644 ms
[2015-09-30T21:58Z] INFO  22:58:07,817 MuTect - [MUTECT] Processed 5000307 reads in 728 ms
[2015-09-30T21:58Z] INFO  22:58:07,817 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:07,873 MuTect - [MUTECT] Processed 29003885 reads in 654 ms
[2015-09-30T21:58Z] INFO  22:58:08,544 MuTect - [MUTECT] Processed 30003912 reads in 671 ms
[2015-09-30T21:58Z] INFO  22:58:08,592 MuTect - [MUTECT] Processed 6000336 reads in 775 ms
[2015-09-30T21:58Z] INFO  22:58:09,056 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:09,190 MuTect - [MUTECT] Processed 31004018 reads in 646 ms
[2015-09-30T21:58Z] INFO  22:58:09,368 MuTect - [MUTECT] Processed 7000410 reads in 776 ms
[2015-09-30T21:58Z] INFO  22:58:09,798 MuTect - [MUTECT] Processed 32004057 reads in 608 ms
[2015-09-30T21:58Z] INFO  22:58:10,076 MuTect - [MUTECT] Processed 8000520 reads in 708 ms
[2015-09-30T21:58Z] INFO  22:58:10,442 MuTect - [MUTECT] Processed 33004109 reads in 644 ms
[2015-09-30T21:58Z] INFO  22:58:10,526 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:10,759 MuTect - [MUTECT] Processed 9000520 reads in 683 ms
[2015-09-30T21:58Z] INFO  22:58:11,206 MuTect - [MUTECT] Processed 34004160 reads in 764 ms
[2015-09-30T21:58Z] INFO  22:58:11,458 MuTect - [MUTECT] Processed 10000642 reads in 699 ms
[2015-09-30T21:58Z] INFO  22:58:11,473 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:11,832 MuTect - [MUTECT] Processed 35004196 reads in 626 ms
[2015-09-30T21:58Z] INFO  22:58:12,118 MuTect - [MUTECT] Processed 11000735 reads in 660 ms
[2015-09-30T21:58Z] INFO  22:58:12,739 MuTect - [MUTECT] Processed 36004243 reads in 907 ms
[2015-09-30T21:58Z] INFO  22:58:12,806 MuTect - [MUTECT] Processed 12000781 reads in 688 ms
[2015-09-30T21:58Z] INFO  22:58:13,467 MuTect - [MUTECT] Processed 37004313 reads in 728 ms
[2015-09-30T21:58Z] INFO  22:58:13,469 MuTect - [MUTECT] Processed 13000843 reads in 663 ms
[2015-09-30T21:58Z] INFO  22:58:13,493 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:13,572 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:14,127 MuTect - [MUTECT] Processed 14000952 reads in 658 ms
[2015-09-30T21:58Z] INFO  22:58:14,136 MuTect - [MUTECT] Processed 38004328 reads in 669 ms
[2015-09-30T21:58Z] INFO  22:58:14,767 MuTect - [MUTECT] Processed 15001007 reads in 640 ms
[2015-09-30T21:58Z] INFO  22:58:14,823 MuTect - [MUTECT] Processed 39004410 reads in 687 ms
[2015-09-30T21:58Z] INFO  22:58:15,139 ProgressMeter -       1:1860034        1.00e+06   30.0 s       29.0 s     10.3%         4.8 m     4.3 m
[2015-09-30T21:58Z] INFO  22:58:15,437 MuTect - [MUTECT] Processed 16001011 reads in 670 ms
[2015-09-30T21:58Z] INFO  22:58:15,534 MuTect - [MUTECT] Processed 40004442 reads in 711 ms
[2015-09-30T21:58Z] INFO  22:58:15,704 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:16,045 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:16,129 MuTect - [MUTECT] Processed 17001042 reads in 692 ms
[2015-09-30T21:58Z] INFO  22:58:16,233 MuTect - [MUTECT] Processed 41004471 reads in 699 ms
[2015-09-30T21:58Z] INFO  22:58:16,819 MuTect - [MUTECT] Processed 18001059 reads in 690 ms
[2015-09-30T21:58Z] INFO  22:58:16,934 MuTect - [MUTECT] Processed 42004492 reads in 701 ms
[2015-09-30T21:58Z] INFO  22:58:17,483 MuTect - [MUTECT] Processed 19001100 reads in 664 ms
[2015-09-30T21:58Z] INFO  22:58:17,611 MuTect - [MUTECT] Processed 43004595 reads in 677 ms
[2015-09-30T21:58Z] INFO  22:58:17,980 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:18,150 MuTect - [MUTECT] Processed 20001179 reads in 667 ms
[2015-09-30T21:58Z] INFO  22:58:18,328 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:18,332 MuTect - [MUTECT] Processed 44004626 reads in 721 ms
[2015-09-30T21:58Z] INFO  22:58:18,831 MuTect - [MUTECT] Processed 21001215 reads in 680 ms
[2015-09-30T21:58Z] INFO  22:58:19,012 MuTect - [MUTECT] Processed 45004644 reads in 680 ms
[2015-09-30T21:58Z] INFO  22:58:19,486 MuTect - [MUTECT] Processed 22001294 reads in 656 ms
[2015-09-30T21:58Z] INFO  22:58:19,680 MuTect - [MUTECT] Processed 46004746 reads in 668 ms
[2015-09-30T21:58Z] INFO  22:58:20,191 MuTect - [MUTECT] Processed 23001321 reads in 705 ms
[2015-09-30T21:58Z] INFO  22:58:20,219 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:20,373 MuTect - [MUTECT] Processed 47004777 reads in 693 ms
[2015-09-30T21:58Z] INFO  22:58:20,537 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:20,859 MuTect - [MUTECT] Processed 24001336 reads in 668 ms
[2015-09-30T21:58Z] INFO  22:58:21,055 MuTect - [MUTECT] Processed 48004894 reads in 682 ms
[2015-09-30T21:58Z] INFO  22:58:21,570 MuTect - [MUTECT] Processed 25001339 reads in 711 ms
[2015-09-30T21:58Z] INFO  22:58:21,743 MuTect - [MUTECT] Processed 49005005 reads in 688 ms
[2015-09-30T21:58Z] INFO  22:58:22,277 MuTect - [MUTECT] Processed 26001421 reads in 707 ms
[2015-09-30T21:58Z] INFO  22:58:22,420 MuTect - [MUTECT] Processed 50005133 reads in 677 ms
[2015-09-30T21:58Z] INFO  22:58:22,538 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:22,963 MuTect - [MUTECT] Processed 27001464 reads in 686 ms
[2015-09-30T21:58Z] INFO  22:58:22,985 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:23,070 MuTect - [MUTECT] Processed 51005224 reads in 650 ms
[2015-09-30T21:58Z] INFO  22:58:23,634 MuTect - [MUTECT] Processed 28001580 reads in 671 ms
[2015-09-30T21:58Z] INFO  22:58:23,749 MuTect - [MUTECT] Processed 52005229 reads in 679 ms
[2015-09-30T21:58Z] INFO  22:58:24,314 MuTect - [MUTECT] Processed 29001659 reads in 680 ms
[2015-09-30T21:58Z] INFO  22:58:24,398 MuTect - [MUTECT] Processed 53005286 reads in 649 ms
[2015-09-30T21:58Z] INFO  22:58:24,691 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:25,033 MuTect - [MUTECT] Processed 30001690 reads in 719 ms
[2015-09-30T21:58Z] INFO  22:58:25,047 MuTect - [MUTECT] Processed 54005324 reads in 649 ms
[2015-09-30T21:58Z] INFO  22:58:25,260 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:25,701 MuTect - [MUTECT] Processed 55005428 reads in 654 ms
[2015-09-30T21:58Z] INFO  22:58:25,795 MuTect - [MUTECT] Processed 31001800 reads in 762 ms
[2015-09-30T21:58Z] INFO  22:58:26,363 MuTect - [MUTECT] Processed 56005459 reads in 662 ms
[2015-09-30T21:58Z] INFO  22:58:26,455 MuTect - [MUTECT] Processed 32001849 reads in 660 ms
[2015-09-30T21:58Z] INFO  22:58:26,824 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:27,030 MuTect - [MUTECT] Processed 57005514 reads in 666 ms
[2015-09-30T21:58Z] INFO  22:58:27,148 MuTect - [MUTECT] Processed 33001898 reads in 693 ms
[2015-09-30T21:58Z] INFO  22:58:27,501 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:27,708 MuTect - [MUTECT] Processed 58005529 reads in 679 ms
[2015-09-30T21:58Z] INFO  22:58:27,836 MuTect - [MUTECT] Processed 34001982 reads in 688 ms
[2015-09-30T21:58Z] INFO  22:58:28,426 MuTect - [MUTECT] Processed 59005680 reads in 718 ms
[2015-09-30T21:58Z] INFO  22:58:28,547 MuTect - [MUTECT] Processed 35002014 reads in 711 ms
[2015-09-30T21:58Z] INFO  22:58:29,107 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:29,134 MuTect - [MUTECT] Processed 60005765 reads in 708 ms
[2015-09-30T21:58Z] INFO  22:58:29,252 MuTect - [MUTECT] Processed 36002134 reads in 705 ms
[2015-09-30T21:58Z] INFO  22:58:29,744 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:29,775 MuTect - [MUTECT] Processed 61005864 reads in 641 ms
[2015-09-30T21:58Z] INFO  22:58:29,954 MuTect - [MUTECT] Processed 37002183 reads in 702 ms
[2015-09-30T21:58Z] INFO  22:58:30,621 MuTect - [MUTECT] Processed 38002203 reads in 667 ms
[2015-09-30T21:58Z] INFO  22:58:30,644 MuTect - [MUTECT] Processed 62005953 reads in 869 ms
[2015-09-30T21:58Z] INFO  22:58:31,263 MuTect - [MUTECT] Processed 39002241 reads in 642 ms
[2015-09-30T21:58Z] INFO  22:58:31,303 MuTect - [MUTECT] Processed 63005986 reads in 659 ms
[2015-09-30T21:58Z] INFO  22:58:31,548 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:31,937 MuTect - [MUTECT] Processed 40002266 reads in 674 ms
[2015-09-30T21:58Z] INFO  22:58:31,954 MuTect - [MUTECT] Processed 64005987 reads in 651 ms
[2015-09-30T21:58Z] INFO  22:58:31,978 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:32,603 MuTect - [MUTECT] Processed 65006031 reads in 648 ms
[2015-09-30T21:58Z] INFO  22:58:32,616 MuTect - [MUTECT] Processed 41002290 reads in 679 ms
[2015-09-30T21:58Z] INFO  22:58:33,291 MuTect - [MUTECT] Processed 66006135 reads in 689 ms
[2015-09-30T21:58Z] INFO  22:58:33,308 MuTect - [MUTECT] Processed 42002364 reads in 692 ms
[2015-09-30T21:58Z] INFO  22:58:33,681 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:33,972 MuTect - [MUTECT] Processed 67006209 reads in 681 ms
[2015-09-30T21:58Z] INFO  22:58:34,003 MuTect - [MUTECT] Processed 43002405 reads in 695 ms
[2015-09-30T21:58Z] INFO  22:58:34,191 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:34,650 MuTect - [MUTECT] Processed 68006283 reads in 678 ms
[2015-09-30T21:58Z] INFO  22:58:34,655 MuTect - [MUTECT] Processed 44002462 reads in 651 ms
[2015-09-30T21:58Z] INFO  22:58:35,290 MuTect - [MUTECT] Processed 69006293 reads in 640 ms
[2015-09-30T21:58Z] INFO  22:58:35,324 MuTect - [MUTECT] Processed 45002579 reads in 670 ms
[2015-09-30T21:58Z] INFO  22:58:35,893 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:35,982 MuTect - [MUTECT] Processed 70006342 reads in 692 ms
[2015-09-30T21:58Z] INFO  22:58:36,009 MuTect - [MUTECT] Processed 46002598 reads in 685 ms
[2015-09-30T21:58Z] INFO  22:58:36,641 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:36,696 MuTect - [MUTECT] Processed 47002678 reads in 687 ms
[2015-09-30T21:58Z] INFO  22:58:36,697 MuTect - [MUTECT] Processed 71006438 reads in 715 ms
[2015-09-30T21:58Z] INFO  22:58:37,346 MuTect - [MUTECT] Processed 48002757 reads in 650 ms
[2015-09-30T21:58Z] INFO  22:58:37,388 MuTect - [MUTECT] Processed 72006445 reads in 691 ms
[2015-09-30T21:58Z] INFO  22:58:38,011 MuTect - [MUTECT] Processed 49002802 reads in 665 ms
[2015-09-30T21:58Z] INFO  22:58:38,672 MuTect - [MUTECT] Processed 50002850 reads in 661 ms
[2015-09-30T21:58Z] INFO  22:58:38,941 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:39,346 MuTect - [MUTECT] Processed 51002892 reads in 674 ms
[2015-09-30T21:58Z] INFO  22:58:40,030 MuTect - [MUTECT] Processed 52002952 reads in 684 ms
[2015-09-30T21:58Z] INFO  22:58:40,710 MuTect - [MUTECT] Processed 73006507 reads in 3322 ms
[2015-09-30T21:58Z] INFO  22:58:40,725 MuTect - [MUTECT] Processed 53002963 reads in 695 ms
[2015-09-30T21:58Z] INFO  22:58:40,859 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:41,362 MuTect - [MUTECT] Processed 54003061 reads in 637 ms
[2015-09-30T21:58Z] INFO  22:58:41,371 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:41,383 MuTect - [MUTECT] Processed 74006553 reads in 673 ms
[2015-09-30T21:58Z] INFO  22:58:41,977 MuTect - [MUTECT] Processed 55003162 reads in 615 ms
[2015-09-30T21:58Z] INFO  22:58:42,054 MuTect - [MUTECT] Processed 75006559 reads in 671 ms
[2015-09-30T21:58Z] INFO  22:58:42,289 ProgressMeter -      1:36474218        1.52e+06   40.0 s       26.0 s     23.4%         2.8 m     2.2 m
[2015-09-30T21:58Z] INFO  22:58:42,615 MuTect - [MUTECT] Processed 56003240 reads in 638 ms
[2015-09-30T21:58Z] INFO  22:58:42,758 MuTect - [MUTECT] Processed 76006618 reads in 704 ms
[2015-09-30T21:58Z] INFO  22:58:43,125 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:43,251 MuTect - [MUTECT] Processed 57003241 reads in 636 ms
[2015-09-30T21:58Z] INFO  22:58:43,441 MuTect - [MUTECT] Processed 77006709 reads in 683 ms
[2015-09-30T21:58Z] INFO  22:58:43,595 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:43,885 MuTect - [MUTECT] Processed 58003359 reads in 634 ms
[2015-09-30T21:58Z] INFO  22:58:44,078 MuTect - [MUTECT] Processed 78006800 reads in 637 ms
[2015-09-30T21:58Z] INFO  22:58:44,513 MuTect - [MUTECT] Processed 59003380 reads in 628 ms
[2015-09-30T21:58Z] INFO  22:58:44,714 MuTect - [MUTECT] Processed 79006818 reads in 636 ms
[2015-09-30T21:58Z] INFO  22:58:45,140 ProgressMeter -       1:6312520        2.12e+06   60.0 s       28.0 s     21.0%         4.8 m     3.8 m
[2015-09-30T21:58Z] INFO  22:58:45,144 MuTect - [MUTECT] Processed 60003429 reads in 631 ms
[2015-09-30T21:58Z] INFO  22:58:45,352 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:45,355 MuTect - [MUTECT] Processed 80006897 reads in 641 ms
[2015-09-30T21:58Z] INFO  22:58:45,792 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:45,802 MuTect - [MUTECT] Processed 61003514 reads in 658 ms
[2015-09-30T21:58Z] INFO  22:58:46,005 MuTect - [MUTECT] Processed 81006985 reads in 650 ms
[2015-09-30T21:58Z] INFO  22:58:46,491 MuTect - [MUTECT] Processed 62003564 reads in 689 ms
[2015-09-30T21:58Z] INFO  22:58:46,648 MuTect - [MUTECT] Processed 82007081 reads in 643 ms
[2015-09-30T21:58Z] INFO  22:58:47,165 MuTect - [MUTECT] Processed 63003589 reads in 674 ms
[2015-09-30T21:58Z] INFO  22:58:47,298 MuTect - [MUTECT] Processed 83007123 reads in 650 ms
[2015-09-30T21:58Z] INFO  22:58:47,646 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:47,821 MuTect - [MUTECT] Processed 64003595 reads in 656 ms
[2015-09-30T21:58Z] INFO  22:58:47,905 MuTect - [MUTECT] Processed 84007191 reads in 607 ms
[2015-09-30T21:58Z] INFO  22:58:47,924 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:48,503 MuTect - [MUTECT] Processed 65003667 reads in 682 ms
[2015-09-30T21:58Z] INFO  22:58:48,536 MuTect - [MUTECT] Processed 85007220 reads in 631 ms
[2015-09-30T21:58Z] INFO  22:58:49,194 MuTect - [MUTECT] Processed 66003683 reads in 691 ms
[2015-09-30T21:58Z] INFO  22:58:49,242 MuTect - [MUTECT] Processed 86007304 reads in 706 ms
[2015-09-30T21:58Z] INFO  22:58:49,866 MuTect - [MUTECT] Processed 67003759 reads in 672 ms
[2015-09-30T21:58Z] INFO  22:58:50,210 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T21:58Z] Varscan
[2015-09-30T21:58Z] Normal Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmpGJwzIL/syn3-X_125953527_155270560-raw-normal.mpileup
[2015-09-30T21:58Z] Tumor Pileup: /home/cancer-dream-syn3/work/varscan/X/tx/tmpGJwzIL/syn3-X_125953527_155270560-raw-tumor.mpileup
[2015-09-30T21:58Z] Min coverage:	5x for Normal, 5x for Tumor
[2015-09-30T21:58Z] Min reads2:	2
[2015-09-30T21:58Z] Min strands2:	1
[2015-09-30T21:58Z] Min var freq:	0.1
[2015-09-30T21:58Z] Min freq for hom:	0.75
[2015-09-30T21:58Z] Normal purity:	1.0
[2015-09-30T21:58Z] Tumor purity:	1.0
[2015-09-30T21:58Z] Min avg qual:	15
[2015-09-30T21:58Z] P-value thresh:	0.98
[2015-09-30T21:58Z] Somatic p-value:	0.05
[2015-09-30T21:58Z] INFO  22:58:50,528 MuTect - [MUTECT] Processed 68003806 reads in 662 ms
[2015-09-30T21:58Z] INFO  22:58:50,679 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:50,734 MuTect - [MUTECT] Processed 87007337 reads in 1492 ms
[2015-09-30T21:58Z] INFO  22:58:51,197 MuTect - [MUTECT] Processed 69003815 reads in 669 ms
[2015-09-30T21:58Z] INFO  22:58:51,392 MuTect - [MUTECT] Processed 88007408 reads in 658 ms
[2015-09-30T21:58Z] INFO  22:58:51,865 MuTect - [MUTECT] Processed 70003890 reads in 668 ms
[2015-09-30T21:58Z] INFO  22:58:52,074 MuTect - [MUTECT] Processed 89007545 reads in 682 ms
[2015-09-30T21:58Z] INFO  22:58:52,383 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:52,545 MuTect - [MUTECT] Processed 71003977 reads in 680 ms
[2015-09-30T21:58Z] INFO  22:58:52,785 MuTect - [MUTECT] Processed 90007578 reads in 711 ms
[2015-09-30T21:58Z] INFO  22:58:52,925 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:53,206 MuTect - [MUTECT] Processed 72004017 reads in 661 ms
[2015-09-30T21:58Z] INFO  22:58:53,502 MuTect - [MUTECT] Processed 91007621 reads in 717 ms
[2015-09-30T21:58Z] INFO  22:58:53,891 MuTect - [MUTECT] Processed 73004039 reads in 685 ms
[2015-09-30T21:58Z] INFO  22:58:54,214 MuTect - [MUTECT] Processed 92007683 reads in 712 ms
[2015-09-30T21:58Z] INFO  22:58:54,516 MuTect - [MUTECT] Processed 74004156 reads in 625 ms
[2015-09-30T21:58Z] INFO  22:58:54,638 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:54,899 MuTect - [MUTECT] Processed 93007702 reads in 685 ms
[2015-09-30T21:58Z] INFO  22:58:55,183 MuTect - [MUTECT] Processed 75004239 reads in 667 ms
[2015-09-30T21:58Z] INFO  22:58:55,397 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:55,625 MuTect - [MUTECT] Processed 94007723 reads in 726 ms
[2015-09-30T21:58Z] INFO  22:58:55,871 MuTect - [MUTECT] Processed 76004350 reads in 688 ms
[2015-09-30T21:58Z] INFO  22:58:56,332 MuTect - [MUTECT] Processed 95007781 reads in 706 ms
[2015-09-30T21:58Z] INFO  22:58:56,486 MuTect - [MUTECT] Processed 77004398 reads in 614 ms
[2015-09-30T21:58Z] INFO  22:58:56,817 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:57,018 MuTect - [MUTECT] Processed 96007806 reads in 687 ms
[2015-09-30T21:58Z] INFO  22:58:57,139 MuTect - [MUTECT] Processed 78004450 reads in 654 ms
[2015-09-30T21:58Z] INFO  22:58:57,717 MuTect - [MUTECT] Processed 97007909 reads in 699 ms
[2015-09-30T21:58Z] INFO  22:58:57,775 MuTect - [MUTECT] Processed 79004511 reads in 636 ms
[2015-09-30T21:58Z] INFO  22:58:57,783 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:58,388 MuTect - [MUTECT] Processed 80004513 reads in 613 ms
[2015-09-30T21:58Z] INFO  22:58:58,425 MuTect - [MUTECT] Processed 98007953 reads in 708 ms
[2015-09-30T21:58Z] INFO  22:58:59,001 MuTect - [MUTECT] Processed 81004555 reads in 613 ms
[2015-09-30T21:58Z] INFO  22:58:59,066 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T21:58Z] INFO  22:58:59,134 MuTect - [MUTECT] Processed 99007971 reads in 709 ms
[2015-09-30T21:58Z] INFO  22:58:59,629 MuTect - [MUTECT] Processed 82004608 reads in 628 ms
[2015-09-30T21:58Z] INFO  22:58:59,853 MuTect - [MUTECT] Processed 100007984 reads in 719 ms
[2015-09-30T21:59Z] INFO  22:59:00,222 MuTect - [MUTECT] Processed 83004640 reads in 593 ms
[2015-09-30T21:59Z] INFO  22:59:00,230 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:00,551 MuTect - [MUTECT] Processed 101007985 reads in 698 ms
[2015-09-30T21:59Z] INFO  22:59:00,849 MuTect - [MUTECT] Processed 84004664 reads in 627 ms
[2015-09-30T21:59Z] INFO  22:59:01,222 MuTect - [MUTECT] Processed 102007993 reads in 671 ms
[2015-09-30T21:59Z] INFO  22:59:01,277 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:01,464 MuTect - [MUTECT] Processed 85004720 reads in 615 ms
[2015-09-30T21:59Z] INFO  22:59:01,905 MuTect - [MUTECT] Processed 103008036 reads in 683 ms
[2015-09-30T21:59Z] INFO  22:59:02,103 MuTect - [MUTECT] Processed 86004846 reads in 639 ms
[2015-09-30T21:59Z] INFO  22:59:02,627 MuTect - [MUTECT] Processed 104008121 reads in 722 ms
[2015-09-30T21:59Z] INFO  22:59:02,710 MuTect - [MUTECT] Processed 87004850 reads in 607 ms
[2015-09-30T21:59Z] INFO  22:59:02,723 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:03,309 MuTect - [MUTECT] Processed 105008157 reads in 682 ms
[2015-09-30T21:59Z] INFO  22:59:03,376 MuTect - [MUTECT] Processed 88004903 reads in 666 ms
[2015-09-30T21:59Z] INFO  22:59:03,754 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:04,046 MuTect - [MUTECT] Processed 89004926 reads in 670 ms
[2015-09-30T21:59Z] INFO  22:59:04,064 MuTect - [MUTECT] Processed 106008180 reads in 755 ms
[2015-09-30T21:59Z] INFO  22:59:04,735 MuTect - [MUTECT] Processed 90004972 reads in 689 ms
[2015-09-30T21:59Z] INFO  22:59:04,802 MuTect - [MUTECT] Processed 107008240 reads in 738 ms
[2015-09-30T21:59Z] INFO  22:59:05,152 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:05,385 MuTect - [MUTECT] Processed 91004994 reads in 650 ms
[2015-09-30T21:59Z] INFO  22:59:05,486 MuTect - [MUTECT] Processed 108008272 reads in 684 ms
[2015-09-30T21:59Z] INFO  22:59:06,015 MuTect - [MUTECT] Processed 92005036 reads in 630 ms
[2015-09-30T21:59Z] INFO  22:59:06,150 MuTect - [MUTECT] Processed 109008298 reads in 664 ms
[2015-09-30T21:59Z] INFO  22:59:06,426 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:06,675 MuTect - [MUTECT] Processed 93005053 reads in 660 ms
[2015-09-30T21:59Z] INFO  22:59:06,819 MuTect - [MUTECT] Processed 110008359 reads in 669 ms
[2015-09-30T21:59Z] INFO  22:59:07,343 MuTect - [MUTECT] Processed 94005131 reads in 668 ms
[2015-09-30T21:59Z] INFO  22:59:07,411 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:07,498 MuTect - [MUTECT] Processed 111008453 reads in 679 ms
[2015-09-30T21:59Z] INFO  22:59:07,978 MuTect - [MUTECT] Processed 95005174 reads in 635 ms
[2015-09-30T21:59Z] INFO  22:59:08,174 MuTect - [MUTECT] Processed 112008512 reads in 676 ms
[2015-09-30T21:59Z] INFO  22:59:08,620 MuTect - [MUTECT] Processed 96005291 reads in 641 ms
[2015-09-30T21:59Z] INFO  22:59:08,649 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:08,895 MuTect - [MUTECT] Processed 113008550 reads in 721 ms
[2015-09-30T21:59Z] INFO  22:59:09,281 MuTect - [MUTECT] Processed 97005373 reads in 662 ms
[2015-09-30T21:59Z] INFO  22:59:09,623 MuTect - [MUTECT] Processed 114008584 reads in 728 ms
[2015-09-30T21:59Z] INFO  22:59:09,830 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:09,905 MuTect - [MUTECT] Processed 98005459 reads in 624 ms
[2015-09-30T21:59Z] INFO  22:59:10,322 MuTect - [MUTECT] Processed 115008656 reads in 699 ms
[2015-09-30T21:59Z] INFO  22:59:10,542 MuTect - [MUTECT] Processed 99005521 reads in 637 ms
[2015-09-30T21:59Z] INFO  22:59:10,755 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:11,004 MuTect - [MUTECT] Processed 116008787 reads in 682 ms
[2015-09-30T21:59Z] INFO  22:59:11,201 MuTect - [MUTECT] Processed 100005563 reads in 659 ms
[2015-09-30T21:59Z] INFO  22:59:11,668 MuTect - [MUTECT] Processed 117008902 reads in 664 ms
[2015-09-30T21:59Z] INFO  22:59:11,879 MuTect - [MUTECT] Processed 101005647 reads in 678 ms
[2015-09-30T21:59Z] INFO  22:59:12,137 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:12,290 ProgressMeter -      1:41452957        3.00e+06   70.0 s       23.0 s     43.4%         2.7 m    91.0 s
[2015-09-30T21:59Z] INFO  22:59:12,333 MuTect - [MUTECT] Processed 118008943 reads in 665 ms
[2015-09-30T21:59Z] INFO  22:59:12,539 MuTect - [MUTECT] Processed 102005721 reads in 660 ms
[2015-09-30T21:59Z] INFO  22:59:12,967 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:13,035 MuTect - [MUTECT] Processed 119008952 reads in 702 ms
[2015-09-30T21:59Z] INFO  22:59:13,183 MuTect - [MUTECT] Processed 103005772 reads in 644 ms
[2015-09-30T21:59Z] INFO  22:59:13,719 MuTect - [MUTECT] Processed 120008967 reads in 684 ms
[2015-09-30T21:59Z] INFO  22:59:13,842 MuTect - [MUTECT] Processed 104005870 reads in 659 ms
[2015-09-30T21:59Z] INFO  22:59:14,428 MuTect - [MUTECT] Processed 121009002 reads in 709 ms
[2015-09-30T21:59Z] INFO  22:59:14,480 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:14,487 MuTect - [MUTECT] Processed 105005921 reads in 645 ms
[2015-09-30T21:59Z] INFO  22:59:15,036 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:15,113 MuTect - [MUTECT] Processed 122009087 reads in 685 ms
[2015-09-30T21:59Z] INFO  22:59:15,129 MuTect - [MUTECT] Processed 106005942 reads in 642 ms
[2015-09-30T21:59Z] INFO  22:59:15,141 ProgressMeter -      1:11167094        3.34e+06   90.0 s       26.0 s     34.5%         4.3 m     2.8 m
[2015-09-30T21:59Z] INFO  22:59:15,768 MuTect - [MUTECT] Processed 123009158 reads in 655 ms
[2015-09-30T21:59Z] INFO  22:59:15,794 MuTect - [MUTECT] Processed 107005987 reads in 665 ms
[2015-09-30T21:59Z] INFO  22:59:16,424 MuTect - [MUTECT] Processed 124009170 reads in 656 ms
[2015-09-30T21:59Z] INFO  22:59:16,467 MuTect - [MUTECT] Processed 108006051 reads in 673 ms
[2015-09-30T21:59Z] INFO  22:59:16,818 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:17,101 MuTect - [MUTECT] Processed 125009181 reads in 677 ms
[2015-09-30T21:59Z] INFO  22:59:17,162 MuTect - [MUTECT] Processed 109006109 reads in 695 ms
[2015-09-30T21:59Z] INFO  22:59:17,453 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:17,774 MuTect - [MUTECT] Processed 126009283 reads in 673 ms
[2015-09-30T21:59Z] INFO  22:59:17,831 MuTect - [MUTECT] Processed 110006148 reads in 669 ms
[2015-09-30T21:59Z] INFO  22:59:18,406 MuTect - [MUTECT] Processed 127009344 reads in 632 ms
[2015-09-30T21:59Z] INFO  22:59:18,465 MuTect - [MUTECT] Processed 111006218 reads in 634 ms
[2015-09-30T21:59Z] INFO  22:59:19,078 MuTect - [MUTECT] Processed 128009411 reads in 672 ms
[2015-09-30T21:59Z] INFO  22:59:19,084 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:19,137 MuTect - [MUTECT] Processed 112006260 reads in 672 ms
[2015-09-30T21:59Z] INFO  22:59:19,635 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:19,764 MuTect - [MUTECT] Processed 129009447 reads in 686 ms
[2015-09-30T21:59Z] INFO  22:59:19,807 MuTect - [MUTECT] Processed 113006327 reads in 669 ms
[2015-09-30T21:59Z] INFO  22:59:20,445 MuTect - [MUTECT] Processed 130009505 reads in 681 ms
[2015-09-30T21:59Z] INFO  22:59:20,457 MuTect - [MUTECT] Processed 114006383 reads in 651 ms
[2015-09-30T21:59Z] INFO  22:59:21,112 MuTect - [MUTECT] Processed 131009611 reads in 667 ms
[2015-09-30T21:59Z] INFO  22:59:21,135 MuTect - [MUTECT] Processed 115006422 reads in 678 ms
[2015-09-30T21:59Z] INFO  22:59:21,410 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:21,848 MuTect - [MUTECT] Processed 116006448 reads in 713 ms
[2015-09-30T21:59Z] INFO  22:59:21,863 MuTect - [MUTECT] Processed 132009708 reads in 751 ms
[2015-09-30T21:59Z] INFO  22:59:21,934 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:22,538 MuTect - [MUTECT] Processed 117006480 reads in 690 ms
[2015-09-30T21:59Z] INFO  22:59:22,565 MuTect - [MUTECT] Processed 133009765 reads in 702 ms
[2015-09-30T21:59Z] INFO  22:59:23,214 MuTect - [MUTECT] Processed 118006525 reads in 676 ms
[2015-09-30T21:59Z] INFO  22:59:23,290 MuTect - [MUTECT] Processed 134009797 reads in 725 ms
[2015-09-30T21:59Z] INFO  22:59:23,787 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:23,869 MuTect - [MUTECT] Processed 119006577 reads in 655 ms
[2015-09-30T21:59Z] INFO  22:59:23,971 MuTect - [MUTECT] Processed 135009831 reads in 681 ms
[2015-09-30T21:59Z] INFO  22:59:24,115 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:24,477 MuTect - [MUTECT] Processed 120006681 reads in 608 ms
[2015-09-30T21:59Z] INFO  22:59:24,612 MuTect - [MUTECT] Processed 136009930 reads in 641 ms
[2015-09-30T21:59Z] INFO  22:59:25,088 MuTect - [MUTECT] Processed 121006801 reads in 611 ms
[2015-09-30T21:59Z] INFO  22:59:25,229 MuTect - [MUTECT] Processed 137009960 reads in 617 ms
[2015-09-30T21:59Z] INFO  22:59:25,687 MuTect - [MUTECT] Processed 122006859 reads in 598 ms
[2015-09-30T21:59Z] INFO  22:59:25,859 MuTect - [MUTECT] Processed 138009994 reads in 630 ms
[2015-09-30T21:59Z] INFO  22:59:26,005 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:26,301 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:26,326 MuTect - [MUTECT] Processed 123006908 reads in 640 ms
[2015-09-30T21:59Z] INFO  22:59:26,539 MuTect - [MUTECT] Processed 139010095 reads in 680 ms
[2015-09-30T21:59Z] INFO  22:59:26,972 MuTect - [MUTECT] Processed 124007013 reads in 646 ms
[2015-09-30T21:59Z] INFO  22:59:27,234 MuTect - [MUTECT] Processed 140010102 reads in 695 ms
[2015-09-30T21:59Z] INFO  22:59:27,644 MuTect - [MUTECT] Processed 125007075 reads in 672 ms
[2015-09-30T21:59Z] INFO  22:59:27,930 MuTect - [MUTECT] Processed 141010180 reads in 696 ms
[2015-09-30T21:59Z] INFO  22:59:28,311 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:28,333 MuTect - [MUTECT] Processed 126007080 reads in 689 ms
[2015-09-30T21:59Z] INFO  22:59:28,596 MuTect - [MUTECT] Processed 142010224 reads in 666 ms
[2015-09-30T21:59Z] INFO  22:59:28,865 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:28,985 MuTect - [MUTECT] Processed 127007182 reads in 652 ms
[2015-09-30T21:59Z] INFO  22:59:29,258 MuTect - [MUTECT] Processed 143010226 reads in 662 ms
[2015-09-30T21:59Z] INFO  22:59:29,624 MuTect - [MUTECT] Processed 128007261 reads in 639 ms
[2015-09-30T21:59Z] INFO  22:59:29,909 MuTect - [MUTECT] Processed 144010246 reads in 651 ms
[2015-09-30T21:59Z] INFO  22:59:30,274 MuTect - [MUTECT] Processed 129007345 reads in 650 ms
[2015-09-30T21:59Z] INFO  22:59:30,561 MuTect - [MUTECT] Processed 145010316 reads in 652 ms
[2015-09-30T21:59Z] INFO  22:59:30,818 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:30,920 MuTect - [MUTECT] Processed 130007355 reads in 646 ms
[2015-09-30T21:59Z] INFO  22:59:31,259 MuTect - [MUTECT] Processed 146010370 reads in 698 ms
[2015-09-30T21:59Z] INFO  22:59:31,271 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:31,536 MuTect - [MUTECT] Processed 131007369 reads in 616 ms
[2015-09-30T21:59Z] INFO  22:59:32,078 MuTect - [MUTECT] Processed 147010389 reads in 819 ms
[2015-09-30T21:59Z] INFO  22:59:32,228 MuTect - [MUTECT] Processed 132007474 reads in 692 ms
[2015-09-30T21:59Z] INFO  22:59:32,882 MuTect - [MUTECT] Processed 133007548 reads in 654 ms
[2015-09-30T21:59Z] INFO  22:59:33,091 MuTect - [MUTECT] Processed 148010427 reads in 1013 ms
[2015-09-30T21:59Z] INFO  22:59:33,388 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:33,498 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:33,575 MuTect - [MUTECT] Processed 134007624 reads in 693 ms
[2015-09-30T21:59Z] INFO  22:59:34,087 MuTect - [MUTECT] Processed 149010446 reads in 996 ms
[2015-09-30T21:59Z] INFO  22:59:34,251 MuTect - [MUTECT] Processed 135007710 reads in 676 ms
[2015-09-30T21:59Z] INFO  22:59:34,825 MuTect - [MUTECT] Processed 150010451 reads in 738 ms
[2015-09-30T21:59Z] INFO  22:59:35,103 MuTect - [MUTECT] Processed 136007750 reads in 852 ms
[2015-09-30T21:59Z] INFO  22:59:35,647 MuTect - [MUTECT] Processed 151010495 reads in 822 ms
[2015-09-30T21:59Z] INFO  22:59:35,758 MuTect - [MUTECT] Processed 137007801 reads in 655 ms
[2015-09-30T21:59Z] INFO  22:59:35,791 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:36,337 MuTect - [MUTECT] Processed 152010549 reads in 690 ms
[2015-09-30T21:59Z] INFO  22:59:36,382 MuTect - [MUTECT] Processed 138007821 reads in 624 ms
[2015-09-30T21:59Z] INFO  22:59:36,956 MuTect - [MUTECT] Processed 153010610 reads in 619 ms
[2015-09-30T21:59Z] INFO  22:59:36,990 MuTect - [MUTECT] Processed 139007836 reads in 608 ms
[2015-09-30T21:59Z] INFO  22:59:37,530 MuTect - [MUTECT] Processed 154010667 reads in 574 ms
[2015-09-30T21:59Z] INFO  22:59:37,597 MuTect - [MUTECT] Processed 140007957 reads in 607 ms
[2015-09-30T21:59Z] INFO  22:59:37,882 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:38,099 MuTect - [MUTECT] Processed 155010717 reads in 569 ms
[2015-09-30T21:59Z] INFO  22:59:38,209 MuTect - [MUTECT] Processed 141008027 reads in 612 ms
[2015-09-30T21:59Z] INFO  22:59:38,402 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:38,742 MuTect - [MUTECT] Processed 156010775 reads in 643 ms
[2015-09-30T21:59Z] INFO  22:59:38,818 MuTect - [MUTECT] Processed 142008063 reads in 609 ms
[2015-09-30T21:59Z] INFO  22:59:39,397 MuTect - [MUTECT] Processed 157010788 reads in 655 ms
[2015-09-30T21:59Z] INFO  22:59:39,475 MuTect - [MUTECT] Processed 143008071 reads in 657 ms
[2015-09-30T21:59Z] INFO  22:59:40,046 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:40,086 MuTect - [MUTECT] Processed 158010805 reads in 689 ms
[2015-09-30T21:59Z] INFO  22:59:40,152 MuTect - [MUTECT] Processed 144008086 reads in 677 ms
[2015-09-30T21:59Z] INFO  22:59:40,551 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:40,727 MuTect - [MUTECT] Processed 159010915 reads in 641 ms
[2015-09-30T21:59Z] INFO  22:59:40,833 MuTect - [MUTECT] Processed 145008090 reads in 681 ms
[2015-09-30T21:59Z] INFO  22:59:41,384 MuTect - [MUTECT] Processed 160010952 reads in 657 ms
[2015-09-30T21:59Z] INFO  22:59:41,490 MuTect - [MUTECT] Processed 146008178 reads in 657 ms
[2015-09-30T21:59Z] INFO  22:59:42,024 MuTect - [MUTECT] Processed 161010988 reads in 640 ms
[2015-09-30T21:59Z] INFO  22:59:42,165 MuTect - [MUTECT] Processed 147008253 reads in 675 ms
[2015-09-30T21:59Z] INFO  22:59:42,291 ProgressMeter -      1:45964915        4.10e+06  100.0 s       24.0 s     61.4%         2.7 m    62.0 s
[2015-09-30T21:59Z] INFO  22:59:42,433 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T21:59Z] 1241673 positions in tumor
[2015-09-30T21:59Z] 1241668 positions shared in normal
[2015-09-30T21:59Z] 1228118 had sufficient coverage for comparison
[2015-09-30T21:59Z] 1227012 were called Reference
[2015-09-30T21:59Z] 0 were mixed SNP-indel calls and filtered
[2015-09-30T21:59Z] 110 were removed by the strand filter
[2015-09-30T21:59Z] 1046 were called Germline
[2015-09-30T21:59Z] 6 were called LOH
[2015-09-30T21:59Z] 47 were called Somatic
[2015-09-30T21:59Z] 7 were called Unknown
[2015-09-30T21:59Z] 0 were called Variant
[2015-09-30T21:59Z] Varscan paired fix
[2015-09-30T21:59Z] Varscan paired fix
[2015-09-30T21:59Z] Resource requests: ; memory: 1.00; cores: 1
[2015-09-30T21:59Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-09-30T21:59Z] bgzip syn3-X_125953527_155270560-raw.snp.vcf
[2015-09-30T21:59Z] INFO  22:59:42,695 MuTect - [MUTECT] Processed 162011010 reads in 671 ms
[2015-09-30T21:59Z] tabix index syn3-X_125953527_155270560-raw.snp.vcf.gz
[2015-09-30T21:59Z] bgzip syn3-X_125953527_155270560-raw.indel.vcf
[2015-09-30T21:59Z] INFO  22:59:42,800 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T21:59Z] tabix index syn3-X_125953527_155270560-raw.indel.vcf.gz
[2015-09-30T21:59Z] INFO  22:59:42,860 MuTect - [MUTECT] Processed 148008370 reads in 695 ms
[2015-09-30T21:59Z] Combine variant files
[2015-09-30T21:59Z] INFO  22:59:43,400 MuTect - [MUTECT] Processed 163011083 reads in 705 ms
[2015-09-30T21:59Z] INFO  22:59:43,549 MuTect - [MUTECT] Processed 149008372 reads in 689 ms
[2015-09-30T21:59Z] INFO  22:59:44,130 MuTect - [MUTECT] Processed 164011116 reads in 730 ms
[2015-09-30T21:59Z] INFO  22:59:44,224 MuTect - [MUTECT] Processed 150008429 reads in 675 ms
[2015-09-30T21:59Z] INFO  22:59:44,467 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:59Z] INFO  22:59:44,469 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53
[2015-09-30T21:59Z] INFO  22:59:44,469 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:59Z] INFO  22:59:44,470 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:59Z] INFO  22:59:44,473 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /home/cancer-dream-syn3/work/varscan/X/tx/tmpGJwzIL/tx/tmpOqcf6J/syn3-X_125953527_155270560-raw.vcf --variant:v0 /home/cancer-dream-syn3/work/varscan/X/tx/tmpGJwzIL/syn3-X_125953527_155270560-raw.snp.vcf.gz --variant:v1 /home/cancer-dream-syn3/work/varscan/X/tx/tmpGJwzIL/syn3-X_125953527_155270560-raw.indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_125953527_155270560-raw-regions.bed --interval_set_rule INTERSECTION
[2015-09-30T21:59Z] INFO  22:59:44,478 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:59Z] INFO  22:59:44,479 HelpFormatter - Date/Time: 2015/09/30 22:59:44
[2015-09-30T21:59Z] INFO  22:59:44,479 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:59Z] INFO  22:59:44,479 HelpFormatter - ---------------------------------------------------------------------------------
[2015-09-30T21:59Z] INFO  22:59:44,552 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:59Z] INFO  22:59:44,751 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:44,856 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2015-09-30T21:59Z] INFO  22:59:44,879 MuTect - [MUTECT] Processed 165011170 reads in 749 ms
[2015-09-30T21:59Z] INFO  22:59:44,893 MuTect - [MUTECT] Processed 151008466 reads in 669 ms
[2015-09-30T21:59Z] INFO  22:59:44,969 IntervalUtils - Processing 1245180 bp from intervals
[2015-09-30T21:59Z] WARN  22:59:44,970 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:59Z] WARN  22:59:44,970 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:59Z] INFO  22:59:45,025 GenomeAnalysisEngine - Preparing for traversal
[2015-09-30T21:59Z] INFO  22:59:45,028 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:59Z] INFO  22:59:45,029 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:59Z] INFO  22:59:45,029 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:59Z] INFO  22:59:45,030 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:59Z] INFO  22:59:45,060 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:45,142 ProgressMeter -      1:15870949        4.52e+06  120.0 s       26.0 s     48.4%         4.1 m     2.1 m
[2015-09-30T21:59Z] INFO  22:59:45,590 MuTect - [MUTECT] Processed 166011197 reads in 711 ms
[2015-09-30T21:59Z] INFO  22:59:45,599 MuTect - [MUTECT] Processed 152008483 reads in 706 ms
[2015-09-30T21:59Z] INFO  22:59:46,159 ProgressMeter -            done      1159.0     1.0 s      16.2 m       99.9%     1.0 s       0.0 s
[2015-09-30T21:59Z] INFO  22:59:46,160 ProgressMeter - Total runtime 1.13 secs, 0.02 min, 0.00 hours
[2015-09-30T21:59Z] INFO  22:59:46,239 MuTect - [MUTECT] Processed 153008488 reads in 640 ms
[2015-09-30T21:59Z] INFO  22:59:46,314 MuTect - [MUTECT] Processed 167011258 reads in 724 ms
[2015-09-30T21:59Z] bgzip syn3-X_125953527_155270560-raw.vcf
[2015-09-30T21:59Z] tabix index syn3-X_125953527_155270560-raw.vcf.gz
[2015-09-30T21:59Z] bgzip syn3-X_125953527_155270560-raw-rejectfix.vcf
[2015-09-30T21:59Z] tabix index syn3-X_125953527_155270560-raw-rejectfix.vcf.gz
[2015-09-30T21:59Z] GATK: VariantAnnotator
[2015-09-30T21:59Z] INFO  22:59:46,918 MuTect - [MUTECT] Processed 154008532 reads in 679 ms
[2015-09-30T21:59Z] INFO  22:59:47,005 MuTect - [MUTECT] Processed 168011349 reads in 691 ms
[2015-09-30T21:59Z] INFO  22:59:47,031 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:47,357 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:47,572 MuTect - [MUTECT] Processed 155008608 reads in 654 ms
[2015-09-30T21:59Z] INFO  22:59:47,655 MuTect - [MUTECT] Processed 169011454 reads in 650 ms
[2015-09-30T21:59Z] INFO  22:59:48,200 MuTect - [MUTECT] Processed 156008684 reads in 628 ms
[2015-09-30T21:59Z] INFO  22:59:48,318 MuTect - [MUTECT] Processed 170011468 reads in 662 ms
[2015-09-30T21:59Z] INFO  22:59:48,490 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:59Z] INFO  22:59:48,493 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T21:59Z] INFO  22:59:48,493 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T21:59Z] INFO  22:59:48,493 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T21:59Z] INFO  22:59:48,496 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/varscan/X/syn3-X_125953527_155270560-raw.vcf.gz --out /home/cancer-dream-syn3/work/varscan/X/tx/tmpjaDFzr/syn3-X_125953527_155270560-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/varscan/X/syn3-X_125953527_155270560-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T21:59Z] INFO  22:59:48,502 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T21:59Z] INFO  22:59:48,502 HelpFormatter - Date/Time: 2015/09/30 22:59:48
[2015-09-30T21:59Z] INFO  22:59:48,503 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:59Z] INFO  22:59:48,503 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T21:59Z] INFO  22:59:48,618 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T21:59Z] INFO  22:59:48,694 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T21:59Z] INFO  22:59:48,701 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T21:59Z] INFO  22:59:48,723 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T21:59Z] INFO  22:59:48,864 MuTect - [MUTECT] Processed 157008732 reads in 664 ms
[2015-09-30T21:59Z] INFO  22:59:49,002 MuTect - [MUTECT] Processed 171011509 reads in 685 ms
[2015-09-30T21:59Z] INFO  22:59:49,053 IntervalUtils - Processing 1159 bp from intervals
[2015-09-30T21:59Z] WARN  22:59:49,057 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:59Z] WARN  22:59:49,057 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T21:59Z] INFO  22:59:49,113 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T21:59Z] INFO  22:59:49,203 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:49,223 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T21:59Z] INFO  22:59:49,224 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T21:59Z] INFO  22:59:49,224 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T21:59Z] INFO  22:59:49,224 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T21:59Z] INFO  22:59:49,325 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T21:59Z] INFO  22:59:49,526 MuTect - [MUTECT] Processed 158008786 reads in 662 ms
[2015-09-30T21:59Z] INFO  22:59:49,635 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:49,662 MuTect - [MUTECT] Processed 172011541 reads in 660 ms
[2015-09-30T21:59Z] INFO  22:59:50,199 MuTect - [MUTECT] Processed 159008822 reads in 673 ms
[2015-09-30T21:59Z] INFO  22:59:50,319 MuTect - [MUTECT] Processed 173011608 reads in 657 ms
[2015-09-30T21:59Z] INFO  22:59:50,904 MuTect - [MUTECT] Processed 160008840 reads in 705 ms
[2015-09-30T21:59Z] INFO  22:59:50,985 MuTect - [MUTECT] Processed 174011654 reads in 666 ms
[2015-09-30T21:59Z] INFO  22:59:51,417 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:51,555 MuTect - [MUTECT] Processed 161008927 reads in 651 ms
[2015-09-30T21:59Z] INFO  22:59:51,704 MuTect - [MUTECT] Processed 175011708 reads in 719 ms
[2015-09-30T21:59Z] INFO  22:59:51,763 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:52,223 MuTect - [MUTECT] Processed 162008991 reads in 668 ms
[2015-09-30T21:59Z] INFO  22:59:52,619 MuTect - [MUTECT] Processed 176011713 reads in 915 ms
[2015-09-30T21:59Z] INFO  22:59:52,885 MuTect - [MUTECT] Processed 163009082 reads in 662 ms
[2015-09-30T21:59Z] INFO  22:59:53,429 MuTect - [MUTECT] Processed 177011846 reads in 810 ms
[2015-09-30T21:59Z] INFO  22:59:53,561 MuTect - [MUTECT] Processed 164009108 reads in 676 ms
[2015-09-30T21:59Z] INFO  22:59:53,728 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:54,103 MuTect - [MUTECT] Processed 178011881 reads in 674 ms
[2015-09-30T21:59Z] INFO  22:59:54,167 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:54,234 MuTect - [MUTECT] Processed 165009182 reads in 673 ms
[2015-09-30T21:59Z] INFO  22:59:54,806 MuTect - [MUTECT] Processed 179011906 reads in 703 ms
[2015-09-30T21:59Z] INFO  22:59:54,871 MuTect - [MUTECT] Processed 166009191 reads in 637 ms
[2015-09-30T21:59Z] INFO  22:59:55,477 MuTect - [MUTECT] Processed 180011994 reads in 671 ms
[2015-09-30T21:59Z] INFO  22:59:55,522 MuTect - [MUTECT] Processed 167009296 reads in 651 ms
[2015-09-30T21:59Z] INFO  22:59:55,555 VariantAnnotator - Processed 992 loci.
[2015-09-30T21:59Z]
[2015-09-30T21:59Z] INFO  22:59:55,578 ProgressMeter -            done      4410.0     6.0 s      24.0 m       99.9%     6.0 s       0.0 s
[2015-09-30T21:59Z] INFO  22:59:55,578 ProgressMeter - Total runtime 6.35 secs, 0.11 min, 0.00 hours
[2015-09-30T21:59Z] INFO  22:59:55,579 MicroScheduler - 4411 reads were filtered out during the traversal out of approximately 90300 total reads (4.88%)
[2015-09-30T21:59Z] INFO  22:59:55,579 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T21:59Z] INFO  22:59:55,579 MicroScheduler -   -> 4397 reads (4.87% of total) failing DuplicateReadFilter
[2015-09-30T21:59Z] INFO  22:59:55,579 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T21:59Z] INFO  22:59:55,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T21:59Z] INFO  22:59:55,580 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T21:59Z] INFO  22:59:55,580 MicroScheduler -   -> 14 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T21:59Z] INFO  22:59:56,077 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:56,143 MuTect - [MUTECT] Processed 181012010 reads in 666 ms
[2015-09-30T21:59Z] INFO  22:59:56,190 MuTect - [MUTECT] Processed 168009331 reads in 668 ms
[2015-09-30T21:59Z] INFO  22:59:56,363 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:56,525 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T21:59Z] INFO  22:59:56,856 MuTect - [MUTECT] Processed 182012045 reads in 713 ms
[2015-09-30T21:59Z] INFO  22:59:56,890 MuTect - [MUTECT] Processed 169009407 reads in 700 ms
[2015-09-30T21:59Z] INFO  22:59:57,514 MuTect - [MUTECT] Processed 183012117 reads in 658 ms
[2015-09-30T21:59Z] INFO  22:59:57,588 MuTect - [MUTECT] Processed 170009448 reads in 698 ms
[2015-09-30T21:59Z] INFO  22:59:58,284 MuTect - [MUTECT] Processed 171009500 reads in 696 ms
[2015-09-30T21:59Z] INFO  22:59:58,461 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:58,530 MuTect - [MUTECT] Processed 184012406 reads in 1016 ms
[2015-09-30T21:59Z] MuTect: MuTect
[2015-09-30T21:59Z] INFO  22:59:58,984 MuTect - [MUTECT] Processed 172009525 reads in 700 ms
[2015-09-30T21:59Z] INFO  22:59:59,510 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T21:59Z] INFO  22:59:59,537 MuTect - [MUTECT] Processed 185012450 reads in 1007 ms
[2015-09-30T21:59Z] INFO  22:59:59,664 MuTect - [MUTECT] Processed 173009589 reads in 680 ms
[2015-09-30T22:00Z] INFO  23:00:00,367 MuTect - [MUTECT] Processed 174009628 reads in 703 ms
[2015-09-30T22:00Z] INFO  23:00:00,601 MuTect - [MUTECT] Processed 186012789 reads in 1064 ms
[2015-09-30T22:00Z] INFO  23:00:00,730 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/1/syn3-1_62231753_93258244-raw-mutect-regions.bed to be BED
[2015-09-30T22:00Z] INFO  23:00:00,785 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:00Z] INFO  23:00:00,786 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:00Z] INFO  23:00:00,786 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:00Z] INFO  23:00:00,786 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:00Z] INFO  23:00:00,789 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/1/syn3-1_62231753_93258244-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/1/tx/tmpyTmnXd/syn3-1_62231753_93258244-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:00Z] INFO  23:00:00,789 HelpFormatter - Date/Time: 2015/09/30 23:00:00
[2015-09-30T22:00Z] INFO  23:00:00,789 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:00Z] INFO  23:00:00,790 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:00Z] INFO  23:00:00,818 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:00Z] INFO  23:00:00,822 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:00Z] INFO  23:00:00,896 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:00Z] INFO  23:00:00,947 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:00Z] INFO  23:00:00,955 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:00Z] INFO  23:00:01,009 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:01,017 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:00Z] INFO  23:00:01,059 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:00Z] INFO  23:00:01,066 MuTect - [MUTECT] Processed 175009668 reads in 699 ms
[2015-09-30T22:00Z] INFO  23:00:01,242 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:00Z] INFO  23:00:01,340 IntervalUtils - Processing 1257634 bp from intervals
[2015-09-30T22:00Z] INFO  23:00:01,344 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:00Z] INFO  23:00:01,344 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:00Z] INFO  23:00:01,518 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:00Z] INFO  23:00:01,693 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:00Z] INFO  23:00:01,693 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:00Z] INFO  23:00:01,694 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:00Z] INFO  23:00:01,695 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:00Z] INFO  23:00:01,750 MuTect - [MUTECT] Processed 187012989 reads in 1149 ms
[2015-09-30T22:00Z] INFO  23:00:01,756 MuTect - [MUTECT] Processed 176009669 reads in 690 ms
[2015-09-30T22:00Z] INFO  23:00:02,409 MuTect - [MUTECT] Processed 177009728 reads in 653 ms
[2015-09-30T22:00Z] INFO  23:00:02,672 MuTect - [MUTECT] Processed 188013237 reads in 922 ms
[2015-09-30T22:00Z] INFO  23:00:02,806 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:03,097 MuTect - [MUTECT] Processed 178009761 reads in 688 ms
[2015-09-30T22:00Z] INFO  23:00:03,505 MuTect - [MUTECT] Processed 189013473 reads in 833 ms
[2015-09-30T22:00Z] INFO  23:00:03,620 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:03,835 MuTect - [MUTECT] Processed 179009780 reads in 738 ms
[2015-09-30T22:00Z] INFO  23:00:04,162 MuTect - [MUTECT] Processed 1000012 reads in 2419 ms
[2015-09-30T22:00Z] INFO  23:00:04,314 MuTect - [MUTECT] Processed 190013652 reads in 809 ms
[2015-09-30T22:00Z] INFO  23:00:04,510 MuTect - [MUTECT] Processed 180009877 reads in 675 ms
[2015-09-30T22:00Z] INFO  23:00:05,217 MuTect - [MUTECT] Processed 2000064 reads in 1055 ms
[2015-09-30T22:00Z] INFO  23:00:05,219 MuTect - [MUTECT] Processed 181009935 reads in 709 ms
[2015-09-30T22:00Z] INFO  23:00:05,293 MuTect - [MUTECT] Processed 191013843 reads in 979 ms
[2015-09-30T22:00Z] INFO  23:00:05,893 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:05,918 MuTect - [MUTECT] Processed 182009959 reads in 699 ms
[2015-09-30T22:00Z] INFO  23:00:06,007 MuTect - [MUTECT] Processed 3000102 reads in 790 ms
[2015-09-30T22:00Z] INFO  23:00:06,038 MuTect - [MUTECT] Processed 192013907 reads in 745 ms
[2015-09-30T22:00Z] INFO  23:00:06,207 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:06,346 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:06,612 MuTect - [MUTECT] Processed 183010015 reads in 694 ms
[2015-09-30T22:00Z] INFO  23:00:06,747 MuTect - [MUTECT] Processed 193014008 reads in 709 ms
[2015-09-30T22:00Z] INFO  23:00:06,790 MuTect - [MUTECT] Processed 4000152 reads in 783 ms
[2015-09-30T22:00Z] INFO  23:00:07,311 MuTect - [MUTECT] Processed 184010068 reads in 699 ms
[2015-09-30T22:00Z] INFO  23:00:07,430 MuTect - [MUTECT] Processed 194014315 reads in 683 ms
[2015-09-30T22:00Z] INFO  23:00:07,526 MuTect - [MUTECT] Processed 5000168 reads in 736 ms
[2015-09-30T22:00Z] INFO  23:00:07,961 MuTect - [MUTECT] Processed 185010097 reads in 650 ms
[2015-09-30T22:00Z] INFO  23:00:08,284 MuTect - [MUTECT] Processed 6000172 reads in 758 ms
[2015-09-30T22:00Z] INFO  23:00:08,295 MuTect - [MUTECT] Processed 195014432 reads in 865 ms
[2015-09-30T22:00Z] INFO  23:00:08,487 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:08,631 MuTect - [MUTECT] Processed 186010164 reads in 670 ms
[2015-09-30T22:00Z] INFO  23:00:08,713 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:09,038 MuTect - [MUTECT] Processed 7000221 reads in 753 ms
[2015-09-30T22:00Z] INFO  23:00:09,077 MuTect - [MUTECT] Processed 196014556 reads in 782 ms
[2015-09-30T22:00Z] INFO  23:00:09,297 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:09,327 MuTect - [MUTECT] Processed 187010188 reads in 696 ms
[2015-09-30T22:00Z] INFO  23:00:09,805 MuTect - [MUTECT] Processed 8000312 reads in 768 ms
[2015-09-30T22:00Z] INFO  23:00:10,034 MuTect - [MUTECT] Processed 188010221 reads in 707 ms
[2015-09-30T22:00Z] INFO  23:00:10,073 MuTect - [MUTECT] Processed 197014619 reads in 996 ms
[2015-09-30T22:00Z] INFO  23:00:10,524 MuTect - [MUTECT] Processed 9000374 reads in 719 ms
[2015-09-30T22:00Z] INFO  23:00:10,738 MuTect - [MUTECT] Processed 189010347 reads in 704 ms
[2015-09-30T22:00Z] INFO  23:00:10,770 MuTect - [MUTECT] Processed 198014765 reads in 697 ms
[2015-09-30T22:00Z] INFO  23:00:11,184 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:11,251 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:11,274 MuTect - [MUTECT] Processed 10000392 reads in 750 ms
[2015-09-30T22:00Z] INFO  23:00:11,409 MuTect - [MUTECT] Processed 190010370 reads in 671 ms
[2015-09-30T22:00Z] INFO  23:00:11,415 MuTect - [MUTECT] Processed 199014800 reads in 645 ms
[2015-09-30T22:00Z] INFO  23:00:11,969 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:11,988 MuTect - [MUTECT] Processed 11000450 reads in 714 ms
[2015-09-30T22:00Z] INFO  23:00:12,039 MuTect - [MUTECT] Processed 200014812 reads in 624 ms
[2015-09-30T22:00Z] INFO  23:00:12,091 MuTect - [MUTECT] Processed 191010389 reads in 682 ms
[2015-09-30T22:00Z] INFO  23:00:12,293 ProgressMeter -      1:53528219        5.42e+06    2.2 m       24.0 s     82.8%         2.6 m    26.0 s
[2015-09-30T22:00Z] INFO  23:00:12,676 MuTect - [MUTECT] Processed 201014853 reads in 637 ms
[2015-09-30T22:00Z] INFO  23:00:12,718 MuTect - [MUTECT] Processed 12000469 reads in 730 ms
[2015-09-30T22:00Z] INFO  23:00:12,808 MuTect - [MUTECT] Processed 192010458 reads in 717 ms
[2015-09-30T22:00Z] INFO  23:00:13,246 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:13,343 MuTect - [MUTECT] Processed 202014878 reads in 667 ms
[2015-09-30T22:00Z] INFO  23:00:13,409 MuTect - [MUTECT] Processed 13000471 reads in 691 ms
[2015-09-30T22:00Z] INFO  23:00:13,540 MuTect - [MUTECT] Processed 193010566 reads in 732 ms
[2015-09-30T22:00Z] INFO  23:00:13,553 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:14,063 MuTect - [MUTECT] Processed 203014909 reads in 720 ms
[2015-09-30T22:00Z] INFO  23:00:14,102 MuTect - [MUTECT] Processed 14000523 reads in 693 ms
[2015-09-30T22:00Z] INFO  23:00:14,204 MuTect - [MUTECT] Processed 194010652 reads in 664 ms
[2015-09-30T22:00Z] INFO  23:00:14,438 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:14,755 MuTect - [MUTECT] Processed 15000610 reads in 652 ms
[2015-09-30T22:00Z] INFO  23:00:14,760 MuTect - [MUTECT] Processed 204015024 reads in 697 ms
[2015-09-30T22:00Z] INFO  23:00:14,862 MuTect - [MUTECT] Processed 195010711 reads in 658 ms
[2015-09-30T22:00Z] INFO  23:00:15,143 ProgressMeter -      1:17570356        5.48e+06    2.5 m       27.0 s     57.5%         4.4 m   111.0 s
[2015-09-30T22:00Z] INFO  23:00:15,412 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:15,444 MuTect - [MUTECT] Processed 205015030 reads in 684 ms
[2015-09-30T22:00Z] INFO  23:00:15,456 MuTect - [MUTECT] Processed 16000623 reads in 702 ms
[2015-09-30T22:00Z] INFO  23:00:15,534 MuTect - [MUTECT] Processed 196010784 reads in 672 ms
[2015-09-30T22:00Z] INFO  23:00:15,827 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:16,128 MuTect - [MUTECT] Processed 206015107 reads in 684 ms
[2015-09-30T22:00Z] INFO  23:00:16,152 MuTect - [MUTECT] Processed 17000632 reads in 696 ms
[2015-09-30T22:00Z] INFO  23:00:16,209 MuTect - [MUTECT] Processed 197010846 reads in 675 ms
[2015-09-30T22:00Z] INFO  23:00:16,817 MuTect - [MUTECT] Processed 207015149 reads in 689 ms
[2015-09-30T22:00Z] INFO  23:00:16,835 MuTect - [MUTECT] Processed 18000651 reads in 683 ms
[2015-09-30T22:00Z] INFO  23:00:16,836 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:16,913 MuTect - [MUTECT] Processed 198010867 reads in 704 ms
[2015-09-30T22:00Z] INFO  23:00:17,556 MuTect - [MUTECT] Processed 19000681 reads in 721 ms
[2015-09-30T22:00Z] INFO  23:00:17,558 MuTect - [MUTECT] Processed 208015218 reads in 741 ms
[2015-09-30T22:00Z] INFO  23:00:17,593 MuTect - [MUTECT] Processed 199010948 reads in 680 ms
[2015-09-30T22:00Z] INFO  23:00:17,645 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:18,221 MuTect - [MUTECT] Processed 209015313 reads in 663 ms
[2015-09-30T22:00Z] INFO  23:00:18,252 MuTect - [MUTECT] Processed 200010974 reads in 659 ms
[2015-09-30T22:00Z] INFO  23:00:18,279 MuTect - [MUTECT] Processed 20000707 reads in 723 ms
[2015-09-30T22:00Z] INFO  23:00:18,309 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:18,877 MuTect - [MUTECT] Processed 210015414 reads in 656 ms
[2015-09-30T22:00Z] INFO  23:00:18,933 MuTect - [MUTECT] Processed 201011029 reads in 681 ms
[2015-09-30T22:00Z] INFO  23:00:19,030 MuTect - [MUTECT] Processed 21000748 reads in 751 ms
[2015-09-30T22:00Z] INFO  23:00:19,357 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:19,569 MuTect - [MUTECT] Processed 211015426 reads in 692 ms
[2015-09-30T22:00Z] INFO  23:00:19,615 MuTect - [MUTECT] Processed 202011089 reads in 682 ms
[2015-09-30T22:00Z] INFO  23:00:19,769 MuTect - [MUTECT] Processed 22000824 reads in 739 ms
[2015-09-30T22:00Z] INFO  23:00:19,834 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:20,278 MuTect - [MUTECT] Processed 212015481 reads in 709 ms
[2015-09-30T22:00Z] INFO  23:00:20,288 MuTect - [MUTECT] Processed 203011146 reads in 672 ms
[2015-09-30T22:00Z] INFO  23:00:20,422 MuTect - [MUTECT] Processed 23000911 reads in 653 ms
[2015-09-30T22:00Z] INFO  23:00:20,561 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:20,973 MuTect - [MUTECT] Processed 204011150 reads in 686 ms
[2015-09-30T22:00Z] INFO  23:00:20,975 MuTect - [MUTECT] Processed 213015487 reads in 697 ms
[2015-09-30T22:00Z] INFO  23:00:21,125 MuTect - [MUTECT] Processed 24000985 reads in 703 ms
[2015-09-30T22:00Z] INFO  23:00:21,628 MuTect - [MUTECT] Processed 214015565 reads in 653 ms
[2015-09-30T22:00Z] INFO  23:00:21,628 MuTect - [MUTECT] Processed 205011222 reads in 655 ms
[2015-09-30T22:00Z] INFO  23:00:21,796 MuTect - [MUTECT] Processed 25001002 reads in 671 ms
[2015-09-30T22:00Z] INFO  23:00:21,824 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:22,099 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:22,301 MuTect - [MUTECT] Processed 206011233 reads in 673 ms
[2015-09-30T22:00Z] INFO  23:00:22,348 MuTect - [MUTECT] Processed 215015684 reads in 720 ms
[2015-09-30T22:00Z] INFO  23:00:22,504 MuTect - [MUTECT] Processed 26001071 reads in 707 ms
[2015-09-30T22:00Z] INFO  23:00:22,787 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:22,996 MuTect - [MUTECT] Processed 207011268 reads in 695 ms
[2015-09-30T22:00Z] INFO  23:00:23,052 MuTect - [MUTECT] Processed 216015770 reads in 704 ms
[2015-09-30T22:00Z] INFO  23:00:23,165 MuTect - [MUTECT] Processed 27001083 reads in 662 ms
[2015-09-30T22:00Z] INFO  23:00:23,646 MuTect - [MUTECT] Processed 208011300 reads in 650 ms
[2015-09-30T22:00Z] INFO  23:00:23,734 MuTect - [MUTECT] Processed 217015866 reads in 682 ms
[2015-09-30T22:00Z] INFO  23:00:23,830 MuTect - [MUTECT] Processed 28001155 reads in 665 ms
[2015-09-30T22:00Z] INFO  23:00:24,260 MuTect - [MUTECT] Processed 209011311 reads in 614 ms
[2015-09-30T22:00Z] INFO  23:00:24,362 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:24,378 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:24,395 MuTect - [MUTECT] Processed 218015869 reads in 661 ms
[2015-09-30T22:00Z] INFO  23:00:24,512 MuTect - [MUTECT] Processed 29001160 reads in 682 ms
[2015-09-30T22:00Z] INFO  23:00:24,878 MuTect - [MUTECT] Processed 210011388 reads in 618 ms
[2015-09-30T22:00Z] INFO  23:00:24,924 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:25,046 MuTect - [MUTECT] Processed 219015944 reads in 651 ms
[2015-09-30T22:00Z] INFO  23:00:25,153 MuTect - [MUTECT] Processed 30001160 reads in 641 ms
[2015-09-30T22:00Z] INFO  23:00:25,498 MuTect - [MUTECT] Processed 211011476 reads in 620 ms
[2015-09-30T22:00Z] INFO  23:00:25,715 MuTect - [MUTECT] Processed 220016052 reads in 669 ms
[2015-09-30T22:00Z] INFO  23:00:25,829 MuTect - [MUTECT] Processed 31001211 reads in 676 ms
[2015-09-30T22:00Z] INFO  23:00:26,153 MuTect - [MUTECT] Processed 212011560 reads in 655 ms
[2015-09-30T22:00Z] INFO  23:00:26,391 MuTect - [MUTECT] Processed 221016107 reads in 676 ms
[2015-09-30T22:00Z] INFO  23:00:26,487 MuTect - [MUTECT] Processed 32001232 reads in 658 ms
[2015-09-30T22:00Z] INFO  23:00:26,796 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:26,826 MuTect - [MUTECT] Processed 213011681 reads in 673 ms
[2015-09-30T22:00Z] INFO  23:00:26,950 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:27,048 MuTect - [MUTECT] Processed 222016119 reads in 657 ms
[2015-09-30T22:00Z] INFO  23:00:27,099 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:27,143 MuTect - [MUTECT] Processed 33001293 reads in 656 ms
[2015-09-30T22:00Z] INFO  23:00:27,469 MuTect - [MUTECT] Processed 214011708 reads in 643 ms
[2015-09-30T22:00Z] INFO  23:00:27,706 MuTect - [MUTECT] Processed 223016147 reads in 658 ms
[2015-09-30T22:00Z] INFO  23:00:27,793 MuTect - [MUTECT] Processed 34001312 reads in 650 ms
[2015-09-30T22:00Z] INFO  23:00:28,099 MuTect - [MUTECT] Processed 215011772 reads in 630 ms
[2015-09-30T22:00Z] INFO  23:00:28,353 MuTect - [MUTECT] Processed 224016233 reads in 647 ms
[2015-09-30T22:00Z] INFO  23:00:28,455 MuTect - [MUTECT] Processed 35001377 reads in 662 ms
[2015-09-30T22:00Z] INFO  23:00:28,751 MuTect - [MUTECT] Processed 216011825 reads in 652 ms
[2015-09-30T22:00Z] INFO  23:00:29,010 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:29,039 MuTect - [MUTECT] Processed 225016334 reads in 686 ms
[2015-09-30T22:00Z] INFO  23:00:29,133 MuTect - [MUTECT] Processed 36001385 reads in 678 ms
[2015-09-30T22:00Z] INFO  23:00:29,358 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:29,380 MuTect - [MUTECT] Processed 217011866 reads in 629 ms
[2015-09-30T22:00Z] INFO  23:00:29,399 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:29,717 MuTect - [MUTECT] Processed 226016396 reads in 678 ms
[2015-09-30T22:00Z] INFO  23:00:29,827 MuTect - [MUTECT] Processed 37001420 reads in 694 ms
[2015-09-30T22:00Z] INFO  23:00:30,019 MuTect - [MUTECT] Processed 218011931 reads in 639 ms
[2015-09-30T22:00Z] INFO  23:00:30,426 MuTect - [MUTECT] Processed 227016407 reads in 709 ms
[2015-09-30T22:00Z] INFO  23:00:30,537 MuTect - [MUTECT] Processed 38001473 reads in 710 ms
[2015-09-30T22:00Z] INFO  23:00:30,667 MuTect - [MUTECT] Processed 219011952 reads in 648 ms
[2015-09-30T22:00Z] INFO  23:00:31,127 MuTect - [MUTECT] Processed 228016487 reads in 701 ms
[2015-09-30T22:00Z] INFO  23:00:31,204 MuTect - [MUTECT] Processed 39001501 reads in 667 ms
[2015-09-30T22:00Z] INFO  23:00:31,313 MuTect - [MUTECT] Processed 220011993 reads in 646 ms
[2015-09-30T22:00Z] INFO  23:00:31,440 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:31,696 ProgressMeter -      1:77763731        1.47e+06   30.0 s       20.0 s     48.5%        61.0 s    31.0 s
[2015-09-30T22:00Z] INFO  23:00:31,783 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:31,829 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:31,844 MuTect - [MUTECT] Processed 229016501 reads in 717 ms
[2015-09-30T22:00Z] INFO  23:00:31,890 MuTect - [MUTECT] Processed 40001524 reads in 686 ms
[2015-09-30T22:00Z] INFO  23:00:31,956 MuTect - [MUTECT] Processed 221011999 reads in 643 ms
[2015-09-30T22:00Z] INFO  23:00:32,522 MuTect - [MUTECT] Processed 41001606 reads in 632 ms
[2015-09-30T22:00Z] INFO  23:00:32,533 MuTect - [MUTECT] Processed 230016586 reads in 689 ms
[2015-09-30T22:00Z] INFO  23:00:32,595 MuTect - [MUTECT] Processed 222012037 reads in 639 ms
[2015-09-30T22:00Z] INFO  23:00:33,209 MuTect - [MUTECT] Processed 231016613 reads in 676 ms
[2015-09-30T22:00Z] INFO  23:00:33,214 MuTect - [MUTECT] Processed 42001623 reads in 692 ms
[2015-09-30T22:00Z] INFO  23:00:33,223 MuTect - [MUTECT] Processed 223012049 reads in 628 ms
[2015-09-30T22:00Z] INFO  23:00:33,885 MuTect - [MUTECT] Processed 232016675 reads in 676 ms
[2015-09-30T22:00Z] INFO  23:00:33,911 MuTect - [MUTECT] Processed 224012117 reads in 688 ms
[2015-09-30T22:00Z] INFO  23:00:33,923 MuTect - [MUTECT] Processed 43001656 reads in 709 ms
[2015-09-30T22:00Z] INFO  23:00:34,003 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:34,252 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:34,339 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:34,561 MuTect - [MUTECT] Processed 233016681 reads in 676 ms
[2015-09-30T22:00Z] INFO  23:00:34,590 MuTect - [MUTECT] Processed 225012126 reads in 679 ms
[2015-09-30T22:00Z] INFO  23:00:34,667 MuTect - [MUTECT] Processed 44001718 reads in 744 ms
[2015-09-30T22:00Z] INFO  23:00:35,242 MuTect - [MUTECT] Processed 234016758 reads in 681 ms
[2015-09-30T22:00Z] INFO  23:00:35,268 MuTect - [MUTECT] Processed 226012181 reads in 678 ms
[2015-09-30T22:00Z] INFO  23:00:35,353 MuTect - [MUTECT] Processed 45001737 reads in 686 ms
[2015-09-30T22:00Z] INFO  23:00:35,909 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:00Z] INFO  23:00:35,912 ProgressMeter -            done        6.56e+06    2.6 m       23.0 s    100.0%         2.6 m     0.0 s
[2015-09-30T22:00Z] INFO  23:00:35,912 ProgressMeter - Total runtime 153.63 secs, 2.56 min, 0.04 hours
[2015-09-30T22:00Z] INFO  23:00:35,921 MuTect - [MUTECT] Processed 235016769 reads in 679 ms
[2015-09-30T22:00Z] INFO  23:00:35,974 MicroScheduler - 176940 reads were filtered out during the traversal out of approximately 2693052 total reads (6.57%)
[2015-09-30T22:00Z] INFO  23:00:35,975 MicroScheduler -   -> 132843 reads (4.93% of total) failing DuplicateReadFilter
[2015-09-30T22:00Z] INFO  23:00:35,975 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:00Z] INFO  23:00:35,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:00Z] INFO  23:00:35,975 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:00Z] INFO  23:00:35,975 MicroScheduler -   -> 44097 reads (1.64% of total) failing UnmappedReadFilter
[2015-09-30T22:00Z] INFO  23:00:36,054 MuTect - [MUTECT] Processed 46001745 reads in 701 ms
[2015-09-30T22:00Z] INFO  23:00:36,225 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:36,624 MuTect - [MUTECT] Processed 236016855 reads in 703 ms
[2015-09-30T22:00Z] INFO  23:00:36,743 MuTect - [MUTECT] Processed 47001771 reads in 689 ms
[2015-09-30T22:00Z] INFO  23:00:36,947 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:00Z] INFO  23:00:37,101 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:37,335 MuTect - [MUTECT] Processed 237016857 reads in 711 ms
[2015-09-30T22:00Z] INFO  23:00:37,464 MuTect - [MUTECT] Processed 48001777 reads in 721 ms
[2015-09-30T22:00Z] INFO  23:00:37,991 MuTect - [MUTECT] Processed 238016871 reads in 656 ms
[2015-09-30T22:00Z] INFO  23:00:38,172 MuTect - [MUTECT] Processed 49001779 reads in 708 ms
[2015-09-30T22:00Z] INFO  23:00:38,460 MuTect - [MUTECT] Inspected 69000 potential candidates
[2015-09-30T22:00Z] bgzip syn3-1_31187762_62229084-raw-mutect.vcf
[2015-09-30T22:00Z] tabix index syn3-1_31187762_62229084-raw-mutect.vcf.gz
[2015-09-30T22:00Z] INFO  23:00:38,656 MuTect - [MUTECT] Processed 239016984 reads in 665 ms
[2015-09-30T22:00Z] INFO  23:00:38,896 MuTect - [MUTECT] Processed 50001828 reads in 724 ms
[2015-09-30T22:00Z] INFO  23:00:39,324 MuTect - [MUTECT] Processed 240017056 reads in 668 ms
[2015-09-30T22:00Z] INFO  23:00:39,619 MuTect - [MUTECT] Processed 51001867 reads in 723 ms
[2015-09-30T22:00Z] INFO  23:00:39,835 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:39,997 MuTect - [MUTECT] Processed 241017102 reads in 673 ms
[2015-09-30T22:00Z] INFO  23:00:40,340 MuTect - [MUTECT] Processed 52001872 reads in 721 ms
[2015-09-30T22:00Z] INFO  23:00:40,658 MuTect - [MUTECT] Processed 242017180 reads in 661 ms
[2015-09-30T22:00Z] INFO  23:00:40,824 MuTect - [MUTECT] Inspected 70000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:41,031 MuTect - [MUTECT] Processed 53001880 reads in 691 ms
[2015-09-30T22:00Z] INFO  23:00:41,308 MuTect - [MUTECT] Processed 243017193 reads in 650 ms
[2015-09-30T22:00Z] MuTect: MuTect
[2015-09-30T22:00Z] INFO  23:00:41,744 MuTect - [MUTECT] Processed 54001968 reads in 713 ms
[2015-09-30T22:00Z] INFO  23:00:41,986 MuTect - [MUTECT] Processed 244017333 reads in 678 ms
[2015-09-30T22:00Z] INFO  23:00:42,435 MuTect - [MUTECT] Processed 55001995 reads in 691 ms
[2015-09-30T22:00Z] INFO  23:00:42,559 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:42,642 MuTect - [MUTECT] Processed 245017419 reads in 656 ms
[2015-09-30T22:00Z] INFO  23:00:43,113 MuTect - [MUTECT] Processed 56002084 reads in 678 ms
[2015-09-30T22:00Z] INFO  23:00:43,163 MuTect - [MUTECT] Inspected 71000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:43,357 MuTect - [MUTECT] Processed 246017520 reads in 715 ms
[2015-09-30T22:00Z] INFO  23:00:43,847 MuTect - [MUTECT] Processed 57002097 reads in 734 ms
[2015-09-30T22:00Z] INFO  23:00:43,860 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/1/syn3-1_93297335_142653959-raw-mutect-regions.bed to be BED
[2015-09-30T22:00Z] INFO  23:00:43,917 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:00Z] INFO  23:00:43,917 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:00Z] INFO  23:00:43,917 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:00Z] INFO  23:00:43,917 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:00Z] INFO  23:00:43,921 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/1/syn3-1_93297335_142653959-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/1/tx/tmpybmVRR/syn3-1_93297335_142653959-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:00Z] INFO  23:00:43,921 HelpFormatter - Date/Time: 2015/09/30 23:00:43
[2015-09-30T22:00Z] INFO  23:00:43,921 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:00Z] INFO  23:00:43,921 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:00Z] INFO  23:00:43,949 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:00Z] INFO  23:00:43,953 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:00Z] INFO  23:00:44,015 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:00Z] INFO  23:00:44,025 MuTect - [MUTECT] Processed 247017549 reads in 668 ms
[2015-09-30T22:00Z] INFO  23:00:44,095 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:00Z] INFO  23:00:44,102 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:00Z] INFO  23:00:44,166 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:00Z] INFO  23:00:44,213 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:00Z] INFO  23:00:44,393 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:00Z] INFO  23:00:44,501 IntervalUtils - Processing 1539614 bp from intervals
[2015-09-30T22:00Z] INFO  23:00:44,505 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:00Z] INFO  23:00:44,505 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:00Z] INFO  23:00:44,603 MuTect - [MUTECT] Processed 58002152 reads in 756 ms
[2015-09-30T22:00Z] INFO  23:00:44,685 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:00Z] INFO  23:00:44,688 MuTect - [MUTECT] Processed 248017652 reads in 663 ms
[2015-09-30T22:00Z] INFO  23:00:44,828 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:00Z] INFO  23:00:44,828 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:00Z] INFO  23:00:44,829 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:00Z] INFO  23:00:44,830 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:00Z] INFO  23:00:45,136 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:45,144 ProgressMeter -      1:21995646        6.85e+06    3.0 m       26.0 s     71.2%         4.2 m    72.0 s
[2015-09-30T22:00Z] INFO  23:00:45,341 MuTect - [MUTECT] Processed 249017739 reads in 653 ms
[2015-09-30T22:00Z] INFO  23:00:45,348 MuTect - [MUTECT] Inspected 72000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:45,349 MuTect - [MUTECT] Processed 59002204 reads in 745 ms
[2015-09-30T22:00Z] INFO  23:00:45,971 MuTect - [MUTECT] Processed 250017798 reads in 630 ms
[2015-09-30T22:00Z] INFO  23:00:46,071 MuTect - [MUTECT] Processed 60002291 reads in 723 ms
[2015-09-30T22:00Z] INFO  23:00:46,625 MuTect - [MUTECT] Processed 251017905 reads in 654 ms
[2015-09-30T22:00Z] INFO  23:00:46,774 MuTect - [MUTECT] Processed 61002316 reads in 703 ms
[2015-09-30T22:00Z] INFO  23:00:47,294 MuTect - [MUTECT] Processed 252018006 reads in 669 ms
[2015-09-30T22:00Z] INFO  23:00:47,371 MuTect - [MUTECT] Processed 1000022 reads in 2492 ms
[2015-09-30T22:00Z] INFO  23:00:47,471 MuTect - [MUTECT] Processed 62002330 reads in 697 ms
[2015-09-30T22:00Z] INFO  23:00:47,532 MuTect - [MUTECT] Inspected 73000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:47,726 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:47,930 MuTect - [MUTECT] Processed 253018105 reads in 636 ms
[2015-09-30T22:00Z] INFO  23:00:48,154 MuTect - [MUTECT] Processed 63002421 reads in 683 ms
[2015-09-30T22:00Z] INFO  23:00:48,171 MuTect - [MUTECT] Processed 2000065 reads in 799 ms
[2015-09-30T22:00Z] INFO  23:00:48,563 MuTect - [MUTECT] Processed 254018171 reads in 633 ms
[2015-09-30T22:00Z] INFO  23:00:48,794 MuTect - [MUTECT] Processed 64002422 reads in 640 ms
[2015-09-30T22:00Z] INFO  23:00:48,860 MuTect - [MUTECT] Processed 3000086 reads in 690 ms
[2015-09-30T22:00Z] INFO  23:00:49,210 MuTect - [MUTECT] Processed 255018310 reads in 647 ms
[2015-09-30T22:00Z] INFO  23:00:49,431 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:49,460 MuTect - [MUTECT] Processed 65002434 reads in 666 ms
[2015-09-30T22:00Z] INFO  23:00:49,576 MuTect - [MUTECT] Inspected 74000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:49,578 MuTect - [MUTECT] Processed 4000148 reads in 718 ms
[2015-09-30T22:00Z] INFO  23:00:49,870 MuTect - [MUTECT] Processed 256018403 reads in 660 ms
[2015-09-30T22:00Z] INFO  23:00:50,197 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:50,199 MuTect - [MUTECT] Processed 66002464 reads in 739 ms
[2015-09-30T22:00Z] INFO  23:00:50,290 MuTect - [MUTECT] Processed 5000174 reads in 712 ms
[2015-09-30T22:00Z] INFO  23:00:50,648 MuTect - [MUTECT] Processed 257018416 reads in 778 ms
[2015-09-30T22:00Z] INFO  23:00:50,877 MuTect - [MUTECT] Processed 67002552 reads in 678 ms
[2015-09-30T22:00Z] INFO  23:00:50,978 MuTect - [MUTECT] Processed 6000195 reads in 688 ms
[2015-09-30T22:00Z] INFO  23:00:51,332 MuTect - [MUTECT] Processed 258018491 reads in 684 ms
[2015-09-30T22:00Z] INFO  23:00:51,557 MuTect - [MUTECT] Processed 68002608 reads in 680 ms
[2015-09-30T22:00Z] INFO  23:00:51,694 MuTect - [MUTECT] Processed 7000223 reads in 716 ms
[2015-09-30T22:00Z] INFO  23:00:51,747 MuTect - [MUTECT] Inspected 75000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:51,897 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:51,983 MuTect - [MUTECT] Processed 259018561 reads in 651 ms
[2015-09-30T22:00Z] INFO  23:00:52,204 MuTect - [MUTECT] Processed 69002623 reads in 647 ms
[2015-09-30T22:00Z] INFO  23:00:52,371 MuTect - [MUTECT] Processed 8000244 reads in 677 ms
[2015-09-30T22:00Z] INFO  23:00:52,508 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:52,642 MuTect - [MUTECT] Processed 260018632 reads in 659 ms
[2015-09-30T22:00Z] INFO  23:00:52,887 MuTect - [MUTECT] Processed 70002678 reads in 683 ms
[2015-09-30T22:00Z] INFO  23:00:53,155 MuTect - [MUTECT] Processed 9000264 reads in 784 ms
[2015-09-30T22:00Z] INFO  23:00:53,312 MuTect - [MUTECT] Processed 261018705 reads in 670 ms
[2015-09-30T22:00Z] INFO  23:00:53,539 MuTect - [MUTECT] Processed 71002732 reads in 652 ms
[2015-09-30T22:00Z] INFO  23:00:53,858 MuTect - [MUTECT] Inspected 76000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:53,867 MuTect - [MUTECT] Processed 10000272 reads in 712 ms
[2015-09-30T22:00Z] INFO  23:00:53,969 MuTect - [MUTECT] Processed 262018794 reads in 657 ms
[2015-09-30T22:00Z] INFO  23:00:54,174 MuTect - [MUTECT] Processed 72002789 reads in 635 ms
[2015-09-30T22:00Z] INFO  23:00:54,376 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:54,605 MuTect - [MUTECT] Processed 263018933 reads in 636 ms
[2015-09-30T22:00Z] INFO  23:00:54,612 MuTect - [MUTECT] Processed 11000281 reads in 745 ms
[2015-09-30T22:00Z] INFO  23:00:54,807 MuTect - [MUTECT] Processed 73002872 reads in 633 ms
[2015-09-30T22:00Z] INFO  23:00:54,848 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:55,243 MuTect - [MUTECT] Processed 264019017 reads in 638 ms
[2015-09-30T22:00Z] INFO  23:00:55,320 MuTect - [MUTECT] Processed 12000331 reads in 708 ms
[2015-09-30T22:00Z] INFO  23:00:55,500 MuTect - [MUTECT] Processed 74002885 reads in 693 ms
[2015-09-30T22:00Z] INFO  23:00:55,919 MuTect - [MUTECT] Processed 265019090 reads in 676 ms
[2015-09-30T22:00Z] INFO  23:00:56,044 MuTect - [MUTECT] Processed 13000357 reads in 724 ms
[2015-09-30T22:00Z] INFO  23:00:56,127 MuTect - [MUTECT] Inspected 77000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:56,177 MuTect - [MUTECT] Processed 75002911 reads in 677 ms
[2015-09-30T22:00Z] INFO  23:00:56,587 MuTect - [MUTECT] Processed 266019133 reads in 668 ms
[2015-09-30T22:00Z] INFO  23:00:56,778 MuTect - [MUTECT] Processed 14000417 reads in 734 ms
[2015-09-30T22:00Z] INFO  23:00:56,837 MuTect - [MUTECT] Processed 76002921 reads in 660 ms
[2015-09-30T22:00Z] INFO  23:00:57,014 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:57,211 MuTect - [MUTECT] Processed 267019172 reads in 624 ms
[2015-09-30T22:00Z] INFO  23:00:57,264 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:57,479 MuTect - [MUTECT] Processed 15000447 reads in 701 ms
[2015-09-30T22:00Z] INFO  23:00:57,521 MuTect - [MUTECT] Processed 77002965 reads in 684 ms
[2015-09-30T22:00Z] INFO  23:00:57,852 MuTect - [MUTECT] Processed 268019214 reads in 641 ms
[2015-09-30T22:00Z] INFO  23:00:58,175 MuTect - [MUTECT] Processed 16000501 reads in 696 ms
[2015-09-30T22:00Z] INFO  23:00:58,203 MuTect - [MUTECT] Processed 78002980 reads in 682 ms
[2015-09-30T22:00Z] INFO  23:00:58,399 MuTect - [MUTECT] Inspected 78000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:58,540 MuTect - [MUTECT] Processed 269019222 reads in 688 ms
[2015-09-30T22:00Z] INFO  23:00:58,870 MuTect - [MUTECT] Processed 79002995 reads in 667 ms
[2015-09-30T22:00Z] INFO  23:00:58,897 MuTect - [MUTECT] Processed 17000559 reads in 722 ms
[2015-09-30T22:00Z] INFO  23:00:59,181 MuTect - [MUTECT] Processed 270019317 reads in 641 ms
[2015-09-30T22:00Z] INFO  23:00:59,541 MuTect - [MUTECT] Processed 80002997 reads in 671 ms
[2015-09-30T22:00Z] INFO  23:00:59,653 MuTect - [MUTECT] Processed 18000595 reads in 756 ms
[2015-09-30T22:00Z] INFO  23:00:59,711 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:59,835 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:00Z] INFO  23:00:59,899 MuTect - [MUTECT] Processed 271019369 reads in 718 ms
[2015-09-30T22:01Z] INFO  23:01:00,085 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:01Z] INFO  23:01:00,090 ProgressMeter -            done        3.11e+06   58.0 s       18.0 s    100.0%        58.0 s     0.0 s
[2015-09-30T22:01Z] INFO  23:01:00,091 ProgressMeter - Total runtime 58.40 secs, 0.97 min, 0.02 hours
[2015-09-30T22:01Z] INFO  23:01:00,158 MicroScheduler - 53601 reads were filtered out during the traversal out of approximately 963707 total reads (5.56%)
[2015-09-30T22:01Z] INFO  23:01:00,158 MicroScheduler -   -> 38421 reads (3.99% of total) failing DuplicateReadFilter
[2015-09-30T22:01Z] INFO  23:01:00,158 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:01Z] INFO  23:01:00,158 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:01Z] INFO  23:01:00,158 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:01Z] INFO  23:01:00,159 MicroScheduler -   -> 15180 reads (1.58% of total) failing UnmappedReadFilter
[2015-09-30T22:01Z] INFO  23:01:00,385 MuTect - [MUTECT] Processed 19000626 reads in 732 ms
[2015-09-30T22:01Z] INFO  23:01:00,507 MuTect - [MUTECT] Inspected 79000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:00,545 MuTect - [MUTECT] Processed 272019376 reads in 646 ms
[2015-09-30T22:01Z] INFO  23:01:01,087 MuTect - [MUTECT] Processed 20000729 reads in 702 ms
[2015-09-30T22:01Z] INFO  23:01:01,154 MuTect - [MUTECT] Processed 273019403 reads in 609 ms
[2015-09-30T22:01Z] INFO  23:01:01,210 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:01Z] bgzip syn3-1_62231753_93258244-raw-mutect.vcf
[2015-09-30T22:01Z] tabix index syn3-1_62231753_93258244-raw-mutect.vcf.gz
[2015-09-30T22:01Z] INFO  23:01:01,785 MuTect - [MUTECT] Processed 274019433 reads in 631 ms
[2015-09-30T22:01Z] INFO  23:01:01,807 MuTect - [MUTECT] Processed 21000739 reads in 720 ms
[2015-09-30T22:01Z] INFO  23:01:02,352 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:02,445 MuTect - [MUTECT] Processed 275019453 reads in 660 ms
[2015-09-30T22:01Z] INFO  23:01:02,483 MuTect - [MUTECT] Processed 22000759 reads in 676 ms
[2015-09-30T22:01Z] INFO  23:01:02,599 MuTect - [MUTECT] Inspected 80000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:03,169 MuTect - [MUTECT] Processed 23000809 reads in 686 ms
[2015-09-30T22:01Z] INFO  23:01:03,170 MuTect - [MUTECT] Processed 276019534 reads in 725 ms
[2015-09-30T22:01Z] INFO  23:01:03,830 MuTect - [MUTECT] Processed 277019554 reads in 660 ms
[2015-09-30T22:01Z] INFO  23:01:03,861 MuTect - [MUTECT] Processed 24000829 reads in 692 ms
[2015-09-30T22:01Z] INFO  23:01:04,507 MuTect - [MUTECT] Processed 278019623 reads in 676 ms
[2015-09-30T22:01Z] INFO  23:01:04,587 MuTect - [MUTECT] Processed 25000842 reads in 726 ms
[2015-09-30T22:01Z] INFO  23:01:04,942 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:01Z] MuTect: MuTect
[2015-09-30T22:01Z] INFO  23:01:04,965 MuTect - [MUTECT] Inspected 81000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:05,188 MuTect - [MUTECT] Processed 279019677 reads in 682 ms
[2015-09-30T22:01Z] INFO  23:01:05,360 MuTect - [MUTECT] Processed 26000894 reads in 773 ms
[2015-09-30T22:01Z] INFO  23:01:05,872 MuTect - [MUTECT] Processed 280019701 reads in 684 ms
[2015-09-30T22:01Z] INFO  23:01:06,034 MuTect - [MUTECT] Processed 27000958 reads in 674 ms
[2015-09-30T22:01Z] INFO  23:01:06,565 MuTect - [MUTECT] Processed 281019707 reads in 693 ms
[2015-09-30T22:01Z] INFO  23:01:06,656 MuTect - [MUTECT] Processed 28000962 reads in 622 ms
[2015-09-30T22:01Z] INFO  23:01:07,158 MuTect - [MUTECT] Inspected 82000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:07,237 MuTect - [MUTECT] Processed 282019783 reads in 672 ms
[2015-09-30T22:01Z] INFO  23:01:07,255 MuTect - [MUTECT] Processed 29001051 reads in 598 ms
[2015-09-30T22:01Z] INFO  23:01:07,391 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/1/syn3-1_142666976_173685474-raw-mutect-regions.bed to be BED
[2015-09-30T22:01Z] INFO  23:01:07,446 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:01Z] INFO  23:01:07,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:01Z] INFO  23:01:07,446 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:01Z] INFO  23:01:07,447 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:01Z] INFO  23:01:07,450 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/1/syn3-1_142666976_173685474-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/1/tx/tmpR594Wz/syn3-1_142666976_173685474-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:01Z] INFO  23:01:07,450 HelpFormatter - Date/Time: 2015/09/30 23:01:07
[2015-09-30T22:01Z] INFO  23:01:07,450 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:01Z] INFO  23:01:07,451 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:01Z] INFO  23:01:07,478 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:01Z] INFO  23:01:07,483 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:01Z] INFO  23:01:07,538 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:01Z] INFO  23:01:07,585 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:01Z] INFO  23:01:07,593 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:01Z] INFO  23:01:07,657 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:01Z] INFO  23:01:07,668 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:01Z] INFO  23:01:07,870 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:01Z] INFO  23:01:07,908 MuTect - [MUTECT] Processed 30001076 reads in 653 ms
[2015-09-30T22:01Z] INFO  23:01:07,921 MuTect - [MUTECT] Processed 283019801 reads in 684 ms
[2015-09-30T22:01Z] INFO  23:01:08,009 IntervalUtils - Processing 2894324 bp from intervals
[2015-09-30T22:01Z] INFO  23:01:08,013 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:01Z] INFO  23:01:08,013 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:01Z] INFO  23:01:08,188 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:01Z] INFO  23:01:08,381 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:01Z] INFO  23:01:08,382 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:01Z] INFO  23:01:08,382 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:01Z] INFO  23:01:08,383 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:01Z] INFO  23:01:08,567 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:08,568 MuTect - [MUTECT] Processed 31001132 reads in 661 ms
[2015-09-30T22:01Z] INFO  23:01:08,599 MuTect - [MUTECT] Processed 284019883 reads in 678 ms
[2015-09-30T22:01Z] INFO  23:01:09,270 MuTect - [MUTECT] Processed 285019889 reads in 671 ms
[2015-09-30T22:01Z] INFO  23:01:09,271 MuTect - [MUTECT] Processed 32001202 reads in 703 ms
[2015-09-30T22:01Z] INFO  23:01:09,571 MuTect - [MUTECT] Inspected 83000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:09,921 MuTect - [MUTECT] Processed 33001224 reads in 650 ms
[2015-09-30T22:01Z] INFO  23:01:09,964 MuTect - [MUTECT] Processed 286019894 reads in 694 ms
[2015-09-30T22:01Z] INFO  23:01:10,574 MuTect - [MUTECT] Processed 34001265 reads in 653 ms
[2015-09-30T22:01Z] INFO  23:01:10,682 MuTect - [MUTECT] Processed 287019925 reads in 718 ms
[2015-09-30T22:01Z] INFO  23:01:11,094 MuTect - [MUTECT] Processed 1000029 reads in 2666 ms
[2015-09-30T22:01Z] INFO  23:01:11,225 MuTect - [MUTECT] Processed 35001380 reads in 651 ms
[2015-09-30T22:01Z] INFO  23:01:11,398 MuTect - [MUTECT] Processed 288019960 reads in 716 ms
[2015-09-30T22:01Z] INFO  23:01:11,908 MuTect - [MUTECT] Processed 36001427 reads in 683 ms
[2015-09-30T22:01Z] INFO  23:01:12,038 MuTect - [MUTECT] Inspected 84000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:12,057 MuTect - [MUTECT] Processed 289020055 reads in 659 ms
[2015-09-30T22:01Z] INFO  23:01:12,243 MuTect - [MUTECT] Processed 2000067 reads in 1149 ms
[2015-09-30T22:01Z] INFO  23:01:12,330 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:12,550 MuTect - [MUTECT] Processed 37001486 reads in 642 ms
[2015-09-30T22:01Z] INFO  23:01:12,692 MuTect - [MUTECT] Processed 290020170 reads in 634 ms
[2015-09-30T22:01Z] INFO  23:01:13,238 MuTect - [MUTECT] Processed 38001531 reads in 688 ms
[2015-09-30T22:01Z] INFO  23:01:13,359 MuTect - [MUTECT] Processed 291020251 reads in 668 ms
[2015-09-30T22:01Z] INFO  23:01:13,737 MuTect - [MUTECT] Processed 3000133 reads in 1494 ms
[2015-09-30T22:01Z] INFO  23:01:13,920 MuTect - [MUTECT] Processed 39001563 reads in 682 ms
[2015-09-30T22:01Z] INFO  23:01:13,979 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:14,017 MuTect - [MUTECT] Processed 292020275 reads in 658 ms
[2015-09-30T22:01Z] INFO  23:01:14,170 MuTect - [MUTECT] Inspected 85000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:14,610 MuTect - [MUTECT] Processed 40001620 reads in 690 ms
[2015-09-30T22:01Z] INFO  23:01:14,644 MuTect - [MUTECT] Processed 293020338 reads in 627 ms
[2015-09-30T22:01Z] INFO  23:01:14,790 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:14,831 ProgressMeter -     1:109538024        1.61e+06   30.0 s       18.0 s     39.3%        76.0 s    46.0 s
[2015-09-30T22:01Z] INFO  23:01:14,894 MuTect - [MUTECT] Processed 4000239 reads in 1157 ms
[2015-09-30T22:01Z] INFO  23:01:15,145 ProgressMeter -      1:26357451        8.20e+06    3.5 m       25.0 s     85.8%         4.1 m    34.0 s
[2015-09-30T22:01Z] INFO  23:01:15,285 MuTect - [MUTECT] Processed 294020430 reads in 641 ms
[2015-09-30T22:01Z] INFO  23:01:15,298 MuTect - [MUTECT] Processed 41001644 reads in 688 ms
[2015-09-30T22:01Z] INFO  23:01:15,683 MuTect - [MUTECT] Processed 5000304 reads in 789 ms
[2015-09-30T22:01Z] INFO  23:01:15,932 MuTect - [MUTECT] Processed 295020571 reads in 647 ms
[2015-09-30T22:01Z] INFO  23:01:15,982 MuTect - [MUTECT] Processed 42001653 reads in 684 ms
[2015-09-30T22:01Z] INFO  23:01:16,359 MuTect - [MUTECT] Processed 6000304 reads in 676 ms
[2015-09-30T22:01Z] INFO  23:01:16,380 MuTect - [MUTECT] Inspected 86000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:16,564 MuTect - [MUTECT] Processed 296020707 reads in 632 ms
[2015-09-30T22:01Z] INFO  23:01:16,653 MuTect - [MUTECT] Processed 43001669 reads in 671 ms
[2015-09-30T22:01Z] INFO  23:01:16,975 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:17,109 MuTect - [MUTECT] Processed 7000400 reads in 750 ms
[2015-09-30T22:01Z] INFO  23:01:17,190 MuTect - [MUTECT] Processed 297020727 reads in 626 ms
[2015-09-30T22:01Z] INFO  23:01:17,278 MuTect - [MUTECT] Processed 44001708 reads in 625 ms
[2015-09-30T22:01Z] INFO  23:01:17,831 MuTect - [MUTECT] Processed 298020815 reads in 641 ms
[2015-09-30T22:01Z] INFO  23:01:17,847 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:17,899 MuTect - [MUTECT] Processed 45001823 reads in 621 ms
[2015-09-30T22:01Z] INFO  23:01:18,070 MuTect - [MUTECT] Processed 8000501 reads in 961 ms
[2015-09-30T22:01Z] INFO  23:01:18,491 MuTect - [MUTECT] Processed 299020861 reads in 660 ms
[2015-09-30T22:01Z] INFO  23:01:18,520 MuTect - [MUTECT] Processed 46001862 reads in 621 ms
[2015-09-30T22:01Z] INFO  23:01:18,571 MuTect - [MUTECT] Inspected 87000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:18,960 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:19,170 MuTect - [MUTECT] Processed 300020880 reads in 679 ms
[2015-09-30T22:01Z] INFO  23:01:19,199 MuTect - [MUTECT] Processed 47001900 reads in 679 ms
[2015-09-30T22:01Z] INFO  23:01:19,262 MuTect - [MUTECT] Processed 9000536 reads in 1192 ms
[2015-09-30T22:01Z] INFO  23:01:19,844 MuTect - [MUTECT] Processed 48001971 reads in 645 ms
[2015-09-30T22:01Z] INFO  23:01:19,848 MuTect - [MUTECT] Processed 301020892 reads in 678 ms
[2015-09-30T22:01Z] INFO  23:01:20,105 MuTect - [MUTECT] Processed 10000678 reads in 843 ms
[2015-09-30T22:01Z] INFO  23:01:20,509 MuTect - [MUTECT] Processed 49001993 reads in 665 ms
[2015-09-30T22:01Z] INFO  23:01:20,516 MuTect - [MUTECT] Processed 302021018 reads in 668 ms
[2015-09-30T22:01Z] INFO  23:01:20,626 MuTect - [MUTECT] Inspected 88000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:20,747 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:20,926 MuTect - [MUTECT] Processed 11000697 reads in 821 ms
[2015-09-30T22:01Z] INFO  23:01:21,127 MuTect - [MUTECT] Processed 50002123 reads in 618 ms
[2015-09-30T22:01Z] INFO  23:01:21,194 MuTect - [MUTECT] Processed 303021036 reads in 678 ms
[2015-09-30T22:01Z] INFO  23:01:21,235 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:21,669 MuTect - [MUTECT] Processed 12000726 reads in 743 ms
[2015-09-30T22:01Z] INFO  23:01:21,771 MuTect - [MUTECT] Processed 51002163 reads in 644 ms
[2015-09-30T22:01Z] INFO  23:01:21,845 MuTect - [MUTECT] Processed 304021109 reads in 651 ms
[2015-09-30T22:01Z] INFO  23:01:22,388 MuTect - [MUTECT] Processed 13000742 reads in 719 ms
[2015-09-30T22:01Z] INFO  23:01:22,448 MuTect - [MUTECT] Processed 52002234 reads in 677 ms
[2015-09-30T22:01Z] INFO  23:01:22,508 MuTect - [MUTECT] Processed 305021221 reads in 663 ms
[2015-09-30T22:01Z] INFO  23:01:22,717 MuTect - [MUTECT] Inspected 89000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:23,111 MuTect - [MUTECT] Processed 53002293 reads in 663 ms
[2015-09-30T22:01Z] INFO  23:01:23,145 MuTect - [MUTECT] Processed 306021296 reads in 637 ms
[2015-09-30T22:01Z] INFO  23:01:23,178 MuTect - [MUTECT] Processed 14001241 reads in 790 ms
[2015-09-30T22:01Z] INFO  23:01:23,443 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:23,591 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:23,804 MuTect - [MUTECT] Processed 307021299 reads in 659 ms
[2015-09-30T22:01Z] INFO  23:01:23,847 MuTect - [MUTECT] Processed 54002313 reads in 736 ms
[2015-09-30T22:01Z] INFO  23:01:23,938 MuTect - [MUTECT] Processed 15001509 reads in 760 ms
[2015-09-30T22:01Z] INFO  23:01:24,422 MuTect - [MUTECT] Processed 308021330 reads in 618 ms
[2015-09-30T22:01Z] INFO  23:01:24,532 MuTect - [MUTECT] Processed 55002320 reads in 685 ms
[2015-09-30T22:01Z] INFO  23:01:24,840 MuTect - [MUTECT] Processed 16001713 reads in 902 ms
[2015-09-30T22:01Z] INFO  23:01:24,843 MuTect - [MUTECT] Inspected 90000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:25,055 MuTect - [MUTECT] Processed 309021399 reads in 632 ms
[2015-09-30T22:01Z] INFO  23:01:25,180 MuTect - [MUTECT] Processed 56002358 reads in 648 ms
[2015-09-30T22:01Z] INFO  23:01:25,650 MuTect - [MUTECT] Processed 17001729 reads in 810 ms
[2015-09-30T22:01Z] INFO  23:01:25,690 MuTect - [MUTECT] Processed 310021423 reads in 636 ms
[2015-09-30T22:01Z] INFO  23:01:25,749 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:25,849 MuTect - [MUTECT] Processed 57002387 reads in 669 ms
[2015-09-30T22:01Z] INFO  23:01:26,317 MuTect - [MUTECT] Processed 311021428 reads in 627 ms
[2015-09-30T22:01Z] INFO  23:01:26,483 MuTect - [MUTECT] Processed 58002441 reads in 634 ms
[2015-09-30T22:01Z] INFO  23:01:26,522 MuTect - [MUTECT] Processed 18002011 reads in 872 ms
[2015-09-30T22:01Z] INFO  23:01:26,941 MuTect - [MUTECT] Processed 312021505 reads in 624 ms
[2015-09-30T22:01Z] INFO  23:01:27,089 MuTect - [MUTECT] Inspected 91000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:27,127 MuTect - [MUTECT] Processed 59002485 reads in 644 ms
[2015-09-30T22:01Z] INFO  23:01:27,292 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:27,555 MuTect - [MUTECT] Processed 313021617 reads in 614 ms
[2015-09-30T22:01Z] INFO  23:01:27,616 MuTect - [MUTECT] Processed 19002164 reads in 1094 ms
[2015-09-30T22:01Z] INFO  23:01:27,786 MuTect - [MUTECT] Processed 60002605 reads in 659 ms
[2015-09-30T22:01Z] INFO  23:01:28,072 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:28,188 MuTect - [MUTECT] Processed 314021683 reads in 633 ms
[2015-09-30T22:01Z] INFO  23:01:28,440 MuTect - [MUTECT] Processed 20002244 reads in 824 ms
[2015-09-30T22:01Z] INFO  23:01:28,504 MuTect - [MUTECT] Processed 61002714 reads in 718 ms
[2015-09-30T22:01Z] INFO  23:01:28,794 MuTect - [MUTECT] Processed 315021753 reads in 606 ms
[2015-09-30T22:01Z] INFO  23:01:29,108 MuTect - [MUTECT] Processed 21002332 reads in 668 ms
[2015-09-30T22:01Z] INFO  23:01:29,164 MuTect - [MUTECT] Processed 62002736 reads in 660 ms
[2015-09-30T22:01Z] INFO  23:01:29,274 MuTect - [MUTECT] Inspected 92000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:29,408 MuTect - [MUTECT] Processed 316021883 reads in 614 ms
[2015-09-30T22:01Z] INFO  23:01:29,726 MuTect - [MUTECT] Processed 22002405 reads in 618 ms
[2015-09-30T22:01Z] INFO  23:01:29,821 MuTect - [MUTECT] Processed 63002812 reads in 657 ms
[2015-09-30T22:01Z] INFO  23:01:30,011 MuTect - [MUTECT] Processed 317022013 reads in 603 ms
[2015-09-30T22:01Z] INFO  23:01:30,219 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:30,349 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:30,353 MuTect - [MUTECT] Processed 23002510 reads in 627 ms
[2015-09-30T22:01Z] INFO  23:01:30,522 MuTect - [MUTECT] Processed 64002933 reads in 701 ms
[2015-09-30T22:01Z] INFO  23:01:30,628 MuTect - [MUTECT] Processed 318022074 reads in 617 ms
[2015-09-30T22:01Z] INFO  23:01:30,977 MuTect - [MUTECT] Processed 24002545 reads in 624 ms
[2015-09-30T22:01Z] INFO  23:01:31,186 MuTect - [MUTECT] Processed 65002964 reads in 664 ms
[2015-09-30T22:01Z] INFO  23:01:31,284 MuTect - [MUTECT] Processed 319022129 reads in 656 ms
[2015-09-30T22:01Z] INFO  23:01:31,361 MuTect - [MUTECT] Inspected 93000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:31,621 MuTect - [MUTECT] Processed 25002570 reads in 644 ms
[2015-09-30T22:01Z] INFO  23:01:31,832 MuTect - [MUTECT] Processed 66003011 reads in 646 ms
[2015-09-30T22:01Z] INFO  23:01:31,948 MuTect - [MUTECT] Processed 320022150 reads in 664 ms
[2015-09-30T22:01Z] INFO  23:01:32,242 MuTect - [MUTECT] Processed 26002595 reads in 621 ms
[2015-09-30T22:01Z] INFO  23:01:32,462 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:32,485 MuTect - [MUTECT] Processed 67003054 reads in 653 ms
[2015-09-30T22:01Z] INFO  23:01:32,613 MuTect - [MUTECT] Processed 321022302 reads in 665 ms
[2015-09-30T22:01Z] INFO  23:01:32,768 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:32,887 MuTect - [MUTECT] Processed 27002625 reads in 645 ms
[2015-09-30T22:01Z] INFO  23:01:33,127 MuTect - [MUTECT] Processed 68003129 reads in 642 ms
[2015-09-30T22:01Z] INFO  23:01:33,304 MuTect - [MUTECT] Processed 322022324 reads in 691 ms
[2015-09-30T22:01Z] INFO  23:01:33,521 MuTect - [MUTECT] Processed 28002701 reads in 634 ms
[2015-09-30T22:01Z] INFO  23:01:33,631 MuTect - [MUTECT] Inspected 94000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:33,807 MuTect - [MUTECT] Processed 69003164 reads in 680 ms
[2015-09-30T22:01Z] INFO  23:01:33,976 MuTect - [MUTECT] Processed 323022379 reads in 672 ms
[2015-09-30T22:01Z] INFO  23:01:34,162 MuTect - [MUTECT] Processed 29002702 reads in 641 ms
[2015-09-30T22:01Z] INFO  23:01:34,512 MuTect - [MUTECT] Processed 70003187 reads in 704 ms
[2015-09-30T22:01Z] INFO  23:01:34,659 MuTect - [MUTECT] Processed 324022446 reads in 683 ms
[2015-09-30T22:01Z] INFO  23:01:34,828 MuTect - [MUTECT] Processed 30002824 reads in 666 ms
[2015-09-30T22:01Z] INFO  23:01:34,972 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:35,198 MuTect - [MUTECT] Processed 71003212 reads in 687 ms
[2015-09-30T22:01Z] INFO  23:01:35,354 MuTect - [MUTECT] Processed 325022488 reads in 695 ms
[2015-09-30T22:01Z] INFO  23:01:35,487 MuTect - [MUTECT] Processed 31002888 reads in 659 ms
[2015-09-30T22:01Z] INFO  23:01:35,867 MuTect - [MUTECT] Processed 72003247 reads in 669 ms
[2015-09-30T22:01Z] INFO  23:01:36,008 MuTect - [MUTECT] Processed 326022542 reads in 654 ms
[2015-09-30T22:01Z] INFO  23:01:36,055 MuTect - [MUTECT] Inspected 95000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:36,204 MuTect - [MUTECT] Processed 32002949 reads in 717 ms
[2015-09-30T22:01Z] INFO  23:01:36,294 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:36,665 MuTect - [MUTECT] Processed 327022642 reads in 656 ms
[2015-09-30T22:01Z] INFO  23:01:36,979 MuTect - [MUTECT] Processed 73003303 reads in 1112 ms
[2015-09-30T22:01Z] INFO  23:01:37,054 MuTect - [MUTECT] Processed 33002990 reads in 850 ms
[2015-09-30T22:01Z] INFO  23:01:37,308 MuTect - [MUTECT] Processed 328022778 reads in 644 ms
[2015-09-30T22:01Z] INFO  23:01:37,654 MuTect - [MUTECT] Processed 74003321 reads in 675 ms
[2015-09-30T22:01Z] INFO  23:01:37,696 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:37,763 MuTect - [MUTECT] Processed 34003001 reads in 709 ms
[2015-09-30T22:01Z] INFO  23:01:37,947 MuTect - [MUTECT] Processed 329022854 reads in 639 ms
[2015-09-30T22:01Z] INFO  23:01:38,294 MuTect - [MUTECT] Inspected 96000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:38,316 MuTect - [MUTECT] Processed 75003339 reads in 662 ms
[2015-09-30T22:01Z] INFO  23:01:38,384 ProgressMeter -     1:146649715        9.76e+05   30.0 s       30.0 s     10.7%         4.7 m     4.2 m
[2015-09-30T22:01Z] INFO  23:01:38,437 MuTect - [MUTECT] Processed 35003016 reads in 674 ms
[2015-09-30T22:01Z] INFO  23:01:38,588 MuTect - [MUTECT] Processed 330022900 reads in 641 ms
[2015-09-30T22:01Z] INFO  23:01:38,982 MuTect - [MUTECT] Processed 76003363 reads in 666 ms
[2015-09-30T22:01Z] INFO  23:01:39,113 MuTect - [MUTECT] Processed 36003017 reads in 676 ms
[2015-09-30T22:01Z] INFO  23:01:39,218 MuTect - [MUTECT] Processed 331022921 reads in 630 ms
[2015-09-30T22:01Z] INFO  23:01:39,296 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:39,639 MuTect - [MUTECT] Processed 77003367 reads in 657 ms
[2015-09-30T22:01Z] INFO  23:01:39,794 MuTect - [MUTECT] Processed 37003104 reads in 681 ms
[2015-09-30T22:01Z] INFO  23:01:39,848 MuTect - [MUTECT] Processed 332023002 reads in 630 ms
[2015-09-30T22:01Z] INFO  23:01:40,001 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:40,342 MuTect - [MUTECT] Processed 78003415 reads in 703 ms
[2015-09-30T22:01Z] INFO  23:01:40,488 MuTect - [MUTECT] Processed 38003160 reads in 694 ms
[2015-09-30T22:01Z] INFO  23:01:40,523 MuTect - [MUTECT] Inspected 97000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:40,528 MuTect - [MUTECT] Processed 333023021 reads in 680 ms
[2015-09-30T22:01Z] INFO  23:01:40,981 MuTect - [MUTECT] Processed 79003437 reads in 639 ms
[2015-09-30T22:01Z] INFO  23:01:41,159 MuTect - [MUTECT] Processed 39003212 reads in 671 ms
[2015-09-30T22:01Z] INFO  23:01:41,172 MuTect - [MUTECT] Processed 334023043 reads in 644 ms
[2015-09-30T22:01Z] INFO  23:01:41,657 MuTect - [MUTECT] Processed 80003486 reads in 676 ms
[2015-09-30T22:01Z] INFO  23:01:41,794 MuTect - [MUTECT] Processed 40003215 reads in 635 ms
[2015-09-30T22:01Z] INFO  23:01:41,828 MuTect - [MUTECT] Processed 335023127 reads in 656 ms
[2015-09-30T22:01Z] INFO  23:01:42,286 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:42,306 MuTect - [MUTECT] Processed 81003551 reads in 649 ms
[2015-09-30T22:01Z] INFO  23:01:42,386 MuTect - [MUTECT] Processed 41003241 reads in 592 ms
[2015-09-30T22:01Z] INFO  23:01:42,499 MuTect - [MUTECT] Processed 336023182 reads in 671 ms
[2015-09-30T22:01Z] INFO  23:01:42,827 MuTect - [MUTECT] Inspected 98000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:42,846 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:42,967 MuTect - [MUTECT] Processed 82003589 reads in 661 ms
[2015-09-30T22:01Z] INFO  23:01:43,111 MuTect - [MUTECT] Processed 42003438 reads in 725 ms
[2015-09-30T22:01Z] INFO  23:01:43,145 MuTect - [MUTECT] Processed 337023205 reads in 646 ms
[2015-09-30T22:01Z] INFO  23:01:43,638 MuTect - [MUTECT] Processed 83003609 reads in 671 ms
[2015-09-30T22:01Z] INFO  23:01:43,799 MuTect - [MUTECT] Processed 338023322 reads in 654 ms
[2015-09-30T22:01Z] INFO  23:01:44,054 MuTect - [MUTECT] Processed 43003523 reads in 943 ms
[2015-09-30T22:01Z] INFO  23:01:44,295 MuTect - [MUTECT] Processed 84003618 reads in 657 ms
[2015-09-30T22:01Z] INFO  23:01:44,449 MuTect - [MUTECT] Processed 339023366 reads in 650 ms
[2015-09-30T22:01Z] INFO  23:01:44,552 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:01Z] INFO  23:01:44,555 ProgressMeter -            done        9.41e+06    4.0 m       25.0 s    100.0%         4.0 m     0.0 s
[2015-09-30T22:01Z] INFO  23:01:44,555 ProgressMeter - Total runtime 239.42 secs, 3.99 min, 0.07 hours
[2015-09-30T22:01Z] INFO  23:01:44,618 MicroScheduler - 284829 reads were filtered out during the traversal out of approximately 4045551 total reads (7.04%)
[2015-09-30T22:01Z] INFO  23:01:44,618 MicroScheduler -   -> 216968 reads (5.36% of total) failing DuplicateReadFilter
[2015-09-30T22:01Z] INFO  23:01:44,618 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:01Z] INFO  23:01:44,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:01Z] INFO  23:01:44,618 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:01Z] INFO  23:01:44,618 MicroScheduler -   -> 67861 reads (1.68% of total) failing UnmappedReadFilter
[2015-09-30T22:01Z] INFO  23:01:44,832 ProgressMeter -     1:114306007        2.96e+06   60.0 s       20.0 s     69.6%        86.0 s    26.0 s
[2015-09-30T22:01Z] INFO  23:01:44,894 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:44,955 MuTect - [MUTECT] Processed 85003620 reads in 660 ms
[2015-09-30T22:01Z] INFO  23:01:44,968 MuTect - [MUTECT] Processed 44003552 reads in 914 ms
[2015-09-30T22:01Z] INFO  23:01:45,625 MuTect - [MUTECT] Processed 86003655 reads in 670 ms
[2015-09-30T22:01Z] INFO  23:01:45,625 MuTect - [MUTECT] Processed 45003681 reads in 657 ms
[2015-09-30T22:01Z] INFO  23:01:45,631 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:01Z] bgzip syn3-1_0_31187470-raw-mutect.vcf
[2015-09-30T22:01Z] tabix index syn3-1_0_31187470-raw-mutect.vcf.gz
[2015-09-30T22:01Z] INFO  23:01:46,292 MuTect - [MUTECT] Processed 87003737 reads in 667 ms
[2015-09-30T22:01Z] INFO  23:01:46,488 MuTect - [MUTECT] Processed 46004031 reads in 863 ms
[2015-09-30T22:01Z] INFO  23:01:46,909 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:46,937 MuTect - [MUTECT] Processed 88003750 reads in 645 ms
[2015-09-30T22:01Z] INFO  23:01:47,393 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:47,407 MuTect - [MUTECT] Processed 47004162 reads in 919 ms
[2015-09-30T22:01Z] INFO  23:01:47,580 MuTect - [MUTECT] Processed 89003825 reads in 643 ms
[2015-09-30T22:01Z] MuTect: MuTect
[2015-09-30T22:01Z] INFO  23:01:48,282 MuTect - [MUTECT] Processed 90003880 reads in 702 ms
[2015-09-30T22:01Z] INFO  23:01:48,418 MuTect - [MUTECT] Processed 48004222 reads in 1011 ms
[2015-09-30T22:01Z] INFO  23:01:48,977 MuTect - [MUTECT] Processed 91003937 reads in 695 ms
[2015-09-30T22:01Z] INFO  23:01:49,246 MuTect - [MUTECT] Processed 49004297 reads in 828 ms
[2015-09-30T22:01Z] INFO  23:01:49,656 MuTect - [MUTECT] Processed 92003952 reads in 678 ms
[2015-09-30T22:01Z] INFO  23:01:49,883 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:50,261 MuTect - [MUTECT] Processed 50004298 reads in 1015 ms
[2015-09-30T22:01Z] INFO  23:01:50,282 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/1/syn3-1_173702591_204798081-raw-mutect-regions.bed to be BED
[2015-09-30T22:01Z] INFO  23:01:50,334 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:01Z] INFO  23:01:50,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:01Z] INFO  23:01:50,335 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:01Z] INFO  23:01:50,335 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:01Z] INFO  23:01:50,338 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/1/syn3-1_173702591_204798081-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/1/tx/tmpsdyOoh/syn3-1_173702591_204798081-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:01Z] INFO  23:01:50,339 HelpFormatter - Date/Time: 2015/09/30 23:01:50
[2015-09-30T22:01Z] INFO  23:01:50,339 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:01Z] INFO  23:01:50,339 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:01Z] INFO  23:01:50,341 MuTect - [MUTECT] Processed 93003957 reads in 686 ms
[2015-09-30T22:01Z] INFO  23:01:50,365 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:01Z] INFO  23:01:50,370 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:01Z] INFO  23:01:50,417 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:01Z] INFO  23:01:50,461 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:01Z] INFO  23:01:50,468 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:01Z] INFO  23:01:50,525 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:01Z] INFO  23:01:50,528 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:50,552 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:01Z] INFO  23:01:50,723 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:01Z] INFO  23:01:50,837 IntervalUtils - Processing 1710105 bp from intervals
[2015-09-30T22:01Z] INFO  23:01:50,841 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:01Z] INFO  23:01:50,841 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:01Z] INFO  23:01:50,991 MuTect - [MUTECT] Processed 51004299 reads in 730 ms
[2015-09-30T22:01Z] INFO  23:01:51,015 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:01Z] INFO  23:01:51,022 MuTect - [MUTECT] Processed 94004014 reads in 681 ms
[2015-09-30T22:01Z] INFO  23:01:51,168 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:01Z] INFO  23:01:51,168 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:01Z] INFO  23:01:51,169 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:01Z] INFO  23:01:51,170 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:01Z] INFO  23:01:51,747 MuTect - [MUTECT] Processed 52004334 reads in 756 ms
[2015-09-30T22:01Z] INFO  23:01:51,757 MuTect - [MUTECT] Processed 95004044 reads in 735 ms
[2015-09-30T22:01Z] INFO  23:01:52,358 MuTect - [MUTECT] Processed 53004384 reads in 611 ms
[2015-09-30T22:01Z] INFO  23:01:52,473 MuTect - [MUTECT] Processed 96004113 reads in 716 ms
[2015-09-30T22:01Z] INFO  23:01:52,537 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:53,016 MuTect - [MUTECT] Processed 54004493 reads in 658 ms
[2015-09-30T22:01Z] INFO  23:01:53,199 MuTect - [MUTECT] Processed 97004146 reads in 726 ms
[2015-09-30T22:01Z] INFO  23:01:53,683 MuTect - [MUTECT] Processed 55004504 reads in 667 ms
[2015-09-30T22:01Z] INFO  23:01:53,842 MuTect - [MUTECT] Processed 1000035 reads in 2628 ms
[2015-09-30T22:01Z] INFO  23:01:53,904 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:53,912 MuTect - [MUTECT] Processed 98004160 reads in 713 ms
[2015-09-30T22:01Z] INFO  23:01:54,339 MuTect - [MUTECT] Processed 56004515 reads in 656 ms
[2015-09-30T22:01Z] INFO  23:01:54,603 MuTect - [MUTECT] Processed 99004255 reads in 691 ms
[2015-09-30T22:01Z] INFO  23:01:54,805 MuTect - [MUTECT] Processed 2000136 reads in 963 ms
[2015-09-30T22:01Z] INFO  23:01:55,015 MuTect - [MUTECT] Processed 57004539 reads in 676 ms
[2015-09-30T22:01Z] INFO  23:01:55,031 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:55,270 MuTect - [MUTECT] Processed 100004257 reads in 667 ms
[2015-09-30T22:01Z] INFO  23:01:55,490 MuTect - [MUTECT] Processed 3000166 reads in 685 ms
[2015-09-30T22:01Z] INFO  23:01:55,709 MuTect - [MUTECT] Processed 58004573 reads in 694 ms
[2015-09-30T22:01Z] INFO  23:01:55,937 MuTect - [MUTECT] Processed 101004278 reads in 667 ms
[2015-09-30T22:01Z] INFO  23:01:56,002 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:56,233 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:56,247 MuTect - [MUTECT] Processed 4000170 reads in 757 ms
[2015-09-30T22:01Z] INFO  23:01:56,361 MuTect - [MUTECT] Processed 59004653 reads in 652 ms
[2015-09-30T22:01Z] INFO  23:01:56,579 MuTect - [MUTECT] Processed 102004348 reads in 642 ms
[2015-09-30T22:01Z] INFO  23:01:57,012 MuTect - [MUTECT] Processed 60004704 reads in 651 ms
[2015-09-30T22:01Z] INFO  23:01:57,041 MuTect - [MUTECT] Processed 5000242 reads in 793 ms
[2015-09-30T22:01Z] INFO  23:01:57,260 MuTect - [MUTECT] Processed 103004369 reads in 681 ms
[2015-09-30T22:01Z] INFO  23:01:57,439 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:57,636 MuTect - [MUTECT] Processed 61004772 reads in 624 ms
[2015-09-30T22:01Z] INFO  23:01:57,813 MuTect - [MUTECT] Processed 6000341 reads in 773 ms
[2015-09-30T22:01Z] INFO  23:01:57,935 MuTect - [MUTECT] Processed 104004382 reads in 675 ms
[2015-09-30T22:01Z] INFO  23:01:58,237 MuTect - [MUTECT] Processed 62004774 reads in 601 ms
[2015-09-30T22:01Z] INFO  23:01:58,424 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:58,577 MuTect - [MUTECT] Processed 7000391 reads in 764 ms
[2015-09-30T22:01Z] INFO  23:01:58,621 MuTect - [MUTECT] Processed 105004432 reads in 686 ms
[2015-09-30T22:01Z] INFO  23:01:58,689 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:01Z] INFO  23:01:58,835 MuTect - [MUTECT] Processed 63004818 reads in 598 ms
[2015-09-30T22:01Z] INFO  23:01:59,282 MuTect - [MUTECT] Processed 8000475 reads in 705 ms
[2015-09-30T22:01Z] INFO  23:01:59,290 MuTect - [MUTECT] Processed 106004481 reads in 669 ms
[2015-09-30T22:01Z] INFO  23:01:59,447 MuTect - [MUTECT] Processed 64004906 reads in 612 ms
[2015-09-30T22:01Z] INFO  23:01:59,978 MuTect - [MUTECT] Processed 107004566 reads in 688 ms
[2015-09-30T22:01Z] INFO  23:01:59,994 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:00,063 MuTect - [MUTECT] Processed 65004984 reads in 616 ms
[2015-09-30T22:02Z] INFO  23:02:00,076 MuTect - [MUTECT] Processed 9000535 reads in 794 ms
[2015-09-30T22:02Z] INFO  23:02:00,650 MuTect - [MUTECT] Processed 108004673 reads in 672 ms
[2015-09-30T22:02Z] INFO  23:02:00,729 MuTect - [MUTECT] Processed 66005025 reads in 666 ms
[2015-09-30T22:02Z] INFO  23:02:00,802 MuTect - [MUTECT] Processed 10000624 reads in 725 ms
[2015-09-30T22:02Z] INFO  23:02:00,826 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:01,268 MuTect - [MUTECT] Processed 109004718 reads in 618 ms
[2015-09-30T22:02Z] INFO  23:02:01,371 MuTect - [MUTECT] Processed 67005057 reads in 642 ms
[2015-09-30T22:02Z] INFO  23:02:01,414 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:01,531 MuTect - [MUTECT] Processed 11000659 reads in 730 ms
[2015-09-30T22:02Z] INFO  23:02:01,882 MuTect - [MUTECT] Processed 110004745 reads in 614 ms
[2015-09-30T22:02Z] INFO  23:02:02,015 MuTect - [MUTECT] Processed 68005162 reads in 644 ms
[2015-09-30T22:02Z] INFO  23:02:02,251 MuTect - [MUTECT] Processed 12000698 reads in 720 ms
[2015-09-30T22:02Z] INFO  23:02:02,514 MuTect - [MUTECT] Processed 111004755 reads in 632 ms
[2015-09-30T22:02Z] INFO  23:02:02,536 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:02,660 MuTect - [MUTECT] Processed 69005233 reads in 645 ms
[2015-09-30T22:02Z] INFO  23:02:02,969 MuTect - [MUTECT] Processed 13000700 reads in 718 ms
[2015-09-30T22:02Z] INFO  23:02:03,054 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:03,150 MuTect - [MUTECT] Processed 112004781 reads in 636 ms
[2015-09-30T22:02Z] INFO  23:02:03,282 MuTect - [MUTECT] Processed 70005329 reads in 622 ms
[2015-09-30T22:02Z] INFO  23:02:03,685 MuTect - [MUTECT] Processed 14000772 reads in 716 ms
[2015-09-30T22:02Z] INFO  23:02:03,818 MuTect - [MUTECT] Processed 113004789 reads in 668 ms
[2015-09-30T22:02Z] INFO  23:02:03,954 MuTect - [MUTECT] Processed 71005345 reads in 672 ms
[2015-09-30T22:02Z] INFO  23:02:04,057 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:04,437 MuTect - [MUTECT] Processed 15000781 reads in 752 ms
[2015-09-30T22:02Z] INFO  23:02:04,466 MuTect - [MUTECT] Processed 114004828 reads in 648 ms
[2015-09-30T22:02Z] INFO  23:02:04,671 MuTect - [MUTECT] Processed 72005364 reads in 717 ms
[2015-09-30T22:02Z] INFO  23:02:04,942 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:05,118 MuTect - [MUTECT] Processed 115004859 reads in 651 ms
[2015-09-30T22:02Z] INFO  23:02:05,155 MuTect - [MUTECT] Processed 16000836 reads in 718 ms
[2015-09-30T22:02Z] INFO  23:02:05,286 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:05,392 MuTect - [MUTECT] Processed 73005379 reads in 721 ms
[2015-09-30T22:02Z] INFO  23:02:05,746 MuTect - [MUTECT] Processed 116004965 reads in 629 ms
[2015-09-30T22:02Z] INFO  23:02:05,874 MuTect - [MUTECT] Processed 17000850 reads in 718 ms
[2015-09-30T22:02Z] INFO  23:02:06,078 MuTect - [MUTECT] Processed 74005481 reads in 686 ms
[2015-09-30T22:02Z] INFO  23:02:06,386 MuTect - [MUTECT] Processed 117005035 reads in 640 ms
[2015-09-30T22:02Z] INFO  23:02:06,495 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:06,543 MuTect - [MUTECT] Processed 18000924 reads in 669 ms
[2015-09-30T22:02Z] INFO  23:02:06,752 MuTect - [MUTECT] Processed 75005529 reads in 674 ms
[2015-09-30T22:02Z] INFO  23:02:07,086 MuTect - [MUTECT] Processed 118005112 reads in 700 ms
[2015-09-30T22:02Z] INFO  23:02:07,271 MuTect - [MUTECT] Processed 19000947 reads in 729 ms
[2015-09-30T22:02Z] INFO  23:02:07,388 MuTect - [MUTECT] Processed 76005554 reads in 636 ms
[2015-09-30T22:02Z] INFO  23:02:07,492 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:07,634 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:07,747 MuTect - [MUTECT] Processed 119005179 reads in 661 ms
[2015-09-30T22:02Z] INFO  23:02:07,990 MuTect - [MUTECT] Processed 20000989 reads in 719 ms
[2015-09-30T22:02Z] INFO  23:02:08,023 MuTect - [MUTECT] Processed 77005637 reads in 635 ms
[2015-09-30T22:02Z] INFO  23:02:08,385 ProgressMeter -     1:151239584        2.32e+06   60.0 s       25.0 s     26.0%         3.8 m     2.8 m
[2015-09-30T22:02Z] INFO  23:02:08,419 MuTect - [MUTECT] Processed 120005207 reads in 672 ms
[2015-09-30T22:02Z] INFO  23:02:08,642 MuTect - [MUTECT] Processed 78005737 reads in 619 ms
[2015-09-30T22:02Z] INFO  23:02:08,696 MuTect - [MUTECT] Processed 21001052 reads in 705 ms
[2015-09-30T22:02Z] INFO  23:02:08,923 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:09,191 MuTect - [MUTECT] Processed 121005253 reads in 772 ms
[2015-09-30T22:02Z] INFO  23:02:09,237 MuTect - [MUTECT] Processed 79005830 reads in 595 ms
[2015-09-30T22:02Z] INFO  23:02:09,410 MuTect - [MUTECT] Processed 22001056 reads in 715 ms
[2015-09-30T22:02Z] INFO  23:02:09,739 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:09,859 MuTect - [MUTECT] Processed 80005877 reads in 622 ms
[2015-09-30T22:02Z] INFO  23:02:09,864 MuTect - [MUTECT] Processed 122005311 reads in 673 ms
[2015-09-30T22:02Z] INFO  23:02:10,214 MuTect - [MUTECT] Processed 23001113 reads in 804 ms
[2015-09-30T22:02Z] INFO  23:02:10,463 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:10,476 MuTect - [MUTECT] Processed 81005956 reads in 617 ms
[2015-09-30T22:02Z] INFO  23:02:10,754 MuTect - [MUTECT] Processed 123005315 reads in 890 ms
[2015-09-30T22:02Z] INFO  23:02:10,933 MuTect - [MUTECT] Processed 24001188 reads in 718 ms
[2015-09-30T22:02Z] INFO  23:02:11,102 MuTect - [MUTECT] Processed 82005979 reads in 626 ms
[2015-09-30T22:02Z] INFO  23:02:11,456 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:11,637 MuTect - [MUTECT] Processed 25001248 reads in 705 ms
[2015-09-30T22:02Z] INFO  23:02:11,783 MuTect - [MUTECT] Processed 83006059 reads in 680 ms
[2015-09-30T22:02Z] INFO  23:02:11,893 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:12,203 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:02Z] INFO  23:02:12,206 ProgressMeter -            done        4.30e+06   87.0 s       20.0 s    100.0%        87.0 s     0.0 s
[2015-09-30T22:02Z] INFO  23:02:12,206 ProgressMeter - Total runtime 87.38 secs, 1.46 min, 0.02 hours
[2015-09-30T22:02Z] INFO  23:02:12,270 MicroScheduler - 87931 reads were filtered out during the traversal out of approximately 1458882 total reads (6.03%)
[2015-09-30T22:02Z] INFO  23:02:12,270 MicroScheduler -   -> 64390 reads (4.41% of total) failing DuplicateReadFilter
[2015-09-30T22:02Z] INFO  23:02:12,270 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:02Z] INFO  23:02:12,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:02Z] INFO  23:02:12,271 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:02Z] INFO  23:02:12,271 MicroScheduler -   -> 23541 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:02Z] INFO  23:02:12,321 MuTect - [MUTECT] Processed 26001306 reads in 684 ms
[2015-09-30T22:02Z] INFO  23:02:12,408 MuTect - [MUTECT] Processed 84006116 reads in 626 ms
[2015-09-30T22:02Z] INFO  23:02:13,035 MuTect - [MUTECT] Processed 27001355 reads in 714 ms
[2015-09-30T22:02Z] INFO  23:02:13,049 MuTect - [MUTECT] Processed 85006151 reads in 641 ms
[2015-09-30T22:02Z] INFO  23:02:13,247 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:02Z] bgzip syn3-1_93297335_142653959-raw-mutect.vcf
[2015-09-30T22:02Z] tabix index syn3-1_93297335_142653959-raw-mutect.vcf.gz
[2015-09-30T22:02Z] INFO  23:02:13,704 MuTect - [MUTECT] Processed 86006157 reads in 655 ms
[2015-09-30T22:02Z] INFO  23:02:13,707 MuTect - [MUTECT] Processed 28001417 reads in 672 ms
[2015-09-30T22:02Z] INFO  23:02:14,015 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:14,176 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:14,352 MuTect - [MUTECT] Processed 87006212 reads in 648 ms
[2015-09-30T22:02Z] INFO  23:02:14,367 MuTect - [MUTECT] Processed 29001533 reads in 660 ms
[2015-09-30T22:02Z] INFO  23:02:15,039 MuTect - [MUTECT] Processed 30001565 reads in 672 ms
[2015-09-30T22:02Z] INFO  23:02:15,039 MuTect - [MUTECT] Processed 88006268 reads in 687 ms
[2015-09-30T22:02Z] MuTect: MuTect
[2015-09-30T22:02Z] INFO  23:02:15,696 MuTect - [MUTECT] Processed 89006334 reads in 657 ms
[2015-09-30T22:02Z] INFO  23:02:15,737 MuTect - [MUTECT] Processed 31001570 reads in 698 ms
[2015-09-30T22:02Z] INFO  23:02:16,256 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:16,384 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:16,385 MuTect - [MUTECT] Processed 90006384 reads in 688 ms
[2015-09-30T22:02Z] INFO  23:02:16,408 MuTect - [MUTECT] Processed 32001572 reads in 671 ms
[2015-09-30T22:02Z] INFO  23:02:17,067 MuTect - [MUTECT] Processed 33001589 reads in 659 ms
[2015-09-30T22:02Z] INFO  23:02:17,076 MuTect - [MUTECT] Processed 91006435 reads in 692 ms
[2015-09-30T22:02Z] INFO  23:02:17,729 MuTect - [MUTECT] Processed 92006452 reads in 653 ms
[2015-09-30T22:02Z] INFO  23:02:17,755 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/1/syn3-1_204839842_235860787-raw-mutect-regions.bed to be BED
[2015-09-30T22:02Z] INFO  23:02:17,759 MuTect - [MUTECT] Processed 34001679 reads in 692 ms
[2015-09-30T22:02Z] INFO  23:02:17,810 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:02Z] INFO  23:02:17,811 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:02Z] INFO  23:02:17,811 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:02Z] INFO  23:02:17,811 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:02Z] INFO  23:02:17,814 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/1/syn3-1_204839842_235860787-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/1/tx/tmpNM0ckG/syn3-1_204839842_235860787-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:02Z] INFO  23:02:17,815 HelpFormatter - Date/Time: 2015/09/30 23:02:17
[2015-09-30T22:02Z] INFO  23:02:17,815 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:02Z] INFO  23:02:17,815 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:02Z] INFO  23:02:17,843 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:02Z] INFO  23:02:17,847 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:02Z] INFO  23:02:17,900 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:02Z] INFO  23:02:17,980 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:02Z] INFO  23:02:17,988 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:02Z] INFO  23:02:18,046 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:02Z] INFO  23:02:18,083 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:02Z] INFO  23:02:18,261 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:02Z] INFO  23:02:18,381 IntervalUtils - Processing 1760157 bp from intervals
[2015-09-30T22:02Z] INFO  23:02:18,385 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:02Z] INFO  23:02:18,385 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:02Z] INFO  23:02:18,443 MuTect - [MUTECT] Processed 35001746 reads in 684 ms
[2015-09-30T22:02Z] INFO  23:02:18,477 MuTect - [MUTECT] Processed 93006667 reads in 748 ms
[2015-09-30T22:02Z] INFO  23:02:18,655 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:18,796 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:02Z] INFO  23:02:18,963 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:02Z] INFO  23:02:18,963 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:02Z] INFO  23:02:18,963 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:02Z] INFO  23:02:18,964 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:02Z] INFO  23:02:19,139 MuTect - [MUTECT] Processed 36001759 reads in 696 ms
[2015-09-30T22:02Z] INFO  23:02:19,172 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:19,229 MuTect - [MUTECT] Processed 94006793 reads in 752 ms
[2015-09-30T22:02Z] INFO  23:02:19,803 MuTect - [MUTECT] Processed 37001806 reads in 664 ms
[2015-09-30T22:02Z] INFO  23:02:20,047 MuTect - [MUTECT] Processed 95006909 reads in 818 ms
[2015-09-30T22:02Z] INFO  23:02:20,489 MuTect - [MUTECT] Processed 38001853 reads in 686 ms
[2015-09-30T22:02Z] INFO  23:02:20,859 MuTect - [MUTECT] Processed 96006934 reads in 812 ms
[2015-09-30T22:02Z] INFO  23:02:20,952 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:21,158 MuTect - [MUTECT] Processed 39001960 reads in 669 ms
[2015-09-30T22:02Z] INFO  23:02:21,171 ProgressMeter -     1:182026165        1.24e+06   30.0 s       24.0 s     28.0%       107.0 s    77.0 s
[2015-09-30T22:02Z] INFO  23:02:21,277 MuTect - [MUTECT] Processed 1000043 reads in 2264 ms
[2015-09-30T22:02Z] INFO  23:02:21,474 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:21,534 MuTect - [MUTECT] Processed 97006937 reads in 675 ms
[2015-09-30T22:02Z] INFO  23:02:21,835 MuTect - [MUTECT] Processed 40001985 reads in 677 ms
[2015-09-30T22:02Z] INFO  23:02:22,111 MuTect - [MUTECT] Processed 2000131 reads in 834 ms
[2015-09-30T22:02Z] INFO  23:02:22,242 MuTect - [MUTECT] Processed 98007010 reads in 708 ms
[2015-09-30T22:02Z] INFO  23:02:22,510 MuTect - [MUTECT] Processed 41002098 reads in 675 ms
[2015-09-30T22:02Z] INFO  23:02:22,841 MuTect - [MUTECT] Processed 3000193 reads in 729 ms
[2015-09-30T22:02Z] INFO  23:02:22,906 MuTect - [MUTECT] Processed 99007038 reads in 664 ms
[2015-09-30T22:02Z] INFO  23:02:23,074 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:23,128 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:23,202 MuTect - [MUTECT] Processed 42002106 reads in 692 ms
[2015-09-30T22:02Z] INFO  23:02:23,553 MuTect - [MUTECT] Processed 100007120 reads in 647 ms
[2015-09-30T22:02Z] INFO  23:02:23,607 MuTect - [MUTECT] Processed 4000223 reads in 767 ms
[2015-09-30T22:02Z] INFO  23:02:23,695 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:23,861 MuTect - [MUTECT] Processed 43002195 reads in 659 ms
[2015-09-30T22:02Z] INFO  23:02:24,301 MuTect - [MUTECT] Processed 101007199 reads in 748 ms
[2015-09-30T22:02Z] INFO  23:02:24,386 MuTect - [MUTECT] Processed 5000238 reads in 779 ms
[2015-09-30T22:02Z] INFO  23:02:24,546 MuTect - [MUTECT] Processed 44002210 reads in 685 ms
[2015-09-30T22:02Z] INFO  23:02:24,978 MuTect - [MUTECT] Processed 102007298 reads in 676 ms
[2015-09-30T22:02Z] INFO  23:02:25,100 MuTect - [MUTECT] Processed 6000242 reads in 714 ms
[2015-09-30T22:02Z] INFO  23:02:25,217 MuTect - [MUTECT] Processed 45002221 reads in 671 ms
[2015-09-30T22:02Z] INFO  23:02:25,403 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:25,494 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:25,667 MuTect - [MUTECT] Processed 103007352 reads in 690 ms
[2015-09-30T22:02Z] INFO  23:02:25,791 MuTect - [MUTECT] Processed 7000277 reads in 691 ms
[2015-09-30T22:02Z] INFO  23:02:25,950 MuTect - [MUTECT] Processed 46002244 reads in 733 ms
[2015-09-30T22:02Z] INFO  23:02:25,955 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:26,362 MuTect - [MUTECT] Processed 104007387 reads in 695 ms
[2015-09-30T22:02Z] INFO  23:02:26,475 MuTect - [MUTECT] Processed 8000306 reads in 683 ms
[2015-09-30T22:02Z] INFO  23:02:26,677 MuTect - [MUTECT] Processed 47002345 reads in 727 ms
[2015-09-30T22:02Z] INFO  23:02:27,043 MuTect - [MUTECT] Processed 105007407 reads in 681 ms
[2015-09-30T22:02Z] INFO  23:02:27,211 MuTect - [MUTECT] Processed 9000360 reads in 737 ms
[2015-09-30T22:02Z] INFO  23:02:27,343 MuTect - [MUTECT] Processed 48002424 reads in 666 ms
[2015-09-30T22:02Z] INFO  23:02:27,733 MuTect - [MUTECT] Processed 106007479 reads in 690 ms
[2015-09-30T22:02Z] INFO  23:02:27,772 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:27,840 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:27,950 MuTect - [MUTECT] Processed 10000396 reads in 739 ms
[2015-09-30T22:02Z] INFO  23:02:28,003 MuTect - [MUTECT] Processed 49002508 reads in 660 ms
[2015-09-30T22:02Z] INFO  23:02:28,140 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:28,391 MuTect - [MUTECT] Processed 107007536 reads in 658 ms
[2015-09-30T22:02Z] INFO  23:02:28,655 MuTect - [MUTECT] Processed 50002547 reads in 652 ms
[2015-09-30T22:02Z] INFO  23:02:28,675 MuTect - [MUTECT] Processed 11000475 reads in 725 ms
[2015-09-30T22:02Z] INFO  23:02:29,056 MuTect - [MUTECT] Processed 108007586 reads in 665 ms
[2015-09-30T22:02Z] INFO  23:02:29,303 MuTect - [MUTECT] Processed 51002628 reads in 648 ms
[2015-09-30T22:02Z] INFO  23:02:29,371 MuTect - [MUTECT] Processed 12000568 reads in 696 ms
[2015-09-30T22:02Z] INFO  23:02:29,705 MuTect - [MUTECT] Processed 109007661 reads in 649 ms
[2015-09-30T22:02Z] INFO  23:02:29,958 MuTect - [MUTECT] Processed 52002714 reads in 655 ms
[2015-09-30T22:02Z] INFO  23:02:30,088 MuTect - [MUTECT] Processed 13000622 reads in 717 ms
[2015-09-30T22:02Z] INFO  23:02:30,207 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:30,265 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:30,356 MuTect - [MUTECT] Processed 110007696 reads in 651 ms
[2015-09-30T22:02Z] INFO  23:02:30,374 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:30,651 MuTect - [MUTECT] Processed 53002765 reads in 693 ms
[2015-09-30T22:02Z] INFO  23:02:30,786 MuTect - [MUTECT] Processed 14000633 reads in 698 ms
[2015-09-30T22:02Z] INFO  23:02:31,023 MuTect - [MUTECT] Processed 111007771 reads in 667 ms
[2015-09-30T22:02Z] INFO  23:02:31,349 MuTect - [MUTECT] Processed 54002813 reads in 698 ms
[2015-09-30T22:02Z] INFO  23:02:31,505 MuTect - [MUTECT] Processed 15000660 reads in 719 ms
[2015-09-30T22:02Z] INFO  23:02:31,685 MuTect - [MUTECT] Processed 112007840 reads in 662 ms
[2015-09-30T22:02Z] INFO  23:02:32,049 MuTect - [MUTECT] Processed 55002880 reads in 700 ms
[2015-09-30T22:02Z] INFO  23:02:32,164 MuTect - [MUTECT] Processed 16000710 reads in 659 ms
[2015-09-30T22:02Z] INFO  23:02:32,316 MuTect - [MUTECT] Processed 113007886 reads in 631 ms
[2015-09-30T22:02Z] INFO  23:02:32,405 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:32,618 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:32,745 MuTect - [MUTECT] Processed 56002886 reads in 696 ms
[2015-09-30T22:02Z] INFO  23:02:32,828 MuTect - [MUTECT] Processed 17000719 reads in 664 ms
[2015-09-30T22:02Z] INFO  23:02:32,951 MuTect - [MUTECT] Processed 114007923 reads in 635 ms
[2015-09-30T22:02Z] INFO  23:02:32,990 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:33,404 MuTect - [MUTECT] Processed 57002940 reads in 659 ms
[2015-09-30T22:02Z] INFO  23:02:33,571 MuTect - [MUTECT] Processed 18000814 reads in 743 ms
[2015-09-30T22:02Z] INFO  23:02:33,576 MuTect - [MUTECT] Processed 115007947 reads in 625 ms
[2015-09-30T22:02Z] INFO  23:02:34,128 MuTect - [MUTECT] Processed 58002953 reads in 724 ms
[2015-09-30T22:02Z] INFO  23:02:34,241 MuTect - [MUTECT] Processed 116007985 reads in 665 ms
[2015-09-30T22:02Z] INFO  23:02:34,276 MuTect - [MUTECT] Processed 19000831 reads in 705 ms
[2015-09-30T22:02Z] INFO  23:02:34,621 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:34,849 MuTect - [MUTECT] Processed 59002961 reads in 721 ms
[2015-09-30T22:02Z] INFO  23:02:34,920 MuTect - [MUTECT] Processed 117008031 reads in 679 ms
[2015-09-30T22:02Z] INFO  23:02:34,992 MuTect - [MUTECT] Processed 20000878 reads in 716 ms
[2015-09-30T22:02Z] INFO  23:02:35,282 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:35,563 MuTect - [MUTECT] Processed 60002982 reads in 714 ms
[2015-09-30T22:02Z] INFO  23:02:35,670 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:35,672 MuTect - [MUTECT] Processed 21000955 reads in 680 ms
[2015-09-30T22:02Z] INFO  23:02:36,294 MuTect - [MUTECT] Processed 61002986 reads in 731 ms
[2015-09-30T22:02Z] INFO  23:02:36,336 MuTect - [MUTECT] Processed 22001036 reads in 664 ms
[2015-09-30T22:02Z] INFO  23:02:36,503 MuTect - [MUTECT] Processed 118008052 reads in 1582 ms
[2015-09-30T22:02Z] INFO  23:02:36,984 MuTect - [MUTECT] Processed 23001117 reads in 648 ms
[2015-09-30T22:02Z] INFO  23:02:37,045 MuTect - [MUTECT] Processed 62003026 reads in 751 ms
[2015-09-30T22:02Z] INFO  23:02:37,171 MuTect - [MUTECT] Processed 119008058 reads in 669 ms
[2015-09-30T22:02Z] INFO  23:02:37,521 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:37,662 MuTect - [MUTECT] Processed 24001122 reads in 678 ms
[2015-09-30T22:02Z] INFO  23:02:37,756 MuTect - [MUTECT] Processed 63003059 reads in 711 ms
[2015-09-30T22:02Z] INFO  23:02:37,831 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:37,840 MuTect - [MUTECT] Processed 120008147 reads in 669 ms
[2015-09-30T22:02Z] INFO  23:02:38,251 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:38,357 MuTect - [MUTECT] Processed 25001150 reads in 695 ms
[2015-09-30T22:02Z] INFO  23:02:38,386 ProgressMeter -     1:154285123        3.56e+06   90.0 s       25.0 s     40.4%         3.7 m     2.2 m
[2015-09-30T22:02Z] INFO  23:02:38,499 MuTect - [MUTECT] Processed 64003082 reads in 743 ms
[2015-09-30T22:02Z] INFO  23:02:38,499 MuTect - [MUTECT] Processed 121008176 reads in 659 ms
[2015-09-30T22:02Z] INFO  23:02:39,020 MuTect - [MUTECT] Processed 26001159 reads in 663 ms
[2015-09-30T22:02Z] INFO  23:02:39,136 MuTect - [MUTECT] Processed 122008237 reads in 637 ms
[2015-09-30T22:02Z] INFO  23:02:39,231 MuTect - [MUTECT] Processed 65003097 reads in 731 ms
[2015-09-30T22:02Z] INFO  23:02:39,688 MuTect - [MUTECT] Processed 27001221 reads in 668 ms
[2015-09-30T22:02Z] INFO  23:02:39,774 MuTect - [MUTECT] Processed 123008325 reads in 638 ms
[2015-09-30T22:02Z] INFO  23:02:39,938 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:39,941 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:39,950 MuTect - [MUTECT] Processed 66003099 reads in 720 ms
[2015-09-30T22:02Z] INFO  23:02:40,369 MuTect - [MUTECT] Processed 28001285 reads in 681 ms
[2015-09-30T22:02Z] INFO  23:02:40,438 MuTect - [MUTECT] Processed 124008413 reads in 664 ms
[2015-09-30T22:02Z] INFO  23:02:40,689 MuTect - [MUTECT] Processed 67003130 reads in 739 ms
[2015-09-30T22:02Z] INFO  23:02:40,842 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:41,041 MuTect - [MUTECT] Processed 29001350 reads in 672 ms
[2015-09-30T22:02Z] INFO  23:02:41,093 MuTect - [MUTECT] Processed 125008490 reads in 655 ms
[2015-09-30T22:02Z] INFO  23:02:41,466 MuTect - [MUTECT] Processed 68003169 reads in 777 ms
[2015-09-30T22:02Z] INFO  23:02:41,727 MuTect - [MUTECT] Processed 126008565 reads in 634 ms
[2015-09-30T22:02Z] INFO  23:02:41,756 MuTect - [MUTECT] Processed 30001364 reads in 715 ms
[2015-09-30T22:02Z] INFO  23:02:42,057 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:42,164 MuTect - [MUTECT] Processed 69003186 reads in 698 ms
[2015-09-30T22:02Z] INFO  23:02:42,399 MuTect - [MUTECT] Processed 127008577 reads in 672 ms
[2015-09-30T22:02Z] INFO  23:02:42,457 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:42,499 MuTect - [MUTECT] Processed 31001417 reads in 743 ms
[2015-09-30T22:02Z] INFO  23:02:42,863 MuTect - [MUTECT] Processed 70003232 reads in 698 ms
[2015-09-30T22:02Z] INFO  23:02:43,076 MuTect - [MUTECT] Processed 128008622 reads in 677 ms
[2015-09-30T22:02Z] INFO  23:02:43,243 MuTect - [MUTECT] Processed 32001473 reads in 744 ms
[2015-09-30T22:02Z] INFO  23:02:43,474 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:43,591 MuTect - [MUTECT] Processed 71003236 reads in 729 ms
[2015-09-30T22:02Z] INFO  23:02:43,780 MuTect - [MUTECT] Processed 129008683 reads in 704 ms
[2015-09-30T22:02Z] INFO  23:02:43,920 MuTect - [MUTECT] Processed 33001559 reads in 677 ms
[2015-09-30T22:02Z] INFO  23:02:44,289 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:44,359 MuTect - [MUTECT] Processed 72003254 reads in 768 ms
[2015-09-30T22:02Z] INFO  23:02:44,435 MuTect - [MUTECT] Processed 130008793 reads in 655 ms
[2015-09-30T22:02Z] INFO  23:02:44,651 MuTect - [MUTECT] Processed 34001573 reads in 731 ms
[2015-09-30T22:02Z] INFO  23:02:45,087 MuTect - [MUTECT] Processed 131008841 reads in 652 ms
[2015-09-30T22:02Z] INFO  23:02:45,088 MuTect - [MUTECT] Processed 73003276 reads in 729 ms
[2015-09-30T22:02Z] INFO  23:02:45,394 MuTect - [MUTECT] Processed 35001623 reads in 743 ms
[2015-09-30T22:02Z] INFO  23:02:45,462 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:45,742 MuTect - [MUTECT] Processed 132008946 reads in 655 ms
[2015-09-30T22:02Z] INFO  23:02:45,853 MuTect - [MUTECT] Processed 74003300 reads in 765 ms
[2015-09-30T22:02Z] INFO  23:02:46,049 MuTect - [MUTECT] Processed 36001640 reads in 655 ms
[2015-09-30T22:02Z] INFO  23:02:46,335 MuTect - [MUTECT] Processed 133008961 reads in 593 ms
[2015-09-30T22:02Z] INFO  23:02:46,378 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:46,419 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:46,601 MuTect - [MUTECT] Processed 75003308 reads in 748 ms
[2015-09-30T22:02Z] INFO  23:02:46,697 MuTect - [MUTECT] Processed 37001675 reads in 648 ms
[2015-09-30T22:02Z] INFO  23:02:46,962 MuTect - [MUTECT] Processed 134009073 reads in 627 ms
[2015-09-30T22:02Z] INFO  23:02:47,319 MuTect - [MUTECT] Processed 76003328 reads in 718 ms
[2015-09-30T22:02Z] INFO  23:02:47,352 MuTect - [MUTECT] Processed 38001784 reads in 655 ms
[2015-09-30T22:02Z] INFO  23:02:47,599 MuTect - [MUTECT] Processed 135009134 reads in 637 ms
[2015-09-30T22:02Z] INFO  23:02:47,607 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:48,007 MuTect - [MUTECT] Processed 39001897 reads in 655 ms
[2015-09-30T22:02Z] INFO  23:02:48,050 MuTect - [MUTECT] Processed 77003351 reads in 731 ms
[2015-09-30T22:02Z] INFO  23:02:48,199 MuTect - [MUTECT] Processed 136009225 reads in 600 ms
[2015-09-30T22:02Z] INFO  23:02:48,494 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:48,674 MuTect - [MUTECT] Processed 40001960 reads in 667 ms
[2015-09-30T22:02Z] INFO  23:02:48,781 MuTect - [MUTECT] Processed 78003391 reads in 731 ms
[2015-09-30T22:02Z] INFO  23:02:48,816 MuTect - [MUTECT] Processed 137009338 reads in 617 ms
[2015-09-30T22:02Z] INFO  23:02:48,966 ProgressMeter -     1:209790221        1.26e+06   30.0 s       23.0 s     22.8%         2.2 m   101.0 s
[2015-09-30T22:02Z] INFO  23:02:49,215 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:49,326 MuTect - [MUTECT] Processed 41002008 reads in 652 ms
[2015-09-30T22:02Z] INFO  23:02:49,438 MuTect - [MUTECT] Processed 138009412 reads in 622 ms
[2015-09-30T22:02Z] INFO  23:02:49,507 MuTect - [MUTECT] Processed 79003410 reads in 726 ms
[2015-09-30T22:02Z] INFO  23:02:49,795 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:49,973 MuTect - [MUTECT] Processed 42002095 reads in 647 ms
[2015-09-30T22:02Z] INFO  23:02:50,052 MuTect - [MUTECT] Processed 139009448 reads in 614 ms
[2015-09-30T22:02Z] INFO  23:02:50,251 MuTect - [MUTECT] Processed 80003455 reads in 744 ms
[2015-09-30T22:02Z] INFO  23:02:50,466 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:50,661 MuTect - [MUTECT] Processed 43002122 reads in 688 ms
[2015-09-30T22:02Z] INFO  23:02:50,683 MuTect - [MUTECT] Processed 140009538 reads in 631 ms
[2015-09-30T22:02Z] INFO  23:02:50,967 MuTect - [MUTECT] Processed 81003456 reads in 716 ms
[2015-09-30T22:02Z] INFO  23:02:51,174 ProgressMeter -     1:200183351        3.11e+06   60.0 s       19.0 s     66.6%        90.0 s    30.0 s
[2015-09-30T22:02Z] INFO  23:02:51,305 MuTect - [MUTECT] Processed 141009546 reads in 622 ms
[2015-09-30T22:02Z] INFO  23:02:51,349 MuTect - [MUTECT] Processed 44002173 reads in 688 ms
[2015-09-30T22:02Z] INFO  23:02:51,663 MuTect - [MUTECT] Processed 82003505 reads in 696 ms
[2015-09-30T22:02Z] INFO  23:02:51,917 MuTect - [MUTECT] Processed 142009605 reads in 612 ms
[2015-09-30T22:02Z] INFO  23:02:51,933 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:52,011 MuTect - [MUTECT] Processed 45002241 reads in 662 ms
[2015-09-30T22:02Z] INFO  23:02:52,181 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:52,402 MuTect - [MUTECT] Processed 83003546 reads in 739 ms
[2015-09-30T22:02Z] INFO  23:02:52,523 MuTect - [MUTECT] Processed 143009607 reads in 606 ms
[2015-09-30T22:02Z] INFO  23:02:52,673 MuTect - [MUTECT] Processed 46002261 reads in 662 ms
[2015-09-30T22:02Z] INFO  23:02:52,726 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:53,130 MuTect - [MUTECT] Processed 84003581 reads in 728 ms
[2015-09-30T22:02Z] INFO  23:02:53,132 MuTect - [MUTECT] Processed 144009712 reads in 609 ms
[2015-09-30T22:02Z] INFO  23:02:53,342 MuTect - [MUTECT] Processed 47002311 reads in 669 ms
[2015-09-30T22:02Z] INFO  23:02:53,740 MuTect - [MUTECT] Processed 145009751 reads in 608 ms
[2015-09-30T22:02Z] INFO  23:02:53,807 MuTect - [MUTECT] Processed 85003674 reads in 677 ms
[2015-09-30T22:02Z] INFO  23:02:54,010 MuTect - [MUTECT] Processed 48002314 reads in 668 ms
[2015-09-30T22:02Z] INFO  23:02:54,363 MuTect - [MUTECT] Processed 146009800 reads in 623 ms
[2015-09-30T22:02Z] INFO  23:02:54,371 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:54,397 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:54,521 MuTect - [MUTECT] Processed 86003687 reads in 714 ms
[2015-09-30T22:02Z] INFO  23:02:54,698 MuTect - [MUTECT] Processed 49002387 reads in 688 ms
[2015-09-30T22:02Z] INFO  23:02:54,826 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:54,970 MuTect - [MUTECT] Processed 147009836 reads in 607 ms
[2015-09-30T22:02Z] INFO  23:02:55,241 MuTect - [MUTECT] Processed 87003723 reads in 720 ms
[2015-09-30T22:02Z] INFO  23:02:55,347 MuTect - [MUTECT] Processed 50002452 reads in 649 ms
[2015-09-30T22:02Z] INFO  23:02:55,562 MuTect - [MUTECT] Processed 148009887 reads in 592 ms
[2015-09-30T22:02Z] INFO  23:02:55,939 MuTect - [MUTECT] Processed 88003807 reads in 698 ms
[2015-09-30T22:02Z] INFO  23:02:56,010 MuTect - [MUTECT] Processed 51002469 reads in 663 ms
[2015-09-30T22:02Z] INFO  23:02:56,187 MuTect - [MUTECT] Processed 149009955 reads in 625 ms
[2015-09-30T22:02Z] INFO  23:02:56,604 MuTect - [MUTECT] Processed 89003895 reads in 665 ms
[2015-09-30T22:02Z] INFO  23:02:56,674 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:56,688 MuTect - [MUTECT] Processed 52002501 reads in 678 ms
[2015-09-30T22:02Z] INFO  23:02:56,801 MuTect - [MUTECT] Processed 150009990 reads in 614 ms
[2015-09-30T22:02Z] INFO  23:02:56,930 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:57,006 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:57,309 MuTect - [MUTECT] Processed 90003918 reads in 705 ms
[2015-09-30T22:02Z] INFO  23:02:57,357 MuTect - [MUTECT] Processed 53002556 reads in 669 ms
[2015-09-30T22:02Z] INFO  23:02:57,419 MuTect - [MUTECT] Processed 151010089 reads in 618 ms
[2015-09-30T22:02Z] INFO  23:02:58,009 MuTect - [MUTECT] Processed 54002636 reads in 652 ms
[2015-09-30T22:02Z] INFO  23:02:58,040 MuTect - [MUTECT] Processed 91003985 reads in 731 ms
[2015-09-30T22:02Z] INFO  23:02:58,044 MuTect - [MUTECT] Processed 152010208 reads in 625 ms
[2015-09-30T22:02Z] INFO  23:02:58,664 MuTect - [MUTECT] Processed 153010262 reads in 620 ms
[2015-09-30T22:02Z] INFO  23:02:58,684 MuTect - [MUTECT] Processed 55002731 reads in 675 ms
[2015-09-30T22:02Z] INFO  23:02:58,813 MuTect - [MUTECT] Processed 92004102 reads in 773 ms
[2015-09-30T22:02Z] INFO  23:02:59,261 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:59,268 MuTect - [MUTECT] Processed 154010349 reads in 604 ms
[2015-09-30T22:02Z] INFO  23:02:59,276 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:59,386 MuTect - [MUTECT] Processed 56002745 reads in 702 ms
[2015-09-30T22:02Z] INFO  23:02:59,445 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:02Z] INFO  23:02:59,566 MuTect - [MUTECT] Processed 93004201 reads in 753 ms
[2015-09-30T22:02Z] INFO  23:02:59,900 MuTect - [MUTECT] Processed 155010432 reads in 632 ms
[2015-09-30T22:03Z] INFO  23:03:00,015 MuTect - [MUTECT] Processed 57002838 reads in 629 ms
[2015-09-30T22:03Z] INFO  23:03:00,299 MuTect - [MUTECT] Processed 94004280 reads in 733 ms
[2015-09-30T22:03Z] INFO  23:03:00,528 MuTect - [MUTECT] Processed 156010461 reads in 628 ms
[2015-09-30T22:03Z] INFO  23:03:00,652 MuTect - [MUTECT] Processed 58002859 reads in 637 ms
[2015-09-30T22:03Z] INFO  23:03:01,099 MuTect - [MUTECT] Processed 95004296 reads in 800 ms
[2015-09-30T22:03Z] INFO  23:03:01,163 MuTect - [MUTECT] Processed 157010514 reads in 635 ms
[2015-09-30T22:03Z] INFO  23:03:01,311 MuTect - [MUTECT] Processed 59002938 reads in 659 ms
[2015-09-30T22:03Z] INFO  23:03:01,575 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:01,607 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:01,623 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:01,762 MuTect - [MUTECT] Processed 158010571 reads in 599 ms
[2015-09-30T22:03Z] INFO  23:03:01,805 MuTect - [MUTECT] Processed 96004331 reads in 706 ms
[2015-09-30T22:03Z] INFO  23:03:01,970 MuTect - [MUTECT] Processed 60002996 reads in 658 ms
[2015-09-30T22:03Z] INFO  23:03:02,379 MuTect - [MUTECT] Processed 159010608 reads in 617 ms
[2015-09-30T22:03Z] INFO  23:03:02,560 MuTect - [MUTECT] Processed 97004344 reads in 755 ms
[2015-09-30T22:03Z] INFO  23:03:02,673 MuTect - [MUTECT] Processed 61003008 reads in 704 ms
[2015-09-30T22:03Z] INFO  23:03:02,993 MuTect - [MUTECT] Processed 160010663 reads in 614 ms
[2015-09-30T22:03Z] INFO  23:03:03,277 MuTect - [MUTECT] Processed 98004442 reads in 717 ms
[2015-09-30T22:03Z] INFO  23:03:03,306 MuTect - [MUTECT] Processed 62003032 reads in 633 ms
[2015-09-30T22:03Z] INFO  23:03:03,620 MuTect - [MUTECT] Processed 161010753 reads in 627 ms
[2015-09-30T22:03Z] INFO  23:03:03,636 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:03,826 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:03,964 MuTect - [MUTECT] Processed 99004524 reads in 686 ms
[2015-09-30T22:03Z] INFO  23:03:04,006 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:04,084 MuTect - [MUTECT] Processed 63003076 reads in 778 ms
[2015-09-30T22:03Z] INFO  23:03:04,262 MuTect - [MUTECT] Processed 162010783 reads in 642 ms
[2015-09-30T22:03Z] INFO  23:03:04,648 MuTect - [MUTECT] Processed 100004601 reads in 685 ms
[2015-09-30T22:03Z] INFO  23:03:04,791 MuTect - [MUTECT] Processed 64003147 reads in 707 ms
[2015-09-30T22:03Z] INFO  23:03:04,912 MuTect - [MUTECT] Processed 163010901 reads in 650 ms
[2015-09-30T22:03Z] INFO  23:03:05,343 MuTect - [MUTECT] Processed 101004671 reads in 695 ms
[2015-09-30T22:03Z] INFO  23:03:05,504 MuTect - [MUTECT] Processed 65003232 reads in 713 ms
[2015-09-30T22:03Z] INFO  23:03:05,594 MuTect - [MUTECT] Processed 164010913 reads in 682 ms
[2015-09-30T22:03Z] INFO  23:03:05,820 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:06,037 MuTect - [MUTECT] Processed 102004718 reads in 694 ms
[2015-09-30T22:03Z] INFO  23:03:06,211 MuTect - [MUTECT] Processed 165010984 reads in 617 ms
[2015-09-30T22:03Z] INFO  23:03:06,219 MuTect - [MUTECT] Processed 66003280 reads in 715 ms
[2015-09-30T22:03Z] INFO  23:03:06,288 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:06,555 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:06,694 MuTect - [MUTECT] Processed 103004758 reads in 657 ms
[2015-09-30T22:03Z] INFO  23:03:06,840 MuTect - [MUTECT] Processed 166011032 reads in 629 ms
[2015-09-30T22:03Z] INFO  23:03:06,941 MuTect - [MUTECT] Processed 67003316 reads in 722 ms
[2015-09-30T22:03Z] INFO  23:03:07,385 MuTect - [MUTECT] Processed 104004767 reads in 691 ms
[2015-09-30T22:03Z] INFO  23:03:07,513 MuTect - [MUTECT] Processed 167011086 reads in 673 ms
[2015-09-30T22:03Z] INFO  23:03:07,691 MuTect - [MUTECT] Processed 68003392 reads in 750 ms
[2015-09-30T22:03Z] INFO  23:03:07,889 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:08,075 MuTect - [MUTECT] Processed 105004770 reads in 690 ms
[2015-09-30T22:03Z] INFO  23:03:08,168 MuTect - [MUTECT] Processed 168011137 reads in 655 ms
[2015-09-30T22:03Z] INFO  23:03:08,437 MuTect - [MUTECT] Processed 69003399 reads in 746 ms
[2015-09-30T22:03Z] INFO  23:03:08,595 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:08,800 MuTect - [MUTECT] Processed 106004825 reads in 725 ms
[2015-09-30T22:03Z] INFO  23:03:08,811 MuTect - [MUTECT] Processed 169011148 reads in 643 ms
[2015-09-30T22:03Z] INFO  23:03:09,163 MuTect - [MUTECT] Processed 70003430 reads in 726 ms
[2015-09-30T22:03Z] INFO  23:03:09,330 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:09,436 MuTect - [MUTECT] Processed 170011208 reads in 625 ms
[2015-09-30T22:03Z] INFO  23:03:09,511 MuTect - [MUTECT] Processed 107004827 reads in 711 ms
[2015-09-30T22:03Z] INFO  23:03:09,879 MuTect - [MUTECT] Processed 71003467 reads in 716 ms
[2015-09-30T22:03Z] INFO  23:03:10,050 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:10,096 MuTect - [MUTECT] Processed 171011293 reads in 660 ms
[2015-09-30T22:03Z] INFO  23:03:10,191 MuTect - [MUTECT] Processed 108004943 reads in 680 ms
[2015-09-30T22:03Z] INFO  23:03:10,579 MuTect - [MUTECT] Processed 72003489 reads in 700 ms
[2015-09-30T22:03Z] INFO  23:03:10,750 MuTect - [MUTECT] Processed 172011299 reads in 654 ms
[2015-09-30T22:03Z] INFO  23:03:10,816 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:10,864 MuTect - [MUTECT] Processed 109004968 reads in 673 ms
[2015-09-30T22:03Z] INFO  23:03:11,267 MuTect - [MUTECT] Processed 73003500 reads in 688 ms
[2015-09-30T22:03Z] INFO  23:03:11,481 MuTect - [MUTECT] Processed 173011417 reads in 731 ms
[2015-09-30T22:03Z] INFO  23:03:11,547 MuTect - [MUTECT] Processed 110005098 reads in 683 ms
[2015-09-30T22:03Z] INFO  23:03:11,893 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:11,973 MuTect - [MUTECT] Processed 74003501 reads in 706 ms
[2015-09-30T22:03Z] INFO  23:03:12,175 MuTect - [MUTECT] Processed 111005115 reads in 628 ms
[2015-09-30T22:03Z] INFO  23:03:12,186 MuTect - [MUTECT] Processed 174011464 reads in 705 ms
[2015-09-30T22:03Z] INFO  23:03:12,429 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:12,674 MuTect - [MUTECT] Processed 75003533 reads in 700 ms
[2015-09-30T22:03Z] INFO  23:03:12,819 MuTect - [MUTECT] Processed 175011511 reads in 633 ms
[2015-09-30T22:03Z] INFO  23:03:12,843 MuTect - [MUTECT] Processed 112005137 reads in 668 ms
[2015-09-30T22:03Z] INFO  23:03:12,899 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:13,336 MuTect - [MUTECT] Processed 76003626 reads in 663 ms
[2015-09-30T22:03Z] INFO  23:03:13,473 MuTect - [MUTECT] Processed 176011579 reads in 654 ms
[2015-09-30T22:03Z] INFO  23:03:13,521 MuTect - [MUTECT] Processed 113005168 reads in 678 ms
[2015-09-30T22:03Z] INFO  23:03:14,053 MuTect - [MUTECT] Processed 77003668 reads in 717 ms
[2015-09-30T22:03Z] INFO  23:03:14,098 MuTect - [MUTECT] Processed 177011643 reads in 625 ms
[2015-09-30T22:03Z] INFO  23:03:14,212 MuTect - [MUTECT] Processed 114005191 reads in 691 ms
[2015-09-30T22:03Z] INFO  23:03:14,307 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:14,613 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:14,749 MuTect - [MUTECT] Processed 78003718 reads in 695 ms
[2015-09-30T22:03Z] INFO  23:03:14,750 MuTect - [MUTECT] Processed 178011660 reads in 651 ms
[2015-09-30T22:03Z] INFO  23:03:14,874 MuTect - [MUTECT] Processed 115005245 reads in 662 ms
[2015-09-30T22:03Z] INFO  23:03:15,377 MuTect - [MUTECT] Processed 179011697 reads in 628 ms
[2015-09-30T22:03Z] INFO  23:03:15,379 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:15,448 MuTect - [MUTECT] Processed 79003730 reads in 700 ms
[2015-09-30T22:03Z] INFO  23:03:15,557 MuTect - [MUTECT] Processed 116005278 reads in 683 ms
[2015-09-30T22:03Z] INFO  23:03:16,016 MuTect - [MUTECT] Processed 180011781 reads in 639 ms
[2015-09-30T22:03Z] INFO  23:03:16,148 MuTect - [MUTECT] Processed 80003735 reads in 700 ms
[2015-09-30T22:03Z] INFO  23:03:16,249 MuTect - [MUTECT] Processed 117005343 reads in 692 ms
[2015-09-30T22:03Z] INFO  23:03:16,636 MuTect - [MUTECT] Processed 181011871 reads in 620 ms
[2015-09-30T22:03Z] INFO  23:03:16,766 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:16,798 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:16,863 MuTect - [MUTECT] Processed 81003766 reads in 715 ms
[2015-09-30T22:03Z] INFO  23:03:16,917 MuTect - [MUTECT] Processed 118005386 reads in 668 ms
[2015-09-30T22:03Z] INFO  23:03:17,291 MuTect - [MUTECT] Processed 182011910 reads in 655 ms
[2015-09-30T22:03Z] INFO  23:03:17,512 MuTect - [MUTECT] Processed 82003775 reads in 649 ms
[2015-09-30T22:03Z] INFO  23:03:17,587 MuTect - [MUTECT] Processed 119005442 reads in 670 ms
[2015-09-30T22:03Z] INFO  23:03:17,813 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:17,940 MuTect - [MUTECT] Processed 183012007 reads in 649 ms
[2015-09-30T22:03Z] INFO  23:03:18,167 MuTect - [MUTECT] Processed 83003816 reads in 655 ms
[2015-09-30T22:03Z] INFO  23:03:18,276 MuTect - [MUTECT] Processed 120005510 reads in 689 ms
[2015-09-30T22:03Z] INFO  23:03:18,387 ProgressMeter -     1:156899105        5.46e+06    2.2 m       23.0 s     60.3%         3.6 m    85.0 s
[2015-09-30T22:03Z] INFO  23:03:18,563 MuTect - [MUTECT] Processed 184012074 reads in 623 ms
[2015-09-30T22:03Z] INFO  23:03:18,848 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:18,856 MuTect - [MUTECT] Processed 84003858 reads in 689 ms
[2015-09-30T22:03Z] INFO  23:03:18,944 MuTect - [MUTECT] Processed 121005581 reads in 668 ms
[2015-09-30T22:03Z] INFO  23:03:18,967 ProgressMeter -     1:223814694        2.69e+06   60.0 s       22.0 s     55.6%       107.0 s    47.0 s
[2015-09-30T22:03Z] INFO  23:03:19,085 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:19,199 MuTect - [MUTECT] Processed 185012138 reads in 636 ms
[2015-09-30T22:03Z] INFO  23:03:19,583 MuTect - [MUTECT] Processed 85003875 reads in 727 ms
[2015-09-30T22:03Z] INFO  23:03:19,626 MuTect - [MUTECT] Processed 122005680 reads in 682 ms
[2015-09-30T22:03Z] INFO  23:03:19,885 MuTect - [MUTECT] Processed 186012144 reads in 686 ms
[2015-09-30T22:03Z] INFO  23:03:20,104 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:20,227 MuTect - [MUTECT] Processed 86003927 reads in 644 ms
[2015-09-30T22:03Z] INFO  23:03:20,328 MuTect - [MUTECT] Processed 123005702 reads in 702 ms
[2015-09-30T22:03Z] INFO  23:03:20,556 MuTect - [MUTECT] Processed 187012174 reads in 671 ms
[2015-09-30T22:03Z] INFO  23:03:20,860 MuTect - [MUTECT] Processed 87003961 reads in 633 ms
[2015-09-30T22:03Z] INFO  23:03:21,022 MuTect - [MUTECT] Processed 124005794 reads in 694 ms
[2015-09-30T22:03Z] INFO  23:03:21,175 ProgressMeter -     1:203186340        4.50e+06   90.0 s       19.0 s     90.8%        99.0 s     9.0 s
[2015-09-30T22:03Z] INFO  23:03:21,210 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:21,241 MuTect - [MUTECT] Processed 188012191 reads in 685 ms
[2015-09-30T22:03Z] INFO  23:03:21,467 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:21,601 MuTect - [MUTECT] Processed 88004000 reads in 741 ms
[2015-09-30T22:03Z] INFO  23:03:21,742 MuTect - [MUTECT] Processed 125005820 reads in 720 ms
[2015-09-30T22:03Z] INFO  23:03:21,957 MuTect - [MUTECT] Processed 189012258 reads in 716 ms
[2015-09-30T22:03Z] INFO  23:03:22,265 MuTect - [MUTECT] Processed 89004111 reads in 664 ms
[2015-09-30T22:03Z] INFO  23:03:22,403 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:22,440 MuTect - [MUTECT] Processed 126005925 reads in 698 ms
[2015-09-30T22:03Z] INFO  23:03:22,655 MuTect - [MUTECT] Processed 190012276 reads in 698 ms
[2015-09-30T22:03Z] INFO  23:03:22,944 MuTect - [MUTECT] Processed 90004128 reads in 679 ms
[2015-09-30T22:03Z] INFO  23:03:23,144 MuTect - [MUTECT] Processed 127006012 reads in 704 ms
[2015-09-30T22:03Z] INFO  23:03:23,316 MuTect - [MUTECT] Processed 191012308 reads in 660 ms
[2015-09-30T22:03Z] INFO  23:03:23,609 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:23,636 MuTect - [MUTECT] Processed 91004174 reads in 692 ms
[2015-09-30T22:03Z] INFO  23:03:23,825 MuTect - [MUTECT] Processed 128006016 reads in 681 ms
[2015-09-30T22:03Z] INFO  23:03:24,000 MuTect - [MUTECT] Processed 192012348 reads in 685 ms
[2015-09-30T22:03Z] INFO  23:03:24,115 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:24,361 MuTect - [MUTECT] Processed 92004184 reads in 725 ms
[2015-09-30T22:03Z] INFO  23:03:24,472 MuTect - [MUTECT] Processed 129006073 reads in 647 ms
[2015-09-30T22:03Z] INFO  23:03:24,689 MuTect - [MUTECT] Processed 193012418 reads in 689 ms
[2015-09-30T22:03Z] INFO  23:03:24,751 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:25,061 MuTect - [MUTECT] Processed 93004184 reads in 700 ms
[2015-09-30T22:03Z] INFO  23:03:25,139 MuTect - [MUTECT] Processed 130006186 reads in 667 ms
[2015-09-30T22:03Z] INFO  23:03:25,343 MuTect - [MUTECT] Processed 194012432 reads in 654 ms
[2015-09-30T22:03Z] INFO  23:03:25,766 MuTect - [MUTECT] Processed 94004219 reads in 705 ms
[2015-09-30T22:03Z] INFO  23:03:25,799 MuTect - [MUTECT] Processed 131006208 reads in 660 ms
[2015-09-30T22:03Z] INFO  23:03:25,864 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:26,003 MuTect - [MUTECT] Processed 195012513 reads in 660 ms
[2015-09-30T22:03Z] INFO  23:03:26,442 MuTect - [MUTECT] Processed 95004254 reads in 676 ms
[2015-09-30T22:03Z] INFO  23:03:26,456 MuTect - [MUTECT] Processed 132006230 reads in 657 ms
[2015-09-30T22:03Z] INFO  23:03:26,664 MuTect - [MUTECT] Processed 196012537 reads in 661 ms
[2015-09-30T22:03Z] INFO  23:03:26,784 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:27,057 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:27,120 MuTect - [MUTECT] Processed 96004328 reads in 678 ms
[2015-09-30T22:03Z] INFO  23:03:27,123 MuTect - [MUTECT] Processed 133006288 reads in 667 ms
[2015-09-30T22:03Z] INFO  23:03:27,373 MuTect - [MUTECT] Processed 197012563 reads in 709 ms
[2015-09-30T22:03Z] INFO  23:03:27,759 MuTect - [MUTECT] Processed 134006315 reads in 636 ms
[2015-09-30T22:03Z] INFO  23:03:27,770 MuTect - [MUTECT] Processed 97004441 reads in 650 ms
[2015-09-30T22:03Z] INFO  23:03:28,069 MuTect - [MUTECT] Processed 198012576 reads in 696 ms
[2015-09-30T22:03Z] INFO  23:03:28,255 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:28,390 MuTect - [MUTECT] Processed 135006426 reads in 631 ms
[2015-09-30T22:03Z] INFO  23:03:28,419 MuTect - [MUTECT] Processed 98004478 reads in 649 ms
[2015-09-30T22:03Z] INFO  23:03:28,790 MuTect - [MUTECT] Processed 199012582 reads in 721 ms
[2015-09-30T22:03Z] INFO  23:03:28,880 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:29,065 MuTect - [MUTECT] Processed 136006453 reads in 675 ms
[2015-09-30T22:03Z] INFO  23:03:29,079 MuTect - [MUTECT] Processed 99004488 reads in 660 ms
[2015-09-30T22:03Z] INFO  23:03:29,158 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:29,456 MuTect - [MUTECT] Processed 200012595 reads in 666 ms
[2015-09-30T22:03Z] INFO  23:03:29,744 MuTect - [MUTECT] Processed 137006456 reads in 679 ms
[2015-09-30T22:03Z] INFO  23:03:29,763 MuTect - [MUTECT] Processed 100004530 reads in 684 ms
[2015-09-30T22:03Z] INFO  23:03:30,129 MuTect - [MUTECT] Processed 201012627 reads in 673 ms
[2015-09-30T22:03Z] INFO  23:03:30,426 MuTect - [MUTECT] Processed 138006467 reads in 682 ms
[2015-09-30T22:03Z] INFO  23:03:30,481 MuTect - [MUTECT] Processed 101004537 reads in 718 ms
[2015-09-30T22:03Z] INFO  23:03:30,598 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:30,780 MuTect - [MUTECT] Processed 202012721 reads in 651 ms
[2015-09-30T22:03Z] INFO  23:03:31,106 MuTect - [MUTECT] Processed 139006575 reads in 680 ms
[2015-09-30T22:03Z] INFO  23:03:31,190 MuTect - [MUTECT] Processed 102004581 reads in 709 ms
[2015-09-30T22:03Z] INFO  23:03:31,349 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:31,430 MuTect - [MUTECT] Processed 203012722 reads in 650 ms
[2015-09-30T22:03Z] INFO  23:03:31,520 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:31,752 MuTect - [MUTECT] Processed 140006665 reads in 646 ms
[2015-09-30T22:03Z] INFO  23:03:31,889 MuTect - [MUTECT] Processed 103004598 reads in 699 ms
[2015-09-30T22:03Z] INFO  23:03:31,926 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:03Z] INFO  23:03:31,930 ProgressMeter -            done        5.02e+06  100.0 s       20.0 s    100.0%       100.0 s     0.0 s
[2015-09-30T22:03Z] INFO  23:03:31,930 ProgressMeter - Total runtime 100.76 secs, 1.68 min, 0.03 hours
[2015-09-30T22:03Z] INFO  23:03:31,995 MicroScheduler - 102365 reads were filtered out during the traversal out of approximately 1666463 total reads (6.14%)
[2015-09-30T22:03Z] INFO  23:03:31,995 MicroScheduler -   -> 75723 reads (4.54% of total) failing DuplicateReadFilter
[2015-09-30T22:03Z] INFO  23:03:31,996 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:03Z] INFO  23:03:31,996 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:03Z] INFO  23:03:31,996 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:03Z] INFO  23:03:31,996 MicroScheduler -   -> 26642 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:03Z] INFO  23:03:32,069 MuTect - [MUTECT] Processed 204012755 reads in 639 ms
[2015-09-30T22:03Z] INFO  23:03:32,577 MuTect - [MUTECT] Processed 104004666 reads in 688 ms
[2015-09-30T22:03Z] INFO  23:03:32,712 MuTect - [MUTECT] Processed 205012777 reads in 643 ms
[2015-09-30T22:03Z] INFO  23:03:32,969 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:03Z] bgzip syn3-1_173702591_204798081-raw-mutect.vcf
[2015-09-30T22:03Z] tabix index syn3-1_173702591_204798081-raw-mutect.vcf.gz
[2015-09-30T22:03Z] INFO  23:03:33,251 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:33,284 MuTect - [MUTECT] Processed 105004775 reads in 707 ms
[2015-09-30T22:03Z] INFO  23:03:33,347 MuTect - [MUTECT] Processed 206012855 reads in 635 ms
[2015-09-30T22:03Z] INFO  23:03:33,782 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:33,962 MuTect - [MUTECT] Processed 106004853 reads in 678 ms
[2015-09-30T22:03Z] INFO  23:03:34,017 MuTect - [MUTECT] Processed 207012907 reads in 670 ms
[2015-09-30T22:03Z] INFO  23:03:34,634 MuTect - [MUTECT] Processed 208012959 reads in 616 ms
[2015-09-30T22:03Z] INFO  23:03:34,715 MuTect - [MUTECT] Processed 107004892 reads in 753 ms
[2015-09-30T22:03Z] INFO  23:03:35,287 MuTect - [MUTECT] Processed 209013012 reads in 654 ms
[2015-09-30T22:03Z] INFO  23:03:35,439 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:35,502 MuTect - [MUTECT] Processed 108004947 reads in 787 ms
[2015-09-30T22:03Z] INFO  23:03:35,901 MuTect - [MUTECT] Processed 210013131 reads in 614 ms
[2015-09-30T22:03Z] INFO  23:03:36,184 MuTect - [MUTECT] Processed 109004973 reads in 682 ms
[2015-09-30T22:03Z] INFO  23:03:36,433 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:36,535 MuTect - [MUTECT] Processed 211013169 reads in 634 ms
[2015-09-30T22:03Z] INFO  23:03:36,879 MuTect - [MUTECT] Processed 110005085 reads in 695 ms
[2015-09-30T22:03Z] MuTect: MuTect
[2015-09-30T22:03Z] INFO  23:03:37,158 MuTect - [MUTECT] Processed 212013263 reads in 623 ms
[2015-09-30T22:03Z] INFO  23:03:37,467 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:37,557 MuTect - [MUTECT] Processed 111005146 reads in 678 ms
[2015-09-30T22:03Z] INFO  23:03:37,851 MuTect - [MUTECT] Processed 213013266 reads in 693 ms
[2015-09-30T22:03Z] INFO  23:03:38,215 MuTect - [MUTECT] Processed 112005264 reads in 658 ms
[2015-09-30T22:03Z] INFO  23:03:38,513 MuTect - [MUTECT] Processed 214013273 reads in 662 ms
[2015-09-30T22:03Z] INFO  23:03:38,739 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:38,872 MuTect - [MUTECT] Processed 113005276 reads in 657 ms
[2015-09-30T22:03Z] INFO  23:03:39,159 MuTect - [MUTECT] Processed 215013310 reads in 646 ms
[2015-09-30T22:03Z] INFO  23:03:39,178 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/1/syn3-1_235865791_249250621-raw-mutect-regions.bed to be BED
[2015-09-30T22:03Z] INFO  23:03:39,235 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:03Z] INFO  23:03:39,235 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:03Z] INFO  23:03:39,235 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:03Z] INFO  23:03:39,235 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:03Z] INFO  23:03:39,239 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/1/syn3-1_235865791_249250621-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/1/tx/tmpMIdSQY/syn3-1_235865791_249250621-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:03Z] INFO  23:03:39,239 HelpFormatter - Date/Time: 2015/09/30 23:03:39
[2015-09-30T22:03Z] INFO  23:03:39,239 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:03Z] INFO  23:03:39,239 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:03Z] INFO  23:03:39,267 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:03Z] INFO  23:03:39,272 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:03Z] INFO  23:03:39,323 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:03Z] INFO  23:03:39,372 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:03Z] INFO  23:03:39,380 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:03Z] INFO  23:03:39,450 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2015-09-30T22:03Z] INFO  23:03:39,462 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:03Z] INFO  23:03:39,529 MuTect - [MUTECT] Processed 114005357 reads in 657 ms
[2015-09-30T22:03Z] INFO  23:03:39,637 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:03Z] INFO  23:03:39,685 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:39,717 IntervalUtils - Processing 670628 bp from intervals
[2015-09-30T22:03Z] INFO  23:03:39,721 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:03Z] INFO  23:03:39,721 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:03Z] INFO  23:03:39,776 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:03Z] INFO  23:03:39,797 MuTect - [MUTECT] Processed 216013316 reads in 638 ms
[2015-09-30T22:03Z] INFO  23:03:40,026 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:03Z] INFO  23:03:40,027 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:03Z] INFO  23:03:40,027 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:03Z] INFO  23:03:40,028 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:03Z] INFO  23:03:40,190 MuTect - [MUTECT] Processed 115005379 reads in 661 ms
[2015-09-30T22:03Z] INFO  23:03:40,515 MuTect - [MUTECT] Processed 217013316 reads in 718 ms
[2015-09-30T22:03Z] INFO  23:03:40,856 MuTect - [MUTECT] Processed 116005408 reads in 666 ms
[2015-09-30T22:03Z] INFO  23:03:40,870 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:41,192 MuTect - [MUTECT] Processed 218013379 reads in 677 ms
[2015-09-30T22:03Z] INFO  23:03:41,523 MuTect - [MUTECT] Processed 117005441 reads in 667 ms
[2015-09-30T22:03Z] INFO  23:03:41,869 MuTect - [MUTECT] Processed 219013393 reads in 677 ms
[2015-09-30T22:03Z] INFO  23:03:41,988 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:42,177 MuTect - [MUTECT] Processed 118005494 reads in 654 ms
[2015-09-30T22:03Z] INFO  23:03:42,528 MuTect - [MUTECT] Processed 220013447 reads in 659 ms
[2015-09-30T22:03Z] INFO  23:03:42,531 MuTect - [MUTECT] Processed 1000025 reads in 2453 ms
[2015-09-30T22:03Z] INFO  23:03:42,814 MuTect - [MUTECT] Processed 119005522 reads in 637 ms
[2015-09-30T22:03Z] INFO  23:03:43,065 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:43,193 MuTect - [MUTECT] Processed 221013448 reads in 665 ms
[2015-09-30T22:03Z] INFO  23:03:43,445 MuTect - [MUTECT] Processed 120005577 reads in 631 ms
[2015-09-30T22:03Z] INFO  23:03:43,576 MuTect - [MUTECT] Processed 2000026 reads in 1045 ms
[2015-09-30T22:03Z] INFO  23:03:43,888 MuTect - [MUTECT] Processed 222013497 reads in 695 ms
[2015-09-30T22:03Z] INFO  23:03:44,074 MuTect - [MUTECT] Processed 121005663 reads in 629 ms
[2015-09-30T22:03Z] INFO  23:03:44,274 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:44,453 MuTect - [MUTECT] Processed 3000037 reads in 877 ms
[2015-09-30T22:03Z] INFO  23:03:44,613 MuTect - [MUTECT] Processed 223013546 reads in 725 ms
[2015-09-30T22:03Z] INFO  23:03:44,684 MuTect - [MUTECT] Processed 122005687 reads in 610 ms
[2015-09-30T22:03Z] INFO  23:03:44,843 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:45,172 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:45,201 MuTect - [MUTECT] Processed 4000107 reads in 748 ms
[2015-09-30T22:03Z] INFO  23:03:45,302 MuTect - [MUTECT] Processed 123005766 reads in 618 ms
[2015-09-30T22:03Z] INFO  23:03:45,326 MuTect - [MUTECT] Processed 224013618 reads in 713 ms
[2015-09-30T22:03Z] INFO  23:03:45,952 MuTect - [MUTECT] Processed 124005846 reads in 650 ms
[2015-09-30T22:03Z] INFO  23:03:45,974 MuTect - [MUTECT] Processed 5000235 reads in 773 ms
[2015-09-30T22:03Z] INFO  23:03:46,043 MuTect - [MUTECT] Processed 225013714 reads in 717 ms
[2015-09-30T22:03Z] INFO  23:03:46,615 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:46,620 MuTect - [MUTECT] Processed 125005935 reads in 668 ms
[2015-09-30T22:03Z] INFO  23:03:46,681 MuTect - [MUTECT] Processed 226013738 reads in 638 ms
[2015-09-30T22:03Z] INFO  23:03:46,697 MuTect - [MUTECT] Processed 6000273 reads in 722 ms
[2015-09-30T22:03Z] INFO  23:03:47,317 MuTect - [MUTECT] Processed 126005997 reads in 697 ms
[2015-09-30T22:03Z] INFO  23:03:47,321 MuTect - [MUTECT] Processed 227013857 reads in 640 ms
[2015-09-30T22:03Z] INFO  23:03:47,449 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:47,456 MuTect - [MUTECT] Processed 7000285 reads in 760 ms
[2015-09-30T22:03Z] INFO  23:03:47,629 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:47,951 MuTect - [MUTECT] Processed 228013957 reads in 630 ms
[2015-09-30T22:03Z] INFO  23:03:48,019 MuTect - [MUTECT] Processed 127006058 reads in 702 ms
[2015-09-30T22:03Z] INFO  23:03:48,189 MuTect - [MUTECT] Processed 8000327 reads in 733 ms
[2015-09-30T22:03Z] INFO  23:03:48,388 ProgressMeter -     1:161135018        6.88e+06    2.7 m       23.0 s     76.0%         3.5 m    50.0 s
[2015-09-30T22:03Z] INFO  23:03:48,578 MuTect - [MUTECT] Processed 229013973 reads in 627 ms
[2015-09-30T22:03Z] INFO  23:03:48,717 MuTect - [MUTECT] Processed 128006178 reads in 698 ms
[2015-09-30T22:03Z] INFO  23:03:48,775 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:48,914 MuTect - [MUTECT] Processed 9000397 reads in 725 ms
[2015-09-30T22:03Z] INFO  23:03:48,968 ProgressMeter -     1:229738330        4.06e+06   90.0 s       22.0 s     82.9%       108.0 s    18.0 s
[2015-09-30T22:03Z] INFO  23:03:49,231 MuTect - [MUTECT] Processed 230013973 reads in 652 ms
[2015-09-30T22:03Z] INFO  23:03:49,386 MuTect - [MUTECT] Processed 129006206 reads in 669 ms
[2015-09-30T22:03Z] INFO  23:03:49,591 MuTect - [MUTECT] Processed 10000443 reads in 676 ms
[2015-09-30T22:03Z] INFO  23:03:49,885 MuTect - [MUTECT] Processed 231014030 reads in 655 ms
[2015-09-30T22:03Z] INFO  23:03:49,903 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:50,082 MuTect - [MUTECT] Processed 130006231 reads in 696 ms
[2015-09-30T22:03Z] INFO  23:03:50,136 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:50,314 MuTect - [MUTECT] Processed 11000461 reads in 724 ms
[2015-09-30T22:03Z] INFO  23:03:50,528 MuTect - [MUTECT] Processed 232014061 reads in 643 ms
[2015-09-30T22:03Z] INFO  23:03:50,740 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:50,786 MuTect - [MUTECT] Processed 131006237 reads in 704 ms
[2015-09-30T22:03Z] INFO  23:03:51,016 MuTect - [MUTECT] Processed 12000532 reads in 702 ms
[2015-09-30T22:03Z] INFO  23:03:51,182 MuTect - [MUTECT] Processed 233014133 reads in 654 ms
[2015-09-30T22:03Z] INFO  23:03:51,494 MuTect - [MUTECT] Processed 132006291 reads in 708 ms
[2015-09-30T22:03Z] INFO  23:03:51,756 MuTect - [MUTECT] Processed 13000556 reads in 740 ms
[2015-09-30T22:03Z] INFO  23:03:51,911 MuTect - [MUTECT] Processed 234014171 reads in 729 ms
[2015-09-30T22:03Z] INFO  23:03:52,202 MuTect - [MUTECT] Processed 133006331 reads in 708 ms
[2015-09-30T22:03Z] INFO  23:03:52,272 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:52,378 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:52,507 MuTect - [MUTECT] Processed 14000636 reads in 750 ms
[2015-09-30T22:03Z] INFO  23:03:52,617 MuTect - [MUTECT] Processed 235014205 reads in 706 ms
[2015-09-30T22:03Z] INFO  23:03:52,844 MuTect - [MUTECT] Processed 134006380 reads in 642 ms
[2015-09-30T22:03Z] INFO  23:03:53,064 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:53,261 MuTect - [MUTECT] Processed 15000683 reads in 755 ms
[2015-09-30T22:03Z] INFO  23:03:53,292 MuTect - [MUTECT] Processed 236014234 reads in 675 ms
[2015-09-30T22:03Z] INFO  23:03:53,544 MuTect - [MUTECT] Processed 135006387 reads in 700 ms
[2015-09-30T22:03Z] INFO  23:03:53,994 MuTect - [MUTECT] Processed 237014283 reads in 702 ms
[2015-09-30T22:03Z] INFO  23:03:54,068 MuTect - [MUTECT] Processed 16000721 reads in 807 ms
[2015-09-30T22:03Z] INFO  23:03:54,239 MuTect - [MUTECT] Processed 136006406 reads in 695 ms
[2015-09-30T22:03Z] INFO  23:03:54,685 MuTect - [MUTECT] Processed 238014360 reads in 691 ms
[2015-09-30T22:03Z] INFO  23:03:54,728 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:54,750 MuTect - [MUTECT] Processed 17000723 reads in 682 ms
[2015-09-30T22:03Z] INFO  23:03:54,920 MuTect - [MUTECT] Processed 137006407 reads in 681 ms
[2015-09-30T22:03Z] INFO  23:03:54,993 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:55,374 MuTect - [MUTECT] Processed 239014412 reads in 689 ms
[2015-09-30T22:03Z] INFO  23:03:55,431 MuTect - [MUTECT] Processed 18000766 reads in 681 ms
[2015-09-30T22:03Z] INFO  23:03:55,582 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:55,585 MuTect - [MUTECT] Processed 138006437 reads in 665 ms
[2015-09-30T22:03Z] INFO  23:03:56,102 MuTect - [MUTECT] Processed 240014541 reads in 728 ms
[2015-09-30T22:03Z] INFO  23:03:56,185 MuTect - [MUTECT] Processed 19000831 reads in 754 ms
[2015-09-30T22:03Z] INFO  23:03:56,227 MuTect - [MUTECT] Processed 139006521 reads in 642 ms
[2015-09-30T22:03Z] INFO  23:03:56,788 MuTect - [MUTECT] Processed 241014580 reads in 686 ms
[2015-09-30T22:03Z] INFO  23:03:56,897 MuTect - [MUTECT] Processed 140006573 reads in 670 ms
[2015-09-30T22:03Z] INFO  23:03:56,899 MuTect - [MUTECT] Processed 20000843 reads in 714 ms
[2015-09-30T22:03Z] INFO  23:03:57,069 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:57,459 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:57,462 MuTect - [MUTECT] Processed 242014655 reads in 674 ms
[2015-09-30T22:03Z] INFO  23:03:57,571 MuTect - [MUTECT] Processed 141006580 reads in 673 ms
[2015-09-30T22:03Z] INFO  23:03:57,630 MuTect - [MUTECT] Processed 21000855 reads in 731 ms
[2015-09-30T22:03Z] INFO  23:03:57,974 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:58,138 MuTect - [MUTECT] Processed 243014674 reads in 676 ms
[2015-09-30T22:03Z] INFO  23:03:58,246 MuTect - [MUTECT] Processed 142006649 reads in 675 ms
[2015-09-30T22:03Z] INFO  23:03:58,319 MuTect - [MUTECT] Processed 22000935 reads in 689 ms
[2015-09-30T22:03Z] INFO  23:03:58,809 MuTect - [MUTECT] Processed 244014712 reads in 671 ms
[2015-09-30T22:03Z] INFO  23:03:58,894 MuTect - [MUTECT] Processed 143006655 reads in 649 ms
[2015-09-30T22:03Z] INFO  23:03:59,037 MuTect - [MUTECT] Processed 23000938 reads in 718 ms
[2015-09-30T22:03Z] INFO  23:03:59,462 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:03Z] INFO  23:03:59,497 MuTect - [MUTECT] Processed 245014717 reads in 688 ms
[2015-09-30T22:03Z] INFO  23:03:59,542 MuTect - [MUTECT] Processed 144006678 reads in 648 ms
[2015-09-30T22:03Z] INFO  23:03:59,770 MuTect - [MUTECT] Processed 24000978 reads in 733 ms
[2015-09-30T22:04Z] INFO  23:04:00,032 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:00,185 MuTect - [MUTECT] Processed 246014776 reads in 688 ms
[2015-09-30T22:04Z] INFO  23:04:00,206 MuTect - [MUTECT] Processed 145006716 reads in 664 ms
[2015-09-30T22:04Z] INFO  23:04:00,449 MuTect - [MUTECT] Inspected 69000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:00,506 MuTect - [MUTECT] Processed 25001011 reads in 736 ms
[2015-09-30T22:04Z] INFO  23:04:00,877 MuTect - [MUTECT] Processed 247014810 reads in 692 ms
[2015-09-30T22:04Z] INFO  23:04:00,891 MuTect - [MUTECT] Processed 146006829 reads in 685 ms
[2015-09-30T22:04Z] INFO  23:04:01,220 MuTect - [MUTECT] Processed 26001065 reads in 714 ms
[2015-09-30T22:04Z] INFO  23:04:01,549 MuTect - [MUTECT] Processed 248014828 reads in 672 ms
[2015-09-30T22:04Z] INFO  23:04:01,574 MuTect - [MUTECT] Processed 147006832 reads in 683 ms
[2015-09-30T22:04Z] INFO  23:04:01,703 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:01,923 MuTect - [MUTECT] Processed 27001111 reads in 703 ms
[2015-09-30T22:04Z] INFO  23:04:02,248 MuTect - [MUTECT] Processed 249014866 reads in 699 ms
[2015-09-30T22:04Z] INFO  23:04:02,280 MuTect - [MUTECT] Processed 148006848 reads in 706 ms
[2015-09-30T22:04Z] INFO  23:04:02,611 MuTect - [MUTECT] Processed 28001147 reads in 688 ms
[2015-09-30T22:04Z] INFO  23:04:02,657 MuTect - [MUTECT] Inspected 70000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:02,898 MuTect - [MUTECT] Processed 250014931 reads in 650 ms
[2015-09-30T22:04Z] INFO  23:04:02,947 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:02,977 MuTect - [MUTECT] Processed 149006849 reads in 697 ms
[2015-09-30T22:04Z] INFO  23:04:03,324 MuTect - [MUTECT] Processed 29001201 reads in 713 ms
[2015-09-30T22:04Z] INFO  23:04:03,546 MuTect - [MUTECT] Processed 251014966 reads in 648 ms
[2015-09-30T22:04Z] INFO  23:04:03,629 MuTect - [MUTECT] Processed 150006859 reads in 652 ms
[2015-09-30T22:04Z] INFO  23:04:04,051 MuTect - [MUTECT] Processed 30001240 reads in 727 ms
[2015-09-30T22:04Z] INFO  23:04:04,137 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:04,172 MuTect - [MUTECT] Processed 252015001 reads in 626 ms
[2015-09-30T22:04Z] INFO  23:04:04,330 MuTect - [MUTECT] Processed 151006903 reads in 701 ms
[2015-09-30T22:04Z] INFO  23:04:04,723 MuTect - [MUTECT] Processed 31001243 reads in 672 ms
[2015-09-30T22:04Z] INFO  23:04:04,845 MuTect - [MUTECT] Processed 253015055 reads in 673 ms
[2015-09-30T22:04Z] INFO  23:04:04,961 MuTect - [MUTECT] Inspected 71000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:05,022 MuTect - [MUTECT] Processed 152006955 reads in 692 ms
[2015-09-30T22:04Z] INFO  23:04:05,379 MuTect - [MUTECT] Processed 32001312 reads in 656 ms
[2015-09-30T22:04Z] INFO  23:04:05,551 MuTect - [MUTECT] Processed 254015154 reads in 706 ms
[2015-09-30T22:04Z] INFO  23:04:05,574 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:05,744 MuTect - [MUTECT] Processed 153006956 reads in 722 ms
[2015-09-30T22:04Z] INFO  23:04:05,885 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:04Z] INFO  23:04:05,929 ProgressMeter -            done        4.76e+06  106.0 s       22.0 s    100.0%       106.0 s     0.0 s
[2015-09-30T22:04Z] INFO  23:04:05,930 ProgressMeter - Total runtime 106.97 secs, 1.78 min, 0.03 hours
[2015-09-30T22:04Z] INFO  23:04:05,996 MicroScheduler - 114877 reads were filtered out during the traversal out of approximately 1825721 total reads (6.29%)
[2015-09-30T22:04Z] INFO  23:04:05,996 MicroScheduler -   -> 85621 reads (4.69% of total) failing DuplicateReadFilter
[2015-09-30T22:04Z] INFO  23:04:05,996 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:04Z] INFO  23:04:05,996 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:04Z] INFO  23:04:05,996 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:04Z] INFO  23:04:05,996 MicroScheduler -   -> 29256 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:04Z] INFO  23:04:06,069 MuTect - [MUTECT] Processed 33001362 reads in 690 ms
[2015-09-30T22:04Z] INFO  23:04:06,219 MuTect - [MUTECT] Processed 255015239 reads in 667 ms
[2015-09-30T22:04Z] INFO  23:04:06,743 MuTect - [MUTECT] Processed 34001411 reads in 674 ms
[2015-09-30T22:04Z] INFO  23:04:06,903 MuTect - [MUTECT] Processed 256015269 reads in 685 ms
[2015-09-30T22:04Z] INFO  23:04:07,080 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:04Z] bgzip syn3-1_204839842_235860787-raw-mutect.vcf
[2015-09-30T22:04Z] tabix index syn3-1_204839842_235860787-raw-mutect.vcf.gz
[2015-09-30T22:04Z] INFO  23:04:07,307 MuTect - [MUTECT] Inspected 72000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:07,429 MuTect - [MUTECT] Processed 35001445 reads in 686 ms
[2015-09-30T22:04Z] INFO  23:04:07,561 MuTect - [MUTECT] Processed 257015299 reads in 658 ms
[2015-09-30T22:04Z] INFO  23:04:07,961 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:08,148 MuTect - [MUTECT] Processed 36001495 reads in 719 ms
[2015-09-30T22:04Z] INFO  23:04:08,234 MuTect - [MUTECT] Processed 258015311 reads in 673 ms
[2015-09-30T22:04Z] INFO  23:04:08,824 MuTect - [MUTECT] Processed 37001554 reads in 676 ms
[2015-09-30T22:04Z] INFO  23:04:08,889 MuTect - [MUTECT] Processed 259015339 reads in 655 ms
[2015-09-30T22:04Z] MuTect: MuTect
[2015-09-30T22:04Z] INFO  23:04:09,581 MuTect - [MUTECT] Processed 38001618 reads in 757 ms
[2015-09-30T22:04Z] INFO  23:04:09,593 MuTect - [MUTECT] Processed 260015411 reads in 704 ms
[2015-09-30T22:04Z] INFO  23:04:09,820 MuTect - [MUTECT] Inspected 73000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:10,029 ProgressMeter -     1:247051941        1.36e+06   30.0 s       22.0 s     78.6%        38.0 s     8.0 s
[2015-09-30T22:04Z] INFO  23:04:10,256 MuTect - [MUTECT] Processed 261015458 reads in 663 ms
[2015-09-30T22:04Z] INFO  23:04:10,413 MuTect - [MUTECT] Processed 39001645 reads in 832 ms
[2015-09-30T22:04Z] INFO  23:04:10,735 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:10,907 MuTect - [MUTECT] Processed 262015560 reads in 651 ms
[2015-09-30T22:04Z] INFO  23:04:11,080 MuTect - [MUTECT] Processed 40001682 reads in 667 ms
[2015-09-30T22:04Z] INFO  23:04:11,589 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/2/syn3-2_0_31134137-raw-mutect-regions.bed to be BED
[2015-09-30T22:04Z] INFO  23:04:11,618 MuTect - [MUTECT] Processed 263015563 reads in 711 ms
[2015-09-30T22:04Z] INFO  23:04:11,645 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:04Z] INFO  23:04:11,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:04Z] INFO  23:04:11,645 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:04Z] INFO  23:04:11,645 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:04Z] INFO  23:04:11,649 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/2/syn3-2_0_31134137-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/2/tx/tmp_tDXE8/syn3-2_0_31134137-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:04Z] INFO  23:04:11,649 HelpFormatter - Date/Time: 2015/09/30 23:04:11
[2015-09-30T22:04Z] INFO  23:04:11,649 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:04Z] INFO  23:04:11,649 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:04Z] INFO  23:04:11,677 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:04Z] INFO  23:04:11,682 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:04Z] INFO  23:04:11,707 MuTect - [MUTECT] Processed 41001722 reads in 627 ms
[2015-09-30T22:04Z] INFO  23:04:11,735 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:04Z] INFO  23:04:11,805 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:04Z] INFO  23:04:11,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:04Z] INFO  23:04:11,882 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2015-09-30T22:04Z] INFO  23:04:11,894 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:04Z] INFO  23:04:12,071 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:04Z] INFO  23:04:12,173 IntervalUtils - Processing 1436475 bp from intervals
[2015-09-30T22:04Z] INFO  23:04:12,175 MuTect - [MUTECT] Inspected 74000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:12,177 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:04Z] INFO  23:04:12,177 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:04Z] INFO  23:04:12,316 MuTect - [MUTECT] Processed 264015573 reads in 698 ms
[2015-09-30T22:04Z] INFO  23:04:12,332 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:04Z] INFO  23:04:12,359 MuTect - [MUTECT] Processed 42001785 reads in 652 ms
[2015-09-30T22:04Z] INFO  23:04:12,483 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:04Z] INFO  23:04:12,483 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:04Z] INFO  23:04:12,483 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:04Z] INFO  23:04:12,484 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:04Z] INFO  23:04:12,966 MuTect - [MUTECT] Processed 265015633 reads in 650 ms
[2015-09-30T22:04Z] INFO  23:04:13,038 MuTect - [MUTECT] Processed 43001805 reads in 679 ms
[2015-09-30T22:04Z] INFO  23:04:13,151 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:13,686 MuTect - [MUTECT] Processed 266015664 reads in 720 ms
[2015-09-30T22:04Z] INFO  23:04:13,738 MuTect - [MUTECT] Processed 44001897 reads in 700 ms
[2015-09-30T22:04Z] INFO  23:04:14,397 MuTect - [MUTECT] Processed 267015706 reads in 711 ms
[2015-09-30T22:04Z] INFO  23:04:14,479 MuTect - [MUTECT] Processed 45001954 reads in 741 ms
[2015-09-30T22:04Z] INFO  23:04:14,688 MuTect - [MUTECT] Inspected 75000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:14,755 MuTect - [MUTECT] Processed 1000066 reads in 2222 ms
[2015-09-30T22:04Z] INFO  23:04:15,148 MuTect - [MUTECT] Processed 268015716 reads in 751 ms
[2015-09-30T22:04Z] INFO  23:04:15,179 MuTect - [MUTECT] Processed 46001967 reads in 700 ms
[2015-09-30T22:04Z] INFO  23:04:15,683 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:15,868 MuTect - [MUTECT] Processed 269015740 reads in 720 ms
[2015-09-30T22:04Z] INFO  23:04:15,883 MuTect - [MUTECT] Processed 2000198 reads in 1128 ms
[2015-09-30T22:04Z] INFO  23:04:15,937 MuTect - [MUTECT] Processed 47001974 reads in 758 ms
[2015-09-30T22:04Z] INFO  23:04:16,539 MuTect - [MUTECT] Processed 270015743 reads in 671 ms
[2015-09-30T22:04Z] INFO  23:04:16,719 MuTect - [MUTECT] Processed 48002028 reads in 782 ms
[2015-09-30T22:04Z] INFO  23:04:16,844 MuTect - [MUTECT] Processed 3000250 reads in 960 ms
[2015-09-30T22:04Z] INFO  23:04:16,998 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:17,239 MuTect - [MUTECT] Processed 271015758 reads in 700 ms
[2015-09-30T22:04Z] INFO  23:04:17,241 MuTect - [MUTECT] Inspected 76000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:17,383 MuTect - [MUTECT] Processed 49002028 reads in 664 ms
[2015-09-30T22:04Z] INFO  23:04:17,685 MuTect - [MUTECT] Processed 4000302 reads in 842 ms
[2015-09-30T22:04Z] INFO  23:04:17,907 MuTect - [MUTECT] Processed 272015778 reads in 668 ms
[2015-09-30T22:04Z] INFO  23:04:18,130 MuTect - [MUTECT] Processed 50002091 reads in 747 ms
[2015-09-30T22:04Z] INFO  23:04:18,157 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:18,389 ProgressMeter -     1:170967051        8.29e+06    3.2 m       22.0 s     94.3%         3.4 m    11.0 s
[2015-09-30T22:04Z] INFO  23:04:18,479 MuTect - [MUTECT] Processed 5000334 reads in 794 ms
[2015-09-30T22:04Z] INFO  23:04:18,562 MuTect - [MUTECT] Processed 273015812 reads in 654 ms
[2015-09-30T22:04Z] INFO  23:04:18,764 MuTect - [MUTECT] Processed 51002133 reads in 634 ms
[2015-09-30T22:04Z] INFO  23:04:19,062 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:04Z] INFO  23:04:19,065 ProgressMeter -            done        1.62e+06   39.0 s       24.0 s    100.0%        39.0 s     0.0 s
[2015-09-30T22:04Z] INFO  23:04:19,065 ProgressMeter - Total runtime 39.04 secs, 0.65 min, 0.01 hours
[2015-09-30T22:04Z] INFO  23:04:19,131 MicroScheduler - 39076 reads were filtered out during the traversal out of approximately 612519 total reads (6.38%)
[2015-09-30T22:04Z] INFO  23:04:19,132 MicroScheduler -   -> 27916 reads (4.56% of total) failing DuplicateReadFilter
[2015-09-30T22:04Z] INFO  23:04:19,132 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:04Z] INFO  23:04:19,132 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:04Z] INFO  23:04:19,132 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:04Z] INFO  23:04:19,132 MicroScheduler -   -> 11160 reads (1.82% of total) failing UnmappedReadFilter
[2015-09-30T22:04Z] INFO  23:04:19,212 MuTect - [MUTECT] Processed 6000373 reads in 732 ms
[2015-09-30T22:04Z] INFO  23:04:19,240 MuTect - [MUTECT] Processed 274015858 reads in 679 ms
[2015-09-30T22:04Z] INFO  23:04:19,318 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:19,570 MuTect - [MUTECT] Inspected 77000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:19,929 MuTect - [MUTECT] Processed 7000468 reads in 718 ms
[2015-09-30T22:04Z] INFO  23:04:19,949 MuTect - [MUTECT] Processed 275015891 reads in 709 ms
[2015-09-30T22:04Z] INFO  23:04:20,134 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:04Z] bgzip syn3-1_235865791_249250621-raw-mutect.vcf
[2015-09-30T22:04Z] tabix index syn3-1_235865791_249250621-raw-mutect.vcf.gz
[2015-09-30T22:04Z] INFO  23:04:20,633 MuTect - [MUTECT] Processed 8000492 reads in 704 ms
[2015-09-30T22:04Z] INFO  23:04:20,649 MuTect - [MUTECT] Processed 276015961 reads in 700 ms
[2015-09-30T22:04Z] INFO  23:04:21,334 MuTect - [MUTECT] Processed 9000578 reads in 701 ms
[2015-09-30T22:04Z] INFO  23:04:21,551 MuTect - [MUTECT] Processed 277016031 reads in 902 ms
[2015-09-30T22:04Z] INFO  23:04:21,811 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:22,055 MuTect - [MUTECT] Processed 10000641 reads in 721 ms
[2015-09-30T22:04Z] INFO  23:04:22,245 MuTect - [MUTECT] Processed 278016073 reads in 694 ms
[2015-09-30T22:04Z] INFO  23:04:22,276 MuTect - [MUTECT] Inspected 78000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:22,778 MuTect - [MUTECT] Processed 11000690 reads in 723 ms
[2015-09-30T22:04Z] MuTect: MuTect
[2015-09-30T22:04Z] INFO  23:04:22,946 MuTect - [MUTECT] Processed 279016112 reads in 701 ms
[2015-09-30T22:04Z] INFO  23:04:23,455 MuTect - [MUTECT] Processed 12000704 reads in 677 ms
[2015-09-30T22:04Z] INFO  23:04:23,639 MuTect - [MUTECT] Processed 280016123 reads in 693 ms
[2015-09-30T22:04Z] INFO  23:04:24,158 MuTect - [MUTECT] Processed 13000810 reads in 703 ms
[2015-09-30T22:04Z] INFO  23:04:24,262 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:24,340 MuTect - [MUTECT] Processed 281016147 reads in 701 ms
[2015-09-30T22:04Z] INFO  23:04:24,748 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/2/syn3-2_31134801_62196287-raw-mutect-regions.bed to be BED
[2015-09-30T22:04Z] INFO  23:04:24,801 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:04Z] INFO  23:04:24,801 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:04Z] INFO  23:04:24,802 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:04Z] INFO  23:04:24,802 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:04Z] INFO  23:04:24,805 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/2/syn3-2_31134801_62196287-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/2/tx/tmplO3h49/syn3-2_31134801_62196287-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:04Z] INFO  23:04:24,805 HelpFormatter - Date/Time: 2015/09/30 23:04:24
[2015-09-30T22:04Z] INFO  23:04:24,805 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:04Z] INFO  23:04:24,805 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:04Z] INFO  23:04:24,818 MuTect - [MUTECT] Inspected 79000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:24,832 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:04Z] INFO  23:04:24,832 MuTect - [MUTECT] Processed 14000871 reads in 674 ms
[2015-09-30T22:04Z] INFO  23:04:24,836 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:04Z] INFO  23:04:24,890 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:04Z] INFO  23:04:24,936 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:04Z] INFO  23:04:24,943 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:04Z] INFO  23:04:25,010 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2015-09-30T22:04Z] INFO  23:04:25,021 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:04Z] INFO  23:04:25,035 MuTect - [MUTECT] Processed 282016194 reads in 695 ms
[2015-09-30T22:04Z] INFO  23:04:25,187 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:04Z] INFO  23:04:25,286 IntervalUtils - Processing 1335510 bp from intervals
[2015-09-30T22:04Z] INFO  23:04:25,290 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:04Z] INFO  23:04:25,290 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:04Z] INFO  23:04:25,440 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:04Z] INFO  23:04:25,480 MuTect - [MUTECT] Processed 15000911 reads in 648 ms
[2015-09-30T22:04Z] INFO  23:04:25,609 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:04Z] INFO  23:04:25,609 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:04Z] INFO  23:04:25,609 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:04Z] INFO  23:04:25,610 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:04Z] INFO  23:04:25,707 MuTect - [MUTECT] Processed 283016195 reads in 672 ms
[2015-09-30T22:04Z] INFO  23:04:26,167 MuTect - [MUTECT] Processed 16000981 reads in 687 ms
[2015-09-30T22:04Z] INFO  23:04:26,410 MuTect - [MUTECT] Processed 284016216 reads in 703 ms
[2015-09-30T22:04Z] INFO  23:04:26,617 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:26,870 MuTect - [MUTECT] Processed 17001048 reads in 702 ms
[2015-09-30T22:04Z] INFO  23:04:26,950 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:04Z] INFO  23:04:26,955 ProgressMeter -            done        8.72e+06    3.3 m       22.0 s    100.0%         3.3 m     0.0 s
[2015-09-30T22:04Z] INFO  23:04:26,955 ProgressMeter - Total runtime 198.57 secs, 3.31 min, 0.06 hours
[2015-09-30T22:04Z] INFO  23:04:27,020 MicroScheduler - 211291 reads were filtered out during the traversal out of approximately 3346661 total reads (6.31%)
[2015-09-30T22:04Z] INFO  23:04:27,021 MicroScheduler -   -> 157140 reads (4.70% of total) failing DuplicateReadFilter
[2015-09-30T22:04Z] INFO  23:04:27,021 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:04Z] INFO  23:04:27,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:04Z] INFO  23:04:27,021 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:04Z] INFO  23:04:27,021 MicroScheduler -   -> 54151 reads (1.62% of total) failing UnmappedReadFilter
[2015-09-30T22:04Z] INFO  23:04:27,605 MuTect - [MUTECT] Processed 18001078 reads in 736 ms
[2015-09-30T22:04Z] INFO  23:04:27,804 MuTect - [MUTECT] Processed 1000036 reads in 2148 ms
[2015-09-30T22:04Z] INFO  23:04:28,032 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:04Z] bgzip syn3-1_142666976_173685474-raw-mutect.vcf
[2015-09-30T22:04Z] tabix index syn3-1_142666976_173685474-raw-mutect.vcf.gz
[2015-09-30T22:04Z] INFO  23:04:28,338 MuTect - [MUTECT] Processed 19001083 reads in 733 ms
[2015-09-30T22:04Z] INFO  23:04:28,524 MuTect - [MUTECT] Processed 2000079 reads in 720 ms
[2015-09-30T22:04Z] INFO  23:04:29,056 MuTect - [MUTECT] Processed 20001127 reads in 717 ms
[2015-09-30T22:04Z] INFO  23:04:29,246 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:29,308 MuTect - [MUTECT] Processed 3000146 reads in 784 ms
[2015-09-30T22:04Z] INFO  23:04:29,659 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:29,734 MuTect - [MUTECT] Processed 21001127 reads in 678 ms
[2015-09-30T22:04Z] INFO  23:04:30,079 MuTect - [MUTECT] Processed 4000183 reads in 771 ms
[2015-09-30T22:04Z] INFO  23:04:30,438 MuTect - [MUTECT] Processed 22001235 reads in 705 ms
[2015-09-30T22:04Z] MuTect: MuTect
[2015-09-30T22:04Z] INFO  23:04:30,882 MuTect - [MUTECT] Processed 5000192 reads in 803 ms
[2015-09-30T22:04Z] INFO  23:04:31,138 MuTect - [MUTECT] Processed 23001321 reads in 700 ms
[2015-09-30T22:04Z] INFO  23:04:31,632 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:31,815 MuTect - [MUTECT] Processed 6000292 reads in 933 ms
[2015-09-30T22:04Z] INFO  23:04:31,853 MuTect - [MUTECT] Processed 24001350 reads in 715 ms
[2015-09-30T22:04Z] INFO  23:04:32,525 MuTect - [MUTECT] Processed 25001405 reads in 672 ms
[2015-09-30T22:04Z] INFO  23:04:32,561 MuTect - [MUTECT] Processed 7000303 reads in 746 ms
[2015-09-30T22:04Z] INFO  23:04:32,565 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:32,983 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/2/syn3-2_62227535_95457199-raw-mutect-regions.bed to be BED
[2015-09-30T22:04Z] INFO  23:04:33,040 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:04Z] INFO  23:04:33,041 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:04Z] INFO  23:04:33,041 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:04Z] INFO  23:04:33,041 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:04Z] INFO  23:04:33,044 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/2/syn3-2_62227535_95457199-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/2/tx/tmp1V7A6I/syn3-2_62227535_95457199-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:04Z] INFO  23:04:33,045 HelpFormatter - Date/Time: 2015/09/30 23:04:33
[2015-09-30T22:04Z] INFO  23:04:33,045 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:04Z] INFO  23:04:33,045 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:04Z] INFO  23:04:33,073 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:04Z] INFO  23:04:33,077 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:04Z] INFO  23:04:33,127 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:04Z] INFO  23:04:33,177 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:04Z] INFO  23:04:33,184 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:04Z] INFO  23:04:33,218 MuTect - [MUTECT] Processed 26001447 reads in 693 ms
[2015-09-30T22:04Z] INFO  23:04:33,243 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:04Z] INFO  23:04:33,254 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:04Z] INFO  23:04:33,288 MuTect - [MUTECT] Processed 8000330 reads in 727 ms
[2015-09-30T22:04Z] INFO  23:04:33,432 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:04Z] INFO  23:04:33,534 IntervalUtils - Processing 1441996 bp from intervals
[2015-09-30T22:04Z] INFO  23:04:33,538 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:04Z] INFO  23:04:33,538 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:04Z] INFO  23:04:33,684 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:04Z] INFO  23:04:33,871 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:04Z] INFO  23:04:33,871 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:04Z] INFO  23:04:33,871 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:04Z] INFO  23:04:33,872 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:04Z] INFO  23:04:33,910 MuTect - [MUTECT] Processed 27001466 reads in 692 ms
[2015-09-30T22:04Z] INFO  23:04:33,984 MuTect - [MUTECT] Processed 9000352 reads in 695 ms
[2015-09-30T22:04Z] INFO  23:04:34,139 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:34,584 MuTect - [MUTECT] Processed 28001549 reads in 674 ms
[2015-09-30T22:04Z] INFO  23:04:34,795 MuTect - [MUTECT] Processed 10000362 reads in 812 ms
[2015-09-30T22:04Z] INFO  23:04:35,302 MuTect - [MUTECT] Processed 29001631 reads in 718 ms
[2015-09-30T22:04Z] INFO  23:04:35,577 MuTect - [MUTECT] Processed 11000362 reads in 782 ms
[2015-09-30T22:04Z] INFO  23:04:35,589 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:36,045 MuTect - [MUTECT] Processed 30001642 reads in 743 ms
[2015-09-30T22:04Z] INFO  23:04:36,296 MuTect - [MUTECT] Processed 12000388 reads in 719 ms
[2015-09-30T22:04Z] INFO  23:04:36,346 MuTect - [MUTECT] Processed 1000027 reads in 2416 ms
[2015-09-30T22:04Z] INFO  23:04:36,505 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:36,780 MuTect - [MUTECT] Processed 31001645 reads in 735 ms
[2015-09-30T22:04Z] INFO  23:04:37,067 MuTect - [MUTECT] Processed 13000431 reads in 771 ms
[2015-09-30T22:04Z] INFO  23:04:37,189 MuTect - [MUTECT] Processed 2000047 reads in 844 ms
[2015-09-30T22:04Z] INFO  23:04:37,556 MuTect - [MUTECT] Processed 32001698 reads in 776 ms
[2015-09-30T22:04Z] INFO  23:04:37,804 MuTect - [MUTECT] Processed 14000480 reads in 736 ms
[2015-09-30T22:04Z] INFO  23:04:37,843 MuTect - [MUTECT] Processed 3000109 reads in 654 ms
[2015-09-30T22:04Z] INFO  23:04:38,213 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:38,281 MuTect - [MUTECT] Processed 33001759 reads in 725 ms
[2015-09-30T22:04Z] INFO  23:04:38,494 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:38,510 MuTect - [MUTECT] Processed 4000112 reads in 667 ms
[2015-09-30T22:04Z] INFO  23:04:38,560 MuTect - [MUTECT] Processed 15000569 reads in 757 ms
[2015-09-30T22:04Z] INFO  23:04:38,998 MuTect - [MUTECT] Processed 34001848 reads in 717 ms
[2015-09-30T22:04Z] INFO  23:04:39,124 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:39,189 MuTect - [MUTECT] Processed 5000149 reads in 679 ms
[2015-09-30T22:04Z] INFO  23:04:39,301 MuTect - [MUTECT] Processed 16000576 reads in 741 ms
[2015-09-30T22:04Z] INFO  23:04:39,731 MuTect - [MUTECT] Processed 35001916 reads in 733 ms
[2015-09-30T22:04Z] INFO  23:04:39,823 MuTect - [MUTECT] Processed 6000159 reads in 634 ms
[2015-09-30T22:04Z] INFO  23:04:40,030 MuTect - [MUTECT] Processed 17000615 reads in 729 ms
[2015-09-30T22:04Z] INFO  23:04:40,416 MuTect - [MUTECT] Processed 36001952 reads in 685 ms
[2015-09-30T22:04Z] INFO  23:04:40,502 MuTect - [MUTECT] Processed 7000228 reads in 679 ms
[2015-09-30T22:04Z] INFO  23:04:40,722 MuTect - [MUTECT] Processed 18000635 reads in 692 ms
[2015-09-30T22:04Z] INFO  23:04:40,951 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:41,011 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:41,111 MuTect - [MUTECT] Processed 37001965 reads in 694 ms
[2015-09-30T22:04Z] INFO  23:04:41,131 MuTect - [MUTECT] Processed 8000255 reads in 629 ms
[2015-09-30T22:04Z] INFO  23:04:41,443 MuTect - [MUTECT] Processed 19000679 reads in 721 ms
[2015-09-30T22:04Z] INFO  23:04:41,643 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:41,795 MuTect - [MUTECT] Processed 38001993 reads in 685 ms
[2015-09-30T22:04Z] INFO  23:04:41,802 MuTect - [MUTECT] Processed 9000285 reads in 671 ms
[2015-09-30T22:04Z] INFO  23:04:42,141 MuTect - [MUTECT] Processed 20000727 reads in 698 ms
[2015-09-30T22:04Z] INFO  23:04:42,459 MuTect - [MUTECT] Processed 10000309 reads in 657 ms
[2015-09-30T22:04Z] INFO  23:04:42,471 MuTect - [MUTECT] Processed 39002027 reads in 675 ms
[2015-09-30T22:04Z] INFO  23:04:42,486 ProgressMeter -      2:11916418        1.14e+06   30.0 s       26.0 s     30.5%        98.0 s    68.0 s
[2015-09-30T22:04Z] INFO  23:04:42,854 MuTect - [MUTECT] Processed 21000760 reads in 713 ms
[2015-09-30T22:04Z] INFO  23:04:43,093 MuTect - [MUTECT] Processed 11000398 reads in 634 ms
[2015-09-30T22:04Z] INFO  23:04:43,168 MuTect - [MUTECT] Processed 40002107 reads in 698 ms
[2015-09-30T22:04Z] INFO  23:04:43,443 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:43,555 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:43,563 MuTect - [MUTECT] Processed 22000789 reads in 708 ms
[2015-09-30T22:04Z] INFO  23:04:43,856 MuTect - [MUTECT] Processed 41002151 reads in 688 ms
[2015-09-30T22:04Z] INFO  23:04:43,858 MuTect - [MUTECT] Processed 12000415 reads in 765 ms
[2015-09-30T22:04Z] INFO  23:04:44,125 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:44,256 MuTect - [MUTECT] Processed 23000822 reads in 694 ms
[2015-09-30T22:04Z] INFO  23:04:44,494 MuTect - [MUTECT] Processed 13000481 reads in 635 ms
[2015-09-30T22:04Z] INFO  23:04:44,527 MuTect - [MUTECT] Processed 42002169 reads in 671 ms
[2015-09-30T22:04Z] INFO  23:04:44,929 MuTect - [MUTECT] Processed 24000869 reads in 673 ms
[2015-09-30T22:04Z] INFO  23:04:45,172 MuTect - [MUTECT] Processed 14000536 reads in 679 ms
[2015-09-30T22:04Z] INFO  23:04:45,240 MuTect - [MUTECT] Processed 43002183 reads in 713 ms
[2015-09-30T22:04Z] INFO  23:04:45,632 MuTect - [MUTECT] Processed 25000906 reads in 703 ms
[2015-09-30T22:04Z] INFO  23:04:45,860 MuTect - [MUTECT] Processed 15000547 reads in 688 ms
[2015-09-30T22:04Z] INFO  23:04:45,879 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:46,049 MuTect - [MUTECT] Processed 44002202 reads in 809 ms
[2015-09-30T22:04Z] INFO  23:04:46,308 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:46,342 MuTect - [MUTECT] Processed 26000940 reads in 710 ms
[2015-09-30T22:04Z] INFO  23:04:46,522 MuTect - [MUTECT] Processed 16000592 reads in 662 ms
[2015-09-30T22:04Z] INFO  23:04:46,775 MuTect - [MUTECT] Processed 45002235 reads in 726 ms
[2015-09-30T22:04Z] INFO  23:04:46,847 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:47,072 MuTect - [MUTECT] Processed 27001009 reads in 730 ms
[2015-09-30T22:04Z] INFO  23:04:47,184 MuTect - [MUTECT] Processed 17000598 reads in 662 ms
[2015-09-30T22:04Z] INFO  23:04:47,461 MuTect - [MUTECT] Processed 46002236 reads in 686 ms
[2015-09-30T22:04Z] INFO  23:04:47,753 MuTect - [MUTECT] Processed 28001048 reads in 681 ms
[2015-09-30T22:04Z] INFO  23:04:47,849 MuTect - [MUTECT] Processed 18000704 reads in 665 ms
[2015-09-30T22:04Z] INFO  23:04:48,146 MuTect - [MUTECT] Processed 47002313 reads in 685 ms
[2015-09-30T22:04Z] INFO  23:04:48,162 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:48,430 MuTect - [MUTECT] Processed 29001083 reads in 677 ms
[2015-09-30T22:04Z] INFO  23:04:48,511 MuTect - [MUTECT] Processed 19000736 reads in 662 ms
[2015-09-30T22:04Z] INFO  23:04:48,878 MuTect - [MUTECT] Processed 48002396 reads in 732 ms
[2015-09-30T22:04Z] INFO  23:04:48,954 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:49,102 MuTect - [MUTECT] Processed 30001142 reads in 672 ms
[2015-09-30T22:04Z] INFO  23:04:49,200 MuTect - [MUTECT] Processed 20000805 reads in 689 ms
[2015-09-30T22:04Z] INFO  23:04:49,320 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:49,522 MuTect - [MUTECT] Processed 49002440 reads in 644 ms
[2015-09-30T22:04Z] INFO  23:04:49,785 MuTect - [MUTECT] Processed 31001154 reads in 683 ms
[2015-09-30T22:04Z] INFO  23:04:49,862 MuTect - [MUTECT] Processed 21000844 reads in 662 ms
[2015-09-30T22:04Z] INFO  23:04:50,208 MuTect - [MUTECT] Processed 50002461 reads in 686 ms
[2015-09-30T22:04Z] INFO  23:04:50,457 MuTect - [MUTECT] Processed 32001210 reads in 672 ms
[2015-09-30T22:04Z] INFO  23:04:50,529 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:50,541 MuTect - [MUTECT] Processed 22000875 reads in 678 ms
[2015-09-30T22:04Z] INFO  23:04:50,889 MuTect - [MUTECT] Processed 51002505 reads in 680 ms
[2015-09-30T22:04Z] INFO  23:04:51,151 MuTect - [MUTECT] Processed 33001256 reads in 694 ms
[2015-09-30T22:04Z] INFO  23:04:51,232 MuTect - [MUTECT] Processed 23000911 reads in 692 ms
[2015-09-30T22:04Z] INFO  23:04:51,439 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:51,592 MuTect - [MUTECT] Processed 52002561 reads in 704 ms
[2015-09-30T22:04Z] INFO  23:04:51,750 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:51,879 MuTect - [MUTECT] Processed 24000957 reads in 647 ms
[2015-09-30T22:04Z] INFO  23:04:51,884 MuTect - [MUTECT] Processed 34001295 reads in 733 ms
[2015-09-30T22:04Z] INFO  23:04:52,290 MuTect - [MUTECT] Processed 53002585 reads in 698 ms
[2015-09-30T22:04Z] INFO  23:04:52,541 MuTect - [MUTECT] Processed 25001013 reads in 662 ms
[2015-09-30T22:04Z] INFO  23:04:52,601 MuTect - [MUTECT] Processed 35001327 reads in 717 ms
[2015-09-30T22:04Z] INFO  23:04:52,940 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:53,041 MuTect - [MUTECT] Processed 54002612 reads in 751 ms
[2015-09-30T22:04Z] INFO  23:04:53,168 MuTect - [MUTECT] Processed 26001095 reads in 627 ms
[2015-09-30T22:04Z] INFO  23:04:53,311 MuTect - [MUTECT] Processed 36001367 reads in 710 ms
[2015-09-30T22:04Z] INFO  23:04:53,763 MuTect - [MUTECT] Processed 55002655 reads in 722 ms
[2015-09-30T22:04Z] INFO  23:04:53,923 MuTect - [MUTECT] Processed 27001155 reads in 755 ms
[2015-09-30T22:04Z] INFO  23:04:53,975 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:53,996 MuTect - [MUTECT] Processed 37001454 reads in 685 ms
[2015-09-30T22:04Z] INFO  23:04:54,163 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:54,423 MuTect - [MUTECT] Processed 56002744 reads in 660 ms
[2015-09-30T22:04Z] INFO  23:04:54,606 MuTect - [MUTECT] Processed 28001199 reads in 683 ms
[2015-09-30T22:04Z] INFO  23:04:54,704 MuTect - [MUTECT] Processed 38001496 reads in 708 ms
[2015-09-30T22:04Z] INFO  23:04:55,097 MuTect - [MUTECT] Processed 57002788 reads in 674 ms
[2015-09-30T22:04Z] INFO  23:04:55,157 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:55,226 MuTect - [MUTECT] Processed 29001340 reads in 620 ms
[2015-09-30T22:04Z] INFO  23:04:55,349 MuTect - [MUTECT] Processed 39001583 reads in 644 ms
[2015-09-30T22:04Z] INFO  23:04:55,612 ProgressMeter -      2:42836994        1.48e+06   30.0 s       20.0 s     40.9%        73.0 s    43.0 s
[2015-09-30T22:04Z] INFO  23:04:55,746 MuTect - [MUTECT] Processed 58002817 reads in 649 ms
[2015-09-30T22:04Z] INFO  23:04:55,869 MuTect - [MUTECT] Processed 30001471 reads in 643 ms
[2015-09-30T22:04Z] INFO  23:04:56,032 MuTect - [MUTECT] Processed 40001613 reads in 684 ms
[2015-09-30T22:04Z] INFO  23:04:56,284 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:56,423 MuTect - [MUTECT] Processed 59002828 reads in 677 ms
[2015-09-30T22:04Z] INFO  23:04:56,560 MuTect - [MUTECT] Processed 31001514 reads in 691 ms
[2015-09-30T22:04Z] INFO  23:04:56,612 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:56,713 MuTect - [MUTECT] Processed 41001639 reads in 681 ms
[2015-09-30T22:04Z] INFO  23:04:57,099 MuTect - [MUTECT] Processed 60002845 reads in 676 ms
[2015-09-30T22:04Z] INFO  23:04:57,206 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:57,208 MuTect - [MUTECT] Processed 32001574 reads in 648 ms
[2015-09-30T22:04Z] INFO  23:04:57,333 MuTect - [MUTECT] Processed 42001679 reads in 620 ms
[2015-09-30T22:04Z] INFO  23:04:57,799 MuTect - [MUTECT] Processed 61002912 reads in 700 ms
[2015-09-30T22:04Z] INFO  23:04:57,845 MuTect - [MUTECT] Processed 33001663 reads in 637 ms
[2015-09-30T22:04Z] INFO  23:04:58,018 MuTect - [MUTECT] Processed 43001692 reads in 685 ms
[2015-09-30T22:04Z] INFO  23:04:58,455 MuTect - [MUTECT] Processed 62003035 reads in 656 ms
[2015-09-30T22:04Z] INFO  23:04:58,532 MuTect - [MUTECT] Processed 34001675 reads in 687 ms
[2015-09-30T22:04Z] INFO  23:04:58,650 MuTect - [MUTECT] Processed 44001748 reads in 632 ms
[2015-09-30T22:04Z] INFO  23:04:58,711 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:59,062 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:59,123 MuTect - [MUTECT] Processed 63003036 reads in 668 ms
[2015-09-30T22:04Z] INFO  23:04:59,258 MuTect - [MUTECT] Processed 35001697 reads in 726 ms
[2015-09-30T22:04Z] INFO  23:04:59,331 MuTect - [MUTECT] Processed 45001772 reads in 681 ms
[2015-09-30T22:04Z] INFO  23:04:59,364 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:04Z] INFO  23:04:59,809 MuTect - [MUTECT] Processed 64003107 reads in 686 ms
[2015-09-30T22:04Z] INFO  23:04:59,966 MuTect - [MUTECT] Processed 46001862 reads in 635 ms
[2015-09-30T22:04Z] INFO  23:04:59,968 MuTect - [MUTECT] Processed 36001709 reads in 710 ms
[2015-09-30T22:05Z] INFO  23:05:00,509 MuTect - [MUTECT] Processed 65003122 reads in 700 ms
[2015-09-30T22:05Z] INFO  23:05:00,600 MuTect - [MUTECT] Processed 47001891 reads in 634 ms
[2015-09-30T22:05Z] INFO  23:05:00,670 MuTect - [MUTECT] Processed 37001770 reads in 702 ms
[2015-09-30T22:05Z] INFO  23:05:01,055 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:01,201 MuTect - [MUTECT] Processed 66003170 reads in 692 ms
[2015-09-30T22:05Z] INFO  23:05:01,232 MuTect - [MUTECT] Processed 48001899 reads in 632 ms
[2015-09-30T22:05Z] INFO  23:05:01,408 MuTect - [MUTECT] Processed 38001839 reads in 738 ms
[2015-09-30T22:05Z] INFO  23:05:01,676 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:01,855 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:01,865 MuTect - [MUTECT] Processed 49001931 reads in 633 ms
[2015-09-30T22:05Z] INFO  23:05:01,914 MuTect - [MUTECT] Processed 67003249 reads in 713 ms
[2015-09-30T22:05Z] INFO  23:05:02,101 MuTect - [MUTECT] Processed 39001955 reads in 693 ms
[2015-09-30T22:05Z] INFO  23:05:02,565 MuTect - [MUTECT] Processed 50001963 reads in 700 ms
[2015-09-30T22:05Z] INFO  23:05:02,600 MuTect - [MUTECT] Processed 68003298 reads in 686 ms
[2015-09-30T22:05Z] INFO  23:05:02,786 MuTect - [MUTECT] Processed 40001991 reads in 685 ms
[2015-09-30T22:05Z] INFO  23:05:03,210 MuTect - [MUTECT] Processed 51002026 reads in 645 ms
[2015-09-30T22:05Z] INFO  23:05:03,311 MuTect - [MUTECT] Processed 69003320 reads in 711 ms
[2015-09-30T22:05Z] INFO  23:05:03,416 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:03,478 MuTect - [MUTECT] Processed 41002056 reads in 691 ms
[2015-09-30T22:05Z] INFO  23:05:03,863 MuTect - [MUTECT] Processed 52002062 reads in 653 ms
[2015-09-30T22:05Z] INFO  23:05:03,874 ProgressMeter -      2:72406466        1.21e+06   30.0 s       24.0 s     34.9%        86.0 s    56.0 s
[2015-09-30T22:05Z] INFO  23:05:03,986 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:04,007 MuTect - [MUTECT] Processed 70003349 reads in 696 ms
[2015-09-30T22:05Z] INFO  23:05:04,083 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:04,141 MuTect - [MUTECT] Processed 42002064 reads in 664 ms
[2015-09-30T22:05Z] INFO  23:05:04,503 MuTect - [MUTECT] Processed 53002169 reads in 640 ms
[2015-09-30T22:05Z] INFO  23:05:04,683 MuTect - [MUTECT] Processed 71003388 reads in 676 ms
[2015-09-30T22:05Z] INFO  23:05:04,828 MuTect - [MUTECT] Processed 43002182 reads in 687 ms
[2015-09-30T22:05Z] INFO  23:05:05,346 MuTect - [MUTECT] Processed 54002229 reads in 843 ms
[2015-09-30T22:05Z] INFO  23:05:05,367 MuTect - [MUTECT] Processed 72003500 reads in 684 ms
[2015-09-30T22:05Z] INFO  23:05:05,538 MuTect - [MUTECT] Processed 44002194 reads in 710 ms
[2015-09-30T22:05Z] INFO  23:05:05,941 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:06,054 MuTect - [MUTECT] Processed 55002365 reads in 708 ms
[2015-09-30T22:05Z] INFO  23:05:06,137 MuTect - [MUTECT] Processed 73003507 reads in 770 ms
[2015-09-30T22:05Z] INFO  23:05:06,235 MuTect - [MUTECT] Processed 45002276 reads in 697 ms
[2015-09-30T22:05Z] INFO  23:05:06,302 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:06,393 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:06,715 MuTect - [MUTECT] Processed 56002471 reads in 661 ms
[2015-09-30T22:05Z] INFO  23:05:06,760 MuTect - [MUTECT] Processed 74003585 reads in 623 ms
[2015-09-30T22:05Z] INFO  23:05:06,934 MuTect - [MUTECT] Processed 46002324 reads in 699 ms
[2015-09-30T22:05Z] INFO  23:05:07,385 MuTect - [MUTECT] Processed 57002513 reads in 670 ms
[2015-09-30T22:05Z] INFO  23:05:07,434 MuTect - [MUTECT] Processed 75003609 reads in 674 ms
[2015-09-30T22:05Z] INFO  23:05:07,604 MuTect - [MUTECT] Processed 47002382 reads in 670 ms
[2015-09-30T22:05Z] INFO  23:05:08,068 MuTect - [MUTECT] Processed 58002563 reads in 683 ms
[2015-09-30T22:05Z] INFO  23:05:08,119 MuTect - [MUTECT] Processed 76003700 reads in 685 ms
[2015-09-30T22:05Z] INFO  23:05:08,267 MuTect - [MUTECT] Processed 48002491 reads in 663 ms
[2015-09-30T22:05Z] INFO  23:05:08,339 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:08,600 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:08,720 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:08,737 MuTect - [MUTECT] Processed 59002636 reads in 669 ms
[2015-09-30T22:05Z] INFO  23:05:08,793 MuTect - [MUTECT] Processed 77003726 reads in 674 ms
[2015-09-30T22:05Z] INFO  23:05:08,940 MuTect - [MUTECT] Processed 49002509 reads in 673 ms
[2015-09-30T22:05Z] INFO  23:05:09,413 MuTect - [MUTECT] Processed 60002684 reads in 676 ms
[2015-09-30T22:05Z] INFO  23:05:09,464 MuTect - [MUTECT] Processed 78003771 reads in 671 ms
[2015-09-30T22:05Z] INFO  23:05:09,577 MuTect - [MUTECT] Processed 50002539 reads in 637 ms
[2015-09-30T22:05Z] INFO  23:05:10,080 MuTect - [MUTECT] Processed 61002703 reads in 667 ms
[2015-09-30T22:05Z] INFO  23:05:10,117 MuTect - [MUTECT] Processed 79003891 reads in 653 ms
[2015-09-30T22:05Z] INFO  23:05:10,201 MuTect - [MUTECT] Processed 51002552 reads in 624 ms
[2015-09-30T22:05Z] INFO  23:05:10,598 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:10,768 MuTect - [MUTECT] Processed 62002792 reads in 688 ms
[2015-09-30T22:05Z] INFO  23:05:10,778 MuTect - [MUTECT] Processed 80003942 reads in 661 ms
[2015-09-30T22:05Z] INFO  23:05:10,850 MuTect - [MUTECT] Processed 52002623 reads in 649 ms
[2015-09-30T22:05Z] INFO  23:05:10,921 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:10,955 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:11,428 MuTect - [MUTECT] Processed 63002805 reads in 660 ms
[2015-09-30T22:05Z] INFO  23:05:11,444 MuTect - [MUTECT] Processed 81004057 reads in 666 ms
[2015-09-30T22:05Z] INFO  23:05:11,527 MuTect - [MUTECT] Processed 53002665 reads in 677 ms
[2015-09-30T22:05Z] INFO  23:05:12,098 MuTect - [MUTECT] Processed 64002823 reads in 670 ms
[2015-09-30T22:05Z] INFO  23:05:12,100 MuTect - [MUTECT] Processed 82004067 reads in 656 ms
[2015-09-30T22:05Z] INFO  23:05:12,139 MuTect - [MUTECT] Processed 54002671 reads in 612 ms
[2015-09-30T22:05Z] INFO  23:05:12,487 ProgressMeter -      2:26652743        2.60e+06   60.0 s       23.0 s     67.2%        89.0 s    29.0 s
[2015-09-30T22:05Z] INFO  23:05:12,759 MuTect - [MUTECT] Processed 65002920 reads in 661 ms
[2015-09-30T22:05Z] INFO  23:05:12,765 MuTect - [MUTECT] Processed 83004165 reads in 665 ms
[2015-09-30T22:05Z] INFO  23:05:12,770 MuTect - [MUTECT] Processed 55002709 reads in 631 ms
[2015-09-30T22:05Z] INFO  23:05:13,078 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:13,094 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:13,418 MuTect - [MUTECT] Processed 84004211 reads in 653 ms
[2015-09-30T22:05Z] INFO  23:05:13,426 MuTect - [MUTECT] Processed 56002839 reads in 656 ms
[2015-09-30T22:05Z] INFO  23:05:13,456 MuTect - [MUTECT] Processed 66002927 reads in 697 ms
[2015-09-30T22:05Z] INFO  23:05:13,466 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:14,070 MuTect - [MUTECT] Processed 85004219 reads in 652 ms
[2015-09-30T22:05Z] INFO  23:05:14,084 MuTect - [MUTECT] Processed 57002953 reads in 658 ms
[2015-09-30T22:05Z] INFO  23:05:14,143 MuTect - [MUTECT] Processed 67003012 reads in 687 ms
[2015-09-30T22:05Z] INFO  23:05:14,724 MuTect - [MUTECT] Processed 86004246 reads in 654 ms
[2015-09-30T22:05Z] INFO  23:05:14,769 MuTect - [MUTECT] Processed 58003009 reads in 685 ms
[2015-09-30T22:05Z] INFO  23:05:14,861 MuTect - [MUTECT] Processed 68003013 reads in 718 ms
[2015-09-30T22:05Z] INFO  23:05:15,142 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:15,383 MuTect - [MUTECT] Processed 87004291 reads in 659 ms
[2015-09-30T22:05Z] INFO  23:05:15,456 MuTect - [MUTECT] Processed 59003071 reads in 687 ms
[2015-09-30T22:05Z] INFO  23:05:15,467 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:15,591 MuTect - [MUTECT] Processed 69003021 reads in 730 ms
[2015-09-30T22:05Z] INFO  23:05:15,724 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:16,052 MuTect - [MUTECT] Processed 88004293 reads in 669 ms
[2015-09-30T22:05Z] INFO  23:05:16,125 MuTect - [MUTECT] Processed 60003093 reads in 669 ms
[2015-09-30T22:05Z] INFO  23:05:16,284 MuTect - [MUTECT] Processed 70003049 reads in 693 ms
[2015-09-30T22:05Z] INFO  23:05:16,721 MuTect - [MUTECT] Processed 89004389 reads in 669 ms
[2015-09-30T22:05Z] INFO  23:05:16,766 MuTect - [MUTECT] Processed 61003103 reads in 641 ms
[2015-09-30T22:05Z] INFO  23:05:16,920 MuTect - [MUTECT] Processed 71003082 reads in 636 ms
[2015-09-30T22:05Z] INFO  23:05:17,365 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:17,396 MuTect - [MUTECT] Processed 62003169 reads in 630 ms
[2015-09-30T22:05Z] INFO  23:05:17,414 MuTect - [MUTECT] Processed 90004474 reads in 693 ms
[2015-09-30T22:05Z] INFO  23:05:17,575 MuTect - [MUTECT] Processed 72003128 reads in 655 ms
[2015-09-30T22:05Z] INFO  23:05:17,959 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:18,035 MuTect - [MUTECT] Processed 63003256 reads in 639 ms
[2015-09-30T22:05Z] INFO  23:05:18,059 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:18,061 MuTect - [MUTECT] Processed 91004502 reads in 647 ms
[2015-09-30T22:05Z] INFO  23:05:18,240 MuTect - [MUTECT] Processed 73003150 reads in 665 ms
[2015-09-30T22:05Z] INFO  23:05:18,684 MuTect - [MUTECT] Processed 64003291 reads in 649 ms
[2015-09-30T22:05Z] INFO  23:05:18,693 MuTect - [MUTECT] Processed 92004527 reads in 632 ms
[2015-09-30T22:05Z] INFO  23:05:18,931 MuTect - [MUTECT] Processed 74003237 reads in 690 ms
[2015-09-30T22:05Z] INFO  23:05:19,319 MuTect - [MUTECT] Processed 65003313 reads in 635 ms
[2015-09-30T22:05Z] INFO  23:05:19,353 MuTect - [MUTECT] Processed 93004612 reads in 660 ms
[2015-09-30T22:05Z] INFO  23:05:19,587 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:19,602 MuTect - [MUTECT] Processed 75003330 reads in 672 ms
[2015-09-30T22:05Z] INFO  23:05:19,945 MuTect - [MUTECT] Processed 66003411 reads in 626 ms
[2015-09-30T22:05Z] INFO  23:05:20,000 MuTect - [MUTECT] Processed 94004622 reads in 647 ms
[2015-09-30T22:05Z] INFO  23:05:20,169 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:20,249 MuTect - [MUTECT] Processed 76003359 reads in 647 ms
[2015-09-30T22:05Z] INFO  23:05:20,365 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:20,569 MuTect - [MUTECT] Processed 67003456 reads in 624 ms
[2015-09-30T22:05Z] INFO  23:05:20,651 MuTect - [MUTECT] Processed 95004717 reads in 651 ms
[2015-09-30T22:05Z] INFO  23:05:20,906 MuTect - [MUTECT] Processed 77003367 reads in 657 ms
[2015-09-30T22:05Z] INFO  23:05:21,216 MuTect - [MUTECT] Processed 68003539 reads in 647 ms
[2015-09-30T22:05Z] INFO  23:05:21,294 MuTect - [MUTECT] Processed 96004721 reads in 643 ms
[2015-09-30T22:05Z] INFO  23:05:21,571 MuTect - [MUTECT] Processed 78003434 reads in 665 ms
[2015-09-30T22:05Z] INFO  23:05:21,695 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:21,836 MuTect - [MUTECT] Processed 69003625 reads in 620 ms
[2015-09-30T22:05Z] INFO  23:05:21,941 MuTect - [MUTECT] Processed 97004767 reads in 647 ms
[2015-09-30T22:05Z] INFO  23:05:22,198 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:22,252 MuTect - [MUTECT] Processed 79003540 reads in 681 ms
[2015-09-30T22:05Z] INFO  23:05:22,459 MuTect - [MUTECT] Processed 70003637 reads in 623 ms
[2015-09-30T22:05Z] INFO  23:05:22,579 MuTect - [MUTECT] Processed 98004799 reads in 638 ms
[2015-09-30T22:05Z] INFO  23:05:22,691 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:22,897 MuTect - [MUTECT] Processed 80003569 reads in 645 ms
[2015-09-30T22:05Z] INFO  23:05:23,095 MuTect - [MUTECT] Processed 71003717 reads in 636 ms
[2015-09-30T22:05Z] INFO  23:05:23,215 MuTect - [MUTECT] Processed 99004805 reads in 636 ms
[2015-09-30T22:05Z] INFO  23:05:23,569 MuTect - [MUTECT] Processed 81003615 reads in 672 ms
[2015-09-30T22:05Z] INFO  23:05:23,738 MuTect - [MUTECT] Processed 72003788 reads in 643 ms
[2015-09-30T22:05Z] INFO  23:05:23,840 MuTect - [MUTECT] Processed 100004909 reads in 625 ms
[2015-09-30T22:05Z] INFO  23:05:23,938 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:24,248 MuTect - [MUTECT] Processed 82003638 reads in 679 ms
[2015-09-30T22:05Z] INFO  23:05:24,284 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:24,395 MuTect - [MUTECT] Processed 73003891 reads in 657 ms
[2015-09-30T22:05Z] INFO  23:05:24,500 MuTect - [MUTECT] Processed 101004930 reads in 660 ms
[2015-09-30T22:05Z] INFO  23:05:24,932 MuTect - [MUTECT] Processed 83003709 reads in 684 ms
[2015-09-30T22:05Z] INFO  23:05:24,986 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:25,090 MuTect - [MUTECT] Processed 74003976 reads in 695 ms
[2015-09-30T22:05Z] INFO  23:05:25,162 MuTect - [MUTECT] Processed 102005039 reads in 662 ms
[2015-09-30T22:05Z] INFO  23:05:25,613 ProgressMeter -      2:55844269        3.02e+06   60.0 s       19.0 s     84.8%        70.0 s    10.0 s
[2015-09-30T22:05Z] INFO  23:05:25,619 MuTect - [MUTECT] Processed 84003719 reads in 687 ms
[2015-09-30T22:05Z] INFO  23:05:25,790 MuTect - [MUTECT] Processed 75003982 reads in 700 ms
[2015-09-30T22:05Z] INFO  23:05:25,834 MuTect - [MUTECT] Processed 103005134 reads in 672 ms
[2015-09-30T22:05Z] INFO  23:05:26,186 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:26,288 MuTect - [MUTECT] Processed 85003833 reads in 669 ms
[2015-09-30T22:05Z] INFO  23:05:26,496 MuTect - [MUTECT] Processed 104005156 reads in 662 ms
[2015-09-30T22:05Z] INFO  23:05:26,528 MuTect - [MUTECT] Processed 76004004 reads in 738 ms
[2015-09-30T22:05Z] INFO  23:05:26,780 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:26,939 MuTect - [MUTECT] Processed 86003835 reads in 651 ms
[2015-09-30T22:05Z] INFO  23:05:27,155 MuTect - [MUTECT] Processed 105005179 reads in 659 ms
[2015-09-30T22:05Z] INFO  23:05:27,267 MuTect - [MUTECT] Processed 77004007 reads in 739 ms
[2015-09-30T22:05Z] INFO  23:05:27,480 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:27,584 MuTect - [MUTECT] Processed 87003855 reads in 645 ms
[2015-09-30T22:05Z] INFO  23:05:27,806 MuTect - [MUTECT] Processed 106005201 reads in 651 ms
[2015-09-30T22:05Z] INFO  23:05:27,965 MuTect - [MUTECT] Processed 78004023 reads in 698 ms
[2015-09-30T22:05Z] INFO  23:05:28,250 MuTect - [MUTECT] Processed 88003906 reads in 666 ms
[2015-09-30T22:05Z] INFO  23:05:28,382 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:28,435 MuTect - [MUTECT] Processed 107005263 reads in 629 ms
[2015-09-30T22:05Z] INFO  23:05:28,613 MuTect - [MUTECT] Processed 79004039 reads in 648 ms
[2015-09-30T22:05Z] INFO  23:05:28,902 MuTect - [MUTECT] Processed 89003964 reads in 652 ms
[2015-09-30T22:05Z] INFO  23:05:29,073 MuTect - [MUTECT] Processed 108005268 reads in 638 ms
[2015-09-30T22:05Z] INFO  23:05:29,150 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:29,283 MuTect - [MUTECT] Processed 80004088 reads in 670 ms
[2015-09-30T22:05Z] INFO  23:05:29,568 MuTect - [MUTECT] Processed 90004015 reads in 666 ms
[2015-09-30T22:05Z] INFO  23:05:29,710 MuTect - [MUTECT] Processed 109005307 reads in 637 ms
[2015-09-30T22:05Z] INFO  23:05:29,921 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:30,004 MuTect - [MUTECT] Processed 81004116 reads in 721 ms
[2015-09-30T22:05Z] INFO  23:05:30,222 MuTect - [MUTECT] Processed 91004037 reads in 654 ms
[2015-09-30T22:05Z] INFO  23:05:30,353 MuTect - [MUTECT] Processed 110005384 reads in 643 ms
[2015-09-30T22:05Z] INFO  23:05:30,683 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:30,703 MuTect - [MUTECT] Processed 82004148 reads in 699 ms
[2015-09-30T22:05Z] INFO  23:05:30,926 MuTect - [MUTECT] Processed 92004064 reads in 704 ms
[2015-09-30T22:05Z] INFO  23:05:30,990 MuTect - [MUTECT] Processed 111005407 reads in 637 ms
[2015-09-30T22:05Z] INFO  23:05:31,398 MuTect - [MUTECT] Processed 83004148 reads in 695 ms
[2015-09-30T22:05Z] INFO  23:05:31,603 MuTect - [MUTECT] Processed 93004079 reads in 677 ms
[2015-09-30T22:05Z] INFO  23:05:31,631 MuTect - [MUTECT] Processed 112005430 reads in 641 ms
[2015-09-30T22:05Z] INFO  23:05:31,867 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:32,058 MuTect - [MUTECT] Processed 84004192 reads in 660 ms
[2015-09-30T22:05Z] INFO  23:05:32,278 MuTect - [MUTECT] Processed 113005472 reads in 646 ms
[2015-09-30T22:05Z] INFO  23:05:32,290 MuTect - [MUTECT] Processed 94004095 reads in 686 ms
[2015-09-30T22:05Z] INFO  23:05:32,488 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:32,703 MuTect - [MUTECT] Processed 85004208 reads in 645 ms
[2015-09-30T22:05Z] INFO  23:05:32,814 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:32,951 MuTect - [MUTECT] Processed 114005515 reads in 674 ms
[2015-09-30T22:05Z] INFO  23:05:33,016 MuTect - [MUTECT] Processed 95004138 reads in 727 ms
[2015-09-30T22:05Z] INFO  23:05:33,336 MuTect - [MUTECT] Processed 86004319 reads in 633 ms
[2015-09-30T22:05Z] INFO  23:05:33,621 MuTect - [MUTECT] Processed 115005577 reads in 670 ms
[2015-09-30T22:05Z] INFO  23:05:33,706 MuTect - [MUTECT] Processed 96004209 reads in 689 ms
[2015-09-30T22:05Z] INFO  23:05:33,875 ProgressMeter -      2:85553991        2.53e+06   60.0 s       23.0 s     68.2%        87.0 s    27.0 s
[2015-09-30T22:05Z] INFO  23:05:34,005 MuTect - [MUTECT] Processed 87004407 reads in 669 ms
[2015-09-30T22:05Z] INFO  23:05:34,112 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:34,305 MuTect - [MUTECT] Processed 116005664 reads in 684 ms
[2015-09-30T22:05Z] INFO  23:05:34,415 MuTect - [MUTECT] Processed 97004217 reads in 710 ms
[2015-09-30T22:05Z] INFO  23:05:34,571 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:05Z] INFO  23:05:34,576 ProgressMeter -            done        3.56e+06   68.0 s       19.0 s    100.0%        68.0 s     0.0 s
[2015-09-30T22:05Z] INFO  23:05:34,576 ProgressMeter - Total runtime 68.97 secs, 1.15 min, 0.02 hours
[2015-09-30T22:05Z] INFO  23:05:34,638 MicroScheduler - 67094 reads were filtered out during the traversal out of approximately 1160831 total reads (5.78%)
[2015-09-30T22:05Z] INFO  23:05:34,638 MicroScheduler -   -> 48853 reads (4.21% of total) failing DuplicateReadFilter
[2015-09-30T22:05Z] INFO  23:05:34,638 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:05Z] INFO  23:05:34,639 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:05Z] INFO  23:05:34,639 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:05Z] INFO  23:05:34,639 MicroScheduler -   -> 18241 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:05Z] INFO  23:05:34,659 MuTect - [MUTECT] Processed 88004470 reads in 654 ms
[2015-09-30T22:05Z] INFO  23:05:34,981 MuTect - [MUTECT] Processed 117005676 reads in 676 ms
[2015-09-30T22:05Z] INFO  23:05:35,234 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:35,323 MuTect - [MUTECT] Processed 89004509 reads in 664 ms
[2015-09-30T22:05Z] INFO  23:05:35,704 MuTect - [MUTECT] Processed 118005732 reads in 723 ms
[2015-09-30T22:05Z] INFO  23:05:35,988 MuTect - [MUTECT] Processed 90004520 reads in 665 ms
[2015-09-30T22:05Z] INFO  23:05:36,161 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:05Z] INFO  23:05:36,317 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:36,393 MuTect - [MUTECT] Processed 119005848 reads in 689 ms
[2015-09-30T22:05Z] INFO  23:05:36,680 MuTect - [MUTECT] Processed 91004538 reads in 692 ms
[2015-09-30T22:05Z] INFO  23:05:37,068 MuTect - [MUTECT] Processed 120005934 reads in 675 ms
[2015-09-30T22:05Z] INFO  23:05:37,384 MuTect - [MUTECT] Processed 92004566 reads in 704 ms
[2015-09-30T22:05Z] INFO  23:05:37,386 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:37,719 MuTect - [MUTECT] Processed 121005998 reads in 651 ms
[2015-09-30T22:05Z] INFO  23:05:38,027 MuTect - [MUTECT] Processed 93004650 reads in 643 ms
[2015-09-30T22:05Z] bgzip syn3-2_31134801_62196287-raw-mutect.vcf
[2015-09-30T22:05Z] INFO  23:05:38,418 MuTect - [MUTECT] Processed 122006004 reads in 699 ms
[2015-09-30T22:05Z] INFO  23:05:38,623 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:38,650 MuTect - [MUTECT] Processed 94004651 reads in 622 ms
[2015-09-30T22:05Z] tabix index syn3-2_31134801_62196287-raw-mutect.vcf.gz
[2015-09-30T22:05Z] INFO  23:05:39,093 MuTect - [MUTECT] Processed 123006112 reads in 675 ms
[2015-09-30T22:05Z] INFO  23:05:39,346 MuTect - [MUTECT] Processed 95004657 reads in 697 ms
[2015-09-30T22:05Z] INFO  23:05:39,643 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:39,784 MuTect - [MUTECT] Processed 124006137 reads in 691 ms
[2015-09-30T22:05Z] INFO  23:05:40,019 MuTect - [MUTECT] Processed 96004698 reads in 673 ms
[2015-09-30T22:05Z] INFO  23:05:40,447 MuTect - [MUTECT] Processed 125006156 reads in 663 ms
[2015-09-30T22:05Z] INFO  23:05:40,660 MuTect - [MUTECT] Processed 97004777 reads in 641 ms
[2015-09-30T22:05Z] INFO  23:05:40,831 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:05Z] MuTect: MuTect
[2015-09-30T22:05Z] INFO  23:05:41,116 MuTect - [MUTECT] Processed 126006196 reads in 669 ms
[2015-09-30T22:05Z] INFO  23:05:41,334 MuTect - [MUTECT] Processed 98004797 reads in 674 ms
[2015-09-30T22:05Z] INFO  23:05:41,799 MuTect - [MUTECT] Processed 127006255 reads in 683 ms
[2015-09-30T22:05Z] INFO  23:05:41,957 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:42,048 MuTect - [MUTECT] Processed 99004800 reads in 714 ms
[2015-09-30T22:05Z] INFO  23:05:42,478 MuTect - [MUTECT] Processed 128006301 reads in 679 ms
[2015-09-30T22:05Z] INFO  23:05:42,488 ProgressMeter -      2:30454601        3.96e+06   90.0 s       22.0 s     98.2%        91.0 s     1.0 s
[2015-09-30T22:05Z] INFO  23:05:42,737 MuTect - [MUTECT] Processed 100004855 reads in 689 ms
[2015-09-30T22:05Z] INFO  23:05:43,038 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/2/syn3-2_95457728_127315933-raw-mutect-regions.bed to be BED
[2015-09-30T22:05Z] INFO  23:05:43,092 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:05Z] INFO  23:05:43,092 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:05Z] INFO  23:05:43,092 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:05Z] INFO  23:05:43,092 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:05Z] INFO  23:05:43,096 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/2/syn3-2_95457728_127315933-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/2/tx/tmpLqPgrg/syn3-2_95457728_127315933-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:05Z] INFO  23:05:43,096 HelpFormatter - Date/Time: 2015/09/30 23:05:43
[2015-09-30T22:05Z] INFO  23:05:43,096 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:05Z] INFO  23:05:43,096 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:05Z] INFO  23:05:43,123 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:05Z] INFO  23:05:43,127 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:05Z] INFO  23:05:43,142 MuTect - [MUTECT] Processed 129006405 reads in 664 ms
[2015-09-30T22:05Z] INFO  23:05:43,176 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:05Z] INFO  23:05:43,224 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:05Z] INFO  23:05:43,231 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:05Z] INFO  23:05:43,294 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:05Z] INFO  23:05:43,331 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:05Z] INFO  23:05:43,366 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:43,435 MuTect - [MUTECT] Processed 101004910 reads in 698 ms
[2015-09-30T22:05Z] INFO  23:05:43,504 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:05Z] INFO  23:05:43,612 IntervalUtils - Processing 1630830 bp from intervals
[2015-09-30T22:05Z] INFO  23:05:43,616 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:05Z] INFO  23:05:43,616 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:05Z] INFO  23:05:43,791 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:05Z] INFO  23:05:43,834 MuTect - [MUTECT] Processed 130006485 reads in 692 ms
[2015-09-30T22:05Z] INFO  23:05:44,191 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:05Z] INFO  23:05:44,202 ProgressMeter -            done        4.02e+06   91.0 s       22.0 s    100.0%        91.0 s     0.0 s
[2015-09-30T22:05Z] INFO  23:05:44,203 ProgressMeter - Total runtime 91.72 secs, 1.53 min, 0.03 hours
[2015-09-30T22:05Z] INFO  23:05:44,267 MicroScheduler - 99750 reads were filtered out during the traversal out of approximately 1551549 total reads (6.43%)
[2015-09-30T22:05Z] INFO  23:05:44,268 MicroScheduler -   -> 74487 reads (4.80% of total) failing DuplicateReadFilter
[2015-09-30T22:05Z] INFO  23:05:44,268 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:05Z] INFO  23:05:44,268 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:05Z] INFO  23:05:44,268 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:05Z] INFO  23:05:44,268 MicroScheduler -   -> 25263 reads (1.63% of total) failing UnmappedReadFilter
[2015-09-30T22:05Z] INFO  23:05:44,373 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:05Z] INFO  23:05:44,374 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:05Z] INFO  23:05:44,374 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:05Z] INFO  23:05:44,375 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:05Z] INFO  23:05:44,558 MuTect - [MUTECT] Processed 102004965 reads in 1123 ms
[2015-09-30T22:05Z] INFO  23:05:45,229 MuTect - [MUTECT] Processed 103005032 reads in 671 ms
[2015-09-30T22:05Z] INFO  23:05:45,296 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:05Z] bgzip syn3-2_0_31134137-raw-mutect.vcf
[2015-09-30T22:05Z] tabix index syn3-2_0_31134137-raw-mutect.vcf.gz
[2015-09-30T22:05Z] INFO  23:05:45,932 MuTect - [MUTECT] Processed 104005067 reads in 703 ms
[2015-09-30T22:05Z] INFO  23:05:46,292 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:46,608 MuTect - [MUTECT] Processed 105005187 reads in 676 ms
[2015-09-30T22:05Z] INFO  23:05:47,276 MuTect - [MUTECT] Processed 1000021 reads in 2820 ms
[2015-09-30T22:05Z] INFO  23:05:47,355 MuTect - [MUTECT] Processed 106005270 reads in 747 ms
[2015-09-30T22:05Z] MuTect: MuTect
[2015-09-30T22:05Z] INFO  23:05:47,978 MuTect - [MUTECT] Processed 107005287 reads in 623 ms
[2015-09-30T22:05Z] INFO  23:05:48,145 MuTect - [MUTECT] Processed 2000039 reads in 869 ms
[2015-09-30T22:05Z] INFO  23:05:48,633 MuTect - [MUTECT] Processed 108005313 reads in 655 ms
[2015-09-30T22:05Z] INFO  23:05:48,825 MuTect - [MUTECT] Processed 3000081 reads in 680 ms
[2015-09-30T22:05Z] INFO  23:05:48,921 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:49,330 MuTect - [MUTECT] Processed 109005349 reads in 697 ms
[2015-09-30T22:05Z] INFO  23:05:49,511 MuTect - [MUTECT] Processed 4000199 reads in 686 ms
[2015-09-30T22:05Z] INFO  23:05:49,885 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/2/syn3-2_127413596_158444156-raw-mutect-regions.bed to be BED
[2015-09-30T22:05Z] INFO  23:05:49,942 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:05Z] INFO  23:05:49,942 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:05Z] INFO  23:05:49,942 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:05Z] INFO  23:05:49,943 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:05Z] INFO  23:05:49,949 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/2/syn3-2_127413596_158444156-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/2/tx/tmpxZyT7W/syn3-2_127413596_158444156-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:05Z] INFO  23:05:49,949 HelpFormatter - Date/Time: 2015/09/30 23:05:49
[2015-09-30T22:05Z] INFO  23:05:49,949 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:05Z] INFO  23:05:49,949 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:05Z] INFO  23:05:49,977 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:05Z] INFO  23:05:49,981 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:05Z] INFO  23:05:50,039 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:05Z] INFO  23:05:50,087 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:05Z] INFO  23:05:50,095 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:05Z] INFO  23:05:50,127 MuTect - [MUTECT] Processed 110005406 reads in 797 ms
[2015-09-30T22:05Z] INFO  23:05:50,155 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:05Z] INFO  23:05:50,188 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:05Z] INFO  23:05:50,196 MuTect - [MUTECT] Processed 5000219 reads in 685 ms
[2015-09-30T22:05Z] INFO  23:05:50,368 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:05Z] INFO  23:05:50,467 IntervalUtils - Processing 1120292 bp from intervals
[2015-09-30T22:05Z] INFO  23:05:50,472 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:05Z] INFO  23:05:50,472 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:05Z] INFO  23:05:50,512 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:50,653 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:05Z] INFO  23:05:50,784 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:05Z] INFO  23:05:50,784 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:05Z] INFO  23:05:50,785 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:05Z] INFO  23:05:50,786 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:05Z] INFO  23:05:50,834 MuTect - [MUTECT] Processed 111005447 reads in 707 ms
[2015-09-30T22:05Z] INFO  23:05:50,855 MuTect - [MUTECT] Processed 6000354 reads in 659 ms
[2015-09-30T22:05Z] INFO  23:05:51,157 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:51,461 MuTect - [MUTECT] Processed 112005464 reads in 627 ms
[2015-09-30T22:05Z] INFO  23:05:51,475 MuTect - [MUTECT] Processed 7000375 reads in 620 ms
[2015-09-30T22:05Z] INFO  23:05:52,094 MuTect - [MUTECT] Processed 8000402 reads in 619 ms
[2015-09-30T22:05Z] INFO  23:05:52,138 MuTect - [MUTECT] Processed 113005561 reads in 677 ms
[2015-09-30T22:05Z] INFO  23:05:52,711 MuTect - [MUTECT] Processed 9000407 reads in 617 ms
[2015-09-30T22:05Z] INFO  23:05:52,830 MuTect - [MUTECT] Processed 114005564 reads in 692 ms
[2015-09-30T22:05Z] INFO  23:05:53,501 MuTect - [MUTECT] Processed 1000053 reads in 2657 ms
[2015-09-30T22:05Z] INFO  23:05:53,569 MuTect - [MUTECT] Processed 115005618 reads in 739 ms
[2015-09-30T22:05Z] INFO  23:05:53,680 MuTect - [MUTECT] Processed 10000420 reads in 969 ms
[2015-09-30T22:05Z] INFO  23:05:54,008 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:54,281 MuTect - [MUTECT] Processed 116005648 reads in 712 ms
[2015-09-30T22:05Z] INFO  23:05:54,347 MuTect - [MUTECT] Processed 2000053 reads in 846 ms
[2015-09-30T22:05Z] INFO  23:05:54,460 MuTect - [MUTECT] Processed 11000756 reads in 780 ms
[2015-09-30T22:05Z] INFO  23:05:54,726 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:55,067 MuTect - [MUTECT] Processed 3000098 reads in 720 ms
[2015-09-30T22:05Z] INFO  23:05:55,130 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:55,180 MuTect - [MUTECT] Processed 117005739 reads in 899 ms
[2015-09-30T22:05Z] INFO  23:05:55,800 MuTect - [MUTECT] Processed 4000114 reads in 733 ms
[2015-09-30T22:05Z] INFO  23:05:55,849 MuTect - [MUTECT] Processed 12000763 reads in 1389 ms
[2015-09-30T22:05Z] INFO  23:05:56,122 MuTect - [MUTECT] Processed 118005771 reads in 942 ms
[2015-09-30T22:05Z] INFO  23:05:56,224 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:56,543 MuTect - [MUTECT] Processed 5000125 reads in 743 ms
[2015-09-30T22:05Z] INFO  23:05:56,631 MuTect - [MUTECT] Processed 13000841 reads in 782 ms
[2015-09-30T22:05Z] INFO  23:05:56,833 MuTect - [MUTECT] Processed 119005834 reads in 711 ms
[2015-09-30T22:05Z] INFO  23:05:57,220 MuTect - [MUTECT] Processed 14000936 reads in 589 ms
[2015-09-30T22:05Z] INFO  23:05:57,234 MuTect - [MUTECT] Processed 6000138 reads in 690 ms
[2015-09-30T22:05Z] INFO  23:05:57,487 MuTect - [MUTECT] Processed 120005842 reads in 654 ms
[2015-09-30T22:05Z] INFO  23:05:57,530 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:57,753 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:57,839 MuTect - [MUTECT] Processed 15000998 reads in 619 ms
[2015-09-30T22:05Z] INFO  23:05:57,950 MuTect - [MUTECT] Processed 7000207 reads in 717 ms
[2015-09-30T22:05Z] INFO  23:05:58,210 MuTect - [MUTECT] Processed 121005861 reads in 723 ms
[2015-09-30T22:05Z] INFO  23:05:58,478 MuTect - [MUTECT] Processed 16001075 reads in 639 ms
[2015-09-30T22:05Z] INFO  23:05:58,651 MuTect - [MUTECT] Processed 8000303 reads in 701 ms
[2015-09-30T22:05Z] INFO  23:05:59,052 MuTect - [MUTECT] Processed 122006151 reads in 842 ms
[2015-09-30T22:05Z] INFO  23:05:59,123 MuTect - [MUTECT] Processed 17001101 reads in 645 ms
[2015-09-30T22:05Z] INFO  23:05:59,336 MuTect - [MUTECT] Processed 9000332 reads in 685 ms
[2015-09-30T22:05Z] INFO  23:05:59,623 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:59,713 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:05Z] INFO  23:05:59,774 MuTect - [MUTECT] Processed 18001178 reads in 651 ms
[2015-09-30T22:06Z] INFO  23:06:00,043 MuTect - [MUTECT] Processed 10000433 reads in 707 ms
[2015-09-30T22:06Z] INFO  23:06:00,088 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:00,348 MuTect - [MUTECT] Processed 123006470 reads in 1296 ms
[2015-09-30T22:06Z] INFO  23:06:00,414 MuTect - [MUTECT] Processed 19001227 reads in 640 ms
[2015-09-30T22:06Z] INFO  23:06:00,757 MuTect - [MUTECT] Processed 11000515 reads in 714 ms
[2015-09-30T22:06Z] INFO  23:06:01,045 MuTect - [MUTECT] Processed 20001328 reads in 631 ms
[2015-09-30T22:06Z] INFO  23:06:01,179 MuTect - [MUTECT] Processed 124006905 reads in 831 ms
[2015-09-30T22:06Z] INFO  23:06:01,449 MuTect - [MUTECT] Processed 12000587 reads in 692 ms
[2015-09-30T22:06Z] INFO  23:06:01,669 MuTect - [MUTECT] Processed 21001361 reads in 624 ms
[2015-09-30T22:06Z] INFO  23:06:01,954 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:02,182 MuTect - [MUTECT] Processed 125007395 reads in 1003 ms
[2015-09-30T22:06Z] INFO  23:06:02,195 MuTect - [MUTECT] Processed 13000636 reads in 746 ms
[2015-09-30T22:06Z] INFO  23:06:02,276 MuTect - [MUTECT] Processed 22001489 reads in 607 ms
[2015-09-30T22:06Z] INFO  23:06:02,569 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:02,882 MuTect - [MUTECT] Processed 23001580 reads in 606 ms
[2015-09-30T22:06Z] INFO  23:06:02,909 MuTect - [MUTECT] Processed 14000666 reads in 713 ms
[2015-09-30T22:06Z] INFO  23:06:03,115 MuTect - [MUTECT] Processed 126008027 reads in 933 ms
[2015-09-30T22:06Z] INFO  23:06:03,487 MuTect - [MUTECT] Processed 24001640 reads in 604 ms
[2015-09-30T22:06Z] INFO  23:06:03,592 MuTect - [MUTECT] Processed 15000672 reads in 684 ms
[2015-09-30T22:06Z] INFO  23:06:03,876 ProgressMeter -      2:91809449        3.70e+06   90.0 s       24.0 s     97.9%        91.0 s     1.0 s
[2015-09-30T22:06Z] INFO  23:06:04,025 MuTect - [MUTECT] Processed 127008042 reads in 909 ms
[2015-09-30T22:06Z] INFO  23:06:04,041 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:04,091 MuTect - [MUTECT] Processed 25001712 reads in 605 ms
[2015-09-30T22:06Z] INFO  23:06:04,310 MuTect - [MUTECT] Processed 16000680 reads in 718 ms
[2015-09-30T22:06Z] INFO  23:06:04,684 MuTect - [MUTECT] Processed 26001766 reads in 593 ms
[2015-09-30T22:06Z] INFO  23:06:04,834 MuTect - [MUTECT] Processed 128008094 reads in 810 ms
[2015-09-30T22:06Z] INFO  23:06:04,968 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:05,041 MuTect - [MUTECT] Processed 17000759 reads in 731 ms
[2015-09-30T22:06Z] INFO  23:06:05,306 MuTect - [MUTECT] Processed 27001777 reads in 622 ms
[2015-09-30T22:06Z] INFO  23:06:05,485 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:05,689 MuTect - [MUTECT] Processed 129008157 reads in 855 ms
[2015-09-30T22:06Z] INFO  23:06:05,740 MuTect - [MUTECT] Processed 18000873 reads in 699 ms
[2015-09-30T22:06Z] INFO  23:06:05,912 MuTect - [MUTECT] Processed 28001826 reads in 606 ms
[2015-09-30T22:06Z] INFO  23:06:06,153 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:06,338 MuTect - [MUTECT] Processed 130008174 reads in 649 ms
[2015-09-30T22:06Z] INFO  23:06:06,487 MuTect - [MUTECT] Processed 19000945 reads in 747 ms
[2015-09-30T22:06Z] INFO  23:06:06,532 MuTect - [MUTECT] Processed 29001884 reads in 620 ms
[2015-09-30T22:06Z] INFO  23:06:07,129 MuTect - [MUTECT] Processed 30001941 reads in 597 ms
[2015-09-30T22:06Z] INFO  23:06:07,244 MuTect - [MUTECT] Processed 20000999 reads in 757 ms
[2015-09-30T22:06Z] INFO  23:06:07,521 MuTect - [MUTECT] Processed 131008213 reads in 1183 ms
[2015-09-30T22:06Z] INFO  23:06:07,610 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:06Z] INFO  23:06:07,613 ProgressMeter -            done        3.75e+06   93.0 s       25.0 s    100.0%        93.0 s     0.0 s
[2015-09-30T22:06Z] INFO  23:06:07,613 ProgressMeter - Total runtime 93.74 secs, 1.56 min, 0.03 hours
[2015-09-30T22:06Z] INFO  23:06:07,680 MicroScheduler - 96826 reads were filtered out during the traversal out of approximately 1557254 total reads (6.22%)
[2015-09-30T22:06Z] INFO  23:06:07,680 MicroScheduler -   -> 71926 reads (4.62% of total) failing DuplicateReadFilter
[2015-09-30T22:06Z] INFO  23:06:07,680 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:06Z] INFO  23:06:07,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:06Z] INFO  23:06:07,680 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:06Z] INFO  23:06:07,681 MicroScheduler -   -> 24900 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:06Z] INFO  23:06:07,713 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:07,746 MuTect - [MUTECT] Processed 31002002 reads in 617 ms
[2015-09-30T22:06Z] INFO  23:06:07,956 MuTect - [MUTECT] Processed 21001084 reads in 712 ms
[2015-09-30T22:06Z] INFO  23:06:08,226 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:08,414 MuTect - [MUTECT] Processed 32002035 reads in 668 ms
[2015-09-30T22:06Z] INFO  23:06:08,623 MuTect - [MUTECT] Processed 22001192 reads in 667 ms
[2015-09-30T22:06Z] INFO  23:06:08,662 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:06Z] bgzip syn3-2_62227535_95457199-raw-mutect.vcf
[2015-09-30T22:06Z] tabix index syn3-2_62227535_95457199-raw-mutect.vcf.gz
[2015-09-30T22:06Z] INFO  23:06:09,086 MuTect - [MUTECT] Processed 33002063 reads in 672 ms
[2015-09-30T22:06Z] INFO  23:06:09,365 MuTect - [MUTECT] Processed 23001264 reads in 742 ms
[2015-09-30T22:06Z] INFO  23:06:09,987 MuTect - [MUTECT] Processed 34002063 reads in 901 ms
[2015-09-30T22:06Z] INFO  23:06:09,992 MuTect - [MUTECT] Processed 24001319 reads in 627 ms
[2015-09-30T22:06Z] INFO  23:06:10,024 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:10,645 MuTect - [MUTECT] Processed 25001396 reads in 653 ms
[2015-09-30T22:06Z] INFO  23:06:10,758 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:11,096 MuTect - [MUTECT] Processed 35002137 reads in 1109 ms
[2015-09-30T22:06Z] MuTect: MuTect
[2015-09-30T22:06Z] INFO  23:06:11,301 MuTect - [MUTECT] Processed 26001458 reads in 656 ms
[2015-09-30T22:06Z] INFO  23:06:11,850 MuTect - [MUTECT] Processed 36002158 reads in 754 ms
[2015-09-30T22:06Z] INFO  23:06:11,909 MuTect - [MUTECT] Processed 27001538 reads in 608 ms
[2015-09-30T22:06Z] INFO  23:06:12,489 MuTect - [MUTECT] Processed 37002252 reads in 639 ms
[2015-09-30T22:06Z] INFO  23:06:12,592 MuTect - [MUTECT] Processed 28001540 reads in 683 ms
[2015-09-30T22:06Z] INFO  23:06:13,239 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/2/syn3-2_158484801_189599894-raw-mutect-regions.bed to be BED
[2015-09-30T22:06Z] INFO  23:06:13,262 MuTect - [MUTECT] Processed 38002271 reads in 773 ms
[2015-09-30T22:06Z] INFO  23:06:13,269 MuTect - [MUTECT] Processed 29001581 reads in 677 ms
[2015-09-30T22:06Z] INFO  23:06:13,293 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:06Z] INFO  23:06:13,294 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:06Z] INFO  23:06:13,294 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:06Z] INFO  23:06:13,294 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:06Z] INFO  23:06:13,298 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/2/syn3-2_158484801_189599894-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/2/tx/tmpGgfLGg/syn3-2_158484801_189599894-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:06Z] INFO  23:06:13,298 HelpFormatter - Date/Time: 2015/09/30 23:06:13
[2015-09-30T22:06Z] INFO  23:06:13,298 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:06Z] INFO  23:06:13,298 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:06Z] INFO  23:06:13,325 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:06Z] INFO  23:06:13,329 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:06Z] INFO  23:06:13,378 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:06Z] INFO  23:06:13,425 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:06Z] INFO  23:06:13,432 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:06Z] INFO  23:06:13,484 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T22:06Z] INFO  23:06:13,495 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:06Z] INFO  23:06:13,670 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:06Z] INFO  23:06:13,776 IntervalUtils - Processing 1652675 bp from intervals
[2015-09-30T22:06Z] INFO  23:06:13,780 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:06Z] INFO  23:06:13,780 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:06Z] INFO  23:06:13,805 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:13,905 MuTect - [MUTECT] Processed 30001643 reads in 636 ms
[2015-09-30T22:06Z] INFO  23:06:13,970 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:06Z] INFO  23:06:14,035 MuTect - [MUTECT] Processed 39002331 reads in 772 ms
[2015-09-30T22:06Z] INFO  23:06:14,078 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:14,154 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:06Z] INFO  23:06:14,154 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:06Z] INFO  23:06:14,154 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:06Z] INFO  23:06:14,155 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:06Z] INFO  23:06:14,376 ProgressMeter -      2:98280490        1.14e+06   30.0 s       26.0 s     24.0%         2.1 m    95.0 s
[2015-09-30T22:06Z] INFO  23:06:14,628 MuTect - [MUTECT] Processed 31001721 reads in 723 ms
[2015-09-30T22:06Z] INFO  23:06:14,676 MuTect - [MUTECT] Processed 40002424 reads in 642 ms
[2015-09-30T22:06Z] INFO  23:06:15,312 MuTect - [MUTECT] Processed 41002541 reads in 636 ms
[2015-09-30T22:06Z] INFO  23:06:15,321 MuTect - [MUTECT] Processed 32001802 reads in 693 ms
[2015-09-30T22:06Z] INFO  23:06:15,969 MuTect - [MUTECT] Processed 42002541 reads in 657 ms
[2015-09-30T22:06Z] INFO  23:06:16,028 MuTect - [MUTECT] Processed 33001815 reads in 707 ms
[2015-09-30T22:06Z] INFO  23:06:16,430 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:16,520 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:16,609 MuTect - [MUTECT] Processed 1000028 reads in 2401 ms
[2015-09-30T22:06Z] INFO  23:06:16,687 MuTect - [MUTECT] Processed 43002613 reads in 718 ms
[2015-09-30T22:06Z] INFO  23:06:16,851 MuTect - [MUTECT] Processed 34001830 reads in 823 ms
[2015-09-30T22:06Z] INFO  23:06:17,392 MuTect - [MUTECT] Processed 44002657 reads in 705 ms
[2015-09-30T22:06Z] INFO  23:06:17,548 MuTect - [MUTECT] Processed 35001876 reads in 697 ms
[2015-09-30T22:06Z] INFO  23:06:17,721 MuTect - [MUTECT] Processed 2000074 reads in 1112 ms
[2015-09-30T22:06Z] INFO  23:06:18,038 MuTect - [MUTECT] Processed 45002781 reads in 646 ms
[2015-09-30T22:06Z] INFO  23:06:18,231 MuTect - [MUTECT] Processed 36001957 reads in 683 ms
[2015-09-30T22:06Z] INFO  23:06:18,465 MuTect - [MUTECT] Processed 3000125 reads in 744 ms
[2015-09-30T22:06Z] INFO  23:06:18,679 MuTect - [MUTECT] Processed 46002814 reads in 641 ms
[2015-09-30T22:06Z] INFO  23:06:18,798 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:18,843 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:18,880 MuTect - [MUTECT] Processed 37001958 reads in 649 ms
[2015-09-30T22:06Z] INFO  23:06:19,017 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:19,225 MuTect - [MUTECT] Processed 4000168 reads in 760 ms
[2015-09-30T22:06Z] INFO  23:06:19,329 MuTect - [MUTECT] Processed 47002863 reads in 650 ms
[2015-09-30T22:06Z] INFO  23:06:19,534 MuTect - [MUTECT] Processed 38002024 reads in 654 ms
[2015-09-30T22:06Z] INFO  23:06:19,982 MuTect - [MUTECT] Processed 5000266 reads in 757 ms
[2015-09-30T22:06Z] INFO  23:06:20,009 MuTect - [MUTECT] Processed 48002888 reads in 680 ms
[2015-09-30T22:06Z] INFO  23:06:20,297 MuTect - [MUTECT] Processed 39002028 reads in 763 ms
[2015-09-30T22:06Z] INFO  23:06:20,633 MuTect - [MUTECT] Processed 49002888 reads in 624 ms
[2015-09-30T22:06Z] INFO  23:06:20,781 MuTect - [MUTECT] Processed 6000297 reads in 799 ms
[2015-09-30T22:06Z] INFO  23:06:20,787 ProgressMeter -     2:132861196        1.25e+06   30.0 s       23.0 s     36.9%        81.0 s    51.0 s
[2015-09-30T22:06Z] INFO  23:06:21,240 MuTect - [MUTECT] Processed 40002455 reads in 943 ms
[2015-09-30T22:06Z] INFO  23:06:21,278 MuTect - [MUTECT] Processed 50002889 reads in 645 ms
[2015-09-30T22:06Z] INFO  23:06:21,340 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:21,454 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:21,561 MuTect - [MUTECT] Processed 7000298 reads in 780 ms
[2015-09-30T22:06Z] INFO  23:06:21,705 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:21,903 MuTect - [MUTECT] Processed 51002902 reads in 625 ms
[2015-09-30T22:06Z] INFO  23:06:22,299 MuTect - [MUTECT] Processed 8000311 reads in 738 ms
[2015-09-30T22:06Z] INFO  23:06:22,521 MuTect - [MUTECT] Processed 52002925 reads in 618 ms
[2015-09-30T22:06Z] INFO  23:06:23,010 MuTect - [MUTECT] Processed 9000330 reads in 711 ms
[2015-09-30T22:06Z] INFO  23:06:23,158 MuTect - [MUTECT] Processed 53002994 reads in 637 ms
[2015-09-30T22:06Z] INFO  23:06:23,628 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:23,717 MuTect - [MUTECT] Processed 10000387 reads in 707 ms
[2015-09-30T22:06Z] INFO  23:06:23,774 MuTect - [MUTECT] Processed 54002996 reads in 616 ms
[2015-09-30T22:06Z] INFO  23:06:24,431 MuTect - [MUTECT] Processed 11000417 reads in 714 ms
[2015-09-30T22:06Z] INFO  23:06:24,433 MuTect - [MUTECT] Processed 55003030 reads in 659 ms
[2015-09-30T22:06Z] INFO  23:06:24,496 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:25,124 MuTect - [MUTECT] Processed 12000461 reads in 693 ms
[2015-09-30T22:06Z] INFO  23:06:25,131 MuTect - [MUTECT] Processed 56003051 reads in 698 ms
[2015-09-30T22:06Z] INFO  23:06:25,773 MuTect - [MUTECT] Processed 41002546 reads in 4533 ms
[2015-09-30T22:06Z] INFO  23:06:25,801 MuTect - [MUTECT] Processed 13000500 reads in 677 ms
[2015-09-30T22:06Z] INFO  23:06:25,814 MuTect - [MUTECT] Processed 57003115 reads in 683 ms
[2015-09-30T22:06Z] INFO  23:06:26,016 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:26,487 MuTect - [MUTECT] Processed 14000520 reads in 686 ms
[2015-09-30T22:06Z] INFO  23:06:26,489 MuTect - [MUTECT] Processed 58003155 reads in 675 ms
[2015-09-30T22:06Z] INFO  23:06:26,683 MuTect - [MUTECT] Processed 42002622 reads in 910 ms
[2015-09-30T22:06Z] INFO  23:06:27,112 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:27,135 MuTect - [MUTECT] Processed 15000540 reads in 648 ms
[2015-09-30T22:06Z] INFO  23:06:27,159 MuTect - [MUTECT] Processed 59003221 reads in 670 ms
[2015-09-30T22:06Z] INFO  23:06:27,190 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:27,364 MuTect - [MUTECT] Processed 43002687 reads in 681 ms
[2015-09-30T22:06Z] INFO  23:06:27,785 MuTect - [MUTECT] Processed 60003268 reads in 626 ms
[2015-09-30T22:06Z] INFO  23:06:27,822 MuTect - [MUTECT] Processed 16000544 reads in 687 ms
[2015-09-30T22:06Z] INFO  23:06:28,056 MuTect - [MUTECT] Processed 44002761 reads in 692 ms
[2015-09-30T22:06Z] INFO  23:06:28,251 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:28,459 MuTect - [MUTECT] Processed 61003293 reads in 674 ms
[2015-09-30T22:06Z] INFO  23:06:28,494 MuTect - [MUTECT] Processed 17000546 reads in 672 ms
[2015-09-30T22:06Z] INFO  23:06:28,760 MuTect - [MUTECT] Processed 45002815 reads in 704 ms
[2015-09-30T22:06Z] INFO  23:06:29,150 MuTect - [MUTECT] Processed 62003336 reads in 691 ms
[2015-09-30T22:06Z] INFO  23:06:29,153 MuTect - [MUTECT] Processed 18000580 reads in 659 ms
[2015-09-30T22:06Z] INFO  23:06:29,461 MuTect - [MUTECT] Processed 46002870 reads in 701 ms
[2015-09-30T22:06Z] INFO  23:06:29,670 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:29,802 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:29,822 MuTect - [MUTECT] Processed 19000584 reads in 669 ms
[2015-09-30T22:06Z] INFO  23:06:29,824 MuTect - [MUTECT] Processed 63003346 reads in 674 ms
[2015-09-30T22:06Z] INFO  23:06:30,179 MuTect - [MUTECT] Processed 47002943 reads in 718 ms
[2015-09-30T22:06Z] INFO  23:06:30,469 MuTect - [MUTECT] Processed 64003396 reads in 645 ms
[2015-09-30T22:06Z] INFO  23:06:30,475 MuTect - [MUTECT] Processed 20000592 reads in 653 ms
[2015-09-30T22:06Z] INFO  23:06:30,684 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:30,875 MuTect - [MUTECT] Processed 48002952 reads in 696 ms
[2015-09-30T22:06Z] INFO  23:06:31,173 MuTect - [MUTECT] Processed 21000666 reads in 698 ms
[2015-09-30T22:06Z] INFO  23:06:31,177 MuTect - [MUTECT] Processed 65003446 reads in 708 ms
[2015-09-30T22:06Z] INFO  23:06:31,607 MuTect - [MUTECT] Processed 49002999 reads in 732 ms
[2015-09-30T22:06Z] INFO  23:06:31,871 MuTect - [MUTECT] Processed 66003494 reads in 694 ms
[2015-09-30T22:06Z] INFO  23:06:31,885 MuTect - [MUTECT] Processed 22000707 reads in 712 ms
[2015-09-30T22:06Z] INFO  23:06:32,173 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:32,296 MuTect - [MUTECT] Processed 50003019 reads in 689 ms
[2015-09-30T22:06Z] INFO  23:06:32,318 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:32,524 MuTect - [MUTECT] Processed 23000757 reads in 638 ms
[2015-09-30T22:06Z] INFO  23:06:32,551 MuTect - [MUTECT] Processed 67003519 reads in 680 ms
[2015-09-30T22:06Z] INFO  23:06:33,001 MuTect - [MUTECT] Processed 51003067 reads in 705 ms
[2015-09-30T22:06Z] INFO  23:06:33,189 MuTect - [MUTECT] Processed 24000816 reads in 666 ms
[2015-09-30T22:06Z] INFO  23:06:33,198 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:33,216 MuTect - [MUTECT] Processed 68003604 reads in 665 ms
[2015-09-30T22:06Z] INFO  23:06:33,675 MuTect - [MUTECT] Processed 52003105 reads in 674 ms
[2015-09-30T22:06Z] INFO  23:06:33,870 MuTect - [MUTECT] Processed 25000833 reads in 681 ms
[2015-09-30T22:06Z] INFO  23:06:33,883 MuTect - [MUTECT] Processed 69003628 reads in 667 ms
[2015-09-30T22:06Z] INFO  23:06:34,347 MuTect - [MUTECT] Processed 53003136 reads in 672 ms
[2015-09-30T22:06Z] INFO  23:06:34,564 MuTect - [MUTECT] Processed 70003632 reads in 681 ms
[2015-09-30T22:06Z] INFO  23:06:34,577 MuTect - [MUTECT] Processed 26000856 reads in 707 ms
[2015-09-30T22:06Z] INFO  23:06:34,763 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:34,839 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:35,015 MuTect - [MUTECT] Processed 54003199 reads in 668 ms
[2015-09-30T22:06Z] INFO  23:06:35,276 MuTect - [MUTECT] Processed 71003669 reads in 712 ms
[2015-09-30T22:06Z] INFO  23:06:35,342 MuTect - [MUTECT] Processed 27000867 reads in 765 ms
[2015-09-30T22:06Z] INFO  23:06:35,595 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:35,732 MuTect - [MUTECT] Processed 55003267 reads in 717 ms
[2015-09-30T22:06Z] INFO  23:06:35,976 MuTect - [MUTECT] Processed 72003676 reads in 700 ms
[2015-09-30T22:06Z] INFO  23:06:36,087 MuTect - [MUTECT] Processed 28000875 reads in 745 ms
[2015-09-30T22:06Z] INFO  23:06:36,424 MuTect - [MUTECT] Processed 56003282 reads in 692 ms
[2015-09-30T22:06Z] INFO  23:06:36,664 MuTect - [MUTECT] Processed 73003780 reads in 688 ms
[2015-09-30T22:06Z] INFO  23:06:36,833 MuTect - [MUTECT] Processed 29000921 reads in 746 ms
[2015-09-30T22:06Z] INFO  23:06:37,124 MuTect - [MUTECT] Processed 57003301 reads in 700 ms
[2015-09-30T22:06Z] INFO  23:06:37,250 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:37,332 MuTect - [MUTECT] Processed 74003894 reads in 668 ms
[2015-09-30T22:06Z] INFO  23:06:37,358 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:37,547 MuTect - [MUTECT] Processed 30000960 reads in 714 ms
[2015-09-30T22:06Z] INFO  23:06:37,808 MuTect - [MUTECT] Processed 58003391 reads in 684 ms
[2015-09-30T22:06Z] INFO  23:06:38,014 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:38,031 MuTect - [MUTECT] Processed 75003954 reads in 699 ms
[2015-09-30T22:06Z] INFO  23:06:38,214 MuTect - [MUTECT] Processed 31000979 reads in 667 ms
[2015-09-30T22:06Z] INFO  23:06:38,520 MuTect - [MUTECT] Processed 59003414 reads in 712 ms
[2015-09-30T22:06Z] INFO  23:06:38,701 MuTect - [MUTECT] Processed 76004020 reads in 669 ms
[2015-09-30T22:06Z] INFO  23:06:38,860 MuTect - [MUTECT] Processed 32001007 reads in 646 ms
[2015-09-30T22:06Z] INFO  23:06:39,228 MuTect - [MUTECT] Processed 60003483 reads in 708 ms
[2015-09-30T22:06Z] INFO  23:06:39,378 MuTect - [MUTECT] Processed 77004091 reads in 678 ms
[2015-09-30T22:06Z] INFO  23:06:39,510 MuTect - [MUTECT] Processed 33001065 reads in 650 ms
[2015-09-30T22:06Z] INFO  23:06:39,927 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:39,959 MuTect - [MUTECT] Processed 61003507 reads in 731 ms
[2015-09-30T22:06Z] INFO  23:06:40,051 MuTect - [MUTECT] Processed 78004126 reads in 673 ms
[2015-09-30T22:06Z] INFO  23:06:40,115 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:40,210 MuTect - [MUTECT] Processed 34001097 reads in 700 ms
[2015-09-30T22:06Z] INFO  23:06:40,685 MuTect - [MUTECT] Processed 62003558 reads in 726 ms
[2015-09-30T22:06Z] INFO  23:06:40,734 MuTect - [MUTECT] Processed 79004135 reads in 683 ms
[2015-09-30T22:06Z] INFO  23:06:40,888 MuTect - [MUTECT] Processed 35001140 reads in 678 ms
[2015-09-30T22:06Z] INFO  23:06:41,162 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:41,353 MuTect - [MUTECT] Processed 63003611 reads in 668 ms
[2015-09-30T22:06Z] INFO  23:06:41,414 MuTect - [MUTECT] Processed 80004166 reads in 680 ms
[2015-09-30T22:06Z] INFO  23:06:41,563 MuTect - [MUTECT] Processed 36001160 reads in 675 ms
[2015-09-30T22:06Z] INFO  23:06:42,091 MuTect - [MUTECT] Processed 81004209 reads in 677 ms
[2015-09-30T22:06Z] INFO  23:06:42,115 MuTect - [MUTECT] Processed 64003658 reads in 762 ms
[2015-09-30T22:06Z] INFO  23:06:42,251 MuTect - [MUTECT] Processed 37001169 reads in 688 ms
[2015-09-30T22:06Z] INFO  23:06:42,593 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:42,608 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:42,786 MuTect - [MUTECT] Processed 82004227 reads in 695 ms
[2015-09-30T22:06Z] INFO  23:06:42,794 MuTect - [MUTECT] Processed 65003701 reads in 679 ms
[2015-09-30T22:06Z] INFO  23:06:42,907 MuTect - [MUTECT] Processed 38001169 reads in 656 ms
[2015-09-30T22:06Z] INFO  23:06:43,450 MuTect - [MUTECT] Processed 83004270 reads in 664 ms
[2015-09-30T22:06Z] INFO  23:06:43,482 MuTect - [MUTECT] Processed 66003724 reads in 688 ms
[2015-09-30T22:06Z] INFO  23:06:43,533 MuTect - [MUTECT] Processed 39001202 reads in 626 ms
[2015-09-30T22:06Z] INFO  23:06:43,728 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:44,088 MuTect - [MUTECT] Processed 84004276 reads in 638 ms
[2015-09-30T22:06Z] INFO  23:06:44,122 MuTect - [MUTECT] Processed 67003744 reads in 640 ms
[2015-09-30T22:06Z] INFO  23:06:44,157 ProgressMeter -     2:170145565        1.56e+06   30.0 s       19.0 s     36.4%        82.0 s    52.0 s
[2015-09-30T22:06Z] INFO  23:06:44,192 MuTect - [MUTECT] Processed 40001251 reads in 659 ms
[2015-09-30T22:06Z] INFO  23:06:44,377 ProgressMeter -     2:109408434        2.70e+06   60.0 s       22.0 s     58.5%       102.0 s    42.0 s
[2015-09-30T22:06Z] INFO  23:06:44,762 MuTect - [MUTECT] Processed 85004368 reads in 674 ms
[2015-09-30T22:06Z] INFO  23:06:44,797 MuTect - [MUTECT] Processed 68003851 reads in 675 ms
[2015-09-30T22:06Z] INFO  23:06:44,888 MuTect - [MUTECT] Processed 41001279 reads in 696 ms
[2015-09-30T22:06Z] INFO  23:06:44,998 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:45,047 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:45,423 MuTect - [MUTECT] Processed 86004399 reads in 661 ms
[2015-09-30T22:06Z] INFO  23:06:45,449 MuTect - [MUTECT] Processed 69003884 reads in 652 ms
[2015-09-30T22:06Z] INFO  23:06:45,573 MuTect - [MUTECT] Processed 42001306 reads in 685 ms
[2015-09-30T22:06Z] INFO  23:06:46,100 MuTect - [MUTECT] Processed 70003982 reads in 651 ms
[2015-09-30T22:06Z] INFO  23:06:46,105 MuTect - [MUTECT] Processed 87004467 reads in 682 ms
[2015-09-30T22:06Z] INFO  23:06:46,124 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:46,292 MuTect - [MUTECT] Processed 43001389 reads in 719 ms
[2015-09-30T22:06Z] INFO  23:06:46,733 MuTect - [MUTECT] Processed 88004519 reads in 628 ms
[2015-09-30T22:06Z] INFO  23:06:46,785 MuTect - [MUTECT] Processed 71004043 reads in 685 ms
[2015-09-30T22:06Z] INFO  23:06:46,978 MuTect - [MUTECT] Processed 44001443 reads in 686 ms
[2015-09-30T22:06Z] INFO  23:06:47,355 MuTect - [MUTECT] Processed 89004533 reads in 622 ms
[2015-09-30T22:06Z] INFO  23:06:47,485 MuTect - [MUTECT] Processed 72004077 reads in 700 ms
[2015-09-30T22:06Z] INFO  23:06:47,535 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:47,611 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:47,678 MuTect - [MUTECT] Processed 45001526 reads in 700 ms
[2015-09-30T22:06Z] INFO  23:06:47,916 MuTect - [MUTECT] Processed 90004610 reads in 561 ms
[2015-09-30T22:06Z] INFO  23:06:48,160 MuTect - [MUTECT] Processed 73004126 reads in 675 ms
[2015-09-30T22:06Z] INFO  23:06:48,362 MuTect - [MUTECT] Processed 46001533 reads in 683 ms
[2015-09-30T22:06Z] INFO  23:06:48,487 MuTect - [MUTECT] Processed 91004677 reads in 571 ms
[2015-09-30T22:06Z] INFO  23:06:48,791 MuTect - [MUTECT] Processed 74004189 reads in 631 ms
[2015-09-30T22:06Z] INFO  23:06:49,046 MuTect - [MUTECT] Processed 47001620 reads in 685 ms
[2015-09-30T22:06Z] INFO  23:06:49,091 MuTect - [MUTECT] Processed 92004700 reads in 604 ms
[2015-09-30T22:06Z] INFO  23:06:49,454 MuTect - [MUTECT] Processed 75004194 reads in 663 ms
[2015-09-30T22:06Z] INFO  23:06:49,728 MuTect - [MUTECT] Processed 48001650 reads in 682 ms
[2015-09-30T22:06Z] INFO  23:06:49,731 MuTect - [MUTECT] Processed 93004753 reads in 640 ms
[2015-09-30T22:06Z] INFO  23:06:49,957 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:50,082 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:50,100 MuTect - [MUTECT] Processed 76004260 reads in 646 ms
[2015-09-30T22:06Z] INFO  23:06:50,327 MuTect - [MUTECT] Processed 94004834 reads in 596 ms
[2015-09-30T22:06Z] INFO  23:06:50,446 MuTect - [MUTECT] Processed 49001712 reads in 718 ms
[2015-09-30T22:06Z] INFO  23:06:50,710 MuTect - [MUTECT] Processed 77004304 reads in 610 ms
[2015-09-30T22:06Z] INFO  23:06:50,788 ProgressMeter -     2:152443852        2.55e+06   60.0 s       23.0 s     83.1%        72.0 s    12.0 s
[2015-09-30T22:06Z] INFO  23:06:50,912 MuTect - [MUTECT] Processed 95004849 reads in 584 ms
[2015-09-30T22:06Z] INFO  23:06:51,138 MuTect - [MUTECT] Processed 50001812 reads in 692 ms
[2015-09-30T22:06Z] INFO  23:06:51,280 MuTect - [MUTECT] Processed 78004385 reads in 570 ms
[2015-09-30T22:06Z] INFO  23:06:51,494 MuTect - [MUTECT] Processed 96004886 reads in 583 ms
[2015-09-30T22:06Z] INFO  23:06:51,673 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:51,834 MuTect - [MUTECT] Processed 51001841 reads in 696 ms
[2015-09-30T22:06Z] INFO  23:06:51,924 MuTect - [MUTECT] Processed 79004401 reads in 644 ms
[2015-09-30T22:06Z] INFO  23:06:52,138 MuTect - [MUTECT] Processed 97004975 reads in 644 ms
[2015-09-30T22:06Z] INFO  23:06:52,528 MuTect - [MUTECT] Processed 52001846 reads in 694 ms
[2015-09-30T22:06Z] INFO  23:06:52,540 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:52,573 MuTect - [MUTECT] Processed 80004458 reads in 649 ms
[2015-09-30T22:06Z] INFO  23:06:52,794 MuTect - [MUTECT] Processed 98005072 reads in 656 ms
[2015-09-30T22:06Z] INFO  23:06:53,085 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:53,205 MuTect - [MUTECT] Processed 53001895 reads in 677 ms
[2015-09-30T22:06Z] INFO  23:06:53,236 MuTect - [MUTECT] Processed 81004508 reads in 663 ms
[2015-09-30T22:06Z] INFO  23:06:53,449 MuTect - [MUTECT] Processed 99005160 reads in 655 ms
[2015-09-30T22:06Z] INFO  23:06:53,871 MuTect - [MUTECT] Processed 54001970 reads in 666 ms
[2015-09-30T22:06Z] INFO  23:06:53,921 MuTect - [MUTECT] Processed 82004544 reads in 685 ms
[2015-09-30T22:06Z] INFO  23:06:54,081 MuTect - [MUTECT] Processed 100005197 reads in 631 ms
[2015-09-30T22:06Z] INFO  23:06:54,325 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:54,575 MuTect - [MUTECT] Processed 55002025 reads in 704 ms
[2015-09-30T22:06Z] INFO  23:06:54,654 MuTect - [MUTECT] Processed 83004605 reads in 733 ms
[2015-09-30T22:06Z] INFO  23:06:54,715 MuTect - [MUTECT] Processed 101005264 reads in 635 ms
[2015-09-30T22:06Z] INFO  23:06:54,909 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:55,227 MuTect - [MUTECT] Processed 56002027 reads in 652 ms
[2015-09-30T22:06Z] INFO  23:06:55,358 MuTect - [MUTECT] Processed 102005303 reads in 643 ms
[2015-09-30T22:06Z] INFO  23:06:55,374 MuTect - [MUTECT] Processed 84004697 reads in 720 ms
[2015-09-30T22:06Z] INFO  23:06:55,737 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:55,901 MuTect - [MUTECT] Processed 57002112 reads in 674 ms
[2015-09-30T22:06Z] INFO  23:06:56,055 MuTect - [MUTECT] Processed 103005321 reads in 697 ms
[2015-09-30T22:06Z] INFO  23:06:56,061 MuTect - [MUTECT] Processed 85004743 reads in 687 ms
[2015-09-30T22:06Z] INFO  23:06:56,543 MuTect - [MUTECT] Processed 58002141 reads in 642 ms
[2015-09-30T22:06Z] INFO  23:06:56,735 MuTect - [MUTECT] Processed 104005342 reads in 680 ms
[2015-09-30T22:06Z] INFO  23:06:56,768 MuTect - [MUTECT] Processed 86004792 reads in 707 ms
[2015-09-30T22:06Z] INFO  23:06:57,017 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:57,204 MuTect - [MUTECT] Processed 59002180 reads in 661 ms
[2015-09-30T22:06Z] INFO  23:06:57,314 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:57,372 MuTect - [MUTECT] Processed 105005380 reads in 637 ms
[2015-09-30T22:06Z] INFO  23:06:57,482 MuTect - [MUTECT] Processed 87004881 reads in 714 ms
[2015-09-30T22:06Z] INFO  23:06:57,886 MuTect - [MUTECT] Processed 60002203 reads in 682 ms
[2015-09-30T22:06Z] INFO  23:06:57,997 MuTect - [MUTECT] Processed 106005412 reads in 625 ms
[2015-09-30T22:06Z] INFO  23:06:58,170 MuTect - [MUTECT] Processed 88004887 reads in 688 ms
[2015-09-30T22:06Z] INFO  23:06:58,409 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:58,536 MuTect - [MUTECT] Processed 61002275 reads in 650 ms
[2015-09-30T22:06Z] INFO  23:06:58,604 MuTect - [MUTECT] Processed 107005436 reads in 607 ms
[2015-09-30T22:06Z] INFO  23:06:58,838 MuTect - [MUTECT] Processed 89004974 reads in 668 ms
[2015-09-30T22:06Z] INFO  23:06:59,188 MuTect - [MUTECT] Processed 62002377 reads in 652 ms
[2015-09-30T22:06Z] INFO  23:06:59,223 MuTect - [MUTECT] Processed 108005509 reads in 619 ms
[2015-09-30T22:06Z] INFO  23:06:59,552 MuTect - [MUTECT] Processed 90005011 reads in 714 ms
[2015-09-30T22:06Z] INFO  23:06:59,657 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:59,817 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:06Z] INFO  23:06:59,856 MuTect - [MUTECT] Processed 63002394 reads in 668 ms
[2015-09-30T22:06Z] INFO  23:06:59,864 MuTect - [MUTECT] Processed 109005589 reads in 641 ms
[2015-09-30T22:06Z] INFO  23:06:59,948 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:06Z] INFO  23:06:59,951 ProgressMeter -            done        3.14e+06   69.0 s       22.0 s    100.0%        69.0 s     0.0 s
[2015-09-30T22:06Z] INFO  23:06:59,952 ProgressMeter - Total runtime 69.17 secs, 1.15 min, 0.02 hours
[2015-09-30T22:07Z] INFO  23:07:00,018 MicroScheduler - 65616 reads were filtered out during the traversal out of approximately 1077470 total reads (6.09%)
[2015-09-30T22:07Z] INFO  23:07:00,018 MicroScheduler -   -> 48558 reads (4.51% of total) failing DuplicateReadFilter
[2015-09-30T22:07Z] INFO  23:07:00,018 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:07Z] INFO  23:07:00,018 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:07Z] INFO  23:07:00,018 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:07Z] INFO  23:07:00,018 MicroScheduler -   -> 17058 reads (1.58% of total) failing UnmappedReadFilter
[2015-09-30T22:07Z] INFO  23:07:00,509 MuTect - [MUTECT] Processed 110005689 reads in 645 ms
[2015-09-30T22:07Z] INFO  23:07:00,527 MuTect - [MUTECT] Processed 64002475 reads in 671 ms
[2015-09-30T22:07Z] INFO  23:07:01,111 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:07Z] INFO  23:07:01,144 MuTect - [MUTECT] Processed 111005742 reads in 635 ms
[2015-09-30T22:07Z] bgzip syn3-2_127413596_158444156-raw-mutect.vcf
[2015-09-30T22:07Z] INFO  23:07:01,210 MuTect - [MUTECT] Processed 65002547 reads in 683 ms
[2015-09-30T22:07Z] tabix index syn3-2_127413596_158444156-raw-mutect.vcf.gz
[2015-09-30T22:07Z] INFO  23:07:01,803 MuTect - [MUTECT] Processed 112005810 reads in 659 ms
[2015-09-30T22:07Z] INFO  23:07:01,888 MuTect - [MUTECT] Processed 66002596 reads in 678 ms
[2015-09-30T22:07Z] INFO  23:07:02,076 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:02,153 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:02,443 MuTect - [MUTECT] Processed 113005877 reads in 640 ms
[2015-09-30T22:07Z] INFO  23:07:02,567 MuTect - [MUTECT] Processed 67002655 reads in 679 ms
[2015-09-30T22:07Z] INFO  23:07:03,113 MuTect - [MUTECT] Processed 114005984 reads in 670 ms
[2015-09-30T22:07Z] INFO  23:07:03,266 MuTect - [MUTECT] Processed 68002705 reads in 699 ms
[2015-09-30T22:07Z] MuTect: MuTect
[2015-09-30T22:07Z] INFO  23:07:03,771 MuTect - [MUTECT] Processed 115005987 reads in 658 ms
[2015-09-30T22:07Z] INFO  23:07:03,934 MuTect - [MUTECT] Processed 69002718 reads in 668 ms
[2015-09-30T22:07Z] INFO  23:07:04,281 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:04,415 MuTect - [MUTECT] Processed 116006028 reads in 644 ms
[2015-09-30T22:07Z] INFO  23:07:04,583 MuTect - [MUTECT] Processed 70002788 reads in 649 ms
[2015-09-30T22:07Z] INFO  23:07:04,617 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:05,061 MuTect - [MUTECT] Processed 117006042 reads in 646 ms
[2015-09-30T22:07Z] INFO  23:07:05,231 MuTect - [MUTECT] Processed 71002812 reads in 648 ms
[2015-09-30T22:07Z] INFO  23:07:05,850 MuTect - [MUTECT] Processed 118006092 reads in 789 ms
[2015-09-30T22:07Z] INFO  23:07:05,945 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/2/syn3-2_189838937_221056966-raw-mutect-regions.bed to be BED
[2015-09-30T22:07Z] INFO  23:07:05,968 MuTect - [MUTECT] Processed 72002870 reads in 737 ms
[2015-09-30T22:07Z] INFO  23:07:06,001 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:07Z] INFO  23:07:06,002 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:07Z] INFO  23:07:06,002 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:07Z] INFO  23:07:06,002 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:07Z] INFO  23:07:06,005 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/2/syn3-2_189838937_221056966-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/2/tx/tmpkVNH7k/syn3-2_189838937_221056966-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:07Z] INFO  23:07:06,006 HelpFormatter - Date/Time: 2015/09/30 23:07:06
[2015-09-30T22:07Z] INFO  23:07:06,006 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:07Z] INFO  23:07:06,006 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:07Z] INFO  23:07:06,106 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:07Z] INFO  23:07:06,207 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:07Z] INFO  23:07:06,258 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:07Z] INFO  23:07:06,398 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:07Z] INFO  23:07:06,406 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:07Z] INFO  23:07:06,542 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
[2015-09-30T22:07Z] INFO  23:07:06,699 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:07Z] INFO  23:07:06,774 MuTect - [MUTECT] Processed 73002875 reads in 806 ms
[2015-09-30T22:07Z] INFO  23:07:06,823 MuTect - [MUTECT] Processed 119006221 reads in 973 ms
[2015-09-30T22:07Z] INFO  23:07:06,887 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:07Z] INFO  23:07:07,001 IntervalUtils - Processing 1927521 bp from intervals
[2015-09-30T22:07Z] INFO  23:07:07,005 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:07Z] INFO  23:07:07,005 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:07Z] INFO  23:07:07,148 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:07,181 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:07Z] INFO  23:07:07,344 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:07Z] INFO  23:07:07,344 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:07Z] INFO  23:07:07,345 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:07Z] INFO  23:07:07,346 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:07Z] INFO  23:07:07,364 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:07,466 MuTect - [MUTECT] Processed 74002936 reads in 692 ms
[2015-09-30T22:07Z] INFO  23:07:07,731 MuTect - [MUTECT] Processed 120006296 reads in 908 ms
[2015-09-30T22:07Z] INFO  23:07:08,175 MuTect - [MUTECT] Processed 75003002 reads in 709 ms
[2015-09-30T22:07Z] INFO  23:07:08,427 MuTect - [MUTECT] Processed 121006329 reads in 696 ms
[2015-09-30T22:07Z] INFO  23:07:08,833 MuTect - [MUTECT] Processed 76003005 reads in 658 ms
[2015-09-30T22:07Z] INFO  23:07:09,123 MuTect - [MUTECT] Processed 122006400 reads in 696 ms
[2015-09-30T22:07Z] INFO  23:07:09,492 MuTect - [MUTECT] Processed 77003077 reads in 659 ms
[2015-09-30T22:07Z] INFO  23:07:09,733 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:09,773 MuTect - [MUTECT] Processed 1000010 reads in 2381 ms
[2015-09-30T22:07Z] INFO  23:07:09,874 MuTect - [MUTECT] Processed 123006444 reads in 751 ms
[2015-09-30T22:07Z] INFO  23:07:09,933 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:10,169 MuTect - [MUTECT] Processed 78003151 reads in 677 ms
[2015-09-30T22:07Z] INFO  23:07:10,535 MuTect - [MUTECT] Processed 124006468 reads in 661 ms
[2015-09-30T22:07Z] INFO  23:07:10,716 MuTect - [MUTECT] Processed 2000085 reads in 943 ms
[2015-09-30T22:07Z] INFO  23:07:10,803 MuTect - [MUTECT] Processed 79003224 reads in 634 ms
[2015-09-30T22:07Z] INFO  23:07:11,199 MuTect - [MUTECT] Processed 125006551 reads in 664 ms
[2015-09-30T22:07Z] INFO  23:07:11,449 MuTect - [MUTECT] Processed 80003229 reads in 646 ms
[2015-09-30T22:07Z] INFO  23:07:11,462 MuTect - [MUTECT] Processed 3000091 reads in 746 ms
[2015-09-30T22:07Z] INFO  23:07:11,878 MuTect - [MUTECT] Processed 126006568 reads in 679 ms
[2015-09-30T22:07Z] INFO  23:07:12,062 MuTect - [MUTECT] Processed 81003320 reads in 613 ms
[2015-09-30T22:07Z] INFO  23:07:12,120 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:12,171 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:12,237 MuTect - [MUTECT] Processed 4000100 reads in 774 ms
[2015-09-30T22:07Z] INFO  23:07:12,261 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:12,536 MuTect - [MUTECT] Processed 127006656 reads in 658 ms
[2015-09-30T22:07Z] INFO  23:07:12,665 MuTect - [MUTECT] Processed 82003409 reads in 602 ms
[2015-09-30T22:07Z] INFO  23:07:12,959 MuTect - [MUTECT] Processed 5000101 reads in 722 ms
[2015-09-30T22:07Z] INFO  23:07:13,182 MuTect - [MUTECT] Processed 128006703 reads in 646 ms
[2015-09-30T22:07Z] INFO  23:07:13,287 MuTect - [MUTECT] Processed 83003461 reads in 623 ms
[2015-09-30T22:07Z] INFO  23:07:13,670 MuTect - [MUTECT] Processed 6000108 reads in 712 ms
[2015-09-30T22:07Z] INFO  23:07:13,787 MuTect - [MUTECT] Processed 129006749 reads in 605 ms
[2015-09-30T22:07Z] INFO  23:07:13,917 MuTect - [MUTECT] Processed 84003486 reads in 630 ms
[2015-09-30T22:07Z] INFO  23:07:14,158 ProgressMeter -     2:179441269        3.05e+06   60.0 s       19.0 s     73.3%        81.0 s    21.0 s
[2015-09-30T22:07Z] INFO  23:07:14,378 ProgressMeter -     2:120282015        4.07e+06   90.0 s       22.0 s     91.0%        98.0 s     8.0 s
[2015-09-30T22:07Z] INFO  23:07:14,409 MuTect - [MUTECT] Processed 7000129 reads in 739 ms
[2015-09-30T22:07Z] INFO  23:07:14,427 MuTect - [MUTECT] Processed 130006759 reads in 640 ms
[2015-09-30T22:07Z] INFO  23:07:14,430 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:14,448 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:14,543 MuTect - [MUTECT] Processed 85003559 reads in 626 ms
[2015-09-30T22:07Z] INFO  23:07:14,989 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:15,086 MuTect - [MUTECT] Processed 131006800 reads in 659 ms
[2015-09-30T22:07Z] INFO  23:07:15,096 MuTect - [MUTECT] Processed 8000166 reads in 686 ms
[2015-09-30T22:07Z] INFO  23:07:15,185 MuTect - [MUTECT] Processed 86003600 reads in 642 ms
[2015-09-30T22:07Z] INFO  23:07:15,777 MuTect - [MUTECT] Processed 9000200 reads in 682 ms
[2015-09-30T22:07Z] INFO  23:07:15,786 MuTect - [MUTECT] Processed 132006832 reads in 700 ms
[2015-09-30T22:07Z] INFO  23:07:15,849 MuTect - [MUTECT] Processed 87003666 reads in 664 ms
[2015-09-30T22:07Z] INFO  23:07:16,457 MuTect - [MUTECT] Processed 10000212 reads in 680 ms
[2015-09-30T22:07Z] INFO  23:07:16,461 MuTect - [MUTECT] Processed 133006893 reads in 675 ms
[2015-09-30T22:07Z] INFO  23:07:16,515 MuTect - [MUTECT] Processed 88003703 reads in 666 ms
[2015-09-30T22:07Z] INFO  23:07:16,889 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:17,112 MuTect - [MUTECT] Processed 134006995 reads in 651 ms
[2015-09-30T22:07Z] INFO  23:07:17,133 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:17,142 MuTect - [MUTECT] Processed 11000314 reads in 685 ms
[2015-09-30T22:07Z] INFO  23:07:17,158 MuTect - [MUTECT] Processed 89003780 reads in 643 ms
[2015-09-30T22:07Z] INFO  23:07:17,609 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:17,790 MuTect - [MUTECT] Processed 135007118 reads in 678 ms
[2015-09-30T22:07Z] INFO  23:07:17,812 MuTect - [MUTECT] Processed 90003788 reads in 654 ms
[2015-09-30T22:07Z] INFO  23:07:17,838 MuTect - [MUTECT] Processed 12000334 reads in 696 ms
[2015-09-30T22:07Z] INFO  23:07:18,423 MuTect - [MUTECT] Processed 136007213 reads in 633 ms
[2015-09-30T22:07Z] INFO  23:07:18,427 MuTect - [MUTECT] Processed 91003817 reads in 615 ms
[2015-09-30T22:07Z] INFO  23:07:18,561 MuTect - [MUTECT] Processed 13000365 reads in 723 ms
[2015-09-30T22:07Z] INFO  23:07:19,060 MuTect - [MUTECT] Processed 92003869 reads in 633 ms
[2015-09-30T22:07Z] INFO  23:07:19,084 MuTect - [MUTECT] Processed 137007338 reads in 661 ms
[2015-09-30T22:07Z] INFO  23:07:19,187 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:19,281 MuTect - [MUTECT] Processed 14000369 reads in 720 ms
[2015-09-30T22:07Z] INFO  23:07:19,421 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:19,652 MuTect - [MUTECT] Processed 93003954 reads in 592 ms
[2015-09-30T22:07Z] INFO  23:07:19,697 MuTect - [MUTECT] Processed 138007371 reads in 613 ms
[2015-09-30T22:07Z] INFO  23:07:19,993 MuTect - [MUTECT] Processed 15000407 reads in 712 ms
[2015-09-30T22:07Z] INFO  23:07:20,214 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:20,273 MuTect - [MUTECT] Processed 94004029 reads in 621 ms
[2015-09-30T22:07Z] INFO  23:07:20,309 MuTect - [MUTECT] Processed 139007382 reads in 612 ms
[2015-09-30T22:07Z] INFO  23:07:20,711 MuTect - [MUTECT] Processed 16000449 reads in 718 ms
[2015-09-30T22:07Z] INFO  23:07:20,888 MuTect - [MUTECT] Processed 95004045 reads in 615 ms
[2015-09-30T22:07Z] INFO  23:07:20,970 MuTect - [MUTECT] Processed 140007410 reads in 661 ms
[2015-09-30T22:07Z] INFO  23:07:21,134 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:21,444 MuTect - [MUTECT] Processed 17000464 reads in 733 ms
[2015-09-30T22:07Z] INFO  23:07:21,506 MuTect - [MUTECT] Processed 96004048 reads in 618 ms
[2015-09-30T22:07Z] INFO  23:07:21,587 MuTect - [MUTECT] Processed 141007439 reads in 617 ms
[2015-09-30T22:07Z] INFO  23:07:21,671 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:22,154 MuTect - [MUTECT] Processed 97004064 reads in 648 ms
[2015-09-30T22:07Z] INFO  23:07:22,171 MuTect - [MUTECT] Processed 18000473 reads in 727 ms
[2015-09-30T22:07Z] INFO  23:07:22,202 MuTect - [MUTECT] Processed 142007463 reads in 615 ms
[2015-09-30T22:07Z] INFO  23:07:22,247 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:07Z] INFO  23:07:22,251 ProgressMeter -            done        4.39e+06   97.0 s       22.0 s    100.0%        97.0 s     0.0 s
[2015-09-30T22:07Z] INFO  23:07:22,251 ProgressMeter - Total runtime 97.88 secs, 1.63 min, 0.03 hours
[2015-09-30T22:07Z] INFO  23:07:22,314 MicroScheduler - 102614 reads were filtered out during the traversal out of approximately 1694345 total reads (6.06%)
[2015-09-30T22:07Z] INFO  23:07:22,315 MicroScheduler -   -> 75548 reads (4.46% of total) failing DuplicateReadFilter
[2015-09-30T22:07Z] INFO  23:07:22,315 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:07Z] INFO  23:07:22,315 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:07Z] INFO  23:07:22,315 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:07Z] INFO  23:07:22,315 MicroScheduler -   -> 27066 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:07Z] INFO  23:07:22,822 MuTect - [MUTECT] Processed 98004149 reads in 668 ms
[2015-09-30T22:07Z] INFO  23:07:22,953 MuTect - [MUTECT] Processed 19000513 reads in 782 ms
[2015-09-30T22:07Z] INFO  23:07:23,008 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:23,318 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:07Z] bgzip syn3-2_95457728_127315933-raw-mutect.vcf
[2015-09-30T22:07Z] INFO  23:07:23,488 MuTect - [MUTECT] Processed 99004154 reads in 666 ms
[2015-09-30T22:07Z] tabix index syn3-2_95457728_127315933-raw-mutect.vcf.gz
[2015-09-30T22:07Z] INFO  23:07:23,695 MuTect - [MUTECT] Processed 20000581 reads in 742 ms
[2015-09-30T22:07Z] INFO  23:07:24,199 MuTect - [MUTECT] Processed 100004182 reads in 711 ms
[2015-09-30T22:07Z] INFO  23:07:24,358 MuTect - [MUTECT] Processed 21000588 reads in 663 ms
[2015-09-30T22:07Z] INFO  23:07:24,375 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:24,925 MuTect - [MUTECT] Processed 101004255 reads in 726 ms
[2015-09-30T22:07Z] INFO  23:07:25,009 MuTect - [MUTECT] Processed 22000592 reads in 651 ms
[2015-09-30T22:07Z] INFO  23:07:25,479 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:25,587 MuTect - [MUTECT] Processed 102004282 reads in 662 ms
[2015-09-30T22:07Z] INFO  23:07:25,698 MuTect - [MUTECT] Processed 23000660 reads in 689 ms
[2015-09-30T22:07Z] MuTect: MuTect
[2015-09-30T22:07Z] INFO  23:07:26,318 MuTect - [MUTECT] Processed 103004315 reads in 731 ms
[2015-09-30T22:07Z] INFO  23:07:26,375 MuTect - [MUTECT] Processed 24000715 reads in 677 ms
[2015-09-30T22:07Z] INFO  23:07:27,030 MuTect - [MUTECT] Processed 104004324 reads in 712 ms
[2015-09-30T22:07Z] INFO  23:07:27,043 MuTect - [MUTECT] Processed 25000720 reads in 668 ms
[2015-09-30T22:07Z] INFO  23:07:27,065 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:27,689 MuTect - [MUTECT] Processed 26000819 reads in 646 ms
[2015-09-30T22:07Z] INFO  23:07:27,729 MuTect - [MUTECT] Processed 105004342 reads in 699 ms
[2015-09-30T22:07Z] INFO  23:07:27,829 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:27,869 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/2/syn3-2_221341378_243199373-raw-mutect-regions.bed to be BED
[2015-09-30T22:07Z] INFO  23:07:27,925 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:07Z] INFO  23:07:27,925 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:07Z] INFO  23:07:27,925 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:07Z] INFO  23:07:27,925 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:07Z] INFO  23:07:27,929 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/2/syn3-2_221341378_243199373-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/2/tx/tmp159X5K/syn3-2_221341378_243199373-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:07Z] INFO  23:07:27,929 HelpFormatter - Date/Time: 2015/09/30 23:07:27
[2015-09-30T22:07Z] INFO  23:07:27,929 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:07Z] INFO  23:07:27,929 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:07Z] INFO  23:07:27,956 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:07Z] INFO  23:07:27,960 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:07Z] INFO  23:07:28,014 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:07Z] INFO  23:07:28,062 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:07Z] INFO  23:07:28,069 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:07Z] INFO  23:07:28,119 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T22:07Z] INFO  23:07:28,146 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:07Z] INFO  23:07:28,321 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:07Z] INFO  23:07:28,354 MuTect - [MUTECT] Processed 27000841 reads in 665 ms
[2015-09-30T22:07Z] INFO  23:07:28,425 IntervalUtils - Processing 1372298 bp from intervals
[2015-09-30T22:07Z] INFO  23:07:28,429 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:07Z] INFO  23:07:28,429 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:07Z] INFO  23:07:28,444 MuTect - [MUTECT] Processed 106004393 reads in 715 ms
[2015-09-30T22:07Z] INFO  23:07:28,746 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:07Z] INFO  23:07:28,889 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:07Z] INFO  23:07:28,889 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:07Z] INFO  23:07:28,890 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:07Z] INFO  23:07:28,891 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:07Z] INFO  23:07:29,041 MuTect - [MUTECT] Processed 28000889 reads in 686 ms
[2015-09-30T22:07Z] INFO  23:07:29,154 MuTect - [MUTECT] Processed 107004397 reads in 710 ms
[2015-09-30T22:07Z] INFO  23:07:29,532 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:29,710 MuTect - [MUTECT] Processed 29000962 reads in 670 ms
[2015-09-30T22:07Z] INFO  23:07:29,786 MuTect - [MUTECT] Processed 108004406 reads in 632 ms
[2015-09-30T22:07Z] INFO  23:07:30,294 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:30,413 MuTect - [MUTECT] Processed 30001011 reads in 703 ms
[2015-09-30T22:07Z] INFO  23:07:30,479 MuTect - [MUTECT] Processed 109004484 reads in 693 ms
[2015-09-30T22:07Z] INFO  23:07:31,096 MuTect - [MUTECT] Processed 31001025 reads in 683 ms
[2015-09-30T22:07Z] INFO  23:07:31,203 MuTect - [MUTECT] Processed 110004552 reads in 724 ms
[2015-09-30T22:07Z] INFO  23:07:31,587 MuTect - [MUTECT] Processed 1000052 reads in 2647 ms
[2015-09-30T22:07Z] INFO  23:07:31,933 MuTect - [MUTECT] Processed 111004571 reads in 730 ms
[2015-09-30T22:07Z] INFO  23:07:31,980 MuTect - [MUTECT] Processed 32001064 reads in 884 ms
[2015-09-30T22:07Z] INFO  23:07:32,050 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:32,300 MuTect - [MUTECT] Processed 2000064 reads in 714 ms
[2015-09-30T22:07Z] INFO  23:07:32,609 MuTect - [MUTECT] Processed 33001092 reads in 629 ms
[2015-09-30T22:07Z] INFO  23:07:32,671 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:07Z] INFO  23:07:32,675 ProgressMeter -            done        4.36e+06   78.0 s       18.0 s    100.0%        78.0 s     0.0 s
[2015-09-30T22:07Z] INFO  23:07:32,675 ProgressMeter - Total runtime 78.52 secs, 1.31 min, 0.02 hours
[2015-09-30T22:07Z] INFO  23:07:32,742 MicroScheduler - 73965 reads were filtered out during the traversal out of approximately 1314502 total reads (5.63%)
[2015-09-30T22:07Z] INFO  23:07:32,742 MicroScheduler -   -> 52661 reads (4.01% of total) failing DuplicateReadFilter
[2015-09-30T22:07Z] INFO  23:07:32,742 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:07Z] INFO  23:07:32,742 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:07Z] INFO  23:07:32,742 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:07Z] INFO  23:07:32,742 MicroScheduler -   -> 21304 reads (1.62% of total) failing UnmappedReadFilter
[2015-09-30T22:07Z] INFO  23:07:32,918 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:32,996 MuTect - [MUTECT] Processed 3000088 reads in 696 ms
[2015-09-30T22:07Z] INFO  23:07:33,234 MuTect - [MUTECT] Processed 34001142 reads in 625 ms
[2015-09-30T22:07Z] INFO  23:07:33,470 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:33,722 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:07Z] INFO  23:07:33,735 MuTect - [MUTECT] Processed 4000119 reads in 739 ms
[2015-09-30T22:07Z] bgzip syn3-2_158484801_189599894-raw-mutect.vcf
[2015-09-30T22:07Z] tabix index syn3-2_158484801_189599894-raw-mutect.vcf.gz
[2015-09-30T22:07Z] INFO  23:07:33,891 MuTect - [MUTECT] Processed 35001183 reads in 657 ms
[2015-09-30T22:07Z] INFO  23:07:34,480 MuTect - [MUTECT] Processed 5000134 reads in 745 ms
[2015-09-30T22:07Z] INFO  23:07:34,582 MuTect - [MUTECT] Processed 36001257 reads in 691 ms
[2015-09-30T22:07Z] INFO  23:07:35,224 MuTect - [MUTECT] Processed 6000181 reads in 744 ms
[2015-09-30T22:07Z] INFO  23:07:35,260 MuTect - [MUTECT] Processed 37001307 reads in 678 ms
[2015-09-30T22:07Z] INFO  23:07:35,438 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:35,959 MuTect - [MUTECT] Processed 38001375 reads in 699 ms
[2015-09-30T22:07Z] INFO  23:07:36,043 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:36,076 MuTect - [MUTECT] Processed 7000233 reads in 852 ms
[2015-09-30T22:07Z] INFO  23:07:36,631 MuTect - [MUTECT] Processed 39001385 reads in 672 ms
[2015-09-30T22:07Z] INFO  23:07:36,837 MuTect - [MUTECT] Processed 8000244 reads in 761 ms
[2015-09-30T22:07Z] MuTect: MuTect
[2015-09-30T22:07Z] INFO  23:07:37,286 MuTect - [MUTECT] Processed 40001470 reads in 655 ms
[2015-09-30T22:07Z] INFO  23:07:37,347 ProgressMeter -     2:201857051        1.76e+06   30.0 s       17.0 s     31.2%        96.0 s    66.0 s
[2015-09-30T22:07Z] INFO  23:07:37,529 MuTect - [MUTECT] Processed 9000245 reads in 692 ms
[2015-09-30T22:07Z] INFO  23:07:37,902 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:37,942 MuTect - [MUTECT] Processed 41001531 reads in 656 ms
[2015-09-30T22:07Z] INFO  23:07:38,224 MuTect - [MUTECT] Processed 10000282 reads in 695 ms
[2015-09-30T22:07Z] INFO  23:07:38,597 MuTect - [MUTECT] Processed 42001575 reads in 655 ms
[2015-09-30T22:07Z] INFO  23:07:38,838 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:38,919 MuTect - [MUTECT] Processed 11000329 reads in 695 ms
[2015-09-30T22:07Z] INFO  23:07:38,959 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/3/syn3-3_0_31203562-raw-mutect-regions.bed to be BED
[2015-09-30T22:07Z] INFO  23:07:39,014 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:07Z] INFO  23:07:39,014 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:07Z] INFO  23:07:39,014 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:07Z] INFO  23:07:39,014 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:07Z] INFO  23:07:39,018 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/3/syn3-3_0_31203562-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/3/tx/tmpWGEKn8/syn3-3_0_31203562-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:07Z] INFO  23:07:39,018 HelpFormatter - Date/Time: 2015/09/30 23:07:39
[2015-09-30T22:07Z] INFO  23:07:39,018 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:07Z] INFO  23:07:39,018 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:07Z] INFO  23:07:39,045 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:07Z] INFO  23:07:39,049 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:07Z] INFO  23:07:39,101 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:07Z] INFO  23:07:39,148 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:07Z] INFO  23:07:39,156 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:07Z] INFO  23:07:39,262 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2015-09-30T22:07Z] INFO  23:07:39,273 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:07Z] INFO  23:07:39,274 MuTect - [MUTECT] Processed 43001589 reads in 677 ms
[2015-09-30T22:07Z] INFO  23:07:39,447 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:07Z] INFO  23:07:39,580 MuTect - [MUTECT] Processed 12000337 reads in 661 ms
[2015-09-30T22:07Z] INFO  23:07:39,798 IntervalUtils - Processing 1186072 bp from intervals
[2015-09-30T22:07Z] INFO  23:07:39,802 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:07Z] INFO  23:07:39,802 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:07Z] INFO  23:07:39,951 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:07Z] INFO  23:07:39,959 MuTect - [MUTECT] Processed 44001679 reads in 685 ms
[2015-09-30T22:07Z] INFO  23:07:40,241 MuTect - [MUTECT] Processed 13000346 reads in 661 ms
[2015-09-30T22:07Z] INFO  23:07:40,334 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:40,616 MuTect - [MUTECT] Processed 45001748 reads in 657 ms
[2015-09-30T22:07Z] INFO  23:07:40,868 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:07Z] INFO  23:07:40,868 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:07Z] INFO  23:07:40,868 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:07Z] INFO  23:07:40,869 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:07Z] INFO  23:07:40,905 MuTect - [MUTECT] Processed 14000380 reads in 664 ms
[2015-09-30T22:07Z] INFO  23:07:41,253 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:41,274 MuTect - [MUTECT] Processed 46001795 reads in 658 ms
[2015-09-30T22:07Z] INFO  23:07:41,597 MuTect - [MUTECT] Processed 15000417 reads in 692 ms
[2015-09-30T22:07Z] INFO  23:07:41,949 MuTect - [MUTECT] Processed 47001820 reads in 675 ms
[2015-09-30T22:07Z] INFO  23:07:42,312 MuTect - [MUTECT] Processed 16000462 reads in 715 ms
[2015-09-30T22:07Z] INFO  23:07:42,630 MuTect - [MUTECT] Processed 48001914 reads in 681 ms
[2015-09-30T22:07Z] INFO  23:07:42,921 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:43,002 MuTect - [MUTECT] Processed 17000476 reads in 690 ms
[2015-09-30T22:07Z] INFO  23:07:43,303 MuTect - [MUTECT] Processed 49001940 reads in 673 ms
[2015-09-30T22:07Z] INFO  23:07:43,442 MuTect - [MUTECT] Processed 1000040 reads in 2454 ms
[2015-09-30T22:07Z] INFO  23:07:43,716 MuTect - [MUTECT] Processed 18000485 reads in 714 ms
[2015-09-30T22:07Z] INFO  23:07:43,781 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:43,999 MuTect - [MUTECT] Processed 50001996 reads in 696 ms
[2015-09-30T22:07Z] INFO  23:07:44,271 MuTect - [MUTECT] Processed 2000119 reads in 828 ms
[2015-09-30T22:07Z] INFO  23:07:44,387 MuTect - [MUTECT] Processed 19000538 reads in 671 ms
[2015-09-30T22:07Z] INFO  23:07:44,686 MuTect - [MUTECT] Processed 51002063 reads in 687 ms
[2015-09-30T22:07Z] INFO  23:07:45,029 MuTect - [MUTECT] Processed 3000169 reads in 759 ms
[2015-09-30T22:07Z] INFO  23:07:45,061 MuTect - [MUTECT] Processed 20000659 reads in 674 ms
[2015-09-30T22:07Z] INFO  23:07:45,350 MuTect - [MUTECT] Processed 52002150 reads in 664 ms
[2015-09-30T22:07Z] INFO  23:07:45,359 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:45,490 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:45,718 MuTect - [MUTECT] Processed 21000697 reads in 657 ms
[2015-09-30T22:07Z] INFO  23:07:45,723 MuTect - [MUTECT] Processed 4000230 reads in 693 ms
[2015-09-30T22:07Z] INFO  23:07:46,045 MuTect - [MUTECT] Processed 53002199 reads in 695 ms
[2015-09-30T22:07Z] INFO  23:07:46,085 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:46,375 MuTect - [MUTECT] Processed 22000730 reads in 657 ms
[2015-09-30T22:07Z] INFO  23:07:46,455 MuTect - [MUTECT] Processed 5000316 reads in 733 ms
[2015-09-30T22:07Z] INFO  23:07:46,726 MuTect - [MUTECT] Processed 54002223 reads in 681 ms
[2015-09-30T22:07Z] INFO  23:07:47,016 MuTect - [MUTECT] Processed 23000786 reads in 641 ms
[2015-09-30T22:07Z] INFO  23:07:47,137 MuTect - [MUTECT] Processed 6000380 reads in 682 ms
[2015-09-30T22:07Z] INFO  23:07:47,402 MuTect - [MUTECT] Processed 55002272 reads in 676 ms
[2015-09-30T22:07Z] INFO  23:07:47,668 MuTect - [MUTECT] Processed 24000815 reads in 651 ms
[2015-09-30T22:07Z] INFO  23:07:47,804 MuTect - [MUTECT] Processed 7000392 reads in 667 ms
[2015-09-30T22:07Z] INFO  23:07:47,857 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:47,955 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:48,098 MuTect - [MUTECT] Processed 56002273 reads in 696 ms
[2015-09-30T22:07Z] INFO  23:07:48,330 MuTect - [MUTECT] Processed 25000847 reads in 663 ms
[2015-09-30T22:07Z] INFO  23:07:48,509 MuTect - [MUTECT] Processed 8000406 reads in 705 ms
[2015-09-30T22:07Z] INFO  23:07:48,615 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:48,787 MuTect - [MUTECT] Processed 57002303 reads in 689 ms
[2015-09-30T22:07Z] INFO  23:07:48,998 MuTect - [MUTECT] Processed 26000864 reads in 667 ms
[2015-09-30T22:07Z] INFO  23:07:49,171 MuTect - [MUTECT] Processed 9000487 reads in 662 ms
[2015-09-30T22:07Z] INFO  23:07:49,492 MuTect - [MUTECT] Processed 58002308 reads in 705 ms
[2015-09-30T22:07Z] INFO  23:07:49,669 MuTect - [MUTECT] Processed 27000883 reads in 672 ms
[2015-09-30T22:07Z] INFO  23:07:49,842 MuTect - [MUTECT] Processed 10000498 reads in 671 ms
[2015-09-30T22:07Z] INFO  23:07:50,198 MuTect - [MUTECT] Processed 59002372 reads in 706 ms
[2015-09-30T22:07Z] INFO  23:07:50,326 MuTect - [MUTECT] Processed 28000895 reads in 657 ms
[2015-09-30T22:07Z] INFO  23:07:50,434 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:50,514 MuTect - [MUTECT] Processed 11000576 reads in 672 ms
[2015-09-30T22:07Z] INFO  23:07:50,554 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:50,925 MuTect - [MUTECT] Processed 60002383 reads in 727 ms
[2015-09-30T22:07Z] INFO  23:07:50,979 MuTect - [MUTECT] Processed 29000911 reads in 653 ms
[2015-09-30T22:07Z] INFO  23:07:51,103 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:51,181 MuTect - [MUTECT] Processed 12000583 reads in 667 ms
[2015-09-30T22:07Z] INFO  23:07:51,612 MuTect - [MUTECT] Processed 61002391 reads in 687 ms
[2015-09-30T22:07Z] INFO  23:07:51,680 MuTect - [MUTECT] Processed 30000985 reads in 701 ms
[2015-09-30T22:07Z] INFO  23:07:51,861 MuTect - [MUTECT] Processed 13000624 reads in 680 ms
[2015-09-30T22:07Z] INFO  23:07:52,278 MuTect - [MUTECT] Processed 62002450 reads in 665 ms
[2015-09-30T22:07Z] INFO  23:07:52,379 MuTect - [MUTECT] Processed 31001015 reads in 699 ms
[2015-09-30T22:07Z] INFO  23:07:52,562 MuTect - [MUTECT] Processed 14000700 reads in 701 ms
[2015-09-30T22:07Z] INFO  23:07:52,858 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:52,957 MuTect - [MUTECT] Processed 63002503 reads in 679 ms
[2015-09-30T22:07Z] INFO  23:07:52,987 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:53,032 MuTect - [MUTECT] Processed 32001045 reads in 653 ms
[2015-09-30T22:07Z] INFO  23:07:53,261 MuTect - [MUTECT] Processed 15000721 reads in 699 ms
[2015-09-30T22:07Z] INFO  23:07:53,352 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:53,671 MuTect - [MUTECT] Processed 64002562 reads in 715 ms
[2015-09-30T22:07Z] INFO  23:07:53,681 MuTect - [MUTECT] Processed 33001056 reads in 649 ms
[2015-09-30T22:07Z] INFO  23:07:53,960 MuTect - [MUTECT] Processed 16000754 reads in 699 ms
[2015-09-30T22:07Z] INFO  23:07:54,352 MuTect - [MUTECT] Processed 65002643 reads in 681 ms
[2015-09-30T22:07Z] INFO  23:07:54,360 MuTect - [MUTECT] Processed 34001120 reads in 679 ms
[2015-09-30T22:07Z] INFO  23:07:54,727 MuTect - [MUTECT] Processed 17000758 reads in 767 ms
[2015-09-30T22:07Z] INFO  23:07:55,010 MuTect - [MUTECT] Processed 66002762 reads in 658 ms
[2015-09-30T22:07Z] INFO  23:07:55,037 MuTect - [MUTECT] Processed 35001218 reads in 677 ms
[2015-09-30T22:07Z] INFO  23:07:55,295 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:55,401 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:55,443 MuTect - [MUTECT] Processed 18000839 reads in 716 ms
[2015-09-30T22:07Z] INFO  23:07:55,636 MuTect - [MUTECT] Processed 67002813 reads in 626 ms
[2015-09-30T22:07Z] INFO  23:07:55,730 MuTect - [MUTECT] Processed 36001291 reads in 693 ms
[2015-09-30T22:07Z] INFO  23:07:55,750 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:56,145 MuTect - [MUTECT] Processed 19000917 reads in 702 ms
[2015-09-30T22:07Z] INFO  23:07:56,303 MuTect - [MUTECT] Processed 68002908 reads in 667 ms
[2015-09-30T22:07Z] INFO  23:07:56,399 MuTect - [MUTECT] Processed 37001366 reads in 669 ms
[2015-09-30T22:07Z] INFO  23:07:56,925 MuTect - [MUTECT] Processed 69002965 reads in 622 ms
[2015-09-30T22:07Z] INFO  23:07:56,982 MuTect - [MUTECT] Processed 20000958 reads in 837 ms
[2015-09-30T22:07Z] INFO  23:07:57,117 MuTect - [MUTECT] Processed 38001374 reads in 718 ms
[2015-09-30T22:07Z] INFO  23:07:57,574 MuTect - [MUTECT] Processed 70003034 reads in 649 ms
[2015-09-30T22:07Z] INFO  23:07:57,656 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:57,679 MuTect - [MUTECT] Processed 21000978 reads in 696 ms
[2015-09-30T22:07Z] INFO  23:07:57,793 MuTect - [MUTECT] Processed 39001462 reads in 676 ms
[2015-09-30T22:07Z] INFO  23:07:57,986 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:58,163 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:07Z] INFO  23:07:58,216 MuTect - [MUTECT] Processed 71003116 reads in 642 ms
[2015-09-30T22:07Z] INFO  23:07:58,366 MuTect - [MUTECT] Processed 22001054 reads in 688 ms
[2015-09-30T22:07Z] INFO  23:07:58,473 MuTect - [MUTECT] Processed 40001505 reads in 680 ms
[2015-09-30T22:07Z] INFO  23:07:58,892 ProgressMeter -     2:233001249        1.33e+06   30.0 s       22.0 s     36.9%        81.0 s    51.0 s
[2015-09-30T22:07Z] INFO  23:07:58,915 MuTect - [MUTECT] Processed 72003178 reads in 699 ms
[2015-09-30T22:07Z] INFO  23:07:59,056 MuTect - [MUTECT] Processed 23001137 reads in 690 ms
[2015-09-30T22:07Z] INFO  23:07:59,158 MuTect - [MUTECT] Processed 41001612 reads in 685 ms
[2015-09-30T22:07Z] INFO  23:07:59,543 MuTect - [MUTECT] Processed 73003239 reads in 628 ms
[2015-09-30T22:07Z] INFO  23:07:59,730 MuTect - [MUTECT] Processed 24001203 reads in 674 ms
[2015-09-30T22:07Z] INFO  23:07:59,837 MuTect - [MUTECT] Processed 42001670 reads in 679 ms
[2015-09-30T22:08Z] INFO  23:08:00,073 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:00,237 MuTect - [MUTECT] Processed 74003309 reads in 694 ms
[2015-09-30T22:08Z] INFO  23:08:00,305 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:00,398 MuTect - [MUTECT] Processed 25001241 reads in 668 ms
[2015-09-30T22:08Z] INFO  23:08:00,538 MuTect - [MUTECT] Processed 43001730 reads in 701 ms
[2015-09-30T22:08Z] INFO  23:08:00,601 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:00,918 MuTect - [MUTECT] Processed 75003363 reads in 681 ms
[2015-09-30T22:08Z] INFO  23:08:01,052 MuTect - [MUTECT] Processed 26001277 reads in 654 ms
[2015-09-30T22:08Z] INFO  23:08:01,229 MuTect - [MUTECT] Processed 44001824 reads in 691 ms
[2015-09-30T22:08Z] INFO  23:08:01,544 MuTect - [MUTECT] Processed 76003406 reads in 626 ms
[2015-09-30T22:08Z] INFO  23:08:01,717 MuTect - [MUTECT] Processed 27001336 reads in 665 ms
[2015-09-30T22:08Z] INFO  23:08:01,907 MuTect - [MUTECT] Processed 45001833 reads in 677 ms
[2015-09-30T22:08Z] INFO  23:08:02,227 MuTect - [MUTECT] Processed 77003422 reads in 683 ms
[2015-09-30T22:08Z] INFO  23:08:02,387 MuTect - [MUTECT] Processed 28001419 reads in 670 ms
[2015-09-30T22:08Z] INFO  23:08:02,397 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:02,498 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:02,601 MuTect - [MUTECT] Processed 46001870 reads in 695 ms
[2015-09-30T22:08Z] INFO  23:08:02,755 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:02,862 MuTect - [MUTECT] Processed 78003469 reads in 635 ms
[2015-09-30T22:08Z] INFO  23:08:03,062 MuTect - [MUTECT] Processed 29001453 reads in 675 ms
[2015-09-30T22:08Z] INFO  23:08:03,335 MuTect - [MUTECT] Processed 47001925 reads in 734 ms
[2015-09-30T22:08Z] INFO  23:08:03,536 MuTect - [MUTECT] Processed 79003471 reads in 674 ms
[2015-09-30T22:08Z] INFO  23:08:03,761 MuTect - [MUTECT] Processed 30001501 reads in 699 ms
[2015-09-30T22:08Z] INFO  23:08:04,019 MuTect - [MUTECT] Processed 48001967 reads in 684 ms
[2015-09-30T22:08Z] INFO  23:08:04,197 MuTect - [MUTECT] Processed 80003476 reads in 661 ms
[2015-09-30T22:08Z] INFO  23:08:04,459 MuTect - [MUTECT] Processed 31001584 reads in 698 ms
[2015-09-30T22:08Z] INFO  23:08:04,755 MuTect - [MUTECT] Processed 49002006 reads in 736 ms
[2015-09-30T22:08Z] INFO  23:08:04,791 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:04,852 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:04,916 MuTect - [MUTECT] Processed 81003536 reads in 719 ms
[2015-09-30T22:08Z] INFO  23:08:05,174 MuTect - [MUTECT] Processed 32001638 reads in 715 ms
[2015-09-30T22:08Z] INFO  23:08:05,338 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:05,458 MuTect - [MUTECT] Processed 50002081 reads in 703 ms
[2015-09-30T22:08Z] INFO  23:08:05,598 MuTect - [MUTECT] Processed 82003578 reads in 682 ms
[2015-09-30T22:08Z] INFO  23:08:05,864 MuTect - [MUTECT] Processed 33001719 reads in 690 ms
[2015-09-30T22:08Z] INFO  23:08:06,144 MuTect - [MUTECT] Processed 51002178 reads in 685 ms
[2015-09-30T22:08Z] INFO  23:08:06,289 MuTect - [MUTECT] Processed 83003580 reads in 691 ms
[2015-09-30T22:08Z] INFO  23:08:06,588 MuTect - [MUTECT] Processed 34001795 reads in 724 ms
[2015-09-30T22:08Z] INFO  23:08:06,910 MuTect - [MUTECT] Processed 52002260 reads in 767 ms
[2015-09-30T22:08Z] INFO  23:08:06,979 MuTect - [MUTECT] Processed 84003627 reads in 690 ms
[2015-09-30T22:08Z] INFO  23:08:07,245 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:07,320 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:07,337 MuTect - [MUTECT] Processed 35001799 reads in 749 ms
[2015-09-30T22:08Z] INFO  23:08:07,348 ProgressMeter -     2:210808000        3.45e+06   60.0 s       17.0 s     62.9%        95.0 s    35.0 s
[2015-09-30T22:08Z] INFO  23:08:07,653 MuTect - [MUTECT] Processed 53002322 reads in 743 ms
[2015-09-30T22:08Z] INFO  23:08:07,724 MuTect - [MUTECT] Processed 85003641 reads in 745 ms
[2015-09-30T22:08Z] INFO  23:08:07,727 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:08,247 MuTect - [MUTECT] Processed 36001832 reads in 910 ms
[2015-09-30T22:08Z] INFO  23:08:08,353 MuTect - [MUTECT] Processed 54002340 reads in 700 ms
[2015-09-30T22:08Z] INFO  23:08:08,505 MuTect - [MUTECT] Processed 86003675 reads in 781 ms
[2015-09-30T22:08Z] INFO  23:08:08,957 MuTect - [MUTECT] Processed 37001881 reads in 710 ms
[2015-09-30T22:08Z] INFO  23:08:09,055 MuTect - [MUTECT] Processed 55002390 reads in 702 ms
[2015-09-30T22:08Z] INFO  23:08:09,224 MuTect - [MUTECT] Processed 87003703 reads in 719 ms
[2015-09-30T22:08Z] INFO  23:08:09,665 MuTect - [MUTECT] Processed 38001887 reads in 708 ms
[2015-09-30T22:08Z] INFO  23:08:09,756 MuTect - [MUTECT] Processed 56002444 reads in 701 ms
[2015-09-30T22:08Z] INFO  23:08:09,789 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:09,838 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:09,915 MuTect - [MUTECT] Processed 88003757 reads in 691 ms
[2015-09-30T22:08Z] INFO  23:08:10,058 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:10,377 MuTect - [MUTECT] Processed 39001923 reads in 712 ms
[2015-09-30T22:08Z] INFO  23:08:10,424 MuTect - [MUTECT] Processed 57002487 reads in 668 ms
[2015-09-30T22:08Z] INFO  23:08:10,590 MuTect - [MUTECT] Processed 89003791 reads in 675 ms
[2015-09-30T22:08Z] INFO  23:08:10,870 ProgressMeter -      3:10326450        1.22e+06   30.0 s       24.0 s     36.5%        82.0 s    52.0 s
[2015-09-30T22:08Z] INFO  23:08:11,040 MuTect - [MUTECT] Processed 40001928 reads in 663 ms
[2015-09-30T22:08Z] INFO  23:08:11,076 MuTect - [MUTECT] Processed 58002517 reads in 652 ms
[2015-09-30T22:08Z] INFO  23:08:11,275 MuTect - [MUTECT] Processed 90003849 reads in 685 ms
[2015-09-30T22:08Z] INFO  23:08:11,711 MuTect - [MUTECT] Processed 41001994 reads in 671 ms
[2015-09-30T22:08Z] INFO  23:08:11,752 MuTect - [MUTECT] Processed 59002549 reads in 676 ms
[2015-09-30T22:08Z] INFO  23:08:11,994 MuTect - [MUTECT] Processed 91003928 reads in 719 ms
[2015-09-30T22:08Z] INFO  23:08:12,103 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:12,315 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:12,388 MuTect - [MUTECT] Processed 42001997 reads in 677 ms
[2015-09-30T22:08Z] INFO  23:08:12,461 MuTect - [MUTECT] Processed 60002616 reads in 709 ms
[2015-09-30T22:08Z] INFO  23:08:12,496 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:12,675 MuTect - [MUTECT] Processed 92004012 reads in 681 ms
[2015-09-30T22:08Z] INFO  23:08:13,092 MuTect - [MUTECT] Processed 43002058 reads in 704 ms
[2015-09-30T22:08Z] INFO  23:08:13,112 MuTect - [MUTECT] Processed 61002745 reads in 651 ms
[2015-09-30T22:08Z] INFO  23:08:13,368 MuTect - [MUTECT] Processed 93004027 reads in 693 ms
[2015-09-30T22:08Z] INFO  23:08:13,773 MuTect - [MUTECT] Processed 44002060 reads in 681 ms
[2015-09-30T22:08Z] INFO  23:08:13,807 MuTect - [MUTECT] Processed 62002827 reads in 695 ms
[2015-09-30T22:08Z] INFO  23:08:14,097 MuTect - [MUTECT] Processed 94004057 reads in 729 ms
[2015-09-30T22:08Z] INFO  23:08:14,428 MuTect - [MUTECT] Processed 45002124 reads in 655 ms
[2015-09-30T22:08Z] INFO  23:08:14,451 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:14,495 MuTect - [MUTECT] Processed 63002875 reads in 688 ms
[2015-09-30T22:08Z] INFO  23:08:14,589 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:14,801 MuTect - [MUTECT] Processed 95004060 reads in 704 ms
[2015-09-30T22:08Z] INFO  23:08:15,038 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:15,086 MuTect - [MUTECT] Processed 46002188 reads in 658 ms
[2015-09-30T22:08Z] INFO  23:08:15,190 MuTect - [MUTECT] Processed 64002905 reads in 695 ms
[2015-09-30T22:08Z] INFO  23:08:15,515 MuTect - [MUTECT] Processed 96004097 reads in 714 ms
[2015-09-30T22:08Z] INFO  23:08:15,747 MuTect - [MUTECT] Processed 47002188 reads in 661 ms
[2015-09-30T22:08Z] INFO  23:08:15,856 MuTect - [MUTECT] Processed 65002986 reads in 666 ms
[2015-09-30T22:08Z] INFO  23:08:16,240 MuTect - [MUTECT] Processed 97004107 reads in 725 ms
[2015-09-30T22:08Z] INFO  23:08:16,404 MuTect - [MUTECT] Processed 48002227 reads in 657 ms
[2015-09-30T22:08Z] INFO  23:08:16,515 MuTect - [MUTECT] Processed 66003096 reads in 659 ms
[2015-09-30T22:08Z] INFO  23:08:16,617 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:16,802 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:16,903 MuTect - [MUTECT] Processed 98004160 reads in 663 ms
[2015-09-30T22:08Z] INFO  23:08:17,093 MuTect - [MUTECT] Processed 49002266 reads in 689 ms
[2015-09-30T22:08Z] INFO  23:08:17,195 MuTect - [MUTECT] Processed 67003176 reads in 680 ms
[2015-09-30T22:08Z] INFO  23:08:17,331 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:17,603 MuTect - [MUTECT] Processed 99004160 reads in 700 ms
[2015-09-30T22:08Z] INFO  23:08:17,809 MuTect - [MUTECT] Processed 50002368 reads in 716 ms
[2015-09-30T22:08Z] INFO  23:08:17,877 MuTect - [MUTECT] Processed 68003203 reads in 682 ms
[2015-09-30T22:08Z] INFO  23:08:18,307 MuTect - [MUTECT] Processed 100004194 reads in 704 ms
[2015-09-30T22:08Z] INFO  23:08:18,479 MuTect - [MUTECT] Processed 51002435 reads in 670 ms
[2015-09-30T22:08Z] INFO  23:08:18,573 MuTect - [MUTECT] Processed 69003261 reads in 696 ms
[2015-09-30T22:08Z] INFO  23:08:18,928 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:18,973 MuTect - [MUTECT] Processed 101004213 reads in 666 ms
[2015-09-30T22:08Z] INFO  23:08:19,116 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:19,133 MuTect - [MUTECT] Processed 52002512 reads in 654 ms
[2015-09-30T22:08Z] INFO  23:08:19,258 MuTect - [MUTECT] Processed 70003266 reads in 685 ms
[2015-09-30T22:08Z] INFO  23:08:19,666 MuTect - [MUTECT] Processed 102004248 reads in 693 ms
[2015-09-30T22:08Z] INFO  23:08:19,783 MuTect - [MUTECT] Processed 53002514 reads in 650 ms
[2015-09-30T22:08Z] INFO  23:08:19,858 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:19,965 MuTect - [MUTECT] Processed 71003300 reads in 707 ms
[2015-09-30T22:08Z] INFO  23:08:20,330 MuTect - [MUTECT] Processed 103004329 reads in 664 ms
[2015-09-30T22:08Z] INFO  23:08:20,446 MuTect - [MUTECT] Processed 54002586 reads in 663 ms
[2015-09-30T22:08Z] INFO  23:08:20,666 MuTect - [MUTECT] Processed 72003334 reads in 701 ms
[2015-09-30T22:08Z] INFO  23:08:20,999 MuTect - [MUTECT] Processed 104004366 reads in 669 ms
[2015-09-30T22:08Z] INFO  23:08:21,117 MuTect - [MUTECT] Processed 55002586 reads in 671 ms
[2015-09-30T22:08Z] INFO  23:08:21,282 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:21,346 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:21,411 MuTect - [MUTECT] Processed 73003344 reads in 745 ms
[2015-09-30T22:08Z] INFO  23:08:21,625 MuTect - [MUTECT] Processed 105004412 reads in 626 ms
[2015-09-30T22:08Z] INFO  23:08:21,768 MuTect - [MUTECT] Processed 56002592 reads in 651 ms
[2015-09-30T22:08Z] INFO  23:08:22,064 MuTect - [MUTECT] Processed 74003399 reads in 653 ms
[2015-09-30T22:08Z] INFO  23:08:22,136 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:22,339 MuTect - [MUTECT] Processed 106004540 reads in 714 ms
[2015-09-30T22:08Z] INFO  23:08:22,440 MuTect - [MUTECT] Processed 57002619 reads in 672 ms
[2015-09-30T22:08Z] INFO  23:08:22,727 MuTect - [MUTECT] Processed 75003412 reads in 663 ms
[2015-09-30T22:08Z] INFO  23:08:23,025 MuTect - [MUTECT] Processed 107004631 reads in 686 ms
[2015-09-30T22:08Z] INFO  23:08:23,094 MuTect - [MUTECT] Processed 58002725 reads in 654 ms
[2015-09-30T22:08Z] INFO  23:08:23,408 MuTect - [MUTECT] Processed 76003499 reads in 680 ms
[2015-09-30T22:08Z] INFO  23:08:23,518 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:23,620 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:23,675 MuTect - [MUTECT] Processed 108004650 reads in 650 ms
[2015-09-30T22:08Z] INFO  23:08:23,745 MuTect - [MUTECT] Processed 59002834 reads in 651 ms
[2015-09-30T22:08Z] INFO  23:08:24,060 MuTect - [MUTECT] Processed 77003622 reads in 653 ms
[2015-09-30T22:08Z] INFO  23:08:24,232 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:24,334 MuTect - [MUTECT] Processed 109004744 reads in 659 ms
[2015-09-30T22:08Z] INFO  23:08:24,389 MuTect - [MUTECT] Processed 60002884 reads in 644 ms
[2015-09-30T22:08Z] INFO  23:08:24,707 MuTect - [MUTECT] Processed 78003709 reads in 647 ms
[2015-09-30T22:08Z] INFO  23:08:24,984 MuTect - [MUTECT] Processed 110004819 reads in 650 ms
[2015-09-30T22:08Z] INFO  23:08:25,032 MuTect - [MUTECT] Processed 61002962 reads in 643 ms
[2015-09-30T22:08Z] INFO  23:08:25,403 MuTect - [MUTECT] Processed 79003744 reads in 696 ms
[2015-09-30T22:08Z] INFO  23:08:25,652 MuTect - [MUTECT] Processed 111004845 reads in 668 ms
[2015-09-30T22:08Z] INFO  23:08:25,676 MuTect - [MUTECT] Processed 62003061 reads in 644 ms
[2015-09-30T22:08Z] INFO  23:08:25,703 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:26,080 MuTect - [MUTECT] Processed 80003802 reads in 677 ms
[2015-09-30T22:08Z] INFO  23:08:26,283 MuTect - [MUTECT] Processed 112004963 reads in 631 ms
[2015-09-30T22:08Z] INFO  23:08:26,324 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:26,354 MuTect - [MUTECT] Processed 63003111 reads in 678 ms
[2015-09-30T22:08Z] INFO  23:08:26,420 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:26,790 MuTect - [MUTECT] Processed 81003833 reads in 710 ms
[2015-09-30T22:08Z] INFO  23:08:26,934 MuTect - [MUTECT] Processed 113004973 reads in 651 ms
[2015-09-30T22:08Z] INFO  23:08:27,050 MuTect - [MUTECT] Processed 64003147 reads in 696 ms
[2015-09-30T22:08Z] INFO  23:08:27,491 MuTect - [MUTECT] Processed 82003912 reads in 701 ms
[2015-09-30T22:08Z] INFO  23:08:27,599 MuTect - [MUTECT] Processed 114004974 reads in 665 ms
[2015-09-30T22:08Z] INFO  23:08:27,704 MuTect - [MUTECT] Processed 65003206 reads in 654 ms
[2015-09-30T22:08Z] INFO  23:08:27,763 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:28,194 MuTect - [MUTECT] Processed 83003999 reads in 703 ms
[2015-09-30T22:08Z] INFO  23:08:28,281 MuTect - [MUTECT] Processed 115005034 reads in 682 ms
[2015-09-30T22:08Z] INFO  23:08:28,371 MuTect - [MUTECT] Processed 66003226 reads in 667 ms
[2015-09-30T22:08Z] INFO  23:08:28,549 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:28,821 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:28,891 MuTect - [MUTECT] Processed 84004133 reads in 697 ms
[2015-09-30T22:08Z] INFO  23:08:28,893 ProgressMeter -     2:238990847        2.64e+06   60.0 s       22.0 s     69.2%        86.0 s    26.0 s
[2015-09-30T22:08Z] INFO  23:08:28,996 MuTect - [MUTECT] Processed 116005166 reads in 715 ms
[2015-09-30T22:08Z] INFO  23:08:29,019 MuTect - [MUTECT] Processed 67003310 reads in 648 ms
[2015-09-30T22:08Z] INFO  23:08:29,643 MuTect - [MUTECT] Processed 85004216 reads in 752 ms
[2015-09-30T22:08Z] INFO  23:08:29,653 MuTect - [MUTECT] Processed 117005222 reads in 657 ms
[2015-09-30T22:08Z] INFO  23:08:29,657 MuTect - [MUTECT] Processed 68003328 reads in 638 ms
[2015-09-30T22:08Z] INFO  23:08:29,967 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:30,310 MuTect - [MUTECT] Processed 118005283 reads in 657 ms
[2015-09-30T22:08Z] INFO  23:08:30,353 MuTect - [MUTECT] Processed 69003439 reads in 696 ms
[2015-09-30T22:08Z] INFO  23:08:30,413 MuTect - [MUTECT] Processed 86004303 reads in 770 ms
[2015-09-30T22:08Z] INFO  23:08:30,746 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:31,033 MuTect - [MUTECT] Processed 119005357 reads in 723 ms
[2015-09-30T22:08Z] INFO  23:08:31,046 MuTect - [MUTECT] Processed 70003505 reads in 693 ms
[2015-09-30T22:08Z] INFO  23:08:31,172 MuTect - [MUTECT] Processed 87004324 reads in 759 ms
[2015-09-30T22:08Z] INFO  23:08:31,289 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:31,693 MuTect - [MUTECT] Processed 71003614 reads in 647 ms
[2015-09-30T22:08Z] INFO  23:08:31,718 MuTect - [MUTECT] Processed 120005364 reads in 685 ms
[2015-09-30T22:08Z] INFO  23:08:31,865 MuTect - [MUTECT] Processed 88004356 reads in 693 ms
[2015-09-30T22:08Z] INFO  23:08:32,164 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:32,330 MuTect - [MUTECT] Processed 72003659 reads in 637 ms
[2015-09-30T22:08Z] INFO  23:08:32,379 MuTect - [MUTECT] Processed 121005400 reads in 661 ms
[2015-09-30T22:08Z] INFO  23:08:32,545 MuTect - [MUTECT] Processed 89004391 reads in 680 ms
[2015-09-30T22:08Z] INFO  23:08:32,994 MuTect - [MUTECT] Processed 73003742 reads in 664 ms
[2015-09-30T22:08Z] INFO  23:08:33,037 MuTect - [MUTECT] Processed 122005513 reads in 658 ms
[2015-09-30T22:08Z] INFO  23:08:33,107 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:33,209 MuTect - [MUTECT] Processed 90004446 reads in 664 ms
[2015-09-30T22:08Z] INFO  23:08:33,545 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:33,655 MuTect - [MUTECT] Processed 74003807 reads in 661 ms
[2015-09-30T22:08Z] INFO  23:08:33,684 MuTect - [MUTECT] Processed 123005596 reads in 647 ms
[2015-09-30T22:08Z] INFO  23:08:33,905 MuTect - [MUTECT] Processed 91004503 reads in 696 ms
[2015-09-30T22:08Z] INFO  23:08:34,308 MuTect - [MUTECT] Processed 75003837 reads in 653 ms
[2015-09-30T22:08Z] INFO  23:08:34,311 MuTect - [MUTECT] Processed 124005623 reads in 627 ms
[2015-09-30T22:08Z] INFO  23:08:34,512 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:34,562 MuTect - [MUTECT] Processed 92004612 reads in 657 ms
[2015-09-30T22:08Z] INFO  23:08:34,942 MuTect - [MUTECT] Processed 125005648 reads in 631 ms
[2015-09-30T22:08Z] INFO  23:08:35,008 MuTect - [MUTECT] Processed 76003907 reads in 700 ms
[2015-09-30T22:08Z] INFO  23:08:35,220 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:35,230 MuTect - [MUTECT] Processed 93004657 reads in 668 ms
[2015-09-30T22:08Z] INFO  23:08:35,563 MuTect - [MUTECT] Processed 126005669 reads in 621 ms
[2015-09-30T22:08Z] INFO  23:08:35,704 MuTect - [MUTECT] Processed 77003959 reads in 696 ms
[2015-09-30T22:08Z] INFO  23:08:35,896 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:35,897 MuTect - [MUTECT] Processed 94004754 reads in 667 ms
[2015-09-30T22:08Z] INFO  23:08:36,185 MuTect - [MUTECT] Processed 127005681 reads in 622 ms
[2015-09-30T22:08Z] INFO  23:08:36,389 MuTect - [MUTECT] Processed 78003992 reads in 685 ms
[2015-09-30T22:08Z] INFO  23:08:36,565 MuTect - [MUTECT] Processed 95004757 reads in 668 ms
[2015-09-30T22:08Z] INFO  23:08:36,804 MuTect - [MUTECT] Processed 128005730 reads in 619 ms
[2015-09-30T22:08Z] INFO  23:08:36,863 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:37,097 MuTect - [MUTECT] Processed 79004012 reads in 708 ms
[2015-09-30T22:08Z] INFO  23:08:37,231 MuTect - [MUTECT] Processed 96004762 reads in 666 ms
[2015-09-30T22:08Z] INFO  23:08:37,300 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:37,349 ProgressMeter -     2:219887700        5.01e+06   90.0 s       17.0 s     89.4%       100.0 s    10.0 s
[2015-09-30T22:08Z] INFO  23:08:37,399 MuTect - [MUTECT] Processed 129005763 reads in 595 ms
[2015-09-30T22:08Z] INFO  23:08:37,760 MuTect - [MUTECT] Processed 80004090 reads in 663 ms
[2015-09-30T22:08Z] INFO  23:08:38,021 MuTect - [MUTECT] Processed 130005810 reads in 622 ms
[2015-09-30T22:08Z] INFO  23:08:38,435 MuTect - [MUTECT] Processed 81004118 reads in 674 ms
[2015-09-30T22:08Z] INFO  23:08:38,966 MuTect - [MUTECT] Processed 97004824 reads in 1735 ms
[2015-09-30T22:08Z] INFO  23:08:38,988 MuTect - [MUTECT] Processed 131005826 reads in 967 ms
[2015-09-30T22:08Z] INFO  23:08:39,103 MuTect - [MUTECT] Processed 82004121 reads in 669 ms
[2015-09-30T22:08Z] INFO  23:08:39,132 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:39,189 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:39,630 MuTect - [MUTECT] Processed 132005839 reads in 642 ms
[2015-09-30T22:08Z] INFO  23:08:39,641 MuTect - [MUTECT] Processed 98004841 reads in 675 ms
[2015-09-30T22:08Z] INFO  23:08:39,706 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:39,780 MuTect - [MUTECT] Processed 83004125 reads in 677 ms
[2015-09-30T22:08Z] INFO  23:08:40,251 MuTect - [MUTECT] Processed 133005852 reads in 621 ms
[2015-09-30T22:08Z] INFO  23:08:40,273 MuTect - [MUTECT] Processed 99004907 reads in 632 ms
[2015-09-30T22:08Z] INFO  23:08:40,492 MuTect - [MUTECT] Processed 84004204 reads in 712 ms
[2015-09-30T22:08Z] INFO  23:08:40,856 MuTect - [MUTECT] Processed 134005932 reads in 605 ms
[2015-09-30T22:08Z] INFO  23:08:40,871 ProgressMeter -      3:16305807        2.55e+06   60.0 s       23.0 s     74.3%        80.0 s    20.0 s
[2015-09-30T22:08Z] INFO  23:08:40,932 MuTect - [MUTECT] Processed 100004999 reads in 659 ms
[2015-09-30T22:08Z] INFO  23:08:41,284 MuTect - [MUTECT] Processed 85004310 reads in 792 ms
[2015-09-30T22:08Z] INFO  23:08:41,469 MuTect - [MUTECT] Processed 135005939 reads in 613 ms
[2015-09-30T22:08Z] INFO  23:08:41,470 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:41,619 MuTect - [MUTECT] Processed 101005116 reads in 687 ms
[2015-09-30T22:08Z] INFO  23:08:41,747 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:41,821 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:41,988 MuTect - [MUTECT] Processed 86004321 reads in 704 ms
[2015-09-30T22:08Z] INFO  23:08:42,077 MuTect - [MUTECT] Processed 136005993 reads in 608 ms
[2015-09-30T22:08Z] INFO  23:08:42,333 MuTect - [MUTECT] Processed 102005217 reads in 714 ms
[2015-09-30T22:08Z] INFO  23:08:42,671 MuTect - [MUTECT] Processed 87004388 reads in 683 ms
[2015-09-30T22:08Z] INFO  23:08:42,681 MuTect - [MUTECT] Processed 137006123 reads in 604 ms
[2015-09-30T22:08Z] INFO  23:08:42,992 MuTect - [MUTECT] Processed 103005365 reads in 659 ms
[2015-09-30T22:08Z] INFO  23:08:43,311 MuTect - [MUTECT] Processed 138006186 reads in 630 ms
[2015-09-30T22:08Z] INFO  23:08:43,369 MuTect - [MUTECT] Processed 88004405 reads in 698 ms
[2015-09-30T22:08Z] INFO  23:08:43,631 MuTect - [MUTECT] Processed 104005373 reads in 639 ms
[2015-09-30T22:08Z] INFO  23:08:43,874 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:43,931 MuTect - [MUTECT] Processed 139006198 reads in 620 ms
[2015-09-30T22:08Z] INFO  23:08:43,976 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:44,046 MuTect - [MUTECT] Processed 89004424 reads in 677 ms
[2015-09-30T22:08Z] INFO  23:08:44,271 MuTect - [MUTECT] Processed 105005515 reads in 640 ms
[2015-09-30T22:08Z] INFO  23:08:44,326 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:44,592 MuTect - [MUTECT] Processed 140006245 reads in 661 ms
[2015-09-30T22:08Z] INFO  23:08:44,696 MuTect - [MUTECT] Processed 90004425 reads in 650 ms
[2015-09-30T22:08Z] INFO  23:08:44,965 MuTect - [MUTECT] Processed 106005562 reads in 694 ms
[2015-09-30T22:08Z] INFO  23:08:45,317 MuTect - [MUTECT] Processed 141006345 reads in 725 ms
[2015-09-30T22:08Z] INFO  23:08:45,340 MuTect - [MUTECT] Processed 91004439 reads in 644 ms
[2015-09-30T22:08Z] INFO  23:08:45,644 MuTect - [MUTECT] Processed 107005589 reads in 679 ms
[2015-09-30T22:08Z] INFO  23:08:45,979 MuTect - [MUTECT] Processed 92004450 reads in 639 ms
[2015-09-30T22:08Z] INFO  23:08:46,003 MuTect - [MUTECT] Processed 142006347 reads in 686 ms
[2015-09-30T22:08Z] INFO  23:08:46,014 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:46,227 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:46,401 MuTect - [MUTECT] Processed 108005740 reads in 757 ms
[2015-09-30T22:08Z] INFO  23:08:46,634 MuTect - [MUTECT] Processed 93004531 reads in 655 ms
[2015-09-30T22:08Z] INFO  23:08:46,638 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:46,687 MuTect - [MUTECT] Processed 143006374 reads in 684 ms
[2015-09-30T22:08Z] INFO  23:08:47,108 MuTect - [MUTECT] Processed 109005798 reads in 707 ms
[2015-09-30T22:08Z] INFO  23:08:47,299 MuTect - [MUTECT] Processed 94004613 reads in 665 ms
[2015-09-30T22:08Z] INFO  23:08:47,349 MuTect - [MUTECT] Processed 144006399 reads in 662 ms
[2015-09-30T22:08Z] INFO  23:08:47,883 MuTect - [MUTECT] Processed 110005854 reads in 775 ms
[2015-09-30T22:08Z] INFO  23:08:47,954 MuTect - [MUTECT] Processed 95004680 reads in 655 ms
[2015-09-30T22:08Z] INFO  23:08:48,007 MuTect - [MUTECT] Processed 145006422 reads in 658 ms
[2015-09-30T22:08Z] INFO  23:08:48,203 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:48,564 MuTect - [MUTECT] Processed 111005878 reads in 681 ms
[2015-09-30T22:08Z] INFO  23:08:48,591 MuTect - [MUTECT] Processed 96004728 reads in 637 ms
[2015-09-30T22:08Z] INFO  23:08:48,597 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:48,667 MuTect - [MUTECT] Processed 146006540 reads in 660 ms
[2015-09-30T22:08Z] INFO  23:08:48,922 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:49,249 MuTect - [MUTECT] Processed 97004743 reads in 658 ms
[2015-09-30T22:08Z] INFO  23:08:49,256 MuTect - [MUTECT] Processed 112005934 reads in 691 ms
[2015-09-30T22:08Z] INFO  23:08:49,352 MuTect - [MUTECT] Processed 147006666 reads in 685 ms
[2015-09-30T22:08Z] INFO  23:08:49,910 MuTect - [MUTECT] Processed 98004813 reads in 661 ms
[2015-09-30T22:08Z] INFO  23:08:49,958 MuTect - [MUTECT] Processed 113005982 reads in 703 ms
[2015-09-30T22:08Z] INFO  23:08:50,037 MuTect - [MUTECT] Processed 148006721 reads in 685 ms
[2015-09-30T22:08Z] INFO  23:08:50,486 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:50,578 MuTect - [MUTECT] Processed 99004918 reads in 668 ms
[2015-09-30T22:08Z] INFO  23:08:50,637 MuTect - [MUTECT] Processed 114006012 reads in 679 ms
[2015-09-30T22:08Z] INFO  23:08:50,676 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:50,747 MuTect - [MUTECT] Processed 149006809 reads in 710 ms
[2015-09-30T22:08Z] INFO  23:08:51,251 MuTect - [MUTECT] Processed 100004962 reads in 673 ms
[2015-09-30T22:08Z] INFO  23:08:51,328 MuTect - [MUTECT] Processed 115006085 reads in 691 ms
[2015-09-30T22:08Z] INFO  23:08:51,440 MuTect - [MUTECT] Processed 150006830 reads in 693 ms
[2015-09-30T22:08Z] INFO  23:08:51,633 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:51,900 MuTect - [MUTECT] Processed 101005016 reads in 649 ms
[2015-09-30T22:08Z] INFO  23:08:51,994 MuTect - [MUTECT] Processed 116006124 reads in 666 ms
[2015-09-30T22:08Z] INFO  23:08:52,102 MuTect - [MUTECT] Processed 151006831 reads in 662 ms
[2015-09-30T22:08Z] INFO  23:08:52,521 MuTect - [MUTECT] Processed 102005033 reads in 621 ms
[2015-09-30T22:08Z] INFO  23:08:52,599 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:52,674 MuTect - [MUTECT] Processed 117006171 reads in 680 ms
[2015-09-30T22:08Z] INFO  23:08:52,757 MuTect - [MUTECT] Processed 152006866 reads in 655 ms
[2015-09-30T22:08Z] INFO  23:08:53,020 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:53,173 MuTect - [MUTECT] Processed 103005042 reads in 652 ms
[2015-09-30T22:08Z] INFO  23:08:53,368 MuTect - [MUTECT] Processed 118006224 reads in 694 ms
[2015-09-30T22:08Z] INFO  23:08:53,419 MuTect - [MUTECT] Processed 153006901 reads in 662 ms
[2015-09-30T22:08Z] INFO  23:08:53,522 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:08Z] INFO  23:08:53,527 ProgressMeter -            done        5.81e+06  106.0 s       18.0 s    100.0%       106.0 s     0.0 s
[2015-09-30T22:08Z] INFO  23:08:53,527 ProgressMeter - Total runtime 106.18 secs, 1.77 min, 0.03 hours
[2015-09-30T22:08Z] INFO  23:08:53,591 MicroScheduler - 109763 reads were filtered out during the traversal out of approximately 1811431 total reads (6.06%)
[2015-09-30T22:08Z] INFO  23:08:53,592 MicroScheduler -   -> 80384 reads (4.44% of total) failing DuplicateReadFilter
[2015-09-30T22:08Z] INFO  23:08:53,592 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:08Z] INFO  23:08:53,592 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:08Z] INFO  23:08:53,592 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:08Z] INFO  23:08:53,592 MicroScheduler -   -> 29379 reads (1.62% of total) failing UnmappedReadFilter
[2015-09-30T22:08Z] INFO  23:08:53,831 MuTect - [MUTECT] Processed 104005117 reads in 658 ms
[2015-09-30T22:08Z] INFO  23:08:53,987 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:54,050 MuTect - [MUTECT] Processed 119006322 reads in 682 ms
[2015-09-30T22:08Z] INFO  23:08:54,482 MuTect - [MUTECT] Processed 105005134 reads in 651 ms
[2015-09-30T22:08Z] INFO  23:08:54,580 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:08Z] bgzip syn3-2_189838937_221056966-raw-mutect.vcf
[2015-09-30T22:08Z] INFO  23:08:54,680 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:08Z] INFO  23:08:54,682 ProgressMeter -            done        3.20e+06   73.0 s       23.0 s    100.0%        73.0 s     0.0 s
[2015-09-30T22:08Z] INFO  23:08:54,682 ProgressMeter - Total runtime 73.81 secs, 1.23 min, 0.02 hours
[2015-09-30T22:08Z] tabix index syn3-2_189838937_221056966-raw-mutect.vcf.gz
[2015-09-30T22:08Z] INFO  23:08:54,748 MicroScheduler - 79555 reads were filtered out during the traversal out of approximately 1259681 total reads (6.32%)
[2015-09-30T22:08Z] INFO  23:08:54,748 MicroScheduler -   -> 59562 reads (4.73% of total) failing DuplicateReadFilter
[2015-09-30T22:08Z] INFO  23:08:54,748 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:08Z] INFO  23:08:54,748 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:08Z] INFO  23:08:54,748 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:08Z] INFO  23:08:54,749 MicroScheduler -   -> 19993 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:08Z] INFO  23:08:54,751 MuTect - [MUTECT] Processed 120006403 reads in 701 ms
[2015-09-30T22:08Z] INFO  23:08:55,379 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:55,413 MuTect - [MUTECT] Processed 121006526 reads in 662 ms
[2015-09-30T22:08Z] INFO  23:08:55,849 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:08Z] bgzip syn3-3_0_31203562-raw-mutect.vcf
[2015-09-30T22:08Z] tabix index syn3-3_0_31203562-raw-mutect.vcf.gz
[2015-09-30T22:08Z] INFO  23:08:56,097 MuTect - [MUTECT] Processed 122006561 reads in 684 ms
[2015-09-30T22:08Z] INFO  23:08:56,792 MuTect - [MUTECT] Processed 123006647 reads in 695 ms
[2015-09-30T22:08Z] MuTect: MuTect
[2015-09-30T22:08Z] INFO  23:08:57,476 MuTect - [MUTECT] Processed 124006767 reads in 684 ms
[2015-09-30T22:08Z] INFO  23:08:57,799 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:08Z] INFO  23:08:58,184 MuTect - [MUTECT] Processed 125006772 reads in 708 ms
[2015-09-30T22:08Z] MuTect: MuTect
[2015-09-30T22:08Z] INFO  23:08:58,843 MuTect - [MUTECT] Processed 126006889 reads in 658 ms
[2015-09-30T22:08Z] INFO  23:08:58,894 ProgressMeter -     2:242523944        3.83e+06   90.0 s       23.0 s     95.6%        94.0 s     4.0 s
[2015-09-30T22:08Z] INFO  23:08:59,022 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/3/syn3-3_31494593_62516713-raw-mutect-regions.bed to be BED
[2015-09-30T22:08Z] INFO  23:08:59,079 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:08Z] INFO  23:08:59,079 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:08Z] INFO  23:08:59,080 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:08Z] INFO  23:08:59,080 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:08Z] INFO  23:08:59,083 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/3/syn3-3_31494593_62516713-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/3/tx/tmp7AD0Gq/syn3-3_31494593_62516713-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:08Z] INFO  23:08:59,083 HelpFormatter - Date/Time: 2015/09/30 23:08:59
[2015-09-30T22:08Z] INFO  23:08:59,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:08Z] INFO  23:08:59,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:08Z] INFO  23:08:59,112 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:08Z] INFO  23:08:59,116 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:08Z] INFO  23:08:59,168 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:08Z] INFO  23:08:59,217 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:08Z] INFO  23:08:59,224 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:08Z] INFO  23:08:59,389 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.16
[2015-09-30T22:08Z] INFO  23:08:59,401 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:08Z] INFO  23:08:59,513 MuTect - [MUTECT] Processed 127006896 reads in 671 ms
[2015-09-30T22:08Z] INFO  23:08:59,574 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:08Z] INFO  23:08:59,704 IntervalUtils - Processing 2635478 bp from intervals
[2015-09-30T22:08Z] INFO  23:08:59,709 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:08Z] INFO  23:08:59,709 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:08Z] INFO  23:08:59,863 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:09Z] INFO  23:09:00,050 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:00,065 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:09Z] INFO  23:09:00,065 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:09Z] INFO  23:09:00,066 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:09Z] INFO  23:09:00,067 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:09Z] INFO  23:09:00,209 MuTect - [MUTECT] Processed 128006904 reads in 696 ms
[2015-09-30T22:09Z] INFO  23:09:00,322 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/3/syn3-3_62518267_93593495-raw-mutect-regions.bed to be BED
[2015-09-30T22:09Z] INFO  23:09:00,376 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:09Z] INFO  23:09:00,377 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:09Z] INFO  23:09:00,377 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:09Z] INFO  23:09:00,377 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:09Z] INFO  23:09:00,380 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/3/syn3-3_62518267_93593495-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/3/tx/tmpybBO3c/syn3-3_62518267_93593495-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:09Z] INFO  23:09:00,380 HelpFormatter - Date/Time: 2015/09/30 23:09:00
[2015-09-30T22:09Z] INFO  23:09:00,380 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:09Z] INFO  23:09:00,381 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:09Z] INFO  23:09:00,407 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:09Z] INFO  23:09:00,411 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:09Z] INFO  23:09:00,465 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:09Z] INFO  23:09:00,513 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:09Z] INFO  23:09:00,520 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:09Z] INFO  23:09:00,543 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:09Z] INFO  23:09:00,554 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:09Z] INFO  23:09:00,728 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:09Z] INFO  23:09:00,802 IntervalUtils - Processing 504096 bp from intervals
[2015-09-30T22:09Z] INFO  23:09:00,806 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:09Z] INFO  23:09:00,806 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:09Z] INFO  23:09:00,860 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:09Z] INFO  23:09:00,889 MuTect - [MUTECT] Processed 129006915 reads in 680 ms
[2015-09-30T22:09Z] INFO  23:09:01,077 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:09Z] INFO  23:09:01,077 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:09Z] INFO  23:09:01,078 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:09Z] INFO  23:09:01,079 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:09Z] INFO  23:09:01,618 MuTect - [MUTECT] Processed 130006930 reads in 729 ms
[2015-09-30T22:09Z] INFO  23:09:02,297 MuTect - [MUTECT] Processed 131006998 reads in 679 ms
[2015-09-30T22:09Z] INFO  23:09:02,414 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:02,624 MuTect - [MUTECT] Processed 1000009 reads in 2370 ms
[2015-09-30T22:09Z] INFO  23:09:03,022 MuTect - [MUTECT] Processed 132007082 reads in 725 ms
[2015-09-30T22:09Z] INFO  23:09:03,543 MuTect - [MUTECT] Processed 2000090 reads in 918 ms
[2015-09-30T22:09Z] INFO  23:09:03,571 MuTect - [MUTECT] Processed 1000041 reads in 2446 ms
[2015-09-30T22:09Z] INFO  23:09:03,721 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:09Z] INFO  23:09:03,725 ProgressMeter -            done        3.97e+06   94.0 s       23.0 s    100.0%        94.0 s     0.0 s
[2015-09-30T22:09Z] INFO  23:09:03,725 ProgressMeter - Total runtime 94.84 secs, 1.58 min, 0.03 hours
[2015-09-30T22:09Z] INFO  23:09:03,808 MicroScheduler - 104986 reads were filtered out during the traversal out of approximately 1593045 total reads (6.59%)
[2015-09-30T22:09Z] INFO  23:09:03,809 MicroScheduler -   -> 79385 reads (4.98% of total) failing DuplicateReadFilter
[2015-09-30T22:09Z] INFO  23:09:03,809 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:09Z] INFO  23:09:03,809 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:09Z] INFO  23:09:03,809 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:09Z] INFO  23:09:03,809 MicroScheduler -   -> 25601 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:09Z] INFO  23:09:04,329 MuTect - [MUTECT] Processed 3000107 reads in 787 ms
[2015-09-30T22:09Z] INFO  23:09:04,399 MuTect - [MUTECT] Processed 2000096 reads in 828 ms
[2015-09-30T22:09Z] INFO  23:09:04,684 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:04,776 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:09Z] bgzip syn3-2_221341378_243199373-raw-mutect.vcf
[2015-09-30T22:09Z] tabix index syn3-2_221341378_243199373-raw-mutect.vcf.gz
[2015-09-30T22:09Z] INFO  23:09:05,026 MuTect - [MUTECT] Processed 4000131 reads in 697 ms
[2015-09-30T22:09Z] INFO  23:09:05,198 MuTect - [MUTECT] Processed 3000124 reads in 799 ms
[2015-09-30T22:09Z] INFO  23:09:05,446 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:05,748 MuTect - [MUTECT] Processed 5000193 reads in 721 ms
[2015-09-30T22:09Z] INFO  23:09:05,921 MuTect - [MUTECT] Processed 4000126 reads in 723 ms
[2015-09-30T22:09Z] INFO  23:09:06,474 MuTect - [MUTECT] Processed 6000258 reads in 727 ms
[2015-09-30T22:09Z] INFO  23:09:07,033 MuTect - [MUTECT] Processed 5000133 reads in 1112 ms
[2015-09-30T22:09Z] INFO  23:09:07,192 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:07,205 MuTect - [MUTECT] Processed 7000258 reads in 731 ms
[2015-09-30T22:09Z] INFO  23:09:07,920 MuTect - [MUTECT] Processed 6000213 reads in 887 ms
[2015-09-30T22:09Z] INFO  23:09:07,926 MuTect - [MUTECT] Processed 8000339 reads in 721 ms
[2015-09-30T22:09Z] MuTect: MuTect
[2015-09-30T22:09Z] INFO  23:09:08,638 MuTect - [MUTECT] Processed 9000436 reads in 712 ms
[2015-09-30T22:09Z] INFO  23:09:08,708 MuTect - [MUTECT] Processed 7000239 reads in 788 ms
[2015-09-30T22:09Z] INFO  23:09:08,743 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:09,317 MuTect - [MUTECT] Processed 10000470 reads in 679 ms
[2015-09-30T22:09Z] INFO  23:09:09,358 MuTect - [MUTECT] Processed 8000244 reads in 650 ms
[2015-09-30T22:09Z] INFO  23:09:09,794 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:10,039 MuTect - [MUTECT] Processed 9000335 reads in 681 ms
[2015-09-30T22:09Z] INFO  23:09:10,062 MuTect - [MUTECT] Processed 11000471 reads in 745 ms
[2015-09-30T22:09Z] INFO  23:09:10,231 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/3/syn3-3_93595554_124625281-raw-mutect-regions.bed to be BED
[2015-09-30T22:09Z] INFO  23:09:10,284 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:09Z] INFO  23:09:10,285 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:09Z] INFO  23:09:10,285 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:09Z] INFO  23:09:10,285 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:09Z] INFO  23:09:10,288 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/3/syn3-3_93595554_124625281-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/3/tx/tmp0jmvAz/syn3-3_93595554_124625281-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:09Z] INFO  23:09:10,288 HelpFormatter - Date/Time: 2015/09/30 23:09:10
[2015-09-30T22:09Z] INFO  23:09:10,289 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:09Z] INFO  23:09:10,289 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:09Z] INFO  23:09:10,316 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:09Z] INFO  23:09:10,320 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:09Z] INFO  23:09:10,371 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:09Z] INFO  23:09:10,418 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:09Z] INFO  23:09:10,425 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:09Z] INFO  23:09:10,447 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:09Z] INFO  23:09:10,458 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:09Z] INFO  23:09:10,715 MuTect - [MUTECT] Processed 10000368 reads in 675 ms
[2015-09-30T22:09Z] INFO  23:09:10,723 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:09Z] INFO  23:09:10,801 MuTect - [MUTECT] Processed 12000544 reads in 739 ms
[2015-09-30T22:09Z] INFO  23:09:10,827 IntervalUtils - Processing 1334187 bp from intervals
[2015-09-30T22:09Z] INFO  23:09:10,831 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:09Z] INFO  23:09:10,832 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:09Z] INFO  23:09:10,983 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:09Z] INFO  23:09:11,144 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:09Z] INFO  23:09:11,144 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:09Z] INFO  23:09:11,144 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:09Z] INFO  23:09:11,145 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:09Z] INFO  23:09:11,151 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:11,393 MuTect - [MUTECT] Processed 11000385 reads in 679 ms
[2015-09-30T22:09Z] INFO  23:09:11,568 MuTect - [MUTECT] Processed 13000589 reads in 767 ms
[2015-09-30T22:09Z] INFO  23:09:12,068 MuTect - [MUTECT] Processed 12000454 reads in 675 ms
[2015-09-30T22:09Z] INFO  23:09:12,268 MuTect - [MUTECT] Processed 14000654 reads in 699 ms
[2015-09-30T22:09Z] INFO  23:09:12,677 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:12,770 MuTect - [MUTECT] Processed 13000478 reads in 702 ms
[2015-09-30T22:09Z] INFO  23:09:12,977 MuTect - [MUTECT] Processed 15000671 reads in 710 ms
[2015-09-30T22:09Z] INFO  23:09:13,490 MuTect - [MUTECT] Processed 14000478 reads in 720 ms
[2015-09-30T22:09Z] INFO  23:09:13,566 MuTect - [MUTECT] Processed 1000007 reads in 2375 ms
[2015-09-30T22:09Z] INFO  23:09:13,585 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:13,655 MuTect - [MUTECT] Processed 16000710 reads in 678 ms
[2015-09-30T22:09Z] INFO  23:09:14,239 MuTect - [MUTECT] Processed 15000490 reads in 749 ms
[2015-09-30T22:09Z] INFO  23:09:14,330 MuTect - [MUTECT] Processed 17000735 reads in 675 ms
[2015-09-30T22:09Z] INFO  23:09:14,439 MuTect - [MUTECT] Processed 2000034 reads in 873 ms
[2015-09-30T22:09Z] INFO  23:09:14,985 MuTect - [MUTECT] Processed 16000594 reads in 746 ms
[2015-09-30T22:09Z] INFO  23:09:15,070 MuTect - [MUTECT] Processed 18000777 reads in 740 ms
[2015-09-30T22:09Z] INFO  23:09:15,135 MuTect - [MUTECT] Processed 3000034 reads in 696 ms
[2015-09-30T22:09Z] INFO  23:09:15,197 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:15,727 MuTect - [MUTECT] Processed 17000636 reads in 742 ms
[2015-09-30T22:09Z] INFO  23:09:15,802 MuTect - [MUTECT] Processed 19000827 reads in 732 ms
[2015-09-30T22:09Z] INFO  23:09:15,822 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:15,825 MuTect - [MUTECT] Processed 4000067 reads in 690 ms
[2015-09-30T22:09Z] INFO  23:09:16,172 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:16,499 MuTect - [MUTECT] Processed 5000100 reads in 674 ms
[2015-09-30T22:09Z] INFO  23:09:16,499 MuTect - [MUTECT] Processed 18000656 reads in 772 ms
[2015-09-30T22:09Z] INFO  23:09:16,539 MuTect - [MUTECT] Processed 20000844 reads in 736 ms
[2015-09-30T22:09Z] INFO  23:09:17,236 MuTect - [MUTECT] Processed 19000672 reads in 737 ms
[2015-09-30T22:09Z] INFO  23:09:17,240 MuTect - [MUTECT] Processed 21000858 reads in 702 ms
[2015-09-30T22:09Z] INFO  23:09:17,286 MuTect - [MUTECT] Processed 6000119 reads in 787 ms
[2015-09-30T22:09Z] INFO  23:09:17,709 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:17,942 MuTect - [MUTECT] Processed 20000705 reads in 706 ms
[2015-09-30T22:09Z] INFO  23:09:17,963 MuTect - [MUTECT] Processed 22000910 reads in 723 ms
[2015-09-30T22:09Z] INFO  23:09:17,982 MuTect - [MUTECT] Processed 7000205 reads in 696 ms
[2015-09-30T22:09Z] INFO  23:09:18,282 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:18,622 MuTect - [MUTECT] Processed 21000724 reads in 680 ms
[2015-09-30T22:09Z] INFO  23:09:18,666 MuTect - [MUTECT] Processed 8000247 reads in 684 ms
[2015-09-30T22:09Z] INFO  23:09:18,669 MuTect - [MUTECT] Processed 23000950 reads in 706 ms
[2015-09-30T22:09Z] INFO  23:09:18,756 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:19,340 MuTect - [MUTECT] Processed 9000311 reads in 674 ms
[2015-09-30T22:09Z] INFO  23:09:19,353 MuTect - [MUTECT] Processed 22000763 reads in 731 ms
[2015-09-30T22:09Z] INFO  23:09:19,413 MuTect - [MUTECT] Processed 24001014 reads in 744 ms
[2015-09-30T22:09Z] INFO  23:09:19,998 MuTect - [MUTECT] Processed 10000326 reads in 658 ms
[2015-09-30T22:09Z] INFO  23:09:20,031 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:20,044 MuTect - [MUTECT] Processed 23000841 reads in 691 ms
[2015-09-30T22:09Z] INFO  23:09:20,069 MuTect - [MUTECT] Processed 25001105 reads in 656 ms
[2015-09-30T22:09Z] INFO  23:09:20,621 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:20,638 MuTect - [MUTECT] Processed 11000345 reads in 640 ms
[2015-09-30T22:09Z] INFO  23:09:20,728 MuTect - [MUTECT] Processed 26001200 reads in 659 ms
[2015-09-30T22:09Z] INFO  23:09:20,758 MuTect - [MUTECT] Processed 24000928 reads in 714 ms
[2015-09-30T22:09Z] INFO  23:09:21,300 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:21,375 MuTect - [MUTECT] Processed 12000405 reads in 737 ms
[2015-09-30T22:09Z] INFO  23:09:21,449 MuTect - [MUTECT] Processed 27001239 reads in 720 ms
[2015-09-30T22:09Z] INFO  23:09:21,451 MuTect - [MUTECT] Processed 25001030 reads in 693 ms
[2015-09-30T22:09Z] INFO  23:09:22,069 MuTect - [MUTECT] Processed 13000437 reads in 694 ms
[2015-09-30T22:09Z] INFO  23:09:22,173 MuTect - [MUTECT] Processed 26001095 reads in 722 ms
[2015-09-30T22:09Z] INFO  23:09:22,306 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:22,322 MuTect - [MUTECT] Processed 28001408 reads in 874 ms
[2015-09-30T22:09Z] INFO  23:09:22,744 MuTect - [MUTECT] Processed 14000444 reads in 675 ms
[2015-09-30T22:09Z] INFO  23:09:22,886 MuTect - [MUTECT] Processed 27001117 reads in 712 ms
[2015-09-30T22:09Z] INFO  23:09:23,197 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:23,458 MuTect - [MUTECT] Processed 15000475 reads in 714 ms
[2015-09-30T22:09Z] INFO  23:09:23,761 MuTect - [MUTECT] Processed 29001418 reads in 1439 ms
[2015-09-30T22:09Z] INFO  23:09:23,782 MuTect - [MUTECT] Processed 28001550 reads in 897 ms
[2015-09-30T22:09Z] INFO  23:09:23,873 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:24,163 MuTect - [MUTECT] Processed 16000482 reads in 705 ms
[2015-09-30T22:09Z] INFO  23:09:24,436 MuTect - [MUTECT] Processed 30001489 reads in 675 ms
[2015-09-30T22:09Z] INFO  23:09:24,699 MuTect - [MUTECT] Processed 29005571 reads in 917 ms
[2015-09-30T22:09Z] INFO  23:09:24,854 MuTect - [MUTECT] Processed 17000506 reads in 691 ms
[2015-09-30T22:09Z] INFO  23:09:25,091 MuTect - [MUTECT] Processed 31001590 reads in 655 ms
[2015-09-30T22:09Z] INFO  23:09:25,154 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:25,477 MuTect - [MUTECT] Processed 30007080 reads in 778 ms
[2015-09-30T22:09Z] INFO  23:09:25,547 MuTect - [MUTECT] Processed 18000581 reads in 693 ms
[2015-09-30T22:09Z] INFO  23:09:25,664 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:25,737 MuTect - [MUTECT] Processed 32001628 reads in 646 ms
[2015-09-30T22:09Z] INFO  23:09:26,239 MuTect - [MUTECT] Processed 19000631 reads in 692 ms
[2015-09-30T22:09Z] INFO  23:09:26,373 MuTect - [MUTECT] Processed 33001692 reads in 636 ms
[2015-09-30T22:09Z] INFO  23:09:26,504 MuTect - [MUTECT] Processed 31007113 reads in 1027 ms
[2015-09-30T22:09Z] INFO  23:09:26,951 MuTect - [MUTECT] Processed 20000663 reads in 712 ms
[2015-09-30T22:09Z] INFO  23:09:27,047 MuTect - [MUTECT] Processed 34001753 reads in 674 ms
[2015-09-30T22:09Z] INFO  23:09:27,183 MuTect - [MUTECT] Processed 32007146 reads in 679 ms
[2015-09-30T22:09Z] INFO  23:09:27,428 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:27,638 MuTect - [MUTECT] Processed 21000748 reads in 687 ms
[2015-09-30T22:09Z] INFO  23:09:27,745 MuTect - [MUTECT] Processed 35001860 reads in 698 ms
[2015-09-30T22:09Z] INFO  23:09:27,877 MuTect - [MUTECT] Processed 33007167 reads in 694 ms
[2015-09-30T22:09Z] INFO  23:09:28,156 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:28,289 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:28,319 MuTect - [MUTECT] Processed 22000753 reads in 681 ms
[2015-09-30T22:09Z] INFO  23:09:28,424 MuTect - [MUTECT] Processed 36001883 reads in 679 ms
[2015-09-30T22:09Z] INFO  23:09:28,616 MuTect - [MUTECT] Processed 34007182 reads in 739 ms
[2015-09-30T22:09Z] INFO  23:09:28,984 MuTect - [MUTECT] Processed 23000847 reads in 665 ms
[2015-09-30T22:09Z] INFO  23:09:29,075 MuTect - [MUTECT] Processed 37001993 reads in 651 ms
[2015-09-30T22:09Z] INFO  23:09:29,369 MuTect - [MUTECT] Processed 35007271 reads in 753 ms
[2015-09-30T22:09Z] INFO  23:09:29,642 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:29,677 MuTect - [MUTECT] Processed 38002064 reads in 602 ms
[2015-09-30T22:09Z] INFO  23:09:29,707 MuTect - [MUTECT] Processed 24000847 reads in 723 ms
[2015-09-30T22:09Z] INFO  23:09:30,068 ProgressMeter -      3:38639028        1.26e+06   30.0 s       23.0 s     16.7%         3.0 m     2.5 m
[2015-09-30T22:09Z] INFO  23:09:30,074 MuTect - [MUTECT] Processed 36007299 reads in 705 ms
[2015-09-30T22:09Z] INFO  23:09:30,315 MuTect - [MUTECT] Processed 39002180 reads in 638 ms
[2015-09-30T22:09Z] INFO  23:09:30,424 MuTect - [MUTECT] Processed 25000901 reads in 717 ms
[2015-09-30T22:09Z] INFO  23:09:30,764 MuTect - [MUTECT] Processed 37007372 reads in 690 ms
[2015-09-30T22:09Z] INFO  23:09:30,921 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:30,942 MuTect - [MUTECT] Processed 40002234 reads in 627 ms
[2015-09-30T22:09Z] INFO  23:09:31,021 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:31,082 ProgressMeter -      3:88285759        1.07e+06   30.0 s       28.0 s     95.9%        31.0 s     1.0 s
[2015-09-30T22:09Z] INFO  23:09:31,134 MuTect - [MUTECT] Processed 26000921 reads in 709 ms
[2015-09-30T22:09Z] INFO  23:09:31,468 MuTect - [MUTECT] Processed 38007401 reads in 704 ms
[2015-09-30T22:09Z] INFO  23:09:31,595 MuTect - [MUTECT] Processed 41002292 reads in 653 ms
[2015-09-30T22:09Z] INFO  23:09:31,847 MuTect - [MUTECT] Processed 27000945 reads in 714 ms
[2015-09-30T22:09Z] INFO  23:09:31,881 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:31,963 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:09Z] INFO  23:09:31,966 ProgressMeter -            done        1.10e+06   30.0 s       28.0 s    100.0%        30.0 s     0.0 s
[2015-09-30T22:09Z] INFO  23:09:31,966 ProgressMeter - Total runtime 30.89 secs, 0.51 min, 0.01 hours
[2015-09-30T22:09Z] INFO  23:09:32,032 MicroScheduler - 31271 reads were filtered out during the traversal out of approximately 466436 total reads (6.70%)
[2015-09-30T22:09Z] INFO  23:09:32,033 MicroScheduler -   -> 23954 reads (5.14% of total) failing DuplicateReadFilter
[2015-09-30T22:09Z] INFO  23:09:32,033 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:09Z] INFO  23:09:32,033 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:09Z] INFO  23:09:32,033 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:09Z] INFO  23:09:32,033 MicroScheduler -   -> 7317 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:09Z] INFO  23:09:32,242 MuTect - [MUTECT] Processed 42002292 reads in 647 ms
[2015-09-30T22:09Z] INFO  23:09:32,569 MuTect - [MUTECT] Processed 28000963 reads in 722 ms
[2015-09-30T22:09Z] INFO  23:09:32,897 MuTect - [MUTECT] Processed 43002368 reads in 655 ms
[2015-09-30T22:09Z] INFO  23:09:33,131 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:09Z] bgzip syn3-3_62518267_93593495-raw-mutect.vcf
[2015-09-30T22:09Z] tabix index syn3-3_62518267_93593495-raw-mutect.vcf.gz
[2015-09-30T22:09Z] INFO  23:09:33,277 MuTect - [MUTECT] Processed 29000968 reads in 708 ms
[2015-09-30T22:09Z] INFO  23:09:33,501 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:33,567 MuTect - [MUTECT] Processed 44002380 reads in 670 ms
[2015-09-30T22:09Z] INFO  23:09:33,994 MuTect - [MUTECT] Processed 30001008 reads in 717 ms
[2015-09-30T22:09Z] INFO  23:09:34,209 MuTect - [MUTECT] Processed 45002514 reads in 642 ms
[2015-09-30T22:09Z] INFO  23:09:34,270 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:34,715 MuTect - [MUTECT] Processed 31001013 reads in 721 ms
[2015-09-30T22:09Z] INFO  23:09:34,857 MuTect - [MUTECT] Processed 46002578 reads in 648 ms
[2015-09-30T22:09Z] MuTect: MuTect
[2015-09-30T22:09Z] INFO  23:09:35,421 MuTect - [MUTECT] Processed 32001028 reads in 706 ms
[2015-09-30T22:09Z] INFO  23:09:35,554 MuTect - [MUTECT] Processed 47002680 reads in 697 ms
[2015-09-30T22:09Z] INFO  23:09:36,133 MuTect - [MUTECT] Processed 33001034 reads in 712 ms
[2015-09-30T22:09Z] INFO  23:09:36,227 MuTect - [MUTECT] Processed 48002714 reads in 672 ms
[2015-09-30T22:09Z] INFO  23:09:36,252 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:36,419 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:36,910 MuTect - [MUTECT] Processed 34001039 reads in 777 ms
[2015-09-30T22:09Z] INFO  23:09:36,911 MuTect - [MUTECT] Processed 49002819 reads in 685 ms
[2015-09-30T22:09Z] INFO  23:09:37,513 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/3/syn3-3_124626733_155649953-raw-mutect-regions.bed to be BED
[2015-09-30T22:09Z] INFO  23:09:37,570 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:09Z] INFO  23:09:37,571 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:09Z] INFO  23:09:37,571 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:09Z] INFO  23:09:37,571 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:09Z] INFO  23:09:37,574 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/3/syn3-3_124626733_155649953-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/3/tx/tmpgwLrjv/syn3-3_124626733_155649953-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:09Z] INFO  23:09:37,575 HelpFormatter - Date/Time: 2015/09/30 23:09:37
[2015-09-30T22:09Z] INFO  23:09:37,575 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:09Z] INFO  23:09:37,575 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:09Z] INFO  23:09:37,656 MuTect - [MUTECT] Processed 50002863 reads in 745 ms
[2015-09-30T22:09Z] INFO  23:09:37,669 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:09Z] INFO  23:09:37,690 MuTect - [MUTECT] Processed 35001062 reads in 780 ms
[2015-09-30T22:09Z] INFO  23:09:37,712 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:09Z] INFO  23:09:37,760 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:09Z] INFO  23:09:37,805 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:09Z] INFO  23:09:37,812 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:09Z] INFO  23:09:38,331 MuTect - [MUTECT] Processed 51002882 reads in 675 ms
[2015-09-30T22:09Z] INFO  23:09:38,439 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.63
[2015-09-30T22:09Z] INFO  23:09:38,450 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:09Z] INFO  23:09:38,618 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:09Z] INFO  23:09:38,730 IntervalUtils - Processing 1640755 bp from intervals
[2015-09-30T22:09Z] INFO  23:09:38,734 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:09Z] INFO  23:09:38,734 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:09Z] INFO  23:09:38,788 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:38,827 MuTect - [MUTECT] Processed 36001063 reads in 1137 ms
[2015-09-30T22:09Z] INFO  23:09:38,999 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:09Z] INFO  23:09:39,032 MuTect - [MUTECT] Processed 52002908 reads in 701 ms
[2015-09-30T22:09Z] INFO  23:09:39,240 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:39,520 MuTect - [MUTECT] Processed 37001119 reads in 693 ms
[2015-09-30T22:09Z] INFO  23:09:39,694 MuTect - [MUTECT] Processed 53002910 reads in 662 ms
[2015-09-30T22:09Z] INFO  23:09:39,785 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:09Z] INFO  23:09:39,785 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:09Z] INFO  23:09:39,785 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:09Z] INFO  23:09:39,786 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:09Z] INFO  23:09:40,251 MuTect - [MUTECT] Processed 38001120 reads in 731 ms
[2015-09-30T22:09Z] INFO  23:09:40,398 MuTect - [MUTECT] Processed 54002921 reads in 704 ms
[2015-09-30T22:09Z] INFO  23:09:40,993 MuTect - [MUTECT] Processed 39001201 reads in 742 ms
[2015-09-30T22:09Z] INFO  23:09:41,117 MuTect - [MUTECT] Processed 55002964 reads in 719 ms
[2015-09-30T22:09Z] INFO  23:09:41,147 ProgressMeter -     3:111763206        1.47e+06   30.0 s       20.0 s     42.8%        70.0 s    40.0 s
[2015-09-30T22:09Z] INFO  23:09:41,231 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:41,719 MuTect - [MUTECT] Processed 40001281 reads in 726 ms
[2015-09-30T22:09Z] INFO  23:09:41,721 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:41,888 MuTect - [MUTECT] Processed 56003012 reads in 771 ms
[2015-09-30T22:09Z] INFO  23:09:42,232 MuTect - [MUTECT] Processed 1000019 reads in 2325 ms
[2015-09-30T22:09Z] INFO  23:09:42,459 MuTect - [MUTECT] Processed 41001346 reads in 740 ms
[2015-09-30T22:09Z] INFO  23:09:42,621 MuTect - [MUTECT] Processed 57003053 reads in 733 ms
[2015-09-30T22:09Z] INFO  23:09:42,983 MuTect - [MUTECT] Processed 2000094 reads in 751 ms
[2015-09-30T22:09Z] INFO  23:09:43,245 MuTect - [MUTECT] Processed 42001381 reads in 786 ms
[2015-09-30T22:09Z] INFO  23:09:43,325 MuTect - [MUTECT] Processed 58003135 reads in 704 ms
[2015-09-30T22:09Z] INFO  23:09:43,614 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:43,741 MuTect - [MUTECT] Processed 3000126 reads in 758 ms
[2015-09-30T22:09Z] INFO  23:09:43,977 MuTect - [MUTECT] Processed 43001431 reads in 732 ms
[2015-09-30T22:09Z] INFO  23:09:43,998 MuTect - [MUTECT] Processed 59003184 reads in 673 ms
[2015-09-30T22:09Z] INFO  23:09:44,002 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:44,319 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:44,442 MuTect - [MUTECT] Processed 4000212 reads in 701 ms
[2015-09-30T22:09Z] INFO  23:09:44,683 MuTect - [MUTECT] Processed 60003228 reads in 685 ms
[2015-09-30T22:09Z] INFO  23:09:44,686 MuTect - [MUTECT] Processed 44001487 reads in 709 ms
[2015-09-30T22:09Z] INFO  23:09:45,125 MuTect - [MUTECT] Processed 5000232 reads in 683 ms
[2015-09-30T22:09Z] INFO  23:09:45,339 MuTect - [MUTECT] Processed 61003253 reads in 656 ms
[2015-09-30T22:09Z] INFO  23:09:45,440 MuTect - [MUTECT] Processed 45001578 reads in 753 ms
[2015-09-30T22:09Z] INFO  23:09:45,971 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:46,002 MuTect - [MUTECT] Processed 62003260 reads in 663 ms
[2015-09-30T22:09Z] INFO  23:09:46,042 MuTect - [MUTECT] Processed 6000244 reads in 917 ms
[2015-09-30T22:09Z] INFO  23:09:46,164 MuTect - [MUTECT] Processed 46001636 reads in 725 ms
[2015-09-30T22:09Z] INFO  23:09:46,681 MuTect - [MUTECT] Processed 63003292 reads in 679 ms
[2015-09-30T22:09Z] INFO  23:09:46,773 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:46,850 MuTect - [MUTECT] Processed 47001739 reads in 686 ms
[2015-09-30T22:09Z] INFO  23:09:46,956 MuTect - [MUTECT] Processed 7000326 reads in 913 ms
[2015-09-30T22:09Z] INFO  23:09:47,039 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:47,388 MuTect - [MUTECT] Processed 64003297 reads in 707 ms
[2015-09-30T22:09Z] INFO  23:09:47,565 MuTect - [MUTECT] Processed 48001804 reads in 715 ms
[2015-09-30T22:09Z] INFO  23:09:47,819 MuTect - [MUTECT] Processed 8000337 reads in 864 ms
[2015-09-30T22:09Z] INFO  23:09:48,049 MuTect - [MUTECT] Processed 65003394 reads in 660 ms
[2015-09-30T22:09Z] INFO  23:09:48,301 MuTect - [MUTECT] Processed 49001826 reads in 736 ms
[2015-09-30T22:09Z] INFO  23:09:48,551 MuTect - [MUTECT] Processed 9000441 reads in 732 ms
[2015-09-30T22:09Z] INFO  23:09:48,718 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:48,724 MuTect - [MUTECT] Processed 66003441 reads in 676 ms
[2015-09-30T22:09Z] INFO  23:09:49,044 MuTect - [MUTECT] Processed 50001869 reads in 743 ms
[2015-09-30T22:09Z] INFO  23:09:49,199 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:49,247 MuTect - [MUTECT] Processed 10000485 reads in 696 ms
[2015-09-30T22:09Z] INFO  23:09:49,436 MuTect - [MUTECT] Processed 67003519 reads in 712 ms
[2015-09-30T22:09Z] INFO  23:09:49,740 MuTect - [MUTECT] Processed 51001881 reads in 696 ms
[2015-09-30T22:09Z] INFO  23:09:49,842 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:49,938 MuTect - [MUTECT] Processed 11000550 reads in 691 ms
[2015-09-30T22:09Z] INFO  23:09:50,131 MuTect - [MUTECT] Processed 68003630 reads in 695 ms
[2015-09-30T22:09Z] INFO  23:09:50,411 MuTect - [MUTECT] Processed 52001908 reads in 670 ms
[2015-09-30T22:09Z] INFO  23:09:50,676 MuTect - [MUTECT] Processed 12000611 reads in 738 ms
[2015-09-30T22:09Z] INFO  23:09:50,822 MuTect - [MUTECT] Processed 69003642 reads in 691 ms
[2015-09-30T22:09Z] INFO  23:09:51,119 MuTect - [MUTECT] Processed 53001910 reads in 708 ms
[2015-09-30T22:09Z] INFO  23:09:51,378 MuTect - [MUTECT] Processed 13000675 reads in 702 ms
[2015-09-30T22:09Z] INFO  23:09:51,470 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:51,507 MuTect - [MUTECT] Processed 70003673 reads in 685 ms
[2015-09-30T22:09Z] INFO  23:09:51,600 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:51,826 MuTect - [MUTECT] Processed 54002020 reads in 708 ms
[2015-09-30T22:09Z] INFO  23:09:52,030 MuTect - [MUTECT] Processed 14000687 reads in 652 ms
[2015-09-30T22:09Z] INFO  23:09:52,166 MuTect - [MUTECT] Processed 71003704 reads in 659 ms
[2015-09-30T22:09Z] INFO  23:09:52,348 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:52,509 MuTect - [MUTECT] Processed 55002071 reads in 683 ms
[2015-09-30T22:09Z] INFO  23:09:52,723 MuTect - [MUTECT] Processed 15000774 reads in 692 ms
[2015-09-30T22:09Z] INFO  23:09:52,804 MuTect - [MUTECT] Processed 72003777 reads in 638 ms
[2015-09-30T22:09Z] INFO  23:09:53,185 MuTect - [MUTECT] Processed 56002129 reads in 676 ms
[2015-09-30T22:09Z] INFO  23:09:53,443 MuTect - [MUTECT] Processed 73003863 reads in 639 ms
[2015-09-30T22:09Z] INFO  23:09:53,475 MuTect - [MUTECT] Processed 16000842 reads in 753 ms
[2015-09-30T22:09Z] INFO  23:09:53,816 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:53,853 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:53,858 MuTect - [MUTECT] Processed 57002160 reads in 672 ms
[2015-09-30T22:09Z] INFO  23:09:54,128 MuTect - [MUTECT] Processed 74003910 reads in 685 ms
[2015-09-30T22:09Z] INFO  23:09:54,201 MuTect - [MUTECT] Processed 17000865 reads in 726 ms
[2015-09-30T22:09Z] INFO  23:09:54,543 MuTect - [MUTECT] Processed 58002248 reads in 686 ms
[2015-09-30T22:09Z] INFO  23:09:54,724 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:54,787 MuTect - [MUTECT] Processed 75003921 reads in 659 ms
[2015-09-30T22:09Z] INFO  23:09:54,913 MuTect - [MUTECT] Processed 18000868 reads in 711 ms
[2015-09-30T22:09Z] INFO  23:09:55,267 MuTect - [MUTECT] Processed 59002252 reads in 724 ms
[2015-09-30T22:09Z] INFO  23:09:55,498 MuTect - [MUTECT] Processed 76003972 reads in 711 ms
[2015-09-30T22:09Z] INFO  23:09:55,610 MuTect - [MUTECT] Processed 19000899 reads in 698 ms
[2015-09-30T22:09Z] INFO  23:09:55,960 MuTect - [MUTECT] Processed 60002258 reads in 693 ms
[2015-09-30T22:09Z] INFO  23:09:56,145 MuTect - [MUTECT] Processed 77004019 reads in 647 ms
[2015-09-30T22:09Z] INFO  23:09:56,203 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:56,284 MuTect - [MUTECT] Processed 20000998 reads in 674 ms
[2015-09-30T22:09Z] INFO  23:09:56,285 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:56,646 MuTect - [MUTECT] Processed 61002358 reads in 686 ms
[2015-09-30T22:09Z] INFO  23:09:56,823 MuTect - [MUTECT] Processed 78004022 reads in 678 ms
[2015-09-30T22:09Z] INFO  23:09:56,940 MuTect - [MUTECT] Processed 21001083 reads in 656 ms
[2015-09-30T22:09Z] INFO  23:09:57,217 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:57,306 MuTect - [MUTECT] Processed 62002401 reads in 660 ms
[2015-09-30T22:09Z] INFO  23:09:57,500 MuTect - [MUTECT] Processed 79004078 reads in 677 ms
[2015-09-30T22:09Z] INFO  23:09:57,623 MuTect - [MUTECT] Processed 22001116 reads in 683 ms
[2015-09-30T22:09Z] INFO  23:09:57,998 MuTect - [MUTECT] Processed 63002414 reads in 692 ms
[2015-09-30T22:09Z] INFO  23:09:58,171 MuTect - [MUTECT] Processed 80004114 reads in 671 ms
[2015-09-30T22:09Z] INFO  23:09:58,301 MuTect - [MUTECT] Processed 23001202 reads in 678 ms
[2015-09-30T22:09Z] INFO  23:09:58,430 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:58,526 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:58,681 MuTect - [MUTECT] Processed 64002461 reads in 683 ms
[2015-09-30T22:09Z] INFO  23:09:58,836 MuTect - [MUTECT] Processed 81004172 reads in 665 ms
[2015-09-30T22:09Z] INFO  23:09:58,962 MuTect - [MUTECT] Processed 24001268 reads in 660 ms
[2015-09-30T22:09Z] INFO  23:09:59,406 MuTect - [MUTECT] Processed 65002464 reads in 725 ms
[2015-09-30T22:09Z] INFO  23:09:59,526 MuTect - [MUTECT] Processed 82004285 reads in 690 ms
[2015-09-30T22:09Z] INFO  23:09:59,564 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:09Z] INFO  23:09:59,612 MuTect - [MUTECT] Processed 25001277 reads in 651 ms
[2015-09-30T22:10Z] INFO  23:10:00,069 ProgressMeter -      3:45872223        2.48e+06   60.0 s       24.0 s     34.7%         2.9 m   112.0 s
[2015-09-30T22:10Z] INFO  23:10:00,110 MuTect - [MUTECT] Processed 66002544 reads in 704 ms
[2015-09-30T22:10Z] INFO  23:10:00,224 MuTect - [MUTECT] Processed 83004317 reads in 697 ms
[2015-09-30T22:10Z] INFO  23:10:00,250 MuTect - [MUTECT] Processed 26001321 reads in 638 ms
[2015-09-30T22:10Z] INFO  23:10:00,750 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:00,779 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:00,817 MuTect - [MUTECT] Processed 67002582 reads in 707 ms
[2015-09-30T22:10Z] INFO  23:10:00,917 MuTect - [MUTECT] Processed 84004347 reads in 694 ms
[2015-09-30T22:10Z] INFO  23:10:00,966 MuTect - [MUTECT] Processed 27001323 reads in 716 ms
[2015-09-30T22:10Z] INFO  23:10:01,465 MuTect - [MUTECT] Processed 68002587 reads in 648 ms
[2015-09-30T22:10Z] INFO  23:10:01,617 MuTect - [MUTECT] Processed 85004440 reads in 700 ms
[2015-09-30T22:10Z] INFO  23:10:01,675 MuTect - [MUTECT] Processed 28001406 reads in 709 ms
[2015-09-30T22:10Z] INFO  23:10:02,001 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:02,123 MuTect - [MUTECT] Processed 69002649 reads in 658 ms
[2015-09-30T22:10Z] INFO  23:10:02,300 MuTect - [MUTECT] Processed 86004446 reads in 683 ms
[2015-09-30T22:10Z] INFO  23:10:02,374 MuTect - [MUTECT] Processed 29001431 reads in 699 ms
[2015-09-30T22:10Z] INFO  23:10:02,792 MuTect - [MUTECT] Processed 70002683 reads in 669 ms
[2015-09-30T22:10Z] INFO  23:10:02,950 MuTect - [MUTECT] Processed 87004529 reads in 650 ms
[2015-09-30T22:10Z] INFO  23:10:03,065 MuTect - [MUTECT] Processed 30001514 reads in 691 ms
[2015-09-30T22:10Z] INFO  23:10:03,125 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:03,244 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:03,495 MuTect - [MUTECT] Processed 71002687 reads in 703 ms
[2015-09-30T22:10Z] INFO  23:10:03,622 MuTect - [MUTECT] Processed 88004596 reads in 672 ms
[2015-09-30T22:10Z] INFO  23:10:03,778 MuTect - [MUTECT] Processed 31001576 reads in 713 ms
[2015-09-30T22:10Z] INFO  23:10:04,181 MuTect - [MUTECT] Processed 72002712 reads in 686 ms
[2015-09-30T22:10Z] INFO  23:10:04,260 MuTect - [MUTECT] Processed 89004681 reads in 638 ms
[2015-09-30T22:10Z] INFO  23:10:04,451 MuTect - [MUTECT] Processed 32001583 reads in 673 ms
[2015-09-30T22:10Z] INFO  23:10:04,506 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:04,864 MuTect - [MUTECT] Processed 73002788 reads in 683 ms
[2015-09-30T22:10Z] INFO  23:10:04,907 MuTect - [MUTECT] Processed 90004683 reads in 647 ms
[2015-09-30T22:10Z] INFO  23:10:05,104 MuTect - [MUTECT] Processed 33001644 reads in 653 ms
[2015-09-30T22:10Z] INFO  23:10:05,409 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:05,552 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:05,557 MuTect - [MUTECT] Processed 91004758 reads in 650 ms
[2015-09-30T22:10Z] INFO  23:10:05,590 MuTect - [MUTECT] Processed 74002860 reads in 726 ms
[2015-09-30T22:10Z] INFO  23:10:05,776 MuTect - [MUTECT] Processed 34001701 reads in 672 ms
[2015-09-30T22:10Z] INFO  23:10:06,220 MuTect - [MUTECT] Processed 92004791 reads in 663 ms
[2015-09-30T22:10Z] INFO  23:10:06,286 MuTect - [MUTECT] Processed 75002953 reads in 696 ms
[2015-09-30T22:10Z] INFO  23:10:06,501 MuTect - [MUTECT] Processed 35001826 reads in 725 ms
[2015-09-30T22:10Z] INFO  23:10:06,882 MuTect - [MUTECT] Processed 93004850 reads in 662 ms
[2015-09-30T22:10Z] INFO  23:10:07,075 MuTect - [MUTECT] Processed 76002968 reads in 789 ms
[2015-09-30T22:10Z] INFO  23:10:07,208 MuTect - [MUTECT] Processed 36001899 reads in 707 ms
[2015-09-30T22:10Z] INFO  23:10:07,227 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:07,533 MuTect - [MUTECT] Processed 94004967 reads in 651 ms
[2015-09-30T22:10Z] INFO  23:10:07,543 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:07,820 MuTect - [MUTECT] Processed 77003034 reads in 745 ms
[2015-09-30T22:10Z] INFO  23:10:07,891 MuTect - [MUTECT] Processed 37001995 reads in 683 ms
[2015-09-30T22:10Z] INFO  23:10:07,915 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:08,170 MuTect - [MUTECT] Processed 95005034 reads in 637 ms
[2015-09-30T22:10Z] INFO  23:10:08,467 MuTect - [MUTECT] Processed 78003124 reads in 647 ms
[2015-09-30T22:10Z] INFO  23:10:08,581 MuTect - [MUTECT] Processed 38002075 reads in 690 ms
[2015-09-30T22:10Z] INFO  23:10:08,845 MuTect - [MUTECT] Processed 96005145 reads in 674 ms
[2015-09-30T22:10Z] INFO  23:10:09,111 MuTect - [MUTECT] Processed 79003128 reads in 644 ms
[2015-09-30T22:10Z] INFO  23:10:09,248 MuTect - [MUTECT] Processed 39002094 reads in 667 ms
[2015-09-30T22:10Z] INFO  23:10:09,533 MuTect - [MUTECT] Processed 97005248 reads in 689 ms
[2015-09-30T22:10Z] INFO  23:10:09,570 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:09,743 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:09,787 ProgressMeter -     3:129116174        1.05e+06   30.0 s       28.0 s     23.4%         2.1 m    98.0 s
[2015-09-30T22:10Z] INFO  23:10:09,789 MuTect - [MUTECT] Processed 80003214 reads in 678 ms
[2015-09-30T22:10Z] INFO  23:10:09,959 MuTect - [MUTECT] Processed 40002128 reads in 711 ms
[2015-09-30T22:10Z] INFO  23:10:10,152 MuTect - [MUTECT] Processed 98005271 reads in 619 ms
[2015-09-30T22:10Z] INFO  23:10:10,244 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:10,507 MuTect - [MUTECT] Processed 81003237 reads in 718 ms
[2015-09-30T22:10Z] INFO  23:10:10,645 MuTect - [MUTECT] Processed 41002173 reads in 686 ms
[2015-09-30T22:10Z] INFO  23:10:10,756 MuTect - [MUTECT] Processed 99005350 reads in 604 ms
[2015-09-30T22:10Z] INFO  23:10:11,148 ProgressMeter -     3:122288194        2.87e+06   60.0 s       20.0 s     84.3%        71.0 s    11.0 s
[2015-09-30T22:10Z] INFO  23:10:11,201 MuTect - [MUTECT] Processed 82003244 reads in 694 ms
[2015-09-30T22:10Z] INFO  23:10:11,337 MuTect - [MUTECT] Processed 42002287 reads in 692 ms
[2015-09-30T22:10Z] INFO  23:10:11,371 MuTect - [MUTECT] Processed 100005409 reads in 615 ms
[2015-09-30T22:10Z] INFO  23:10:11,918 MuTect - [MUTECT] Processed 83003261 reads in 716 ms
[2015-09-30T22:10Z] INFO  23:10:11,947 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:12,018 MuTect - [MUTECT] Processed 101005418 reads in 647 ms
[2015-09-30T22:10Z] INFO  23:10:12,022 MuTect - [MUTECT] Processed 43002308 reads in 685 ms
[2015-09-30T22:10Z] INFO  23:10:12,128 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:12,610 MuTect - [MUTECT] Processed 84003309 reads in 693 ms
[2015-09-30T22:10Z] INFO  23:10:12,633 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:12,637 MuTect - [MUTECT] Processed 102005462 reads in 619 ms
[2015-09-30T22:10Z] INFO  23:10:12,707 MuTect - [MUTECT] Processed 44002381 reads in 684 ms
[2015-09-30T22:10Z] INFO  23:10:13,253 MuTect - [MUTECT] Processed 103005564 reads in 616 ms
[2015-09-30T22:10Z] INFO  23:10:13,320 MuTect - [MUTECT] Processed 85003380 reads in 710 ms
[2015-09-30T22:10Z] INFO  23:10:13,375 MuTect - [MUTECT] Processed 45002458 reads in 669 ms
[2015-09-30T22:10Z] INFO  23:10:13,894 MuTect - [MUTECT] Processed 104005660 reads in 641 ms
[2015-09-30T22:10Z] INFO  23:10:13,995 MuTect - [MUTECT] Processed 86003518 reads in 675 ms
[2015-09-30T22:10Z] INFO  23:10:14,069 MuTect - [MUTECT] Processed 46002531 reads in 694 ms
[2015-09-30T22:10Z] INFO  23:10:14,142 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:14,475 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:14,512 MuTect - [MUTECT] Processed 105005692 reads in 618 ms
[2015-09-30T22:10Z] INFO  23:10:14,695 MuTect - [MUTECT] Processed 87003602 reads in 700 ms
[2015-09-30T22:10Z] INFO  23:10:14,786 MuTect - [MUTECT] Processed 47002617 reads in 717 ms
[2015-09-30T22:10Z] INFO  23:10:15,130 MuTect - [MUTECT] Processed 106005803 reads in 618 ms
[2015-09-30T22:10Z] INFO  23:10:15,158 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:15,372 MuTect - [MUTECT] Processed 88003615 reads in 677 ms
[2015-09-30T22:10Z] INFO  23:10:15,575 MuTect - [MUTECT] Processed 48002671 reads in 789 ms
[2015-09-30T22:10Z] INFO  23:10:15,773 MuTect - [MUTECT] Processed 107005821 reads in 643 ms
[2015-09-30T22:10Z] INFO  23:10:16,028 MuTect - [MUTECT] Processed 89003660 reads in 656 ms
[2015-09-30T22:10Z] INFO  23:10:16,357 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:16,433 MuTect - [MUTECT] Processed 49002701 reads in 858 ms
[2015-09-30T22:10Z] INFO  23:10:16,445 MuTect - [MUTECT] Processed 108005891 reads in 672 ms
[2015-09-30T22:10Z] INFO  23:10:16,631 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:16,704 MuTect - [MUTECT] Processed 90003821 reads in 675 ms
[2015-09-30T22:10Z] INFO  23:10:17,085 MuTect - [MUTECT] Processed 109005970 reads in 640 ms
[2015-09-30T22:10Z] INFO  23:10:17,105 MuTect - [MUTECT] Processed 50002789 reads in 672 ms
[2015-09-30T22:10Z] INFO  23:10:17,376 MuTect - [MUTECT] Processed 91003904 reads in 673 ms
[2015-09-30T22:10Z] INFO  23:10:17,514 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:17,755 MuTect - [MUTECT] Processed 110005973 reads in 670 ms
[2015-09-30T22:10Z] INFO  23:10:17,833 MuTect - [MUTECT] Processed 51002803 reads in 728 ms
[2015-09-30T22:10Z] INFO  23:10:18,065 MuTect - [MUTECT] Processed 92003933 reads in 689 ms
[2015-09-30T22:10Z] INFO  23:10:18,400 MuTect - [MUTECT] Processed 111006008 reads in 645 ms
[2015-09-30T22:10Z] INFO  23:10:18,526 MuTect - [MUTECT] Processed 52002825 reads in 693 ms
[2015-09-30T22:10Z] INFO  23:10:18,578 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:18,729 MuTect - [MUTECT] Processed 93004044 reads in 664 ms
[2015-09-30T22:10Z] INFO  23:10:19,017 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:19,041 MuTect - [MUTECT] Processed 112006061 reads in 641 ms
[2015-09-30T22:10Z] INFO  23:10:19,239 MuTect - [MUTECT] Processed 53002847 reads in 713 ms
[2015-09-30T22:10Z] INFO  23:10:19,432 MuTect - [MUTECT] Processed 94004073 reads in 703 ms
[2015-09-30T22:10Z] INFO  23:10:19,671 MuTect - [MUTECT] Processed 113006108 reads in 630 ms
[2015-09-30T22:10Z] INFO  23:10:19,926 MuTect - [MUTECT] Processed 54002920 reads in 687 ms
[2015-09-30T22:10Z] INFO  23:10:20,069 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:20,133 MuTect - [MUTECT] Processed 95004119 reads in 701 ms
[2015-09-30T22:10Z] INFO  23:10:20,313 MuTect - [MUTECT] Processed 114006115 reads in 642 ms
[2015-09-30T22:10Z] INFO  23:10:20,614 MuTect - [MUTECT] Processed 55002934 reads in 688 ms
[2015-09-30T22:10Z] INFO  23:10:20,798 MuTect - [MUTECT] Processed 96004162 reads in 665 ms
[2015-09-30T22:10Z] INFO  23:10:20,857 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:21,025 MuTect - [MUTECT] Processed 115006189 reads in 712 ms
[2015-09-30T22:10Z] INFO  23:10:21,322 MuTect - [MUTECT] Processed 56002965 reads in 708 ms
[2015-09-30T22:10Z] INFO  23:10:21,473 MuTect - [MUTECT] Processed 97004203 reads in 675 ms
[2015-09-30T22:10Z] INFO  23:10:21,498 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:21,692 MuTect - [MUTECT] Processed 116006189 reads in 667 ms
[2015-09-30T22:10Z] INFO  23:10:21,996 MuTect - [MUTECT] Processed 57003020 reads in 674 ms
[2015-09-30T22:10Z] INFO  23:10:22,148 MuTect - [MUTECT] Processed 98004264 reads in 675 ms
[2015-09-30T22:10Z] INFO  23:10:22,377 MuTect - [MUTECT] Processed 117006241 reads in 685 ms
[2015-09-30T22:10Z] INFO  23:10:22,689 MuTect - [MUTECT] Processed 58003082 reads in 693 ms
[2015-09-30T22:10Z] INFO  23:10:22,694 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:22,855 MuTect - [MUTECT] Processed 99004268 reads in 707 ms
[2015-09-30T22:10Z] INFO  23:10:23,001 MuTect - [MUTECT] Processed 118006350 reads in 624 ms
[2015-09-30T22:10Z] INFO  23:10:23,081 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:23,435 MuTect - [MUTECT] Processed 59003092 reads in 746 ms
[2015-09-30T22:10Z] INFO  23:10:23,544 MuTect - [MUTECT] Processed 100004292 reads in 689 ms
[2015-09-30T22:10Z] INFO  23:10:23,634 MuTect - [MUTECT] Processed 119006375 reads in 633 ms
[2015-09-30T22:10Z] INFO  23:10:23,943 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:24,142 MuTect - [MUTECT] Processed 60003112 reads in 707 ms
[2015-09-30T22:10Z] INFO  23:10:24,219 MuTect - [MUTECT] Processed 101004428 reads in 675 ms
[2015-09-30T22:10Z] INFO  23:10:24,292 MuTect - [MUTECT] Processed 120006406 reads in 658 ms
[2015-09-30T22:10Z] INFO  23:10:24,744 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:10Z] INFO  23:10:24,747 ProgressMeter -            done        3.38e+06   73.0 s       21.0 s    100.0%        73.0 s     0.0 s
[2015-09-30T22:10Z] INFO  23:10:24,747 ProgressMeter - Total runtime 73.60 secs, 1.23 min, 0.02 hours
[2015-09-30T22:10Z] INFO  23:10:24,814 MicroScheduler - 71650 reads were filtered out during the traversal out of approximately 1216026 total reads (5.89%)
[2015-09-30T22:10Z] INFO  23:10:24,814 MicroScheduler -   -> 52358 reads (4.31% of total) failing DuplicateReadFilter
[2015-09-30T22:10Z] INFO  23:10:24,814 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:10Z] INFO  23:10:24,814 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:10Z] INFO  23:10:24,815 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:10Z] INFO  23:10:24,815 MicroScheduler -   -> 19292 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:10Z] INFO  23:10:24,856 MuTect - [MUTECT] Processed 61003139 reads in 714 ms
[2015-09-30T22:10Z] INFO  23:10:24,914 MuTect - [MUTECT] Processed 121006468 reads in 622 ms
[2015-09-30T22:10Z] INFO  23:10:25,244 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:25,397 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:25,540 MuTect - [MUTECT] Processed 122006485 reads in 626 ms
[2015-09-30T22:10Z] INFO  23:10:25,594 MuTect - [MUTECT] Processed 62003170 reads in 738 ms
[2015-09-30T22:10Z] INFO  23:10:25,836 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:10Z] bgzip syn3-3_93595554_124625281-raw-mutect.vcf
[2015-09-30T22:10Z] tabix index syn3-3_93595554_124625281-raw-mutect.vcf.gz
[2015-09-30T22:10Z] INFO  23:10:26,169 MuTect - [MUTECT] Processed 123006557 reads in 629 ms
[2015-09-30T22:10Z] INFO  23:10:26,312 MuTect - [MUTECT] Processed 63003209 reads in 718 ms
[2015-09-30T22:10Z] INFO  23:10:26,765 MuTect - [MUTECT] Processed 124006625 reads in 596 ms
[2015-09-30T22:10Z] INFO  23:10:27,030 MuTect - [MUTECT] Processed 64003318 reads in 717 ms
[2015-09-30T22:10Z] INFO  23:10:27,249 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:27,360 MuTect - [MUTECT] Processed 125006679 reads in 595 ms
[2015-09-30T22:10Z] INFO  23:10:27,760 MuTect - [MUTECT] Processed 65003335 reads in 731 ms
[2015-09-30T22:10Z] INFO  23:10:27,885 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:27,976 MuTect - [MUTECT] Processed 126006769 reads in 616 ms
[2015-09-30T22:10Z] MuTect: MuTect
[2015-09-30T22:10Z] INFO  23:10:28,465 MuTect - [MUTECT] Processed 66003414 reads in 705 ms
[2015-09-30T22:10Z] INFO  23:10:28,604 MuTect - [MUTECT] Processed 127006815 reads in 628 ms
[2015-09-30T22:10Z] INFO  23:10:29,155 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:29,190 MuTect - [MUTECT] Processed 67003420 reads in 725 ms
[2015-09-30T22:10Z] INFO  23:10:29,208 MuTect - [MUTECT] Processed 128006927 reads in 604 ms
[2015-09-30T22:10Z] INFO  23:10:29,817 MuTect - [MUTECT] Processed 129006996 reads in 609 ms
[2015-09-30T22:10Z] INFO  23:10:29,905 MuTect - [MUTECT] Processed 68003462 reads in 715 ms
[2015-09-30T22:10Z] INFO  23:10:30,070 ProgressMeter -      3:48679125        3.64e+06   90.0 s       24.0 s     51.0%         2.9 m    86.0 s
[2015-09-30T22:10Z] INFO  23:10:30,262 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/3/syn3-3_155652401_186761310-raw-mutect-regions.bed to be BED
[2015-09-30T22:10Z] INFO  23:10:30,319 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:10Z] INFO  23:10:30,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:10Z] INFO  23:10:30,320 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:10Z] INFO  23:10:30,320 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:10Z] INFO  23:10:30,324 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/3/syn3-3_155652401_186761310-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/3/tx/tmpQLlpNG/syn3-3_155652401_186761310-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:10Z] INFO  23:10:30,324 HelpFormatter - Date/Time: 2015/09/30 23:10:30
[2015-09-30T22:10Z] INFO  23:10:30,324 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:10Z] INFO  23:10:30,324 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:10Z] INFO  23:10:30,352 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:10Z] INFO  23:10:30,356 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:10Z] INFO  23:10:30,406 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:10Z] INFO  23:10:30,415 MuTect - [MUTECT] Processed 130007051 reads in 598 ms
[2015-09-30T22:10Z] INFO  23:10:30,455 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:10Z] INFO  23:10:30,462 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:10Z] INFO  23:10:30,508 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:10Z] INFO  23:10:30,520 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:10Z] INFO  23:10:30,611 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:30,616 MuTect - [MUTECT] Processed 69003500 reads in 711 ms
[2015-09-30T22:10Z] INFO  23:10:30,692 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:10Z] INFO  23:10:30,790 IntervalUtils - Processing 1196842 bp from intervals
[2015-09-30T22:10Z] INFO  23:10:30,794 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:10Z] INFO  23:10:30,794 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:10Z] INFO  23:10:30,961 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:10Z] INFO  23:10:31,037 MuTect - [MUTECT] Processed 131007185 reads in 622 ms
[2015-09-30T22:10Z] INFO  23:10:31,111 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:10Z] INFO  23:10:31,111 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:10Z] INFO  23:10:31,111 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:10Z] INFO  23:10:31,112 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:10Z] INFO  23:10:31,113 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:31,295 MuTect - [MUTECT] Processed 70003570 reads in 679 ms
[2015-09-30T22:10Z] INFO  23:10:31,681 MuTect - [MUTECT] Processed 132007227 reads in 644 ms
[2015-09-30T22:10Z] INFO  23:10:32,026 MuTect - [MUTECT] Processed 71003652 reads in 731 ms
[2015-09-30T22:10Z] INFO  23:10:32,340 MuTect - [MUTECT] Processed 133007308 reads in 659 ms
[2015-09-30T22:10Z] INFO  23:10:32,695 MuTect - [MUTECT] Processed 72003673 reads in 669 ms
[2015-09-30T22:10Z] INFO  23:10:33,012 MuTect - [MUTECT] Processed 134007355 reads in 672 ms
[2015-09-30T22:10Z] INFO  23:10:33,050 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:33,325 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:33,360 MuTect - [MUTECT] Processed 73003698 reads in 665 ms
[2015-09-30T22:10Z] INFO  23:10:33,683 MuTect - [MUTECT] Processed 135007402 reads in 671 ms
[2015-09-30T22:10Z] INFO  23:10:33,774 MuTect - [MUTECT] Processed 1000093 reads in 2614 ms
[2015-09-30T22:10Z] INFO  23:10:34,018 MuTect - [MUTECT] Processed 74003700 reads in 658 ms
[2015-09-30T22:10Z] INFO  23:10:34,365 MuTect - [MUTECT] Processed 136007466 reads in 682 ms
[2015-09-30T22:10Z] INFO  23:10:34,695 MuTect - [MUTECT] Processed 75003773 reads in 677 ms
[2015-09-30T22:10Z] INFO  23:10:34,715 MuTect - [MUTECT] Processed 2000099 reads in 942 ms
[2015-09-30T22:10Z] INFO  23:10:35,012 MuTect - [MUTECT] Processed 137007533 reads in 647 ms
[2015-09-30T22:10Z] INFO  23:10:35,376 MuTect - [MUTECT] Processed 76003814 reads in 681 ms
[2015-09-30T22:10Z] INFO  23:10:35,442 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:35,462 MuTect - [MUTECT] Processed 3000146 reads in 747 ms
[2015-09-30T22:10Z] INFO  23:10:35,635 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:35,657 MuTect - [MUTECT] Processed 138007553 reads in 645 ms
[2015-09-30T22:10Z] INFO  23:10:35,919 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:36,034 MuTect - [MUTECT] Processed 77003874 reads in 658 ms
[2015-09-30T22:10Z] INFO  23:10:36,167 MuTect - [MUTECT] Processed 4000192 reads in 705 ms
[2015-09-30T22:10Z] INFO  23:10:36,300 MuTect - [MUTECT] Processed 139007630 reads in 643 ms
[2015-09-30T22:10Z] INFO  23:10:36,759 MuTect - [MUTECT] Processed 78003974 reads in 725 ms
[2015-09-30T22:10Z] INFO  23:10:36,935 MuTect - [MUTECT] Processed 5000224 reads in 767 ms
[2015-09-30T22:10Z] INFO  23:10:36,964 MuTect - [MUTECT] Processed 140007659 reads in 664 ms
[2015-09-30T22:10Z] INFO  23:10:37,461 MuTect - [MUTECT] Processed 79003978 reads in 702 ms
[2015-09-30T22:10Z] INFO  23:10:37,606 MuTect - [MUTECT] Processed 141007770 reads in 641 ms
[2015-09-30T22:10Z] INFO  23:10:37,643 MuTect - [MUTECT] Processed 6000244 reads in 709 ms
[2015-09-30T22:10Z] INFO  23:10:37,827 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:37,976 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:38,169 MuTect - [MUTECT] Processed 80004014 reads in 708 ms
[2015-09-30T22:10Z] INFO  23:10:38,245 MuTect - [MUTECT] Processed 142007847 reads in 640 ms
[2015-09-30T22:10Z] INFO  23:10:38,386 MuTect - [MUTECT] Processed 7000254 reads in 743 ms
[2015-09-30T22:10Z] INFO  23:10:38,556 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:38,825 MuTect - [MUTECT] Processed 81004110 reads in 656 ms
[2015-09-30T22:10Z] INFO  23:10:38,883 MuTect - [MUTECT] Processed 143007847 reads in 638 ms
[2015-09-30T22:10Z] INFO  23:10:39,072 MuTect - [MUTECT] Processed 8000267 reads in 686 ms
[2015-09-30T22:10Z] INFO  23:10:39,472 MuTect - [MUTECT] Processed 82004194 reads in 647 ms
[2015-09-30T22:10Z] INFO  23:10:39,538 MuTect - [MUTECT] Processed 144007905 reads in 655 ms
[2015-09-30T22:10Z] INFO  23:10:39,788 ProgressMeter -     3:137802945        2.57e+06   60.0 s       23.0 s     54.4%       110.0 s    50.0 s
[2015-09-30T22:10Z] INFO  23:10:39,790 MuTect - [MUTECT] Processed 9000347 reads in 718 ms
[2015-09-30T22:10Z] INFO  23:10:40,143 MuTect - [MUTECT] Processed 83004255 reads in 671 ms
[2015-09-30T22:10Z] INFO  23:10:40,208 MuTect - [MUTECT] Processed 145007908 reads in 670 ms
[2015-09-30T22:10Z] INFO  23:10:40,267 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:40,294 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:40,429 MuTect - [MUTECT] Processed 10000398 reads in 639 ms
[2015-09-30T22:10Z] INFO  23:10:40,788 MuTect - [MUTECT] Processed 84004314 reads in 644 ms
[2015-09-30T22:10Z] INFO  23:10:40,864 MuTect - [MUTECT] Processed 146007913 reads in 656 ms
[2015-09-30T22:10Z] INFO  23:10:41,434 MuTect - [MUTECT] Processed 85004318 reads in 646 ms
[2015-09-30T22:10Z] INFO  23:10:41,528 MuTect - [MUTECT] Processed 147007941 reads in 664 ms
[2015-09-30T22:10Z] INFO  23:10:41,628 MuTect - [MUTECT] Processed 11000425 reads in 1199 ms
[2015-09-30T22:10Z] INFO  23:10:41,637 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:42,090 MuTect - [MUTECT] Processed 86004366 reads in 657 ms
[2015-09-30T22:10Z] INFO  23:10:42,202 MuTect - [MUTECT] Processed 148008010 reads in 673 ms
[2015-09-30T22:10Z] INFO  23:10:42,381 MuTect - [MUTECT] Processed 12000457 reads in 753 ms
[2015-09-30T22:10Z] INFO  23:10:42,628 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:42,662 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:42,753 MuTect - [MUTECT] Processed 87004385 reads in 663 ms
[2015-09-30T22:10Z] INFO  23:10:42,868 MuTect - [MUTECT] Processed 149008056 reads in 667 ms
[2015-09-30T22:10Z] INFO  23:10:43,012 MuTect - [MUTECT] Processed 13000457 reads in 631 ms
[2015-09-30T22:10Z] INFO  23:10:43,419 MuTect - [MUTECT] Processed 88004416 reads in 666 ms
[2015-09-30T22:10Z] INFO  23:10:43,509 MuTect - [MUTECT] Processed 150008101 reads in 641 ms
[2015-09-30T22:10Z] INFO  23:10:43,752 MuTect - [MUTECT] Processed 14000489 reads in 740 ms
[2015-09-30T22:10Z] INFO  23:10:44,080 MuTect - [MUTECT] Processed 89004433 reads in 661 ms
[2015-09-30T22:10Z] INFO  23:10:44,143 MuTect - [MUTECT] Processed 151008119 reads in 634 ms
[2015-09-30T22:10Z] INFO  23:10:44,249 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:44,765 MuTect - [MUTECT] Processed 15000577 reads in 1013 ms
[2015-09-30T22:10Z] INFO  23:10:44,778 MuTect - [MUTECT] Processed 90004438 reads in 698 ms
[2015-09-30T22:10Z] INFO  23:10:44,789 MuTect - [MUTECT] Processed 152008267 reads in 646 ms
[2015-09-30T22:10Z] INFO  23:10:44,851 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:45,000 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:45,396 MuTect - [MUTECT] Processed 153008346 reads in 607 ms
[2015-09-30T22:10Z] INFO  23:10:45,472 MuTect - [MUTECT] Processed 16000612 reads in 707 ms
[2015-09-30T22:10Z] INFO  23:10:45,477 MuTect - [MUTECT] Processed 91004455 reads in 699 ms
[2015-09-30T22:10Z] INFO  23:10:46,125 MuTect - [MUTECT] Processed 154008373 reads in 729 ms
[2015-09-30T22:10Z] INFO  23:10:46,186 MuTect - [MUTECT] Processed 92004497 reads in 709 ms
[2015-09-30T22:10Z] INFO  23:10:46,295 MuTect - [MUTECT] Processed 17000640 reads in 823 ms
[2015-09-30T22:10Z] INFO  23:10:46,767 MuTect - [MUTECT] Processed 155008483 reads in 641 ms
[2015-09-30T22:10Z] INFO  23:10:46,876 MuTect - [MUTECT] Processed 93004565 reads in 690 ms
[2015-09-30T22:10Z] INFO  23:10:46,892 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:47,025 MuTect - [MUTECT] Processed 18000717 reads in 730 ms
[2015-09-30T22:10Z] INFO  23:10:47,147 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:47,394 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:47,399 MuTect - [MUTECT] Processed 156008579 reads in 633 ms
[2015-09-30T22:10Z] INFO  23:10:47,577 MuTect - [MUTECT] Processed 94004635 reads in 701 ms
[2015-09-30T22:10Z] INFO  23:10:47,706 MuTect - [MUTECT] Processed 19000720 reads in 681 ms
[2015-09-30T22:10Z] INFO  23:10:48,034 MuTect - [MUTECT] Processed 157008664 reads in 635 ms
[2015-09-30T22:10Z] INFO  23:10:48,283 MuTect - [MUTECT] Processed 95004723 reads in 706 ms
[2015-09-30T22:10Z] INFO  23:10:48,367 MuTect - [MUTECT] Processed 20000748 reads in 661 ms
[2015-09-30T22:10Z] INFO  23:10:48,639 MuTect - [MUTECT] Processed 158008733 reads in 605 ms
[2015-09-30T22:10Z] INFO  23:10:48,952 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:48,979 MuTect - [MUTECT] Processed 96004742 reads in 696 ms
[2015-09-30T22:10Z] INFO  23:10:48,998 MuTect - [MUTECT] Processed 21000826 reads in 631 ms
[2015-09-30T22:10Z] INFO  23:10:49,252 MuTect - [MUTECT] Processed 159008763 reads in 613 ms
[2015-09-30T22:10Z] INFO  23:10:49,658 MuTect - [MUTECT] Processed 22000882 reads in 660 ms
[2015-09-30T22:10Z] INFO  23:10:49,659 MuTect - [MUTECT] Processed 97004772 reads in 680 ms
[2015-09-30T22:10Z] INFO  23:10:49,713 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:49,886 MuTect - [MUTECT] Processed 160008827 reads in 634 ms
[2015-09-30T22:10Z] INFO  23:10:50,002 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:50,306 MuTect - [MUTECT] Processed 23000922 reads in 648 ms
[2015-09-30T22:10Z] INFO  23:10:50,367 MuTect - [MUTECT] Processed 98004832 reads in 708 ms
[2015-09-30T22:10Z] INFO  23:10:50,512 MuTect - [MUTECT] Processed 161008930 reads in 626 ms
[2015-09-30T22:10Z] INFO  23:10:50,953 MuTect - [MUTECT] Processed 24000936 reads in 647 ms
[2015-09-30T22:10Z] INFO  23:10:51,063 MuTect - [MUTECT] Processed 99004890 reads in 696 ms
[2015-09-30T22:10Z] INFO  23:10:51,078 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:51,114 MuTect - [MUTECT] Processed 162008995 reads in 602 ms
[2015-09-30T22:10Z] INFO  23:10:51,585 MuTect - [MUTECT] Processed 25000977 reads in 632 ms
[2015-09-30T22:10Z] INFO  23:10:51,744 MuTect - [MUTECT] Processed 163009008 reads in 630 ms
[2015-09-30T22:10Z] INFO  23:10:51,845 MuTect - [MUTECT] Processed 100004909 reads in 782 ms
[2015-09-30T22:10Z] INFO  23:10:52,159 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:52,269 MuTect - [MUTECT] Processed 26001011 reads in 684 ms
[2015-09-30T22:10Z] INFO  23:10:52,375 MuTect - [MUTECT] Processed 164009080 reads in 631 ms
[2015-09-30T22:10Z] INFO  23:10:52,572 MuTect - [MUTECT] Processed 101004949 reads in 727 ms
[2015-09-30T22:10Z] INFO  23:10:52,710 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:52,907 MuTect - [MUTECT] Processed 27001053 reads in 638 ms
[2015-09-30T22:10Z] INFO  23:10:52,994 MuTect - [MUTECT] Processed 165009149 reads in 619 ms
[2015-09-30T22:10Z] INFO  23:10:53,210 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:53,280 MuTect - [MUTECT] Processed 102004975 reads in 708 ms
[2015-09-30T22:10Z] INFO  23:10:53,523 MuTect - [MUTECT] Processed 28001187 reads in 616 ms
[2015-09-30T22:10Z] INFO  23:10:53,612 MuTect - [MUTECT] Processed 166009267 reads in 617 ms
[2015-09-30T22:10Z] INFO  23:10:53,981 MuTect - [MUTECT] Processed 103004987 reads in 701 ms
[2015-09-30T22:10Z] INFO  23:10:54,178 MuTect - [MUTECT] Processed 29001220 reads in 655 ms
[2015-09-30T22:10Z] INFO  23:10:54,223 MuTect - [MUTECT] Processed 167009316 reads in 612 ms
[2015-09-30T22:10Z] INFO  23:10:54,498 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:54,650 MuTect - [MUTECT] Processed 104005043 reads in 669 ms
[2015-09-30T22:10Z] INFO  23:10:54,853 MuTect - [MUTECT] Processed 30001264 reads in 675 ms
[2015-09-30T22:10Z] INFO  23:10:54,870 MuTect - [MUTECT] Processed 168009420 reads in 647 ms
[2015-09-30T22:10Z] INFO  23:10:55,267 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:55,302 MuTect - [MUTECT] Processed 105005081 reads in 652 ms
[2015-09-30T22:10Z] INFO  23:10:55,351 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:55,503 MuTect - [MUTECT] Processed 169009442 reads in 633 ms
[2015-09-30T22:10Z] INFO  23:10:55,542 MuTect - [MUTECT] Processed 31001356 reads in 689 ms
[2015-09-30T22:10Z] INFO  23:10:55,957 MuTect - [MUTECT] Processed 106005187 reads in 655 ms
[2015-09-30T22:10Z] INFO  23:10:56,144 MuTect - [MUTECT] Processed 170009577 reads in 641 ms
[2015-09-30T22:10Z] INFO  23:10:56,243 MuTect - [MUTECT] Processed 32001452 reads in 701 ms
[2015-09-30T22:10Z] INFO  23:10:56,655 MuTect - [MUTECT] Processed 107005254 reads in 698 ms
[2015-09-30T22:10Z] INFO  23:10:56,806 MuTect - [MUTECT] Processed 171009634 reads in 662 ms
[2015-09-30T22:10Z] INFO  23:10:56,879 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:56,932 MuTect - [MUTECT] Processed 33001522 reads in 689 ms
[2015-09-30T22:10Z] INFO  23:10:57,359 MuTect - [MUTECT] Processed 108005296 reads in 704 ms
[2015-09-30T22:10Z] INFO  23:10:57,448 MuTect - [MUTECT] Processed 172009729 reads in 642 ms
[2015-09-30T22:10Z] INFO  23:10:57,510 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:57,603 MuTect - [MUTECT] Processed 34001612 reads in 671 ms
[2015-09-30T22:10Z] INFO  23:10:57,676 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:58,066 MuTect - [MUTECT] Processed 109005306 reads in 707 ms
[2015-09-30T22:10Z] INFO  23:10:58,076 MuTect - [MUTECT] Processed 173009732 reads in 628 ms
[2015-09-30T22:10Z] INFO  23:10:58,263 MuTect - [MUTECT] Processed 35001700 reads in 660 ms
[2015-09-30T22:10Z] INFO  23:10:58,716 MuTect - [MUTECT] Processed 174009739 reads in 640 ms
[2015-09-30T22:10Z] INFO  23:10:58,797 MuTect - [MUTECT] Processed 110005316 reads in 731 ms
[2015-09-30T22:10Z] INFO  23:10:58,942 MuTect - [MUTECT] Processed 36001743 reads in 678 ms
[2015-09-30T22:10Z] INFO  23:10:59,210 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:10Z] INFO  23:10:59,353 MuTect - [MUTECT] Processed 175009762 reads in 637 ms
[2015-09-30T22:10Z] INFO  23:10:59,592 MuTect - [MUTECT] Processed 111005365 reads in 795 ms
[2015-09-30T22:10Z] INFO  23:10:59,637 MuTect - [MUTECT] Processed 37001752 reads in 696 ms
[2015-09-30T22:10Z] INFO  23:10:59,705 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:00,009 MuTect - [MUTECT] Processed 176009909 reads in 656 ms
[2015-09-30T22:11Z] INFO  23:11:00,071 ProgressMeter -      3:50471941        4.83e+06  120.0 s       24.0 s     65.9%         3.0 m    62.0 s
[2015-09-30T22:11Z] INFO  23:11:00,284 MuTect - [MUTECT] Processed 112005383 reads in 692 ms
[2015-09-30T22:11Z] INFO  23:11:00,321 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:00,390 MuTect - [MUTECT] Processed 38001762 reads in 753 ms
[2015-09-30T22:11Z] INFO  23:11:00,691 MuTect - [MUTECT] Processed 177009965 reads in 682 ms
[2015-09-30T22:11Z] INFO  23:11:00,997 MuTect - [MUTECT] Processed 113005435 reads in 713 ms
[2015-09-30T22:11Z] INFO  23:11:01,102 MuTect - [MUTECT] Processed 39001795 reads in 712 ms
[2015-09-30T22:11Z] INFO  23:11:01,113 ProgressMeter -     3:176752283        1.41e+06   30.0 s       21.0 s     49.4%        60.0 s    30.0 s
[2015-09-30T22:11Z] INFO  23:11:01,354 MuTect - [MUTECT] Processed 178010066 reads in 663 ms
[2015-09-30T22:11Z] INFO  23:11:01,705 MuTect - [MUTECT] Processed 114005463 reads in 708 ms
[2015-09-30T22:11Z] INFO  23:11:01,803 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:01,804 MuTect - [MUTECT] Processed 40001830 reads in 702 ms
[2015-09-30T22:11Z] INFO  23:11:02,014 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:02,023 MuTect - [MUTECT] Processed 179010066 reads in 669 ms
[2015-09-30T22:11Z] INFO  23:11:02,431 MuTect - [MUTECT] Processed 115005517 reads in 726 ms
[2015-09-30T22:11Z] INFO  23:11:02,489 MuTect - [MUTECT] Processed 41001914 reads in 685 ms
[2015-09-30T22:11Z] INFO  23:11:02,673 MuTect - [MUTECT] Processed 180010123 reads in 650 ms
[2015-09-30T22:11Z] INFO  23:11:02,969 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:03,132 MuTect - [MUTECT] Processed 116005550 reads in 701 ms
[2015-09-30T22:11Z] INFO  23:11:03,166 MuTect - [MUTECT] Processed 42001930 reads in 677 ms
[2015-09-30T22:11Z] INFO  23:11:03,285 MuTect - [MUTECT] Processed 181010187 reads in 612 ms
[2015-09-30T22:11Z] INFO  23:11:03,843 MuTect - [MUTECT] Processed 117005574 reads in 711 ms
[2015-09-30T22:11Z] INFO  23:11:03,857 MuTect - [MUTECT] Processed 43001952 reads in 691 ms
[2015-09-30T22:11Z] INFO  23:11:03,898 MuTect - [MUTECT] Processed 182010233 reads in 613 ms
[2015-09-30T22:11Z] INFO  23:11:04,158 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:04,312 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:04,547 MuTect - [MUTECT] Processed 118005650 reads in 704 ms
[2015-09-30T22:11Z] INFO  23:11:04,563 MuTect - [MUTECT] Processed 44001985 reads in 706 ms
[2015-09-30T22:11Z] INFO  23:11:04,579 MuTect - [MUTECT] Processed 183010300 reads in 680 ms
[2015-09-30T22:11Z] INFO  23:11:05,198 MuTect - [MUTECT] Processed 184010311 reads in 619 ms
[2015-09-30T22:11Z] INFO  23:11:05,249 MuTect - [MUTECT] Processed 45001986 reads in 686 ms
[2015-09-30T22:11Z] INFO  23:11:05,260 MuTect - [MUTECT] Processed 119005659 reads in 713 ms
[2015-09-30T22:11Z] INFO  23:11:05,395 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:05,846 MuTect - [MUTECT] Processed 185010435 reads in 649 ms
[2015-09-30T22:11Z] INFO  23:11:05,923 MuTect - [MUTECT] Processed 46002020 reads in 674 ms
[2015-09-30T22:11Z] INFO  23:11:05,965 MuTect - [MUTECT] Processed 120005692 reads in 705 ms
[2015-09-30T22:11Z] INFO  23:11:06,314 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:06,459 MuTect - [MUTECT] Processed 186010511 reads in 613 ms
[2015-09-30T22:11Z] INFO  23:11:06,617 MuTect - [MUTECT] Processed 47002048 reads in 694 ms
[2015-09-30T22:11Z] INFO  23:11:06,687 MuTect - [MUTECT] Processed 121005739 reads in 722 ms
[2015-09-30T22:11Z] INFO  23:11:06,926 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:07,085 MuTect - [MUTECT] Processed 187010575 reads in 626 ms
[2015-09-30T22:11Z] INFO  23:11:07,271 MuTect - [MUTECT] Processed 48002087 reads in 654 ms
[2015-09-30T22:11Z] INFO  23:11:07,390 MuTect - [MUTECT] Processed 122005773 reads in 703 ms
[2015-09-30T22:11Z] INFO  23:11:07,684 MuTect - [MUTECT] Processed 188010609 reads in 599 ms
[2015-09-30T22:11Z] INFO  23:11:07,858 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:07,980 MuTect - [MUTECT] Processed 49002120 reads in 709 ms
[2015-09-30T22:11Z] INFO  23:11:08,117 MuTect - [MUTECT] Processed 123005781 reads in 727 ms
[2015-09-30T22:11Z] INFO  23:11:08,315 MuTect - [MUTECT] Processed 189010689 reads in 631 ms
[2015-09-30T22:11Z] INFO  23:11:08,360 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:08,678 MuTect - [MUTECT] Processed 50002128 reads in 698 ms
[2015-09-30T22:11Z] INFO  23:11:08,832 MuTect - [MUTECT] Processed 124005836 reads in 715 ms
[2015-09-30T22:11Z] INFO  23:11:08,929 MuTect - [MUTECT] Processed 190010726 reads in 614 ms
[2015-09-30T22:11Z] INFO  23:11:09,367 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:09,387 MuTect - [MUTECT] Processed 51002192 reads in 708 ms
[2015-09-30T22:11Z] INFO  23:11:09,532 MuTect - [MUTECT] Processed 191010782 reads in 603 ms
[2015-09-30T22:11Z] INFO  23:11:09,560 MuTect - [MUTECT] Processed 125005841 reads in 728 ms
[2015-09-30T22:11Z] INFO  23:11:09,789 ProgressMeter -     3:151130754        4.12e+06   90.0 s       21.0 s     91.6%        98.0 s     8.0 s
[2015-09-30T22:11Z] INFO  23:11:10,043 MuTect - [MUTECT] Processed 52002265 reads in 657 ms
[2015-09-30T22:11Z] INFO  23:11:10,129 MuTect - [MUTECT] Processed 192010808 reads in 597 ms
[2015-09-30T22:11Z] INFO  23:11:10,283 MuTect - [MUTECT] Processed 126005936 reads in 723 ms
[2015-09-30T22:11Z] INFO  23:11:10,360 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:10,511 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:10,697 MuTect - [MUTECT] Processed 53002338 reads in 654 ms
[2015-09-30T22:11Z] INFO  23:11:10,746 MuTect - [MUTECT] Processed 193010828 reads in 617 ms
[2015-09-30T22:11Z] INFO  23:11:11,028 MuTect - [MUTECT] Processed 127006008 reads in 745 ms
[2015-09-30T22:11Z] INFO  23:11:11,369 MuTect - [MUTECT] Processed 194010955 reads in 623 ms
[2015-09-30T22:11Z] INFO  23:11:11,408 MuTect - [MUTECT] Processed 54002386 reads in 711 ms
[2015-09-30T22:11Z] INFO  23:11:11,706 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:11,760 MuTect - [MUTECT] Processed 128006077 reads in 732 ms
[2015-09-30T22:11Z] INFO  23:11:11,992 MuTect - [MUTECT] Processed 195010960 reads in 623 ms
[2015-09-30T22:11Z] INFO  23:11:12,072 MuTect - [MUTECT] Processed 55002438 reads in 664 ms
[2015-09-30T22:11Z] INFO  23:11:12,375 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:12,451 MuTect - [MUTECT] Processed 129006121 reads in 691 ms
[2015-09-30T22:11Z] INFO  23:11:12,614 MuTect - [MUTECT] Processed 196011033 reads in 622 ms
[2015-09-30T22:11Z] INFO  23:11:12,754 MuTect - [MUTECT] Processed 56002529 reads in 682 ms
[2015-09-30T22:11Z] INFO  23:11:12,988 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:13,168 MuTect - [MUTECT] Processed 130006150 reads in 717 ms
[2015-09-30T22:11Z] INFO  23:11:13,222 MuTect - [MUTECT] Processed 197011060 reads in 608 ms
[2015-09-30T22:11Z] INFO  23:11:13,461 MuTect - [MUTECT] Processed 57002549 reads in 707 ms
[2015-09-30T22:11Z] INFO  23:11:13,827 MuTect - [MUTECT] Processed 198011155 reads in 605 ms
[2015-09-30T22:11Z] INFO  23:11:13,894 MuTect - [MUTECT] Processed 131006172 reads in 726 ms
[2015-09-30T22:11Z] INFO  23:11:14,087 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:14,145 MuTect - [MUTECT] Processed 58002629 reads in 684 ms
[2015-09-30T22:11Z] INFO  23:11:14,454 MuTect - [MUTECT] Processed 199011230 reads in 627 ms
[2015-09-30T22:11Z] INFO  23:11:14,630 MuTect - [MUTECT] Processed 132006198 reads in 736 ms
[2015-09-30T22:11Z] INFO  23:11:14,649 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:14,807 MuTect - [MUTECT] Processed 59002722 reads in 662 ms
[2015-09-30T22:11Z] INFO  23:11:15,059 MuTect - [MUTECT] Processed 200011335 reads in 605 ms
[2015-09-30T22:11Z] INFO  23:11:15,322 MuTect - [MUTECT] Processed 133006237 reads in 692 ms
[2015-09-30T22:11Z] INFO  23:11:15,498 MuTect - [MUTECT] Processed 60002746 reads in 691 ms
[2015-09-30T22:11Z] INFO  23:11:15,593 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:15,666 MuTect - [MUTECT] Processed 201011459 reads in 607 ms
[2015-09-30T22:11Z] INFO  23:11:16,062 MuTect - [MUTECT] Processed 134006316 reads in 740 ms
[2015-09-30T22:11Z] INFO  23:11:16,142 MuTect - [MUTECT] Processed 61002819 reads in 644 ms
[2015-09-30T22:11Z] INFO  23:11:16,283 MuTect - [MUTECT] Processed 202011516 reads in 617 ms
[2015-09-30T22:11Z] INFO  23:11:16,317 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:16,527 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:11Z] INFO  23:11:16,532 ProgressMeter -            done        4.43e+06   96.0 s       21.0 s    100.0%        96.0 s     0.0 s
[2015-09-30T22:11Z] INFO  23:11:16,532 ProgressMeter - Total runtime 96.75 secs, 1.61 min, 0.03 hours
[2015-09-30T22:11Z] INFO  23:11:16,616 MicroScheduler - 99358 reads were filtered out during the traversal out of approximately 1610597 total reads (6.17%)
[2015-09-30T22:11Z] INFO  23:11:16,616 MicroScheduler -   -> 73675 reads (4.57% of total) failing DuplicateReadFilter
[2015-09-30T22:11Z] INFO  23:11:16,616 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:11Z] INFO  23:11:16,616 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:11Z] INFO  23:11:16,617 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:11Z] INFO  23:11:16,617 MicroScheduler -   -> 25683 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:11Z] INFO  23:11:16,706 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:16,780 MuTect - [MUTECT] Processed 62002931 reads in 638 ms
[2015-09-30T22:11Z] INFO  23:11:16,919 MuTect - [MUTECT] Processed 203011587 reads in 636 ms
[2015-09-30T22:11Z] INFO  23:11:17,413 MuTect - [MUTECT] Processed 63003040 reads in 633 ms
[2015-09-30T22:11Z] INFO  23:11:17,584 MuTect - [MUTECT] Processed 204011649 reads in 665 ms
[2015-09-30T22:11Z] INFO  23:11:17,635 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:11Z] bgzip syn3-3_124626733_155649953-raw-mutect.vcf
[2015-09-30T22:11Z] tabix index syn3-3_124626733_155649953-raw-mutect.vcf.gz
[2015-09-30T22:11Z] INFO  23:11:18,069 MuTect - [MUTECT] Processed 64003102 reads in 656 ms
[2015-09-30T22:11Z] INFO  23:11:18,225 MuTect - [MUTECT] Processed 205011719 reads in 641 ms
[2015-09-30T22:11Z] INFO  23:11:18,457 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:18,672 MuTect - [MUTECT] Processed 65003170 reads in 603 ms
[2015-09-30T22:11Z] INFO  23:11:18,771 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:18,884 MuTect - [MUTECT] Processed 206011840 reads in 659 ms
[2015-09-30T22:11Z] INFO  23:11:19,305 MuTect - [MUTECT] Processed 66003196 reads in 633 ms
[2015-09-30T22:11Z] INFO  23:11:19,532 MuTect - [MUTECT] Processed 207011923 reads in 648 ms
[2015-09-30T22:11Z] MuTect: MuTect
[2015-09-30T22:11Z] INFO  23:11:19,976 MuTect - [MUTECT] Processed 67003213 reads in 671 ms
[2015-09-30T22:11Z] INFO  23:11:20,231 MuTect - [MUTECT] Processed 208012036 reads in 699 ms
[2015-09-30T22:11Z] INFO  23:11:20,594 MuTect - [MUTECT] Processed 68003253 reads in 618 ms
[2015-09-30T22:11Z] INFO  23:11:20,598 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:20,885 MuTect - [MUTECT] Processed 209012090 reads in 654 ms
[2015-09-30T22:11Z] INFO  23:11:20,919 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:21,222 MuTect - [MUTECT] Processed 69003325 reads in 628 ms
[2015-09-30T22:11Z] INFO  23:11:21,553 MuTect - [MUTECT] Processed 210012191 reads in 668 ms
[2015-09-30T22:11Z] INFO  23:11:21,808 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/3/syn3-3_186768753_198022430-raw-mutect-regions.bed to be BED
[2015-09-30T22:11Z] INFO  23:11:21,860 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:11Z] INFO  23:11:21,861 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:11Z] INFO  23:11:21,861 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:11Z] INFO  23:11:21,861 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:11Z] INFO  23:11:21,864 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/3/syn3-3_186768753_198022430-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/3/tx/tmpLm47bA/syn3-3_186768753_198022430-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:11Z] INFO  23:11:21,865 HelpFormatter - Date/Time: 2015/09/30 23:11:21
[2015-09-30T22:11Z] INFO  23:11:21,865 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:11Z] INFO  23:11:21,865 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:11Z] INFO  23:11:21,869 MuTect - [MUTECT] Processed 70003388 reads in 647 ms
[2015-09-30T22:11Z] INFO  23:11:21,891 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:11Z] INFO  23:11:21,895 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:11Z] INFO  23:11:21,948 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:11Z] INFO  23:11:21,994 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:11Z] INFO  23:11:22,001 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:11Z] INFO  23:11:22,049 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T22:11Z] INFO  23:11:22,084 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:11Z] INFO  23:11:22,212 MuTect - [MUTECT] Processed 211012330 reads in 659 ms
[2015-09-30T22:11Z] INFO  23:11:22,252 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:11Z] INFO  23:11:22,328 IntervalUtils - Processing 589876 bp from intervals
[2015-09-30T22:11Z] INFO  23:11:22,332 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:11Z] INFO  23:11:22,332 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:11Z] INFO  23:11:22,384 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:11Z] INFO  23:11:22,496 MuTect - [MUTECT] Processed 71003392 reads in 627 ms
[2015-09-30T22:11Z] INFO  23:11:22,644 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:11Z] INFO  23:11:22,644 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:11Z] INFO  23:11:22,645 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:11Z] INFO  23:11:22,646 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:11Z] INFO  23:11:22,676 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:22,827 MuTect - [MUTECT] Processed 212012397 reads in 615 ms
[2015-09-30T22:11Z] INFO  23:11:23,007 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:23,135 MuTect - [MUTECT] Processed 72003472 reads in 639 ms
[2015-09-30T22:11Z] INFO  23:11:23,464 MuTect - [MUTECT] Processed 213012404 reads in 637 ms
[2015-09-30T22:11Z] INFO  23:11:23,781 MuTect - [MUTECT] Processed 73003537 reads in 645 ms
[2015-09-30T22:11Z] INFO  23:11:24,132 MuTect - [MUTECT] Processed 214012465 reads in 668 ms
[2015-09-30T22:11Z] INFO  23:11:24,453 MuTect - [MUTECT] Processed 74003586 reads in 673 ms
[2015-09-30T22:11Z] INFO  23:11:24,792 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:24,799 MuTect - [MUTECT] Processed 215012542 reads in 667 ms
[2015-09-30T22:11Z] INFO  23:11:24,958 MuTect - [MUTECT] Processed 1000031 reads in 2265 ms
[2015-09-30T22:11Z] INFO  23:11:25,132 MuTect - [MUTECT] Processed 75003636 reads in 679 ms
[2015-09-30T22:11Z] INFO  23:11:25,396 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:25,446 MuTect - [MUTECT] Processed 216012559 reads in 647 ms
[2015-09-30T22:11Z] INFO  23:11:25,831 MuTect - [MUTECT] Processed 76003642 reads in 699 ms
[2015-09-30T22:11Z] INFO  23:11:25,903 MuTect - [MUTECT] Processed 2000043 reads in 945 ms
[2015-09-30T22:11Z] INFO  23:11:26,103 MuTect - [MUTECT] Processed 217012639 reads in 657 ms
[2015-09-30T22:11Z] INFO  23:11:26,494 MuTect - [MUTECT] Processed 77003714 reads in 663 ms
[2015-09-30T22:11Z] INFO  23:11:26,751 MuTect - [MUTECT] Processed 218012641 reads in 648 ms
[2015-09-30T22:11Z] INFO  23:11:26,887 MuTect - [MUTECT] Processed 3000052 reads in 984 ms
[2015-09-30T22:11Z] INFO  23:11:27,114 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:27,143 MuTect - [MUTECT] Processed 78003820 reads in 649 ms
[2015-09-30T22:11Z] INFO  23:11:27,285 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:27,395 MuTect - [MUTECT] Processed 219012736 reads in 644 ms
[2015-09-30T22:11Z] INFO  23:11:27,706 MuTect - [MUTECT] Processed 4000119 reads in 819 ms
[2015-09-30T22:11Z] INFO  23:11:27,713 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:27,777 MuTect - [MUTECT] Processed 79003853 reads in 634 ms
[2015-09-30T22:11Z] INFO  23:11:28,044 MuTect - [MUTECT] Processed 220012808 reads in 649 ms
[2015-09-30T22:11Z] INFO  23:11:28,453 MuTect - [MUTECT] Processed 80003859 reads in 676 ms
[2015-09-30T22:11Z] INFO  23:11:28,486 MuTect - [MUTECT] Processed 5000123 reads in 780 ms
[2015-09-30T22:11Z] INFO  23:11:28,697 MuTect - [MUTECT] Processed 221012868 reads in 653 ms
[2015-09-30T22:11Z] INFO  23:11:29,079 MuTect - [MUTECT] Processed 81003916 reads in 626 ms
[2015-09-30T22:11Z] INFO  23:11:29,250 MuTect - [MUTECT] Processed 6000204 reads in 764 ms
[2015-09-30T22:11Z] INFO  23:11:29,407 MuTect - [MUTECT] Processed 222012880 reads in 710 ms
[2015-09-30T22:11Z] INFO  23:11:29,489 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:29,707 MuTect - [MUTECT] Processed 82003942 reads in 628 ms
[2015-09-30T22:11Z] INFO  23:11:30,072 ProgressMeter -      3:53003269        6.28e+06    2.5 m       23.0 s     81.9%         3.1 m    33.0 s
[2015-09-30T22:11Z] INFO  23:11:30,073 MuTect - [MUTECT] Processed 223012901 reads in 666 ms
[2015-09-30T22:11Z] INFO  23:11:30,083 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:30,323 MuTect - [MUTECT] Processed 83003979 reads in 616 ms
[2015-09-30T22:11Z] INFO  23:11:30,341 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:30,491 MuTect - [MUTECT] Processed 7000280 reads in 1241 ms
[2015-09-30T22:11Z] INFO  23:11:30,783 MuTect - [MUTECT] Processed 224012957 reads in 710 ms
[2015-09-30T22:11Z] INFO  23:11:30,948 MuTect - [MUTECT] Processed 84004041 reads in 625 ms
[2015-09-30T22:11Z] INFO  23:11:31,114 ProgressMeter -     3:185979601        2.93e+06   60.0 s       20.0 s     94.9%        63.0 s     3.0 s
[2015-09-30T22:11Z] INFO  23:11:31,385 MuTect - [MUTECT] Processed 8000325 reads in 894 ms
[2015-09-30T22:11Z] INFO  23:11:31,479 MuTect - [MUTECT] Processed 225013008 reads in 696 ms
[2015-09-30T22:11Z] INFO  23:11:31,528 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:31,585 MuTect - [MUTECT] Processed 85004099 reads in 637 ms
[2015-09-30T22:11Z] INFO  23:11:32,166 MuTect - [MUTECT] Processed 9000332 reads in 780 ms
[2015-09-30T22:11Z] INFO  23:11:32,227 MuTect - [MUTECT] Processed 86004181 reads in 642 ms
[2015-09-30T22:11Z] INFO  23:11:32,252 MuTect - [MUTECT] Processed 226013094 reads in 773 ms
[2015-09-30T22:11Z] INFO  23:11:32,380 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:32,860 MuTect - [MUTECT] Processed 87004241 reads in 633 ms
[2015-09-30T22:11Z] INFO  23:11:32,953 MuTect - [MUTECT] Processed 10000332 reads in 788 ms
[2015-09-30T22:11Z] INFO  23:11:32,973 MuTect - [MUTECT] Processed 227013211 reads in 721 ms
[2015-09-30T22:11Z] INFO  23:11:33,187 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:33,521 MuTect - [MUTECT] Processed 88004245 reads in 661 ms
[2015-09-30T22:11Z] INFO  23:11:33,654 MuTect - [MUTECT] Processed 228013228 reads in 681 ms
[2015-09-30T22:11Z] INFO  23:11:33,656 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:33,673 MuTect - [MUTECT] Processed 11000401 reads in 720 ms
[2015-09-30T22:11Z] INFO  23:11:34,164 MuTect - [MUTECT] Processed 89004246 reads in 643 ms
[2015-09-30T22:11Z] INFO  23:11:34,323 MuTect - [MUTECT] Processed 229013334 reads in 669 ms
[2015-09-30T22:11Z] INFO  23:11:34,359 MuTect - [MUTECT] Processed 12000423 reads in 686 ms
[2015-09-30T22:11Z] INFO  23:11:34,572 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:11Z] INFO  23:11:34,577 ProgressMeter -            done        3.13e+06   63.0 s       20.0 s    100.0%        63.0 s     0.0 s
[2015-09-30T22:11Z] INFO  23:11:34,577 ProgressMeter - Total runtime 63.47 secs, 1.06 min, 0.02 hours
[2015-09-30T22:11Z] INFO  23:11:34,642 MicroScheduler - 62937 reads were filtered out during the traversal out of approximately 1064398 total reads (5.91%)
[2015-09-30T22:11Z] INFO  23:11:34,642 MicroScheduler -   -> 45896 reads (4.31% of total) failing DuplicateReadFilter
[2015-09-30T22:11Z] INFO  23:11:34,642 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:11Z] INFO  23:11:34,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:11Z] INFO  23:11:34,642 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:11Z] INFO  23:11:34,642 MicroScheduler -   -> 17041 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:11Z] INFO  23:11:34,880 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:34,959 MuTect - [MUTECT] Processed 230013347 reads in 636 ms
[2015-09-30T22:11Z] INFO  23:11:35,060 MuTect - [MUTECT] Processed 13000458 reads in 700 ms
[2015-09-30T22:11Z] INFO  23:11:35,592 MuTect - [MUTECT] Processed 231013417 reads in 633 ms
[2015-09-30T22:11Z] INFO  23:11:35,648 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:11Z] INFO  23:11:35,677 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:11Z] bgzip syn3-3_155652401_186761310-raw-mutect.vcf
[2015-09-30T22:11Z] INFO  23:11:35,760 MuTect - [MUTECT] Processed 14000563 reads in 701 ms
[2015-09-30T22:11Z] tabix index syn3-3_155652401_186761310-raw-mutect.vcf.gz
[2015-09-30T22:11Z] INFO  23:11:36,284 MuTect - [MUTECT] Processed 232013451 reads in 692 ms
[2015-09-30T22:11Z] INFO  23:11:36,480 MuTect - [MUTECT] Processed 15000617 reads in 720 ms
[2015-09-30T22:11Z] INFO  23:11:36,981 MuTect - [MUTECT] Processed 233013452 reads in 697 ms
[2015-09-30T22:11Z] INFO  23:11:37,107 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:37,459 MuTect - [MUTECT] Processed 16000641 reads in 979 ms
[2015-09-30T22:11Z] INFO  23:11:37,698 MuTect - [MUTECT] Processed 234013481 reads in 717 ms
[2015-09-30T22:11Z] MuTect: MuTect
[2015-09-30T22:11Z] INFO  23:11:38,163 MuTect - [MUTECT] Processed 17000664 reads in 704 ms
[2015-09-30T22:11Z] INFO  23:11:38,389 MuTect - [MUTECT] Processed 235013530 reads in 691 ms
[2015-09-30T22:11Z] INFO  23:11:38,568 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:38,874 MuTect - [MUTECT] Processed 18000664 reads in 711 ms
[2015-09-30T22:11Z] INFO  23:11:39,071 MuTect - [MUTECT] Processed 236013589 reads in 682 ms
[2015-09-30T22:11Z] INFO  23:11:39,470 MuTect - [MUTECT] Inspected 69000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:39,646 MuTect - [MUTECT] Processed 19000746 reads in 772 ms
[2015-09-30T22:11Z] INFO  23:11:39,743 MuTect - [MUTECT] Processed 237013634 reads in 672 ms
[2015-09-30T22:11Z] INFO  23:11:40,042 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/4/syn3-4_0_31018607-raw-mutect-regions.bed to be BED
[2015-09-30T22:11Z] INFO  23:11:40,097 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:11Z] INFO  23:11:40,097 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:11Z] INFO  23:11:40,097 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:11Z] INFO  23:11:40,097 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:11Z] INFO  23:11:40,101 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/4/syn3-4_0_31018607-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/4/tx/tmpQjMicU/syn3-4_0_31018607-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:11Z] INFO  23:11:40,101 HelpFormatter - Date/Time: 2015/09/30 23:11:40
[2015-09-30T22:11Z] INFO  23:11:40,101 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:11Z] INFO  23:11:40,101 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:11Z] INFO  23:11:40,128 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:11Z] INFO  23:11:40,133 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:11Z] INFO  23:11:40,185 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:11Z] INFO  23:11:40,233 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:11Z] INFO  23:11:40,240 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:11Z] INFO  23:11:40,263 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:11Z] INFO  23:11:40,285 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:11Z] INFO  23:11:40,380 MuTect - [MUTECT] Processed 20000762 reads in 734 ms
[2015-09-30T22:11Z] INFO  23:11:40,457 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:11Z] INFO  23:11:40,458 MuTect - [MUTECT] Processed 238013660 reads in 715 ms
[2015-09-30T22:11Z] INFO  23:11:40,552 IntervalUtils - Processing 1291749 bp from intervals
[2015-09-30T22:11Z] INFO  23:11:40,557 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:11Z] INFO  23:11:40,557 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:11Z] INFO  23:11:40,766 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:11Z] INFO  23:11:40,858 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:40,922 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:11Z] INFO  23:11:40,922 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:11Z] INFO  23:11:40,922 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:11Z] INFO  23:11:40,923 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:11Z] INFO  23:11:41,105 MuTect - [MUTECT] Processed 21000836 reads in 725 ms
[2015-09-30T22:11Z] INFO  23:11:41,191 MuTect - [MUTECT] Processed 239013669 reads in 733 ms
[2015-09-30T22:11Z] INFO  23:11:41,807 MuTect - [MUTECT] Processed 22000882 reads in 702 ms
[2015-09-30T22:11Z] INFO  23:11:41,902 MuTect - [MUTECT] Processed 240013720 reads in 710 ms
[2015-09-30T22:11Z] INFO  23:11:41,985 MuTect - [MUTECT] Inspected 70000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:42,500 MuTect - [MUTECT] Processed 23000883 reads in 693 ms
[2015-09-30T22:11Z] INFO  23:11:42,601 MuTect - [MUTECT] Processed 241013728 reads in 700 ms
[2015-09-30T22:11Z] INFO  23:11:43,219 MuTect - [MUTECT] Processed 24000928 reads in 719 ms
[2015-09-30T22:11Z] INFO  23:11:43,277 MuTect - [MUTECT] Processed 242013840 reads in 675 ms
[2015-09-30T22:11Z] INFO  23:11:43,367 MuTect - [MUTECT] Processed 1000221 reads in 2399 ms
[2015-09-30T22:11Z] INFO  23:11:43,497 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:43,960 MuTect - [MUTECT] Processed 243013927 reads in 684 ms
[2015-09-30T22:11Z] INFO  23:11:44,033 MuTect - [MUTECT] Processed 25000976 reads in 814 ms
[2015-09-30T22:11Z] INFO  23:11:44,335 MuTect - [MUTECT] Inspected 71000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:44,572 MuTect - [MUTECT] Processed 2000222 reads in 1205 ms
[2015-09-30T22:11Z] INFO  23:11:44,652 MuTect - [MUTECT] Processed 244013965 reads in 692 ms
[2015-09-30T22:11Z] INFO  23:11:44,974 MuTect - [MUTECT] Processed 26001108 reads in 941 ms
[2015-09-30T22:11Z] INFO  23:11:45,333 MuTect - [MUTECT] Processed 245014000 reads in 681 ms
[2015-09-30T22:11Z] INFO  23:11:45,461 MuTect - [MUTECT] Processed 3000278 reads in 889 ms
[2015-09-30T22:11Z] INFO  23:11:45,745 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:45,994 MuTect - [MUTECT] Processed 27001188 reads in 1020 ms
[2015-09-30T22:11Z] INFO  23:11:46,089 MuTect - [MUTECT] Processed 246014011 reads in 756 ms
[2015-09-30T22:11Z] INFO  23:11:46,112 MuTect - [MUTECT] Processed 4000392 reads in 651 ms
[2015-09-30T22:11Z] INFO  23:11:46,721 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:46,760 MuTect - [MUTECT] Processed 5000399 reads in 648 ms
[2015-09-30T22:11Z] INFO  23:11:46,792 MuTect - [MUTECT] Processed 247014106 reads in 703 ms
[2015-09-30T22:11Z] INFO  23:11:46,861 MuTect - [MUTECT] Processed 28001280 reads in 867 ms
[2015-09-30T22:11Z] INFO  23:11:46,873 MuTect - [MUTECT] Inspected 72000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:47,394 MuTect - [MUTECT] Processed 6000490 reads in 634 ms
[2015-09-30T22:11Z] INFO  23:11:47,489 MuTect - [MUTECT] Processed 248014152 reads in 697 ms
[2015-09-30T22:11Z] INFO  23:11:47,629 MuTect - [MUTECT] Processed 29001281 reads in 768 ms
[2015-09-30T22:11Z] INFO  23:11:48,041 MuTect - [MUTECT] Processed 7000553 reads in 647 ms
[2015-09-30T22:11Z] INFO  23:11:48,050 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:48,178 MuTect - [MUTECT] Processed 249014236 reads in 689 ms
[2015-09-30T22:11Z] INFO  23:11:48,359 MuTect - [MUTECT] Processed 30001381 reads in 730 ms
[2015-09-30T22:11Z] INFO  23:11:48,667 MuTect - [MUTECT] Processed 8000621 reads in 626 ms
[2015-09-30T22:11Z] INFO  23:11:48,842 MuTect - [MUTECT] Processed 250014258 reads in 664 ms
[2015-09-30T22:11Z] INFO  23:11:49,015 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:49,364 MuTect - [MUTECT] Processed 9000675 reads in 697 ms
[2015-09-30T22:11Z] INFO  23:11:49,394 MuTect - [MUTECT] Inspected 73000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:49,490 MuTect - [MUTECT] Processed 251014267 reads in 647 ms
[2015-09-30T22:11Z] INFO  23:11:50,010 MuTect - [MUTECT] Processed 31001487 reads in 1651 ms
[2015-09-30T22:11Z] INFO  23:11:50,075 MuTect - [MUTECT] Processed 10000800 reads in 711 ms
[2015-09-30T22:11Z] INFO  23:11:50,123 MuTect - [MUTECT] Processed 252014329 reads in 634 ms
[2015-09-30T22:11Z] INFO  23:11:50,408 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:50,742 MuTect - [MUTECT] Processed 11000893 reads in 667 ms
[2015-09-30T22:11Z] INFO  23:11:50,773 MuTect - [MUTECT] Processed 253014384 reads in 649 ms
[2015-09-30T22:11Z] INFO  23:11:51,411 MuTect - [MUTECT] Processed 12000920 reads in 669 ms
[2015-09-30T22:11Z] INFO  23:11:51,446 MuTect - [MUTECT] Processed 254014422 reads in 674 ms
[2015-09-30T22:11Z] INFO  23:11:51,509 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:51,615 MuTect - [MUTECT] Inspected 74000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:52,080 MuTect - [MUTECT] Processed 13000957 reads in 669 ms
[2015-09-30T22:11Z] INFO  23:11:52,134 MuTect - [MUTECT] Processed 255014506 reads in 688 ms
[2015-09-30T22:11Z] INFO  23:11:52,204 MuTect - [MUTECT] Processed 32001584 reads in 2194 ms
[2015-09-30T22:11Z] INFO  23:11:52,602 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:52,647 ProgressMeter -     3:195515390        9.29e+05   30.0 s       32.0 s     59.0%        50.0 s    20.0 s
[2015-09-30T22:11Z] INFO  23:11:52,762 MuTect - [MUTECT] Processed 14001037 reads in 681 ms
[2015-09-30T22:11Z] INFO  23:11:52,787 MuTect - [MUTECT] Processed 256014544 reads in 653 ms
[2015-09-30T22:11Z] INFO  23:11:53,189 MuTect - [MUTECT] Processed 33001662 reads in 985 ms
[2015-09-30T22:11Z] INFO  23:11:53,468 MuTect - [MUTECT] Processed 15001161 reads in 707 ms
[2015-09-30T22:11Z] INFO  23:11:53,492 MuTect - [MUTECT] Processed 257014577 reads in 705 ms
[2015-09-30T22:11Z] INFO  23:11:53,767 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:53,795 MuTect - [MUTECT] Inspected 75000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:53,859 MuTect - [MUTECT] Processed 34001795 reads in 670 ms
[2015-09-30T22:11Z] INFO  23:11:54,171 MuTect - [MUTECT] Processed 258014604 reads in 679 ms
[2015-09-30T22:11Z] INFO  23:11:54,187 MuTect - [MUTECT] Processed 16001258 reads in 719 ms
[2015-09-30T22:11Z] INFO  23:11:54,601 MuTect - [MUTECT] Processed 35001943 reads in 742 ms
[2015-09-30T22:11Z] INFO  23:11:54,861 MuTect - [MUTECT] Processed 259014691 reads in 690 ms
[2015-09-30T22:11Z] INFO  23:11:54,871 MuTect - [MUTECT] Processed 17001278 reads in 684 ms
[2015-09-30T22:11Z] INFO  23:11:54,908 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:55,471 MuTect - [MUTECT] Processed 36002012 reads in 870 ms
[2015-09-30T22:11Z] INFO  23:11:55,528 MuTect - [MUTECT] Processed 260014725 reads in 667 ms
[2015-09-30T22:11Z] INFO  23:11:55,537 MuTect - [MUTECT] Processed 18001285 reads in 666 ms
[2015-09-30T22:11Z] INFO  23:11:56,191 MuTect - [MUTECT] Processed 261014765 reads in 663 ms
[2015-09-30T22:11Z] INFO  23:11:56,191 MuTect - [MUTECT] Processed 37002086 reads in 720 ms
[2015-09-30T22:11Z] INFO  23:11:56,197 MuTect - [MUTECT] Inspected 76000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:56,223 MuTect - [MUTECT] Processed 19001357 reads in 686 ms
[2015-09-30T22:11Z] INFO  23:11:56,523 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:56,824 MuTect - [MUTECT] Processed 262014781 reads in 633 ms
[2015-09-30T22:11Z] INFO  23:11:56,900 MuTect - [MUTECT] Processed 38002198 reads in 709 ms
[2015-09-30T22:11Z] INFO  23:11:56,903 MuTect - [MUTECT] Processed 20001400 reads in 680 ms
[2015-09-30T22:11Z] INFO  23:11:57,241 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:11Z] INFO  23:11:57,243 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:57,244 ProgressMeter -            done        7.63e+06    3.0 m       23.0 s    100.0%         3.0 m     0.0 s
[2015-09-30T22:11Z] INFO  23:11:57,244 ProgressMeter - Total runtime 177.18 secs, 2.95 min, 0.05 hours
[2015-09-30T22:11Z] INFO  23:11:57,308 MicroScheduler - 206979 reads were filtered out during the traversal out of approximately 3098426 total reads (6.68%)
[2015-09-30T22:11Z] INFO  23:11:57,308 MicroScheduler -   -> 156060 reads (5.04% of total) failing DuplicateReadFilter
[2015-09-30T22:11Z] INFO  23:11:57,309 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:11Z] INFO  23:11:57,309 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:11Z] INFO  23:11:57,309 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:11Z] INFO  23:11:57,309 MicroScheduler -   -> 50919 reads (1.64% of total) failing UnmappedReadFilter
[2015-09-30T22:11Z] INFO  23:11:57,617 MuTect - [MUTECT] Processed 21001456 reads in 714 ms
[2015-09-30T22:11Z] INFO  23:11:57,668 MuTect - [MUTECT] Processed 39002240 reads in 768 ms
[2015-09-30T22:11Z] INFO  23:11:58,248 MuTect - [MUTECT] Processed 22001531 reads in 631 ms
[2015-09-30T22:11Z] INFO  23:11:58,279 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:11Z] bgzip syn3-3_31494593_62516713-raw-mutect.vcf
[2015-09-30T22:11Z] INFO  23:11:58,372 MuTect - [MUTECT] Processed 40002331 reads in 704 ms
[2015-09-30T22:11Z] tabix index syn3-3_31494593_62516713-raw-mutect.vcf.gz
[2015-09-30T22:11Z] INFO  23:11:58,844 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:58,930 MuTect - [MUTECT] Processed 23001548 reads in 682 ms
[2015-09-30T22:11Z] INFO  23:11:59,066 MuTect - [MUTECT] Processed 41002359 reads in 694 ms
[2015-09-30T22:11Z] INFO  23:11:59,398 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:11Z] INFO  23:11:59,617 MuTect - [MUTECT] Processed 24001599 reads in 687 ms
[2015-09-30T22:11Z] INFO  23:11:59,767 MuTect - [MUTECT] Processed 42002364 reads in 701 ms
[2015-09-30T22:12Z] INFO  23:12:00,306 MuTect - [MUTECT] Processed 25001604 reads in 689 ms
[2015-09-30T22:12Z] INFO  23:12:00,456 MuTect - [MUTECT] Processed 43002404 reads in 689 ms
[2015-09-30T22:12Z] MuTect: MuTect
[2015-09-30T22:12Z] INFO  23:12:00,990 MuTect - [MUTECT] Processed 26001690 reads in 684 ms
[2015-09-30T22:12Z] INFO  23:12:01,118 MuTect - [MUTECT] Processed 44002484 reads in 662 ms
[2015-09-30T22:12Z] INFO  23:12:01,236 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:01,669 MuTect - [MUTECT] Processed 27001744 reads in 679 ms
[2015-09-30T22:12Z] INFO  23:12:01,747 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:01,767 MuTect - [MUTECT] Processed 45002492 reads in 649 ms
[2015-09-30T22:12Z] INFO  23:12:02,330 MuTect - [MUTECT] Processed 28001876 reads in 661 ms
[2015-09-30T22:12Z] INFO  23:12:02,412 MuTect - [MUTECT] Processed 46002536 reads in 645 ms
[2015-09-30T22:12Z] INFO  23:12:02,900 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/4/syn3-4_31031389_62067173-raw-mutect-regions.bed to be BED
[2015-09-30T22:12Z] INFO  23:12:02,957 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:12Z] INFO  23:12:02,957 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:12Z] INFO  23:12:02,957 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:12Z] INFO  23:12:02,957 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:12Z] INFO  23:12:02,961 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/4/syn3-4_31031389_62067173-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/4/tx/tmpbNr_7J/syn3-4_31031389_62067173-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:12Z] INFO  23:12:02,961 HelpFormatter - Date/Time: 2015/09/30 23:12:02
[2015-09-30T22:12Z] INFO  23:12:02,961 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:12Z] INFO  23:12:02,961 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:12Z] INFO  23:12:02,989 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:12Z] INFO  23:12:02,993 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:12Z] INFO  23:12:03,021 MuTect - [MUTECT] Processed 29001917 reads in 691 ms
[2015-09-30T22:12Z] INFO  23:12:03,045 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:12Z] INFO  23:12:03,090 MuTect - [MUTECT] Processed 47002596 reads in 678 ms
[2015-09-30T22:12Z] INFO  23:12:03,101 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:12Z] INFO  23:12:03,109 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:12Z] INFO  23:12:03,150 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:12Z] INFO  23:12:03,175 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:12Z] INFO  23:12:03,350 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:12Z] INFO  23:12:03,387 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:03,433 IntervalUtils - Processing 850491 bp from intervals
[2015-09-30T22:12Z] INFO  23:12:03,437 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:12Z] INFO  23:12:03,437 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:12Z] INFO  23:12:03,492 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:12Z] INFO  23:12:03,696 MuTect - [MUTECT] Processed 30001961 reads in 675 ms
[2015-09-30T22:12Z] INFO  23:12:03,713 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:12Z] INFO  23:12:03,713 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:12Z] INFO  23:12:03,713 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:12Z] INFO  23:12:03,714 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:12Z] INFO  23:12:03,738 MuTect - [MUTECT] Processed 48002655 reads in 648 ms
[2015-09-30T22:12Z] INFO  23:12:04,044 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:04,383 MuTect - [MUTECT] Processed 31002022 reads in 687 ms
[2015-09-30T22:12Z] INFO  23:12:04,471 MuTect - [MUTECT] Processed 49002667 reads in 733 ms
[2015-09-30T22:12Z] INFO  23:12:05,056 MuTect - [MUTECT] Processed 32002129 reads in 672 ms
[2015-09-30T22:12Z] INFO  23:12:05,098 MuTect - [MUTECT] Processed 50002754 reads in 627 ms
[2015-09-30T22:12Z] INFO  23:12:05,704 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:05,738 MuTect - [MUTECT] Processed 51002763 reads in 640 ms
[2015-09-30T22:12Z] INFO  23:12:05,742 MuTect - [MUTECT] Processed 33002196 reads in 687 ms
[2015-09-30T22:12Z] INFO  23:12:06,196 MuTect - [MUTECT] Processed 1000000 reads in 2429 ms
[2015-09-30T22:12Z] INFO  23:12:06,395 MuTect - [MUTECT] Processed 52002784 reads in 657 ms
[2015-09-30T22:12Z] INFO  23:12:06,479 MuTect - [MUTECT] Processed 34002297 reads in 737 ms
[2015-09-30T22:12Z] INFO  23:12:06,657 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:06,963 MuTect - [MUTECT] Processed 2000027 reads in 767 ms
[2015-09-30T22:12Z] INFO  23:12:07,071 MuTect - [MUTECT] Processed 53002899 reads in 676 ms
[2015-09-30T22:12Z] INFO  23:12:07,175 MuTect - [MUTECT] Processed 35002350 reads in 696 ms
[2015-09-30T22:12Z] INFO  23:12:07,687 MuTect - [MUTECT] Processed 3000083 reads in 724 ms
[2015-09-30T22:12Z] INFO  23:12:07,808 MuTect - [MUTECT] Processed 54002947 reads in 737 ms
[2015-09-30T22:12Z] INFO  23:12:07,934 MuTect - [MUTECT] Processed 36002389 reads in 759 ms
[2015-09-30T22:12Z] INFO  23:12:08,130 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:08,266 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:08,409 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:12Z] INFO  23:12:08,413 ProgressMeter -            done        1.63e+06   45.0 s       27.0 s    100.0%        45.0 s     0.0 s
[2015-09-30T22:12Z] INFO  23:12:08,413 MuTect - [MUTECT] Processed 4000136 reads in 726 ms
[2015-09-30T22:12Z] INFO  23:12:08,414 ProgressMeter - Total runtime 45.77 secs, 0.76 min, 0.01 hours
[2015-09-30T22:12Z] INFO  23:12:08,477 MicroScheduler - 40817 reads were filtered out during the traversal out of approximately 655565 total reads (6.23%)
[2015-09-30T22:12Z] INFO  23:12:08,477 MicroScheduler -   -> 30610 reads (4.67% of total) failing DuplicateReadFilter
[2015-09-30T22:12Z] INFO  23:12:08,477 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:12Z] INFO  23:12:08,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:12Z] INFO  23:12:08,478 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:12Z] INFO  23:12:08,478 MicroScheduler -   -> 10207 reads (1.56% of total) failing UnmappedReadFilter
[2015-09-30T22:12Z] INFO  23:12:08,656 MuTect - [MUTECT] Processed 37002476 reads in 722 ms
[2015-09-30T22:12Z] INFO  23:12:09,093 MuTect - [MUTECT] Processed 5000172 reads in 680 ms
[2015-09-30T22:12Z] INFO  23:12:09,133 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:09,351 MuTect - [MUTECT] Processed 38002486 reads in 695 ms
[2015-09-30T22:12Z] INFO  23:12:09,475 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:12Z] bgzip syn3-3_186768753_198022430-raw-mutect.vcf
[2015-09-30T22:12Z] tabix index syn3-3_186768753_198022430-raw-mutect.vcf.gz
[2015-09-30T22:12Z] INFO  23:12:09,780 MuTect - [MUTECT] Processed 6000275 reads in 687 ms
[2015-09-30T22:12Z] INFO  23:12:10,038 MuTect - [MUTECT] Processed 39002543 reads in 687 ms
[2015-09-30T22:12Z] INFO  23:12:10,446 MuTect - [MUTECT] Processed 7000379 reads in 666 ms
[2015-09-30T22:12Z] INFO  23:12:10,663 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:10,734 MuTect - [MUTECT] Processed 40002549 reads in 696 ms
[2015-09-30T22:12Z] INFO  23:12:10,925 ProgressMeter -       4:2943215        9.48e+05   30.0 s       31.0 s     27.2%       110.0 s    80.0 s
[2015-09-30T22:12Z] INFO  23:12:11,101 MuTect - [MUTECT] Processed 8000408 reads in 655 ms
[2015-09-30T22:12Z] INFO  23:12:11,403 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:11,433 MuTect - [MUTECT] Processed 41002558 reads in 699 ms
[2015-09-30T22:12Z] INFO  23:12:11,830 MuTect - [MUTECT] Processed 9000444 reads in 729 ms
[2015-09-30T22:12Z] INFO  23:12:12,091 MuTect - [MUTECT] Processed 42002641 reads in 658 ms
[2015-09-30T22:12Z] INFO  23:12:12,515 MuTect - [MUTECT] Processed 10000492 reads in 685 ms
[2015-09-30T22:12Z] INFO  23:12:12,743 MuTect - [MUTECT] Processed 43002701 reads in 652 ms
[2015-09-30T22:12Z] INFO  23:12:13,189 MuTect - [MUTECT] Processed 11000497 reads in 674 ms
[2015-09-30T22:12Z] INFO  23:12:13,190 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:13,362 MuTect - [MUTECT] Processed 44002713 reads in 619 ms
[2015-09-30T22:12Z] INFO  23:12:13,870 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:13,879 MuTect - [MUTECT] Processed 12000529 reads in 690 ms
[2015-09-30T22:12Z] INFO  23:12:13,981 MuTect - [MUTECT] Processed 45002825 reads in 619 ms
[2015-09-30T22:12Z] MuTect: MuTect
[2015-09-30T22:12Z] INFO  23:12:14,564 MuTect - [MUTECT] Processed 13000544 reads in 684 ms
[2015-09-30T22:12Z] INFO  23:12:14,615 MuTect - [MUTECT] Processed 46002906 reads in 634 ms
[2015-09-30T22:12Z] INFO  23:12:15,228 MuTect - [MUTECT] Processed 14000546 reads in 665 ms
[2015-09-30T22:12Z] INFO  23:12:15,252 MuTect - [MUTECT] Processed 47002914 reads in 637 ms
[2015-09-30T22:12Z] INFO  23:12:15,643 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:15,885 MuTect - [MUTECT] Processed 48002918 reads in 633 ms
[2015-09-30T22:12Z] INFO  23:12:15,919 MuTect - [MUTECT] Processed 15000597 reads in 691 ms
[2015-09-30T22:12Z] INFO  23:12:16,000 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:16,305 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/4/syn3-4_62292837_93511697-raw-mutect-regions.bed to be BED
[2015-09-30T22:12Z] INFO  23:12:16,361 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:12Z] INFO  23:12:16,362 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:12Z] INFO  23:12:16,362 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:12Z] INFO  23:12:16,362 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:12Z] INFO  23:12:16,365 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/4/syn3-4_62292837_93511697-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/4/tx/tmpbhpyqe/syn3-4_62292837_93511697-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:12Z] INFO  23:12:16,366 HelpFormatter - Date/Time: 2015/09/30 23:12:16
[2015-09-30T22:12Z] INFO  23:12:16,366 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:12Z] INFO  23:12:16,366 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:12Z] INFO  23:12:16,394 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:12Z] INFO  23:12:16,398 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:12Z] INFO  23:12:16,454 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:12Z] INFO  23:12:16,503 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:12Z] INFO  23:12:16,510 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:12Z] INFO  23:12:16,532 MuTect - [MUTECT] Processed 49002981 reads in 647 ms
[2015-09-30T22:12Z] INFO  23:12:16,533 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:12Z] INFO  23:12:16,543 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:12Z] INFO  23:12:16,639 MuTect - [MUTECT] Processed 16000637 reads in 720 ms
[2015-09-30T22:12Z] INFO  23:12:16,724 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:12Z] INFO  23:12:16,828 IntervalUtils - Processing 1281025 bp from intervals
[2015-09-30T22:12Z] INFO  23:12:16,832 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:12Z] INFO  23:12:16,833 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:12Z] INFO  23:12:16,989 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:12Z] INFO  23:12:17,162 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:12Z] INFO  23:12:17,163 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:12Z] INFO  23:12:17,163 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:12Z] INFO  23:12:17,164 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:12Z] INFO  23:12:17,235 MuTect - [MUTECT] Processed 50003084 reads in 702 ms
[2015-09-30T22:12Z] INFO  23:12:17,333 MuTect - [MUTECT] Processed 17000663 reads in 694 ms
[2015-09-30T22:12Z] INFO  23:12:17,997 MuTect - [MUTECT] Processed 51003182 reads in 763 ms
[2015-09-30T22:12Z] INFO  23:12:18,044 MuTect - [MUTECT] Processed 18000761 reads in 711 ms
[2015-09-30T22:12Z] INFO  23:12:18,126 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:18,147 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:18,731 MuTect - [MUTECT] Processed 19000834 reads in 686 ms
[2015-09-30T22:12Z] INFO  23:12:18,856 MuTect - [MUTECT] Processed 52003239 reads in 859 ms
[2015-09-30T22:12Z] INFO  23:12:19,412 MuTect - [MUTECT] Processed 20000857 reads in 682 ms
[2015-09-30T22:12Z] INFO  23:12:19,623 MuTect - [MUTECT] Processed 53003251 reads in 766 ms
[2015-09-30T22:12Z] INFO  23:12:19,829 MuTect - [MUTECT] Processed 1000068 reads in 2618 ms
[2015-09-30T22:12Z] INFO  23:12:20,114 MuTect - [MUTECT] Processed 21000860 reads in 702 ms
[2015-09-30T22:12Z] INFO  23:12:20,396 MuTect - [MUTECT] Processed 54003304 reads in 774 ms
[2015-09-30T22:12Z] INFO  23:12:20,568 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:20,713 MuTect - [MUTECT] Processed 2000075 reads in 884 ms
[2015-09-30T22:12Z] INFO  23:12:20,758 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:20,812 MuTect - [MUTECT] Processed 22000893 reads in 698 ms
[2015-09-30T22:12Z] INFO  23:12:21,189 MuTect - [MUTECT] Processed 55003417 reads in 793 ms
[2015-09-30T22:12Z] INFO  23:12:21,494 MuTect - [MUTECT] Processed 23000938 reads in 682 ms
[2015-09-30T22:12Z] INFO  23:12:21,612 MuTect - [MUTECT] Processed 3000079 reads in 899 ms
[2015-09-30T22:12Z] INFO  23:12:21,849 MuTect - [MUTECT] Processed 56003459 reads in 660 ms
[2015-09-30T22:12Z] INFO  23:12:22,096 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:22,189 MuTect - [MUTECT] Processed 24000972 reads in 694 ms
[2015-09-30T22:12Z] INFO  23:12:22,330 MuTect - [MUTECT] Processed 4000123 reads in 718 ms
[2015-09-30T22:12Z] INFO  23:12:22,520 MuTect - [MUTECT] Processed 57003531 reads in 671 ms
[2015-09-30T22:12Z] INFO  23:12:22,910 MuTect - [MUTECT] Processed 25001001 reads in 722 ms
[2015-09-30T22:12Z] INFO  23:12:23,042 MuTect - [MUTECT] Processed 5000137 reads in 712 ms
[2015-09-30T22:12Z] INFO  23:12:23,061 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:23,160 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:23,200 MuTect - [MUTECT] Processed 58003581 reads in 680 ms
[2015-09-30T22:12Z] INFO  23:12:23,637 MuTect - [MUTECT] Processed 26001002 reads in 727 ms
[2015-09-30T22:12Z] INFO  23:12:23,754 MuTect - [MUTECT] Processed 6000195 reads in 712 ms
[2015-09-30T22:12Z] INFO  23:12:23,903 MuTect - [MUTECT] Processed 59003645 reads in 703 ms
[2015-09-30T22:12Z] INFO  23:12:24,361 MuTect - [MUTECT] Processed 27001026 reads in 724 ms
[2015-09-30T22:12Z] INFO  23:12:24,459 MuTect - [MUTECT] Processed 7000281 reads in 705 ms
[2015-09-30T22:12Z] INFO  23:12:24,617 MuTect - [MUTECT] Processed 60003730 reads in 713 ms
[2015-09-30T22:12Z] INFO  23:12:24,759 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:25,132 MuTect - [MUTECT] Processed 28001028 reads in 771 ms
[2015-09-30T22:12Z] INFO  23:12:25,132 MuTect - [MUTECT] Processed 8000316 reads in 673 ms
[2015-09-30T22:12Z] INFO  23:12:25,323 MuTect - [MUTECT] Processed 61003785 reads in 707 ms
[2015-09-30T22:12Z] INFO  23:12:25,550 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:25,626 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:25,851 MuTect - [MUTECT] Processed 29001057 reads in 719 ms
[2015-09-30T22:12Z] INFO  23:12:25,893 MuTect - [MUTECT] Processed 9000379 reads in 761 ms
[2015-09-30T22:12Z] INFO  23:12:26,017 MuTect - [MUTECT] Processed 62003872 reads in 694 ms
[2015-09-30T22:12Z] INFO  23:12:26,556 MuTect - [MUTECT] Processed 30001074 reads in 705 ms
[2015-09-30T22:12Z] INFO  23:12:26,592 MuTect - [MUTECT] Processed 10000451 reads in 699 ms
[2015-09-30T22:12Z] INFO  23:12:26,709 MuTect - [MUTECT] Processed 63003912 reads in 692 ms
[2015-09-30T22:12Z] INFO  23:12:27,253 MuTect - [MUTECT] Processed 31001127 reads in 697 ms
[2015-09-30T22:12Z] INFO  23:12:27,304 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:27,359 MuTect - [MUTECT] Processed 11000466 reads in 767 ms
[2015-09-30T22:12Z] INFO  23:12:27,412 MuTect - [MUTECT] Processed 64003962 reads in 703 ms
[2015-09-30T22:12Z] INFO  23:12:27,907 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:27,987 MuTect - [MUTECT] Processed 32001127 reads in 734 ms
[2015-09-30T22:12Z] INFO  23:12:28,102 MuTect - [MUTECT] Processed 12000466 reads in 743 ms
[2015-09-30T22:12Z] INFO  23:12:28,122 MuTect - [MUTECT] Processed 65004055 reads in 710 ms
[2015-09-30T22:12Z] INFO  23:12:28,356 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:28,718 MuTect - [MUTECT] Processed 33001130 reads in 731 ms
[2015-09-30T22:12Z] INFO  23:12:28,836 MuTect - [MUTECT] Processed 13000506 reads in 734 ms
[2015-09-30T22:12Z] INFO  23:12:28,878 MuTect - [MUTECT] Processed 66004111 reads in 756 ms
[2015-09-30T22:12Z] INFO  23:12:29,453 MuTect - [MUTECT] Processed 34001131 reads in 735 ms
[2015-09-30T22:12Z] INFO  23:12:29,615 MuTect - [MUTECT] Processed 67004133 reads in 737 ms
[2015-09-30T22:12Z] INFO  23:12:29,637 MuTect - [MUTECT] Processed 14000552 reads in 801 ms
[2015-09-30T22:12Z] INFO  23:12:29,878 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:30,172 MuTect - [MUTECT] Processed 35001157 reads in 719 ms
[2015-09-30T22:12Z] INFO  23:12:30,219 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:30,343 MuTect - [MUTECT] Processed 15000623 reads in 706 ms
[2015-09-30T22:12Z] INFO  23:12:30,346 MuTect - [MUTECT] Processed 68004244 reads in 731 ms
[2015-09-30T22:12Z] INFO  23:12:30,869 MuTect - [MUTECT] Processed 36001174 reads in 697 ms
[2015-09-30T22:12Z] INFO  23:12:30,873 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:31,054 MuTect - [MUTECT] Processed 16000657 reads in 711 ms
[2015-09-30T22:12Z] INFO  23:12:31,055 MuTect - [MUTECT] Processed 69004327 reads in 709 ms
[2015-09-30T22:12Z] INFO  23:12:31,576 MuTect - [MUTECT] Processed 37001222 reads in 707 ms
[2015-09-30T22:12Z] INFO  23:12:31,693 MuTect - [MUTECT] Processed 17000675 reads in 639 ms
[2015-09-30T22:12Z] INFO  23:12:31,751 MuTect - [MUTECT] Processed 70004376 reads in 696 ms
[2015-09-30T22:12Z] INFO  23:12:32,291 MuTect - [MUTECT] Processed 38001226 reads in 715 ms
[2015-09-30T22:12Z] INFO  23:12:32,335 MuTect - [MUTECT] Processed 18000697 reads in 642 ms
[2015-09-30T22:12Z] INFO  23:12:32,419 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:32,433 MuTect - [MUTECT] Processed 71004403 reads in 682 ms
[2015-09-30T22:12Z] INFO  23:12:32,637 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:32,976 MuTect - [MUTECT] Processed 19000765 reads in 641 ms
[2015-09-30T22:12Z] INFO  23:12:32,982 MuTect - [MUTECT] Processed 39001284 reads in 690 ms
[2015-09-30T22:12Z] INFO  23:12:33,143 MuTect - [MUTECT] Processed 72004481 reads in 710 ms
[2015-09-30T22:12Z] INFO  23:12:33,640 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:33,651 MuTect - [MUTECT] Processed 20000798 reads in 675 ms
[2015-09-30T22:12Z] INFO  23:12:33,715 ProgressMeter -      4:49561801        1.41e+06   30.0 s       21.0 s     66.5%        45.0 s    15.0 s
[2015-09-30T22:12Z] INFO  23:12:33,823 MuTect - [MUTECT] Processed 73004494 reads in 680 ms
[2015-09-30T22:12Z] INFO  23:12:34,057 MuTect - [MUTECT] Processed 40001293 reads in 1076 ms
[2015-09-30T22:12Z] INFO  23:12:34,295 MuTect - [MUTECT] Processed 21000800 reads in 644 ms
[2015-09-30T22:12Z] INFO  23:12:34,553 MuTect - [MUTECT] Processed 74004573 reads in 730 ms
[2015-09-30T22:12Z] INFO  23:12:34,740 MuTect - [MUTECT] Processed 41001435 reads in 683 ms
[2015-09-30T22:12Z] INFO  23:12:34,942 MuTect - [MUTECT] Processed 22000848 reads in 647 ms
[2015-09-30T22:12Z] INFO  23:12:34,942 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:34,986 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:35,309 MuTect - [MUTECT] Processed 75004585 reads in 756 ms
[2015-09-30T22:12Z] INFO  23:12:35,427 MuTect - [MUTECT] Processed 42001490 reads in 687 ms
[2015-09-30T22:12Z] INFO  23:12:35,608 MuTect - [MUTECT] Processed 23000853 reads in 666 ms
[2015-09-30T22:12Z] INFO  23:12:36,057 MuTect - [MUTECT] Processed 76004636 reads in 748 ms
[2015-09-30T22:12Z] INFO  23:12:36,121 MuTect - [MUTECT] Processed 43001589 reads in 694 ms
[2015-09-30T22:12Z] INFO  23:12:36,167 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:36,243 MuTect - [MUTECT] Processed 24000939 reads in 635 ms
[2015-09-30T22:12Z] INFO  23:12:36,765 MuTect - [MUTECT] Processed 77004692 reads in 708 ms
[2015-09-30T22:12Z] INFO  23:12:36,825 MuTect - [MUTECT] Processed 44001591 reads in 704 ms
[2015-09-30T22:12Z] INFO  23:12:36,924 MuTect - [MUTECT] Processed 25000949 reads in 681 ms
[2015-09-30T22:12Z] INFO  23:12:37,379 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:37,461 MuTect - [MUTECT] Processed 78004788 reads in 696 ms
[2015-09-30T22:12Z] INFO  23:12:37,513 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:37,550 MuTect - [MUTECT] Processed 45001635 reads in 725 ms
[2015-09-30T22:12Z] INFO  23:12:37,643 MuTect - [MUTECT] Processed 26001005 reads in 719 ms
[2015-09-30T22:12Z] INFO  23:12:38,192 MuTect - [MUTECT] Processed 79004865 reads in 731 ms
[2015-09-30T22:12Z] INFO  23:12:38,261 MuTect - [MUTECT] Processed 46001706 reads in 711 ms
[2015-09-30T22:12Z] INFO  23:12:38,386 MuTect - [MUTECT] Processed 27001047 reads in 742 ms
[2015-09-30T22:12Z] INFO  23:12:38,655 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:38,908 MuTect - [MUTECT] Processed 80004986 reads in 716 ms
[2015-09-30T22:12Z] INFO  23:12:38,993 MuTect - [MUTECT] Processed 47001783 reads in 732 ms
[2015-09-30T22:12Z] INFO  23:12:39,038 MuTect - [MUTECT] Processed 28001051 reads in 653 ms
[2015-09-30T22:12Z] INFO  23:12:39,553 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:39,627 MuTect - [MUTECT] Processed 81005072 reads in 719 ms
[2015-09-30T22:12Z] INFO  23:12:39,693 MuTect - [MUTECT] Processed 48001823 reads in 700 ms
[2015-09-30T22:12Z] INFO  23:12:39,731 MuTect - [MUTECT] Processed 29001063 reads in 693 ms
[2015-09-30T22:12Z] INFO  23:12:40,148 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:40,395 MuTect - [MUTECT] Processed 82005221 reads in 768 ms
[2015-09-30T22:12Z] INFO  23:12:40,398 MuTect - [MUTECT] Processed 49001870 reads in 705 ms
[2015-09-30T22:12Z] INFO  23:12:40,414 MuTect - [MUTECT] Processed 30001073 reads in 683 ms
[2015-09-30T22:12Z] INFO  23:12:40,926 ProgressMeter -       4:8393983        1.99e+06   60.0 s       30.0 s     57.8%       103.0 s    43.0 s
[2015-09-30T22:12Z] INFO  23:12:41,046 MuTect - [MUTECT] Processed 31001126 reads in 632 ms
[2015-09-30T22:12Z] INFO  23:12:41,076 MuTect - [MUTECT] Processed 83005271 reads in 681 ms
[2015-09-30T22:12Z] INFO  23:12:41,103 MuTect - [MUTECT] Processed 50001948 reads in 705 ms
[2015-09-30T22:12Z] INFO  23:12:41,175 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:41,671 MuTect - [MUTECT] Processed 32001211 reads in 625 ms
[2015-09-30T22:12Z] INFO  23:12:41,761 MuTect - [MUTECT] Processed 84005282 reads in 685 ms
[2015-09-30T22:12Z] INFO  23:12:41,828 MuTect - [MUTECT] Processed 51001969 reads in 725 ms
[2015-09-30T22:12Z] INFO  23:12:41,974 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:42,332 MuTect - [MUTECT] Processed 33001286 reads in 661 ms
[2015-09-30T22:12Z] INFO  23:12:42,484 MuTect - [MUTECT] Processed 85005420 reads in 723 ms
[2015-09-30T22:12Z] INFO  23:12:42,596 MuTect - [MUTECT] Processed 52002053 reads in 768 ms
[2015-09-30T22:12Z] INFO  23:12:42,708 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:43,008 MuTect - [MUTECT] Processed 34001313 reads in 676 ms
[2015-09-30T22:12Z] INFO  23:12:43,232 MuTect - [MUTECT] Processed 86005488 reads in 748 ms
[2015-09-30T22:12Z] INFO  23:12:43,306 MuTect - [MUTECT] Processed 53002067 reads in 710 ms
[2015-09-30T22:12Z] INFO  23:12:43,642 MuTect - [MUTECT] Processed 35001400 reads in 634 ms
[2015-09-30T22:12Z] INFO  23:12:43,962 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:44,039 MuTect - [MUTECT] Processed 54002152 reads in 733 ms
[2015-09-30T22:12Z] INFO  23:12:44,120 MuTect - [MUTECT] Processed 87005492 reads in 888 ms
[2015-09-30T22:12Z] INFO  23:12:44,290 MuTect - [MUTECT] Processed 36001408 reads in 648 ms
[2015-09-30T22:12Z] INFO  23:12:44,751 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:44,772 MuTect - [MUTECT] Processed 55002152 reads in 733 ms
[2015-09-30T22:12Z] INFO  23:12:44,917 MuTect - [MUTECT] Processed 88005566 reads in 797 ms
[2015-09-30T22:12Z] INFO  23:12:44,984 MuTect - [MUTECT] Processed 37001471 reads in 694 ms
[2015-09-30T22:12Z] INFO  23:12:45,005 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:45,455 MuTect - [MUTECT] Processed 56002187 reads in 683 ms
[2015-09-30T22:12Z] INFO  23:12:45,648 MuTect - [MUTECT] Processed 89005605 reads in 730 ms
[2015-09-30T22:12Z] INFO  23:12:45,679 MuTect - [MUTECT] Processed 38001487 reads in 695 ms
[2015-09-30T22:12Z] INFO  23:12:46,152 MuTect - [MUTECT] Processed 57002199 reads in 697 ms
[2015-09-30T22:12Z] INFO  23:12:46,348 MuTect - [MUTECT] Processed 90005654 reads in 701 ms
[2015-09-30T22:12Z] INFO  23:12:46,371 MuTect - [MUTECT] Processed 39001494 reads in 692 ms
[2015-09-30T22:12Z] INFO  23:12:46,500 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:46,856 MuTect - [MUTECT] Processed 58002245 reads in 704 ms
[2015-09-30T22:12Z] INFO  23:12:47,032 MuTect - [MUTECT] Processed 91005715 reads in 684 ms
[2015-09-30T22:12Z] INFO  23:12:47,072 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:47,089 MuTect - [MUTECT] Processed 40001559 reads in 718 ms
[2015-09-30T22:12Z] INFO  23:12:47,166 ProgressMeter -      4:77492173        1.70e+06   30.0 s       17.0 s     50.3%        59.0 s    29.0 s
[2015-09-30T22:12Z] INFO  23:12:47,512 MuTect - [MUTECT] Processed 59002290 reads in 656 ms
[2015-09-30T22:12Z] INFO  23:12:47,656 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:47,730 MuTect - [MUTECT] Processed 92005764 reads in 698 ms
[2015-09-30T22:12Z] INFO  23:12:47,788 MuTect - [MUTECT] Processed 41001649 reads in 699 ms
[2015-09-30T22:12Z] INFO  23:12:48,149 MuTect - [MUTECT] Processed 60002357 reads in 637 ms
[2015-09-30T22:12Z] INFO  23:12:48,305 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:12Z] INFO  23:12:48,308 ProgressMeter -            done        2.20e+06   44.0 s       20.0 s    100.0%        44.0 s     0.0 s
[2015-09-30T22:12Z] INFO  23:12:48,308 ProgressMeter - Total runtime 44.60 secs, 0.74 min, 0.01 hours
[2015-09-30T22:12Z] INFO  23:12:48,373 MicroScheduler - 40878 reads were filtered out during the traversal out of approximately 718427 total reads (5.69%)
[2015-09-30T22:12Z] INFO  23:12:48,373 MicroScheduler -   -> 29574 reads (4.12% of total) failing DuplicateReadFilter
[2015-09-30T22:12Z] INFO  23:12:48,374 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:12Z] INFO  23:12:48,374 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:12Z] INFO  23:12:48,374 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:12Z] INFO  23:12:48,374 MicroScheduler -   -> 11304 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:12Z] INFO  23:12:48,400 MuTect - [MUTECT] Processed 93005801 reads in 670 ms
[2015-09-30T22:12Z] INFO  23:12:48,414 MuTect - [MUTECT] Processed 42001656 reads in 626 ms
[2015-09-30T22:12Z] INFO  23:12:49,061 MuTect - [MUTECT] Processed 43001693 reads in 647 ms
[2015-09-30T22:12Z] INFO  23:12:49,107 MuTect - [MUTECT] Processed 94005805 reads in 707 ms
[2015-09-30T22:12Z] INFO  23:12:49,382 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:12Z] bgzip syn3-4_31031389_62067173-raw-mutect.vcf
[2015-09-30T22:12Z] INFO  23:12:49,516 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:12Z] tabix index syn3-4_31031389_62067173-raw-mutect.vcf.gz
[2015-09-30T22:12Z] INFO  23:12:49,711 MuTect - [MUTECT] Processed 44001735 reads in 650 ms
[2015-09-30T22:12Z] INFO  23:12:49,788 MuTect - [MUTECT] Processed 95005887 reads in 681 ms
[2015-09-30T22:12Z] INFO  23:12:49,944 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:50,401 MuTect - [MUTECT] Processed 45001736 reads in 690 ms
[2015-09-30T22:12Z] INFO  23:12:50,435 MuTect - [MUTECT] Processed 96005897 reads in 647 ms
[2015-09-30T22:12Z] INFO  23:12:51,067 MuTect - [MUTECT] Processed 46001791 reads in 666 ms
[2015-09-30T22:12Z] INFO  23:12:51,114 MuTect - [MUTECT] Processed 97005905 reads in 679 ms
[2015-09-30T22:12Z] INFO  23:12:51,709 MuTect - [MUTECT] Processed 47001878 reads in 642 ms
[2015-09-30T22:12Z] INFO  23:12:51,808 MuTect - [MUTECT] Processed 98005975 reads in 694 ms
[2015-09-30T22:12Z] MuTect: MuTect
[2015-09-30T22:12Z] INFO  23:12:51,945 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:52,209 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:52,369 MuTect - [MUTECT] Processed 48001944 reads in 660 ms
[2015-09-30T22:12Z] INFO  23:12:52,508 MuTect - [MUTECT] Processed 99005986 reads in 700 ms
[2015-09-30T22:12Z] INFO  23:12:53,058 MuTect - [MUTECT] Processed 49001963 reads in 689 ms
[2015-09-30T22:12Z] INFO  23:12:53,218 MuTect - [MUTECT] Processed 100006015 reads in 710 ms
[2015-09-30T22:12Z] INFO  23:12:53,739 MuTect - [MUTECT] Processed 50001997 reads in 681 ms
[2015-09-30T22:12Z] INFO  23:12:53,906 MuTect - [MUTECT] Processed 101006076 reads in 688 ms
[2015-09-30T22:12Z] INFO  23:12:54,158 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/4/syn3-4_94005855_125588163-raw-mutect-regions.bed to be BED
[2015-09-30T22:12Z] INFO  23:12:54,212 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:12Z] INFO  23:12:54,213 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:12Z] INFO  23:12:54,213 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:12Z] INFO  23:12:54,213 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:12Z] INFO  23:12:54,217 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/4/syn3-4_94005855_125588163-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/4/tx/tmpTHZUyX/syn3-4_94005855_125588163-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:12Z] INFO  23:12:54,217 HelpFormatter - Date/Time: 2015/09/30 23:12:54
[2015-09-30T22:12Z] INFO  23:12:54,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:12Z] INFO  23:12:54,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:12Z] INFO  23:12:54,244 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:12Z] INFO  23:12:54,248 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:12Z] INFO  23:12:54,298 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:12Z] INFO  23:12:54,306 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:54,347 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:12Z] INFO  23:12:54,354 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:12Z] INFO  23:12:54,377 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:12Z] INFO  23:12:54,388 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:12Z] INFO  23:12:54,441 MuTect - [MUTECT] Processed 51002048 reads in 702 ms
[2015-09-30T22:12Z] INFO  23:12:54,564 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:12Z] INFO  23:12:54,631 MuTect - [MUTECT] Processed 102006092 reads in 725 ms
[2015-09-30T22:12Z] INFO  23:12:54,655 IntervalUtils - Processing 1026851 bp from intervals
[2015-09-30T22:12Z] INFO  23:12:54,659 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:12Z] INFO  23:12:54,659 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:12Z] INFO  23:12:54,720 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:54,837 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:12Z] INFO  23:12:54,988 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:12Z] INFO  23:12:54,988 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:12Z] INFO  23:12:54,989 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:12Z] INFO  23:12:54,990 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:12Z] INFO  23:12:55,127 MuTect - [MUTECT] Processed 52002100 reads in 686 ms
[2015-09-30T22:12Z] INFO  23:12:55,327 MuTect - [MUTECT] Processed 103006104 reads in 696 ms
[2015-09-30T22:12Z] INFO  23:12:55,784 MuTect - [MUTECT] Processed 53002138 reads in 657 ms
[2015-09-30T22:12Z] INFO  23:12:56,018 MuTect - [MUTECT] Processed 104006167 reads in 690 ms
[2015-09-30T22:12Z] INFO  23:12:56,502 MuTect - [MUTECT] Processed 54002153 reads in 718 ms
[2015-09-30T22:12Z] INFO  23:12:56,654 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:56,741 MuTect - [MUTECT] Processed 105006182 reads in 724 ms
[2015-09-30T22:12Z] INFO  23:12:57,175 MuTect - [MUTECT] Processed 55002186 reads in 673 ms
[2015-09-30T22:12Z] INFO  23:12:57,224 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:57,447 MuTect - [MUTECT] Processed 1000057 reads in 2411 ms
[2015-09-30T22:12Z] INFO  23:12:57,503 MuTect - [MUTECT] Processed 106006276 reads in 762 ms
[2015-09-30T22:12Z] INFO  23:12:57,866 MuTect - [MUTECT] Processed 56002222 reads in 691 ms
[2015-09-30T22:12Z] INFO  23:12:58,273 MuTect - [MUTECT] Processed 107006316 reads in 770 ms
[2015-09-30T22:12Z] INFO  23:12:58,408 MuTect - [MUTECT] Processed 2000062 reads in 961 ms
[2015-09-30T22:12Z] INFO  23:12:58,522 MuTect - [MUTECT] Processed 57002243 reads in 656 ms
[2015-09-30T22:12Z] INFO  23:12:58,929 MuTect - [MUTECT] Processed 108006389 reads in 656 ms
[2015-09-30T22:12Z] INFO  23:12:59,027 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:59,183 MuTect - [MUTECT] Processed 58002314 reads in 661 ms
[2015-09-30T22:12Z] INFO  23:12:59,268 MuTect - [MUTECT] Processed 3000144 reads in 860 ms
[2015-09-30T22:12Z] INFO  23:12:59,572 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:12Z] INFO  23:12:59,622 MuTect - [MUTECT] Processed 109006397 reads in 693 ms
[2015-09-30T22:12Z] INFO  23:12:59,879 MuTect - [MUTECT] Processed 59002320 reads in 696 ms
[2015-09-30T22:12Z] INFO  23:12:59,900 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:00,041 MuTect - [MUTECT] Processed 4000168 reads in 773 ms
[2015-09-30T22:13Z] INFO  23:13:00,324 MuTect - [MUTECT] Processed 110006460 reads in 702 ms
[2015-09-30T22:13Z] INFO  23:13:00,536 MuTect - [MUTECT] Processed 60002367 reads in 657 ms
[2015-09-30T22:13Z] INFO  23:13:00,842 MuTect - [MUTECT] Processed 5000216 reads in 801 ms
[2015-09-30T22:13Z] INFO  23:13:01,007 MuTect - [MUTECT] Processed 111006468 reads in 683 ms
[2015-09-30T22:13Z] INFO  23:13:01,226 MuTect - [MUTECT] Processed 61002404 reads in 690 ms
[2015-09-30T22:13Z] INFO  23:13:01,496 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:01,526 MuTect - [MUTECT] Processed 6000252 reads in 684 ms
[2015-09-30T22:13Z] INFO  23:13:01,698 MuTect - [MUTECT] Processed 112006543 reads in 691 ms
[2015-09-30T22:13Z] INFO  23:13:01,906 MuTect - [MUTECT] Processed 62002488 reads in 680 ms
[2015-09-30T22:13Z] INFO  23:13:02,016 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:02,236 MuTect - [MUTECT] Processed 7000269 reads in 710 ms
[2015-09-30T22:13Z] INFO  23:13:02,379 MuTect - [MUTECT] Processed 113006605 reads in 681 ms
[2015-09-30T22:13Z] INFO  23:13:02,556 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:02,598 MuTect - [MUTECT] Processed 63002524 reads in 692 ms
[2015-09-30T22:13Z] INFO  23:13:03,005 MuTect - [MUTECT] Processed 8000323 reads in 769 ms
[2015-09-30T22:13Z] INFO  23:13:03,066 MuTect - [MUTECT] Processed 114006635 reads in 687 ms
[2015-09-30T22:13Z] INFO  23:13:03,251 MuTect - [MUTECT] Processed 64002575 reads in 653 ms
[2015-09-30T22:13Z] INFO  23:13:03,730 MuTect - [MUTECT] Processed 9000405 reads in 725 ms
[2015-09-30T22:13Z] INFO  23:13:03,761 MuTect - [MUTECT] Processed 115006664 reads in 694 ms
[2015-09-30T22:13Z] INFO  23:13:03,895 MuTect - [MUTECT] Processed 65002657 reads in 644 ms
[2015-09-30T22:13Z] INFO  23:13:04,240 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:04,478 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:04,481 MuTect - [MUTECT] Processed 116006723 reads in 721 ms
[2015-09-30T22:13Z] INFO  23:13:04,484 MuTect - [MUTECT] Processed 10000432 reads in 754 ms
[2015-09-30T22:13Z] INFO  23:13:04,546 MuTect - [MUTECT] Processed 66002666 reads in 651 ms
[2015-09-30T22:13Z] INFO  23:13:05,179 MuTect - [MUTECT] Processed 67002717 reads in 633 ms
[2015-09-30T22:13Z] INFO  23:13:05,204 MuTect - [MUTECT] Processed 117006780 reads in 723 ms
[2015-09-30T22:13Z] INFO  23:13:05,214 MuTect - [MUTECT] Processed 11000487 reads in 730 ms
[2015-09-30T22:13Z] INFO  23:13:05,343 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:05,841 MuTect - [MUTECT] Processed 68002794 reads in 662 ms
[2015-09-30T22:13Z] INFO  23:13:05,888 MuTect - [MUTECT] Processed 12000578 reads in 673 ms
[2015-09-30T22:13Z] INFO  23:13:05,911 MuTect - [MUTECT] Processed 118006856 reads in 707 ms
[2015-09-30T22:13Z] INFO  23:13:06,516 MuTect - [MUTECT] Processed 69002796 reads in 675 ms
[2015-09-30T22:13Z] INFO  23:13:06,587 MuTect - [MUTECT] Processed 13000600 reads in 700 ms
[2015-09-30T22:13Z] INFO  23:13:06,598 MuTect - [MUTECT] Processed 119006928 reads in 687 ms
[2015-09-30T22:13Z] INFO  23:13:06,789 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:07,195 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:07,218 MuTect - [MUTECT] Processed 70002831 reads in 702 ms
[2015-09-30T22:13Z] INFO  23:13:07,332 MuTect - [MUTECT] Processed 14000624 reads in 745 ms
[2015-09-30T22:13Z] INFO  23:13:07,333 MuTect - [MUTECT] Processed 120006961 reads in 735 ms
[2015-09-30T22:13Z] INFO  23:13:07,905 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:07,927 MuTect - [MUTECT] Processed 71002831 reads in 709 ms
[2015-09-30T22:13Z] INFO  23:13:08,021 MuTect - [MUTECT] Processed 121006973 reads in 688 ms
[2015-09-30T22:13Z] INFO  23:13:08,106 MuTect - [MUTECT] Processed 15000635 reads in 774 ms
[2015-09-30T22:13Z] INFO  23:13:08,601 MuTect - [MUTECT] Processed 72002922 reads in 674 ms
[2015-09-30T22:13Z] INFO  23:13:08,730 MuTect - [MUTECT] Processed 122006981 reads in 709 ms
[2015-09-30T22:13Z] INFO  23:13:08,834 MuTect - [MUTECT] Processed 16000686 reads in 728 ms
[2015-09-30T22:13Z] INFO  23:13:09,292 MuTect - [MUTECT] Processed 73003001 reads in 691 ms
[2015-09-30T22:13Z] INFO  23:13:09,388 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:09,441 MuTect - [MUTECT] Processed 123007001 reads in 711 ms
[2015-09-30T22:13Z] INFO  23:13:09,492 MuTect - [MUTECT] Processed 17000781 reads in 658 ms
[2015-09-30T22:13Z] INFO  23:13:09,643 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:10,006 MuTect - [MUTECT] Processed 74003021 reads in 714 ms
[2015-09-30T22:13Z] INFO  23:13:10,138 MuTect - [MUTECT] Processed 124007023 reads in 697 ms
[2015-09-30T22:13Z] INFO  23:13:10,150 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:13Z] INFO  23:13:10,155 ProgressMeter -            done        3.33e+06   89.0 s       26.0 s    100.0%        89.0 s     0.0 s
[2015-09-30T22:13Z] INFO  23:13:10,155 ProgressMeter - Total runtime 89.23 secs, 1.49 min, 0.02 hours
[2015-09-30T22:13Z] INFO  23:13:10,174 MuTect - [MUTECT] Processed 18000789 reads in 682 ms
[2015-09-30T22:13Z] INFO  23:13:10,218 MicroScheduler - 100178 reads were filtered out during the traversal out of approximately 1492691 total reads (6.71%)
[2015-09-30T22:13Z] INFO  23:13:10,219 MicroScheduler -   -> 75987 reads (5.09% of total) failing DuplicateReadFilter
[2015-09-30T22:13Z] INFO  23:13:10,219 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:13Z] INFO  23:13:10,219 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:13Z] INFO  23:13:10,219 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:13Z] INFO  23:13:10,219 MicroScheduler -   -> 24191 reads (1.62% of total) failing UnmappedReadFilter
[2015-09-30T22:13Z] INFO  23:13:10,336 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:10,721 MuTect - [MUTECT] Processed 75003100 reads in 715 ms
[2015-09-30T22:13Z] INFO  23:13:10,967 MuTect - [MUTECT] Processed 19000795 reads in 792 ms
[2015-09-30T22:13Z] INFO  23:13:11,222 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:13Z] INFO  23:13:11,459 MuTect - [MUTECT] Processed 76003133 reads in 738 ms
[2015-09-30T22:13Z] INFO  23:13:11,612 MuTect - [MUTECT] Processed 20000847 reads in 646 ms
[2015-09-30T22:13Z] INFO  23:13:11,930 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:13Z] bgzip syn3-4_0_31018607-raw-mutect.vcf
[2015-09-30T22:13Z] INFO  23:13:12,159 MuTect - [MUTECT] Processed 77003155 reads in 700 ms
[2015-09-30T22:13Z] INFO  23:13:12,271 MuTect - [MUTECT] Processed 21000867 reads in 659 ms
[2015-09-30T22:13Z] INFO  23:13:12,633 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:13Z] tabix index syn3-4_0_31018607-raw-mutect.vcf.gz
[2015-09-30T22:13Z] INFO  23:13:12,836 MuTect - [MUTECT] Processed 78003160 reads in 677 ms
[2015-09-30T22:13Z] INFO  23:13:12,920 MuTect - [MUTECT] Processed 22000883 reads in 649 ms
[2015-09-30T22:13Z] INFO  23:13:13,525 MuTect - [MUTECT] Processed 79003240 reads in 689 ms
[2015-09-30T22:13Z] INFO  23:13:13,588 MuTect - [MUTECT] Processed 23000894 reads in 668 ms
[2015-09-30T22:13Z] INFO  23:13:14,296 MuTect - [MUTECT] Processed 24000972 reads in 708 ms
[2015-09-30T22:13Z] INFO  23:13:14,301 MuTect - [MUTECT] Processed 80003274 reads in 776 ms
[2015-09-30T22:13Z] INFO  23:13:14,541 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:14,974 MuTect - [MUTECT] Processed 81003368 reads in 673 ms
[2015-09-30T22:13Z] INFO  23:13:15,005 MuTect - [MUTECT] Processed 25001014 reads in 709 ms
[2015-09-30T22:13Z] INFO  23:13:15,212 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:13Z] MuTect: MuTect
[2015-09-30T22:13Z] INFO  23:13:15,651 MuTect - [MUTECT] Processed 82003453 reads in 677 ms
[2015-09-30T22:13Z] INFO  23:13:15,688 MuTect - [MUTECT] Processed 26001044 reads in 683 ms
[2015-09-30T22:13Z] INFO  23:13:16,351 MuTect - [MUTECT] Processed 83003505 reads in 700 ms
[2015-09-30T22:13Z] INFO  23:13:16,430 MuTect - [MUTECT] Processed 27001067 reads in 742 ms
[2015-09-30T22:13Z] INFO  23:13:16,987 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:17,049 MuTect - [MUTECT] Processed 84003566 reads in 698 ms
[2015-09-30T22:13Z] INFO  23:13:17,167 ProgressMeter -      4:90757036        3.27e+06   60.0 s       18.0 s     98.1%        61.0 s     1.0 s
[2015-09-30T22:13Z] INFO  23:13:17,173 MuTect - [MUTECT] Processed 28001093 reads in 743 ms
[2015-09-30T22:13Z] INFO  23:13:17,668 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/4/syn3-4_125589908_156618518-raw-mutect-regions.bed to be BED
[2015-09-30T22:13Z] INFO  23:13:17,721 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:13Z] INFO  23:13:17,722 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:13Z] INFO  23:13:17,722 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:13Z] INFO  23:13:17,722 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:13Z] INFO  23:13:17,725 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/4/syn3-4_125589908_156618518-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/4/tx/tmprDj2PK/syn3-4_125589908_156618518-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:13Z] INFO  23:13:17,726 HelpFormatter - Date/Time: 2015/09/30 23:13:17
[2015-09-30T22:13Z] INFO  23:13:17,726 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:13Z] INFO  23:13:17,726 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:13Z] INFO  23:13:17,754 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:13Z] INFO  23:13:17,758 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:13Z] INFO  23:13:17,788 MuTect - [MUTECT] Processed 85003583 reads in 739 ms
[2015-09-30T22:13Z] INFO  23:13:17,810 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:13Z] INFO  23:13:17,855 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:13Z] INFO  23:13:17,863 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:13Z] INFO  23:13:17,874 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:17,899 MuTect - [MUTECT] Processed 29001147 reads in 726 ms
[2015-09-30T22:13Z] INFO  23:13:17,900 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:13Z] INFO  23:13:17,923 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:13Z] INFO  23:13:18,094 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:13Z] INFO  23:13:18,123 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:13Z] INFO  23:13:18,126 ProgressMeter -            done        3.30e+06   60.0 s       18.0 s    100.0%        60.0 s     0.0 s
[2015-09-30T22:13Z] INFO  23:13:18,126 ProgressMeter - Total runtime 60.96 secs, 1.02 min, 0.02 hours
[2015-09-30T22:13Z] INFO  23:13:18,185 IntervalUtils - Processing 792406 bp from intervals
[2015-09-30T22:13Z] INFO  23:13:18,189 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:13Z] INFO  23:13:18,189 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:13Z] INFO  23:13:18,194 MicroScheduler - 56423 reads were filtered out during the traversal out of approximately 1015225 total reads (5.56%)
[2015-09-30T22:13Z] INFO  23:13:18,194 MicroScheduler -   -> 40566 reads (4.00% of total) failing DuplicateReadFilter
[2015-09-30T22:13Z] INFO  23:13:18,194 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:13Z] INFO  23:13:18,194 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:13Z] INFO  23:13:18,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:13Z] INFO  23:13:18,194 MicroScheduler -   -> 15857 reads (1.56% of total) failing UnmappedReadFilter
[2015-09-30T22:13Z] INFO  23:13:18,243 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:13Z] INFO  23:13:18,496 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:13Z] INFO  23:13:18,496 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:13Z] INFO  23:13:18,497 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:13Z] INFO  23:13:18,498 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:13Z] INFO  23:13:18,613 MuTect - [MUTECT] Processed 30001204 reads in 714 ms
[2015-09-30T22:13Z] INFO  23:13:19,145 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:13Z] bgzip syn3-4_62292837_93511697-raw-mutect.vcf
[2015-09-30T22:13Z] tabix index syn3-4_62292837_93511697-raw-mutect.vcf.gz
[2015-09-30T22:13Z] INFO  23:13:19,339 MuTect - [MUTECT] Processed 31001220 reads in 726 ms
[2015-09-30T22:13Z] INFO  23:13:20,063 MuTect - [MUTECT] Processed 32001318 reads in 724 ms
[2015-09-30T22:13Z] INFO  23:13:20,467 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:20,777 MuTect - [MUTECT] Processed 33001321 reads in 714 ms
[2015-09-30T22:13Z] INFO  23:13:21,195 MuTect - [MUTECT] Processed 1000002 reads in 2650 ms
[2015-09-30T22:13Z] INFO  23:13:21,490 MuTect - [MUTECT] Processed 34001367 reads in 713 ms
[2015-09-30T22:13Z] MuTect: MuTect
[2015-09-30T22:13Z] INFO  23:13:22,096 MuTect - [MUTECT] Processed 2000015 reads in 901 ms
[2015-09-30T22:13Z] INFO  23:13:22,202 MuTect - [MUTECT] Processed 35001459 reads in 712 ms
[2015-09-30T22:13Z] INFO  23:13:22,889 MuTect - [MUTECT] Processed 3000052 reads in 793 ms
[2015-09-30T22:13Z] INFO  23:13:22,901 MuTect - [MUTECT] Processed 36001509 reads in 699 ms
[2015-09-30T22:13Z] INFO  23:13:22,959 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:23,452 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:23,622 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/4/syn3-4_156624795_188926424-raw-mutect-regions.bed to be BED
[2015-09-30T22:13Z] INFO  23:13:23,634 MuTect - [MUTECT] Processed 4000104 reads in 745 ms
[2015-09-30T22:13Z] INFO  23:13:23,656 MuTect - [MUTECT] Processed 37001605 reads in 755 ms
[2015-09-30T22:13Z] INFO  23:13:23,675 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:13Z] INFO  23:13:23,676 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:13Z] INFO  23:13:23,676 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:13Z] INFO  23:13:23,676 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:13Z] INFO  23:13:23,679 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/4/syn3-4_156624795_188926424-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/4/tx/tmpoRULvL/syn3-4_156624795_188926424-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:13Z] INFO  23:13:23,679 HelpFormatter - Date/Time: 2015/09/30 23:13:23
[2015-09-30T22:13Z] INFO  23:13:23,679 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:13Z] INFO  23:13:23,680 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:13Z] INFO  23:13:23,705 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:13Z] INFO  23:13:23,709 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:13Z] INFO  23:13:23,760 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:13Z] INFO  23:13:23,805 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:13Z] INFO  23:13:23,812 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:13Z] INFO  23:13:23,834 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:13Z] INFO  23:13:23,845 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:13Z] INFO  23:13:24,037 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:13Z] INFO  23:13:24,121 IntervalUtils - Processing 813870 bp from intervals
[2015-09-30T22:13Z] INFO  23:13:24,124 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:13Z] INFO  23:13:24,125 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:13Z] INFO  23:13:24,174 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:13Z] INFO  23:13:24,357 MuTect - [MUTECT] Processed 38001655 reads in 701 ms
[2015-09-30T22:13Z] INFO  23:13:24,397 MuTect - [MUTECT] Processed 5000113 reads in 763 ms
[2015-09-30T22:13Z] INFO  23:13:24,444 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:13Z] INFO  23:13:24,444 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:13Z] INFO  23:13:24,445 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:13Z] INFO  23:13:24,446 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:13Z] INFO  23:13:24,991 ProgressMeter -     4:111554411        1.40e+06   30.0 s       21.0 s     58.0%        51.0 s    21.0 s
[2015-09-30T22:13Z] INFO  23:13:25,060 MuTect - [MUTECT] Processed 39001697 reads in 703 ms
[2015-09-30T22:13Z] INFO  23:13:25,168 MuTect - [MUTECT] Processed 6000164 reads in 771 ms
[2015-09-30T22:13Z] INFO  23:13:25,567 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:25,763 MuTect - [MUTECT] Processed 40001730 reads in 703 ms
[2015-09-30T22:13Z] INFO  23:13:26,123 MuTect - [MUTECT] Processed 7000213 reads in 955 ms
[2015-09-30T22:13Z] INFO  23:13:26,487 MuTect - [MUTECT] Processed 41001760 reads in 724 ms
[2015-09-30T22:13Z] INFO  23:13:26,492 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:26,878 MuTect - [MUTECT] Processed 8000239 reads in 755 ms
[2015-09-30T22:13Z] INFO  23:13:27,159 MuTect - [MUTECT] Processed 1000028 reads in 2668 ms
[2015-09-30T22:13Z] INFO  23:13:27,207 MuTect - [MUTECT] Processed 42001761 reads in 720 ms
[2015-09-30T22:13Z] INFO  23:13:27,721 MuTect - [MUTECT] Processed 9000269 reads in 843 ms
[2015-09-30T22:13Z] INFO  23:13:27,912 MuTect - [MUTECT] Processed 2000072 reads in 753 ms
[2015-09-30T22:13Z] INFO  23:13:27,940 MuTect - [MUTECT] Processed 43001785 reads in 733 ms
[2015-09-30T22:13Z] INFO  23:13:28,056 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:28,501 MuTect - [MUTECT] Processed 10000305 reads in 780 ms
[2015-09-30T22:13Z] INFO  23:13:28,643 MuTect - [MUTECT] Processed 44001887 reads in 703 ms
[2015-09-30T22:13Z] INFO  23:13:28,714 MuTect - [MUTECT] Processed 3000162 reads in 802 ms
[2015-09-30T22:13Z] INFO  23:13:29,209 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:29,239 MuTect - [MUTECT] Processed 11000314 reads in 738 ms
[2015-09-30T22:13Z] INFO  23:13:29,325 MuTect - [MUTECT] Processed 45001966 reads in 682 ms
[2015-09-30T22:13Z] INFO  23:13:29,399 MuTect - [MUTECT] Processed 4000200 reads in 685 ms
[2015-09-30T22:13Z] INFO  23:13:29,456 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:29,974 MuTect - [MUTECT] Processed 12000327 reads in 734 ms
[2015-09-30T22:13Z] INFO  23:13:29,988 MuTect - [MUTECT] Processed 46002035 reads in 663 ms
[2015-09-30T22:13Z] INFO  23:13:30,094 MuTect - [MUTECT] Processed 5000220 reads in 695 ms
[2015-09-30T22:13Z] INFO  23:13:30,635 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:30,661 MuTect - [MUTECT] Processed 47002092 reads in 673 ms
[2015-09-30T22:13Z] INFO  23:13:30,716 MuTect - [MUTECT] Processed 13000352 reads in 742 ms
[2015-09-30T22:13Z] INFO  23:13:30,797 MuTect - [MUTECT] Processed 6000246 reads in 703 ms
[2015-09-30T22:13Z] INFO  23:13:31,363 MuTect - [MUTECT] Processed 48002156 reads in 702 ms
[2015-09-30T22:13Z] INFO  23:13:31,440 MuTect - [MUTECT] Processed 14000404 reads in 725 ms
[2015-09-30T22:13Z] INFO  23:13:31,477 MuTect - [MUTECT] Processed 7000291 reads in 680 ms
[2015-09-30T22:13Z] INFO  23:13:31,695 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:32,073 MuTect - [MUTECT] Processed 49002203 reads in 710 ms
[2015-09-30T22:13Z] INFO  23:13:32,175 MuTect - [MUTECT] Processed 8000326 reads in 698 ms
[2015-09-30T22:13Z] INFO  23:13:32,186 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:32,186 MuTect - [MUTECT] Processed 15000466 reads in 746 ms
[2015-09-30T22:13Z] INFO  23:13:32,789 MuTect - [MUTECT] Processed 50002231 reads in 716 ms
[2015-09-30T22:13Z] INFO  23:13:32,852 MuTect - [MUTECT] Processed 9000333 reads in 677 ms
[2015-09-30T22:13Z] INFO  23:13:32,919 MuTect - [MUTECT] Processed 16000466 reads in 733 ms
[2015-09-30T22:13Z] INFO  23:13:33,277 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:33,517 MuTect - [MUTECT] Processed 51002238 reads in 728 ms
[2015-09-30T22:13Z] INFO  23:13:33,612 MuTect - [MUTECT] Processed 10000353 reads in 760 ms
[2015-09-30T22:13Z] INFO  23:13:33,709 MuTect - [MUTECT] Processed 17000493 reads in 790 ms
[2015-09-30T22:13Z] INFO  23:13:34,263 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:34,279 MuTect - [MUTECT] Processed 11000454 reads in 667 ms
[2015-09-30T22:13Z] INFO  23:13:34,306 MuTect - [MUTECT] Processed 52002278 reads in 789 ms
[2015-09-30T22:13Z] INFO  23:13:34,427 MuTect - [MUTECT] Processed 18000552 reads in 718 ms
[2015-09-30T22:13Z] INFO  23:13:34,844 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:34,975 MuTect - [MUTECT] Processed 12000516 reads in 696 ms
[2015-09-30T22:13Z] INFO  23:13:34,995 MuTect - [MUTECT] Processed 53002320 reads in 688 ms
[2015-09-30T22:13Z] INFO  23:13:35,165 MuTect - [MUTECT] Processed 19000583 reads in 738 ms
[2015-09-30T22:13Z] INFO  23:13:35,606 MuTect - [MUTECT] Processed 13000537 reads in 631 ms
[2015-09-30T22:13Z] INFO  23:13:35,717 MuTect - [MUTECT] Processed 54002327 reads in 723 ms
[2015-09-30T22:13Z] INFO  23:13:35,861 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:35,937 MuTect - [MUTECT] Processed 20000602 reads in 772 ms
[2015-09-30T22:13Z] INFO  23:13:36,301 MuTect - [MUTECT] Processed 14000541 reads in 695 ms
[2015-09-30T22:13Z] INFO  23:13:36,481 MuTect - [MUTECT] Processed 55002340 reads in 764 ms
[2015-09-30T22:13Z] INFO  23:13:36,705 MuTect - [MUTECT] Processed 21000606 reads in 768 ms
[2015-09-30T22:13Z] INFO  23:13:36,932 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:37,019 MuTect - [MUTECT] Processed 15000578 reads in 718 ms
[2015-09-30T22:13Z] INFO  23:13:37,192 MuTect - [MUTECT] Processed 56002366 reads in 711 ms
[2015-09-30T22:13Z] INFO  23:13:37,415 MuTect - [MUTECT] Processed 22000637 reads in 710 ms
[2015-09-30T22:13Z] INFO  23:13:37,563 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:37,871 MuTect - [MUTECT] Processed 16000594 reads in 852 ms
[2015-09-30T22:13Z] INFO  23:13:37,920 MuTect - [MUTECT] Processed 57002384 reads in 728 ms
[2015-09-30T22:13Z] INFO  23:13:38,190 MuTect - [MUTECT] Processed 23000706 reads in 775 ms
[2015-09-30T22:13Z] INFO  23:13:38,583 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:38,633 MuTect - [MUTECT] Processed 17000676 reads in 762 ms
[2015-09-30T22:13Z] INFO  23:13:38,738 MuTect - [MUTECT] Processed 58002408 reads in 818 ms
[2015-09-30T22:13Z] INFO  23:13:38,942 MuTect - [MUTECT] Processed 24000833 reads in 751 ms
[2015-09-30T22:13Z] INFO  23:13:39,429 MuTect - [MUTECT] Processed 59002488 reads in 691 ms
[2015-09-30T22:13Z] INFO  23:13:39,451 MuTect - [MUTECT] Processed 18000736 reads in 818 ms
[2015-09-30T22:13Z] INFO  23:13:39,780 MuTect - [MUTECT] Processed 25000881 reads in 839 ms
[2015-09-30T22:13Z] INFO  23:13:39,793 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:40,138 MuTect - [MUTECT] Processed 60002508 reads in 709 ms
[2015-09-30T22:13Z] INFO  23:13:40,203 MuTect - [MUTECT] Processed 19000739 reads in 752 ms
[2015-09-30T22:13Z] INFO  23:13:40,419 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:40,515 MuTect - [MUTECT] Processed 26000888 reads in 735 ms
[2015-09-30T22:13Z] INFO  23:13:40,831 MuTect - [MUTECT] Processed 61002514 reads in 693 ms
[2015-09-30T22:13Z] INFO  23:13:40,890 MuTect - [MUTECT] Processed 20000781 reads in 687 ms
[2015-09-30T22:13Z] INFO  23:13:41,205 MuTect - [MUTECT] Processed 27000915 reads in 690 ms
[2015-09-30T22:13Z] INFO  23:13:41,398 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:41,496 MuTect - [MUTECT] Processed 62002558 reads in 665 ms
[2015-09-30T22:13Z] INFO  23:13:41,581 MuTect - [MUTECT] Processed 21000788 reads in 691 ms
[2015-09-30T22:13Z] INFO  23:13:41,918 MuTect - [MUTECT] Processed 28000916 reads in 713 ms
[2015-09-30T22:13Z] INFO  23:13:42,193 MuTect - [MUTECT] Processed 63002559 reads in 697 ms
[2015-09-30T22:13Z] INFO  23:13:42,274 MuTect - [MUTECT] Processed 22000807 reads in 693 ms
[2015-09-30T22:13Z] INFO  23:13:42,413 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:42,639 MuTect - [MUTECT] Processed 29000926 reads in 721 ms
[2015-09-30T22:13Z] INFO  23:13:42,898 MuTect - [MUTECT] Processed 64002613 reads in 705 ms
[2015-09-30T22:13Z] INFO  23:13:42,960 MuTect - [MUTECT] Processed 23000886 reads in 686 ms
[2015-09-30T22:13Z] INFO  23:13:43,097 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:43,356 MuTect - [MUTECT] Processed 30000997 reads in 717 ms
[2015-09-30T22:13Z] INFO  23:13:43,582 MuTect - [MUTECT] Processed 24000912 reads in 622 ms
[2015-09-30T22:13Z] INFO  23:13:43,616 MuTect - [MUTECT] Processed 65002650 reads in 718 ms
[2015-09-30T22:13Z] INFO  23:13:43,997 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:44,085 MuTect - [MUTECT] Processed 31001061 reads in 729 ms
[2015-09-30T22:13Z] INFO  23:13:44,123 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:13Z] INFO  23:13:44,127 ProgressMeter -            done        2.52e+06   49.0 s       19.0 s    100.0%        49.0 s     0.0 s
[2015-09-30T22:13Z] INFO  23:13:44,127 ProgressMeter - Total runtime 49.14 secs, 0.82 min, 0.01 hours
[2015-09-30T22:13Z] INFO  23:13:44,194 MicroScheduler - 43160 reads were filtered out during the traversal out of approximately 781790 total reads (5.52%)
[2015-09-30T22:13Z] INFO  23:13:44,194 MicroScheduler -   -> 30761 reads (3.93% of total) failing DuplicateReadFilter
[2015-09-30T22:13Z] INFO  23:13:44,194 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:13Z] INFO  23:13:44,195 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:13Z] INFO  23:13:44,195 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:13Z] INFO  23:13:44,195 MicroScheduler -   -> 12399 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:13Z] INFO  23:13:44,262 MuTect - [MUTECT] Processed 25000927 reads in 680 ms
[2015-09-30T22:13Z] INFO  23:13:44,805 MuTect - [MUTECT] Processed 32001093 reads in 720 ms
[2015-09-30T22:13Z] INFO  23:13:44,874 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:44,924 MuTect - [MUTECT] Processed 26000939 reads in 662 ms
[2015-09-30T22:13Z] INFO  23:13:45,286 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:13Z] bgzip syn3-4_94005855_125588163-raw-mutect.vcf
[2015-09-30T22:13Z] tabix index syn3-4_94005855_125588163-raw-mutect.vcf.gz
[2015-09-30T22:13Z] INFO  23:13:45,497 MuTect - [MUTECT] Processed 33001115 reads in 692 ms
[2015-09-30T22:13Z] INFO  23:13:45,574 MuTect - [MUTECT] Processed 27001051 reads in 650 ms
[2015-09-30T22:13Z] INFO  23:13:45,838 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:46,222 MuTect - [MUTECT] Processed 34001149 reads in 725 ms
[2015-09-30T22:13Z] INFO  23:13:46,269 MuTect - [MUTECT] Processed 28001100 reads in 695 ms
[2015-09-30T22:13Z] INFO  23:13:46,972 MuTect - [MUTECT] Processed 35001250 reads in 750 ms
[2015-09-30T22:13Z] INFO  23:13:46,975 MuTect - [MUTECT] Processed 29001171 reads in 706 ms
[2015-09-30T22:13Z] INFO  23:13:47,573 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:13Z] MuTect: MuTect
[2015-09-30T22:13Z] INFO  23:13:47,692 MuTect - [MUTECT] Processed 36001278 reads in 720 ms
[2015-09-30T22:13Z] INFO  23:13:47,722 MuTect - [MUTECT] Processed 30001182 reads in 747 ms
[2015-09-30T22:13Z] INFO  23:13:48,370 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:48,388 MuTect - [MUTECT] Processed 37001295 reads in 696 ms
[2015-09-30T22:13Z] INFO  23:13:48,424 MuTect - [MUTECT] Processed 31001216 reads in 702 ms
[2015-09-30T22:13Z] INFO  23:13:48,499 ProgressMeter -     4:151246974        1.25e+06   30.0 s       24.0 s     68.7%        43.0 s    13.0 s
[2015-09-30T22:13Z] INFO  23:13:49,091 MuTect - [MUTECT] Processed 38001307 reads in 703 ms
[2015-09-30T22:13Z] INFO  23:13:49,139 MuTect - [MUTECT] Processed 32001222 reads in 715 ms
[2015-09-30T22:13Z] INFO  23:13:49,689 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/4/syn3-4_189012293_191154276-raw-mutect-regions.bed to be BED
[2015-09-30T22:13Z] INFO  23:13:49,745 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:13Z] INFO  23:13:49,746 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:13Z] INFO  23:13:49,746 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:13Z] INFO  23:13:49,746 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:13Z] INFO  23:13:49,749 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/4/syn3-4_189012293_191154276-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/4/tx/tmp9XhBeO/syn3-4_189012293_191154276-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:13Z] INFO  23:13:49,750 HelpFormatter - Date/Time: 2015/09/30 23:13:49
[2015-09-30T22:13Z] INFO  23:13:49,750 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:13Z] INFO  23:13:49,750 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:13Z] INFO  23:13:49,777 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:13Z] INFO  23:13:49,781 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:13Z] INFO  23:13:49,845 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:13Z] INFO  23:13:49,848 MuTect - [MUTECT] Processed 33001252 reads in 709 ms
[2015-09-30T22:13Z] INFO  23:13:49,848 MuTect - [MUTECT] Processed 39001341 reads in 757 ms
[2015-09-30T22:13Z] INFO  23:13:49,892 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:13Z] INFO  23:13:49,900 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:13Z] INFO  23:13:49,941 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:13Z] INFO  23:13:49,977 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:13Z] INFO  23:13:50,155 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:13Z] INFO  23:13:50,204 IntervalUtils - Processing 26832 bp from intervals
[2015-09-30T22:13Z] INFO  23:13:50,208 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:13Z] INFO  23:13:50,208 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:13Z] INFO  23:13:50,260 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:13Z] INFO  23:13:50,301 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:50,438 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:13Z] INFO  23:13:50,439 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:13Z] INFO  23:13:50,439 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:13Z] INFO  23:13:50,440 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:13Z] INFO  23:13:50,523 MuTect - [MUTECT] Processed 40001411 reads in 675 ms
[2015-09-30T22:13Z] INFO  23:13:50,542 MuTect - [MUTECT] Processed 34001349 reads in 694 ms
[2015-09-30T22:13Z] INFO  23:13:50,995 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:51,230 MuTect - [MUTECT] Processed 35001439 reads in 688 ms
[2015-09-30T22:13Z] INFO  23:13:51,248 MuTect - [MUTECT] Processed 41001425 reads in 724 ms
[2015-09-30T22:13Z] INFO  23:13:51,914 MuTect - [MUTECT] Processed 42001470 reads in 667 ms
[2015-09-30T22:13Z] INFO  23:13:51,940 MuTect - [MUTECT] Processed 36001473 reads in 710 ms
[2015-09-30T22:13Z] INFO  23:13:52,608 MuTect - [MUTECT] Processed 43001561 reads in 694 ms
[2015-09-30T22:13Z] INFO  23:13:52,661 MuTect - [MUTECT] Processed 37001485 reads in 721 ms
[2015-09-30T22:13Z] INFO  23:13:52,822 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:53,038 MuTect - [MUTECT] Processed 1000052 reads in 2551 ms
[2015-09-30T22:13Z] INFO  23:13:53,306 MuTect - [MUTECT] Processed 44001588 reads in 698 ms
[2015-09-30T22:13Z] INFO  23:13:53,367 MuTect - [MUTECT] Processed 38001529 reads in 706 ms
[2015-09-30T22:13Z] INFO  23:13:53,478 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:53,964 MuTect - [MUTECT] Processed 45001641 reads in 658 ms
[2015-09-30T22:13Z] INFO  23:13:54,122 MuTect - [MUTECT] Processed 39001592 reads in 755 ms
[2015-09-30T22:13Z] INFO  23:13:54,447 ProgressMeter -     4:184930417        1.38e+06   30.0 s       21.0 s     74.8%        40.0 s    10.0 s
[2015-09-30T22:13Z] INFO  23:13:54,560 MuTect - [MUTECT] Processed 2000105 reads in 1522 ms
[2015-09-30T22:13Z] INFO  23:13:54,619 MuTect - [MUTECT] Processed 46001662 reads in 655 ms
[2015-09-30T22:13Z] INFO  23:13:54,835 MuTect - [MUTECT] Processed 40001653 reads in 713 ms
[2015-09-30T22:13Z] INFO  23:13:55,309 MuTect - [MUTECT] Processed 47001663 reads in 690 ms
[2015-09-30T22:13Z] INFO  23:13:55,318 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:55,538 MuTect - [MUTECT] Processed 41001690 reads in 703 ms
[2015-09-30T22:13Z] INFO  23:13:55,616 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:55,987 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:55,994 MuTect - [MUTECT] Processed 48001729 reads in 685 ms
[2015-09-30T22:13Z] INFO  23:13:56,264 MuTect - [MUTECT] Processed 42001720 reads in 726 ms
[2015-09-30T22:13Z] INFO  23:13:56,649 MuTect - [MUTECT] Processed 49001770 reads in 655 ms
[2015-09-30T22:13Z] INFO  23:13:56,972 MuTect - [MUTECT] Processed 43001758 reads in 708 ms
[2015-09-30T22:13Z] INFO  23:13:57,278 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:13Z] INFO  23:13:57,283 ProgressMeter -            done        5.96e+04    6.0 s      114.0 s     99.7%         6.0 s     0.0 s
[2015-09-30T22:13Z] INFO  23:13:57,283 ProgressMeter - Total runtime 6.84 secs, 0.11 min, 0.00 hours
[2015-09-30T22:13Z] INFO  23:13:57,308 MuTect - [MUTECT] Processed 50001823 reads in 659 ms
[2015-09-30T22:13Z] INFO  23:13:57,350 MicroScheduler - 2335 reads were filtered out during the traversal out of approximately 31997 total reads (7.30%)
[2015-09-30T22:13Z] INFO  23:13:57,350 MicroScheduler -   -> 1765 reads (5.52% of total) failing DuplicateReadFilter
[2015-09-30T22:13Z] INFO  23:13:57,351 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:13Z] INFO  23:13:57,351 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:13Z] INFO  23:13:57,351 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:13Z] INFO  23:13:57,351 MicroScheduler -   -> 570 reads (1.78% of total) failing UnmappedReadFilter
[2015-09-30T22:13Z] INFO  23:13:57,666 MuTect - [MUTECT] Processed 44001804 reads in 694 ms
[2015-09-30T22:13Z] INFO  23:13:57,762 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:57,977 MuTect - [MUTECT] Processed 51001909 reads in 669 ms
[2015-09-30T22:13Z] INFO  23:13:58,387 MuTect - [MUTECT] Processed 45001838 reads in 721 ms
[2015-09-30T22:13Z] INFO  23:13:58,503 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:13Z] INFO  23:13:58,638 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:13Z] bgzip syn3-4_189012293_191154276-raw-mutect.vcf
[2015-09-30T22:13Z] INFO  23:13:58,691 MuTect - [MUTECT] Processed 52001958 reads in 714 ms
[2015-09-30T22:13Z] tabix index syn3-4_189012293_191154276-raw-mutect.vcf.gz
[2015-09-30T22:13Z] INFO  23:13:59,100 MuTect - [MUTECT] Processed 46001926 reads in 713 ms
[2015-09-30T22:13Z] INFO  23:13:59,385 MuTect - [MUTECT] Processed 53002038 reads in 694 ms
[2015-09-30T22:13Z] INFO  23:13:59,825 MuTect - [MUTECT] Processed 47001962 reads in 725 ms
[2015-09-30T22:14Z] INFO  23:14:00,101 MuTect - [MUTECT] Processed 54002050 reads in 716 ms
[2015-09-30T22:14Z] INFO  23:14:00,417 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:00,571 MuTect - [MUTECT] Processed 48001967 reads in 746 ms
[2015-09-30T22:14Z] INFO  23:14:00,752 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:14Z] INFO  23:14:00,755 ProgressMeter -            done        1.89e+06   42.0 s       22.0 s    100.0%        42.0 s     0.0 s
[2015-09-30T22:14Z] INFO  23:14:00,755 ProgressMeter - Total runtime 42.26 secs, 0.70 min, 0.01 hours
[2015-09-30T22:14Z] INFO  23:14:00,820 MicroScheduler - 37101 reads were filtered out during the traversal out of approximately 649528 total reads (5.71%)
[2015-09-30T22:14Z] INFO  23:14:00,820 MicroScheduler -   -> 26638 reads (4.10% of total) failing DuplicateReadFilter
[2015-09-30T22:14Z] INFO  23:14:00,821 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:14Z] INFO  23:14:00,821 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:14Z] INFO  23:14:00,821 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:14Z] INFO  23:14:00,821 MicroScheduler -   -> 10463 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:14Z] MuTect: MuTect
[2015-09-30T22:14Z] INFO  23:14:01,257 MuTect - [MUTECT] Processed 49001976 reads in 686 ms
[2015-09-30T22:14Z] INFO  23:14:01,820 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:14Z] bgzip syn3-4_125589908_156618518-raw-mutect.vcf
[2015-09-30T22:14Z] tabix index syn3-4_125589908_156618518-raw-mutect.vcf.gz
[2015-09-30T22:14Z] INFO  23:14:01,979 MuTect - [MUTECT] Processed 50002028 reads in 722 ms
[2015-09-30T22:14Z] INFO  23:14:02,715 MuTect - [MUTECT] Processed 51002115 reads in 736 ms
[2015-09-30T22:14Z] INFO  23:14:02,851 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:03,157 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/5/syn3-5_0_31268043-raw-mutect-regions.bed to be BED
[2015-09-30T22:14Z] INFO  23:14:03,213 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:03,213 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:14Z] INFO  23:14:03,213 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:14Z] INFO  23:14:03,213 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:14Z] INFO  23:14:03,217 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/5/syn3-5_0_31268043-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/5/tx/tmp_6CO43/syn3-5_0_31268043-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:14Z] INFO  23:14:03,217 HelpFormatter - Date/Time: 2015/09/30 23:14:03
[2015-09-30T22:14Z] INFO  23:14:03,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:03,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:03,245 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:14Z] INFO  23:14:03,249 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:14Z] INFO  23:14:03,302 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:14Z] INFO  23:14:03,349 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:14Z] INFO  23:14:03,357 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:14Z] INFO  23:14:03,399 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:14Z] INFO  23:14:03,407 MuTect - [MUTECT] Processed 52002166 reads in 692 ms
[2015-09-30T22:14Z] INFO  23:14:03,410 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:14Z] INFO  23:14:03,585 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:14Z] INFO  23:14:03,664 IntervalUtils - Processing 657750 bp from intervals
[2015-09-30T22:14Z] INFO  23:14:03,668 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:14Z] INFO  23:14:03,668 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:14Z] INFO  23:14:03,722 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:14Z] INFO  23:14:03,944 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:14Z] INFO  23:14:03,945 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:14Z] INFO  23:14:03,945 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:14Z] INFO  23:14:03,946 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:14Z] INFO  23:14:04,106 MuTect - [MUTECT] Processed 53002216 reads in 699 ms
[2015-09-30T22:14Z] MuTect: MuTect
[2015-09-30T22:14Z] INFO  23:14:04,780 MuTect - [MUTECT] Processed 54002256 reads in 674 ms
[2015-09-30T22:14Z] INFO  23:14:05,443 MuTect - [MUTECT] Processed 55002273 reads in 663 ms
[2015-09-30T22:14Z] INFO  23:14:05,466 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:05,962 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:14Z] INFO  23:14:05,966 ProgressMeter -            done        1.93e+06   41.0 s       21.0 s    100.0%        41.0 s     0.0 s
[2015-09-30T22:14Z] INFO  23:14:05,966 ProgressMeter - Total runtime 41.52 secs, 0.69 min, 0.01 hours
[2015-09-30T22:14Z] INFO  23:14:06,031 MicroScheduler - 38078 reads were filtered out during the traversal out of approximately 662815 total reads (5.74%)
[2015-09-30T22:14Z] INFO  23:14:06,031 MicroScheduler -   -> 27439 reads (4.14% of total) failing DuplicateReadFilter
[2015-09-30T22:14Z] INFO  23:14:06,031 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:14Z] INFO  23:14:06,032 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:14Z] INFO  23:14:06,032 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:14Z] INFO  23:14:06,032 MicroScheduler -   -> 10639 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:14Z] INFO  23:14:06,252 MuTect - [MUTECT] Processed 1000004 reads in 2260 ms
[2015-09-30T22:14Z] INFO  23:14:06,399 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/5/syn3-5_31293868_62597714-raw-mutect-regions.bed to be BED
[2015-09-30T22:14Z] INFO  23:14:06,456 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:06,456 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:14Z] INFO  23:14:06,456 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:14Z] INFO  23:14:06,456 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:14Z] INFO  23:14:06,460 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/5/syn3-5_31293868_62597714-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/5/tx/tmpyVnCg7/syn3-5_31293868_62597714-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:14Z] INFO  23:14:06,460 HelpFormatter - Date/Time: 2015/09/30 23:14:06
[2015-09-30T22:14Z] INFO  23:14:06,460 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:06,460 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:06,487 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:14Z] INFO  23:14:06,492 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:14Z] INFO  23:14:06,547 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:14Z] INFO  23:14:06,595 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:14Z] INFO  23:14:06,602 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:14Z] INFO  23:14:06,625 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:14Z] INFO  23:14:06,637 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:14Z] INFO  23:14:06,813 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:14Z] INFO  23:14:06,907 IntervalUtils - Processing 1117535 bp from intervals
[2015-09-30T22:14Z] INFO  23:14:06,911 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:14Z] INFO  23:14:06,911 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:14Z] INFO  23:14:07,018 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:14Z] INFO  23:14:07,087 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:14Z] INFO  23:14:07,235 MuTect - [MUTECT] Processed 2000098 reads in 983 ms
[2015-09-30T22:14Z] INFO  23:14:07,880 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:14Z] INFO  23:14:07,880 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:14Z] INFO  23:14:07,880 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:14Z] INFO  23:14:07,881 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:14Z] INFO  23:14:08,278 MuTect - [MUTECT] Processed 3000131 reads in 1043 ms
[2015-09-30T22:14Z] INFO  23:14:08,615 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:09,340 MuTect - [MUTECT] Processed 4000195 reads in 1062 ms
[2015-09-30T22:14Z] bgzip syn3-4_156624795_188926424-raw-mutect.vcf
[2015-09-30T22:14Z] tabix index syn3-4_156624795_188926424-raw-mutect.vcf.gz
[2015-09-30T22:14Z] INFO  23:14:10,315 MuTect - [MUTECT] Processed 5000214 reads in 975 ms
[2015-09-30T22:14Z] INFO  23:14:10,734 MuTect - [MUTECT] Processed 1000063 reads in 2760 ms
[2015-09-30T22:14Z] INFO  23:14:11,043 MuTect - [MUTECT] Processed 6000266 reads in 728 ms
[2015-09-30T22:14Z] INFO  23:14:11,434 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:11,491 MuTect - [MUTECT] Processed 2000071 reads in 757 ms
[2015-09-30T22:14Z] INFO  23:14:11,778 MuTect - [MUTECT] Processed 7000300 reads in 735 ms
[2015-09-30T22:14Z] INFO  23:14:12,254 MuTect - [MUTECT] Processed 3000116 reads in 763 ms
[2015-09-30T22:14Z] INFO  23:14:12,572 MuTect - [MUTECT] Processed 8000332 reads in 794 ms
[2015-09-30T22:14Z] INFO  23:14:12,700 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:14Z] MuTect: MuTect
[2015-09-30T22:14Z] INFO  23:14:13,000 MuTect - [MUTECT] Processed 4000234 reads in 746 ms
[2015-09-30T22:14Z] INFO  23:14:13,290 MuTect - [MUTECT] Processed 9000402 reads in 718 ms
[2015-09-30T22:14Z] INFO  23:14:13,699 MuTect - [MUTECT] Processed 5000275 reads in 699 ms
[2015-09-30T22:14Z] INFO  23:14:13,905 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:14,061 MuTect - [MUTECT] Processed 10000497 reads in 771 ms
[2015-09-30T22:14Z] INFO  23:14:14,416 MuTect - [MUTECT] Processed 6000276 reads in 717 ms
[2015-09-30T22:14Z] INFO  23:14:14,771 MuTect - [MUTECT] Processed 11000579 reads in 710 ms
[2015-09-30T22:14Z] INFO  23:14:15,163 MuTect - [MUTECT] Processed 7000298 reads in 747 ms
[2015-09-30T22:14Z] INFO  23:14:15,196 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/5/syn3-5_63256014_94276127-raw-mutect-regions.bed to be BED
[2015-09-30T22:14Z] INFO  23:14:15,253 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:15,253 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:14Z] INFO  23:14:15,253 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:14Z] INFO  23:14:15,253 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:14Z] INFO  23:14:15,257 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/5/syn3-5_63256014_94276127-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/5/tx/tmpi2vl7W/syn3-5_63256014_94276127-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:14Z] INFO  23:14:15,257 HelpFormatter - Date/Time: 2015/09/30 23:14:15
[2015-09-30T22:14Z] INFO  23:14:15,257 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:15,257 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:15,285 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:14Z] INFO  23:14:15,289 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:14Z] INFO  23:14:15,347 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:14Z] INFO  23:14:15,359 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:15,395 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:14Z] INFO  23:14:15,403 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:14Z] INFO  23:14:15,426 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:14Z] INFO  23:14:15,433 MuTect - [MUTECT] Processed 12000587 reads in 662 ms
[2015-09-30T22:14Z] INFO  23:14:15,437 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:14Z] INFO  23:14:15,616 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:14Z] INFO  23:14:15,713 IntervalUtils - Processing 1272246 bp from intervals
[2015-09-30T22:14Z] INFO  23:14:15,717 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:14Z] INFO  23:14:15,717 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:14Z] INFO  23:14:15,878 MuTect - [MUTECT] Processed 8000348 reads in 715 ms
[2015-09-30T22:14Z] INFO  23:14:15,888 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:14Z] INFO  23:14:16,101 MuTect - [MUTECT] Processed 13000720 reads in 668 ms
[2015-09-30T22:14Z] INFO  23:14:16,336 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:16,603 MuTect - [MUTECT] Processed 9000376 reads in 725 ms
[2015-09-30T22:14Z] INFO  23:14:16,770 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:14Z] INFO  23:14:16,770 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:14Z] INFO  23:14:16,770 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:14Z] INFO  23:14:16,771 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:14Z] INFO  23:14:16,807 MuTect - [MUTECT] Processed 14000821 reads in 706 ms
[2015-09-30T22:14Z] INFO  23:14:17,344 MuTect - [MUTECT] Processed 10000430 reads in 740 ms
[2015-09-30T22:14Z] INFO  23:14:17,527 MuTect - [MUTECT] Processed 15000904 reads in 720 ms
[2015-09-30T22:14Z] INFO  23:14:17,922 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:18,105 MuTect - [MUTECT] Processed 11000545 reads in 761 ms
[2015-09-30T22:14Z] INFO  23:14:18,219 MuTect - [MUTECT] Processed 16001032 reads in 692 ms
[2015-09-30T22:14Z] INFO  23:14:18,513 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:18,809 MuTect - [MUTECT] Processed 12000584 reads in 704 ms
[2015-09-30T22:14Z] INFO  23:14:18,941 MuTect - [MUTECT] Processed 17001070 reads in 722 ms
[2015-09-30T22:14Z] INFO  23:14:19,231 MuTect - [MUTECT] Processed 1000014 reads in 2386 ms
[2015-09-30T22:14Z] INFO  23:14:19,559 MuTect - [MUTECT] Processed 13000658 reads in 751 ms
[2015-09-30T22:14Z] INFO  23:14:19,642 MuTect - [MUTECT] Processed 18001126 reads in 700 ms
[2015-09-30T22:14Z] INFO  23:14:20,213 MuTect - [MUTECT] Processed 2000063 reads in 983 ms
[2015-09-30T22:14Z] INFO  23:14:20,310 MuTect - [MUTECT] Processed 19001265 reads in 669 ms
[2015-09-30T22:14Z] INFO  23:14:20,413 MuTect - [MUTECT] Processed 14001208 reads in 854 ms
[2015-09-30T22:14Z] INFO  23:14:20,871 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:20,954 MuTect - [MUTECT] Processed 20001362 reads in 644 ms
[2015-09-30T22:14Z] INFO  23:14:21,180 MuTect - [MUTECT] Processed 15001468 reads in 767 ms
[2015-09-30T22:14Z] INFO  23:14:21,679 MuTect - [MUTECT] Processed 21001415 reads in 725 ms
[2015-09-30T22:14Z] INFO  23:14:22,084 MuTect - [MUTECT] Processed 3000069 reads in 1871 ms
[2015-09-30T22:14Z] INFO  23:14:22,116 MuTect - [MUTECT] Processed 16001486 reads in 936 ms
[2015-09-30T22:14Z] INFO  23:14:22,372 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:22,405 MuTect - [MUTECT] Processed 22001424 reads in 726 ms
[2015-09-30T22:14Z] INFO  23:14:22,417 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:22,821 MuTect - [MUTECT] Processed 17001496 reads in 705 ms
[2015-09-30T22:14Z] INFO  23:14:22,896 MuTect - [MUTECT] Processed 4000093 reads in 812 ms
[2015-09-30T22:14Z] INFO  23:14:23,029 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:23,073 MuTect - [MUTECT] Processed 23001429 reads in 668 ms
[2015-09-30T22:14Z] INFO  23:14:23,503 MuTect - [MUTECT] Processed 18001508 reads in 682 ms
[2015-09-30T22:14Z] INFO  23:14:23,722 MuTect - [MUTECT] Processed 5000093 reads in 826 ms
[2015-09-30T22:14Z] INFO  23:14:23,831 MuTect - [MUTECT] Processed 24001468 reads in 758 ms
[2015-09-30T22:14Z] INFO  23:14:24,219 MuTect - [MUTECT] Processed 19001566 reads in 716 ms
[2015-09-30T22:14Z] INFO  23:14:24,495 MuTect - [MUTECT] Processed 6000150 reads in 773 ms
[2015-09-30T22:14Z] INFO  23:14:24,551 MuTect - [MUTECT] Processed 25001505 reads in 720 ms
[2015-09-30T22:14Z] INFO  23:14:24,992 MuTect - [MUTECT] Processed 20001627 reads in 773 ms
[2015-09-30T22:14Z] INFO  23:14:25,065 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:25,192 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:25,211 MuTect - [MUTECT] Processed 26001547 reads in 660 ms
[2015-09-30T22:14Z] INFO  23:14:25,270 MuTect - [MUTECT] Processed 7000214 reads in 775 ms
[2015-09-30T22:14Z] INFO  23:14:25,506 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:25,740 MuTect - [MUTECT] Processed 21001658 reads in 748 ms
[2015-09-30T22:14Z] INFO  23:14:25,972 MuTect - [MUTECT] Processed 27001588 reads in 761 ms
[2015-09-30T22:14Z] INFO  23:14:25,998 MuTect - [MUTECT] Processed 8000237 reads in 728 ms
[2015-09-30T22:14Z] INFO  23:14:26,515 MuTect - [MUTECT] Processed 22001688 reads in 775 ms
[2015-09-30T22:14Z] INFO  23:14:26,627 MuTect - [MUTECT] Processed 28001674 reads in 655 ms
[2015-09-30T22:14Z] INFO  23:14:26,712 MuTect - [MUTECT] Processed 9000274 reads in 714 ms
[2015-09-30T22:14Z] INFO  23:14:27,237 MuTect - [MUTECT] Processed 23001735 reads in 722 ms
[2015-09-30T22:14Z] INFO  23:14:27,299 MuTect - [MUTECT] Processed 29001751 reads in 672 ms
[2015-09-30T22:14Z] INFO  23:14:27,380 MuTect - [MUTECT] Processed 10000331 reads in 667 ms
[2015-09-30T22:14Z] INFO  23:14:27,646 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:27,710 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:27,929 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:27,939 MuTect - [MUTECT] Processed 30001831 reads in 640 ms
[2015-09-30T22:14Z] INFO  23:14:27,948 MuTect - [MUTECT] Processed 24001761 reads in 711 ms
[2015-09-30T22:14Z] INFO  23:14:28,028 MuTect - [MUTECT] Processed 11000383 reads in 649 ms
[2015-09-30T22:14Z] INFO  23:14:28,639 MuTect - [MUTECT] Processed 31001891 reads in 700 ms
[2015-09-30T22:14Z] INFO  23:14:28,681 MuTect - [MUTECT] Processed 25001768 reads in 733 ms
[2015-09-30T22:14Z] INFO  23:14:28,726 MuTect - [MUTECT] Processed 12000394 reads in 698 ms
[2015-09-30T22:14Z] INFO  23:14:29,443 MuTect - [MUTECT] Processed 26001847 reads in 762 ms
[2015-09-30T22:14Z] INFO  23:14:29,475 MuTect - [MUTECT] Processed 32001926 reads in 836 ms
[2015-09-30T22:14Z] INFO  23:14:29,477 MuTect - [MUTECT] Processed 13000444 reads in 751 ms
[2015-09-30T22:14Z] INFO  23:14:30,156 MuTect - [MUTECT] Processed 27001851 reads in 713 ms
[2015-09-30T22:14Z] INFO  23:14:30,172 MuTect - [MUTECT] Processed 33001954 reads in 697 ms
[2015-09-30T22:14Z] INFO  23:14:30,214 MuTect - [MUTECT] Processed 14000444 reads in 737 ms
[2015-09-30T22:14Z] INFO  23:14:30,263 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:30,281 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:30,349 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:30,807 MuTect - [MUTECT] Processed 34001975 reads in 635 ms
[2015-09-30T22:14Z] INFO  23:14:30,878 MuTect - [MUTECT] Processed 28001876 reads in 722 ms
[2015-09-30T22:14Z] INFO  23:14:30,927 MuTect - [MUTECT] Processed 15000498 reads in 713 ms
[2015-09-30T22:14Z] INFO  23:14:31,469 MuTect - [MUTECT] Processed 35001992 reads in 662 ms
[2015-09-30T22:14Z] INFO  23:14:31,610 MuTect - [MUTECT] Processed 29001897 reads in 732 ms
[2015-09-30T22:14Z] INFO  23:14:31,631 MuTect - [MUTECT] Processed 16000577 reads in 704 ms
[2015-09-30T22:14Z] INFO  23:14:32,142 MuTect - [MUTECT] Processed 36002007 reads in 673 ms
[2015-09-30T22:14Z] INFO  23:14:32,312 MuTect - [MUTECT] Processed 30001923 reads in 701 ms
[2015-09-30T22:14Z] INFO  23:14:32,362 MuTect - [MUTECT] Processed 17000585 reads in 731 ms
[2015-09-30T22:14Z] INFO  23:14:32,820 MuTect - [MUTECT] Processed 37002108 reads in 678 ms
[2015-09-30T22:14Z] INFO  23:14:32,867 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:33,003 MuTect - [MUTECT] Processed 31001979 reads in 692 ms
[2015-09-30T22:14Z] INFO  23:14:33,084 MuTect - [MUTECT] Processed 18000728 reads in 722 ms
[2015-09-30T22:14Z] INFO  23:14:33,126 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:33,498 MuTect - [MUTECT] Processed 38002110 reads in 678 ms
[2015-09-30T22:14Z] INFO  23:14:33,656 MuTect - [MUTECT] Processed 19001019 reads in 572 ms
[2015-09-30T22:14Z] INFO  23:14:33,712 MuTect - [MUTECT] Processed 32001989 reads in 709 ms
[2015-09-30T22:14Z] INFO  23:14:33,947 ProgressMeter -      5:10435199        1.10e+06   30.0 s       27.0 s     58.3%        51.0 s    21.0 s
[2015-09-30T22:14Z] INFO  23:14:34,145 MuTect - [MUTECT] Processed 39002167 reads in 646 ms
[2015-09-30T22:14Z] INFO  23:14:34,258 MuTect - [MUTECT] Processed 20001059 reads in 602 ms
[2015-09-30T22:14Z] INFO  23:14:34,407 MuTect - [MUTECT] Processed 33002060 reads in 695 ms
[2015-09-30T22:14Z] INFO  23:14:34,804 MuTect - [MUTECT] Processed 40002267 reads in 660 ms
[2015-09-30T22:14Z] INFO  23:14:34,871 MuTect - [MUTECT] Processed 21001126 reads in 613 ms
[2015-09-30T22:14Z] INFO  23:14:35,080 MuTect - [MUTECT] Processed 34002118 reads in 673 ms
[2015-09-30T22:14Z] INFO  23:14:35,262 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:35,467 MuTect - [MUTECT] Processed 41002293 reads in 663 ms
[2015-09-30T22:14Z] INFO  23:14:35,491 MuTect - [MUTECT] Processed 22001133 reads in 620 ms
[2015-09-30T22:14Z] INFO  23:14:35,699 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:35,772 MuTect - [MUTECT] Processed 35002161 reads in 692 ms
[2015-09-30T22:14Z] INFO  23:14:36,199 MuTect - [MUTECT] Processed 23001135 reads in 707 ms
[2015-09-30T22:14Z] INFO  23:14:36,203 MuTect - [MUTECT] Processed 42002310 reads in 736 ms
[2015-09-30T22:14Z] INFO  23:14:36,529 MuTect - [MUTECT] Processed 36002234 reads in 757 ms
[2015-09-30T22:14Z] INFO  23:14:36,725 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:36,894 MuTect - [MUTECT] Processed 24001195 reads in 696 ms
[2015-09-30T22:14Z] INFO  23:14:37,089 MuTect - [MUTECT] Processed 43002401 reads in 886 ms
[2015-09-30T22:14Z] INFO  23:14:37,235 MuTect - [MUTECT] Processed 37002277 reads in 706 ms
[2015-09-30T22:14Z] INFO  23:14:37,488 MuTect - [MUTECT] Processed 25001547 reads in 594 ms
[2015-09-30T22:14Z] INFO  23:14:37,821 MuTect - [MUTECT] Processed 44002422 reads in 732 ms
[2015-09-30T22:14Z] INFO  23:14:37,883 ProgressMeter -      5:39110712        1.40e+06   30.0 s       21.0 s     44.1%        68.0 s    38.0 s
[2015-09-30T22:14Z] INFO  23:14:37,923 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:38,043 MuTect - [MUTECT] Processed 38002351 reads in 808 ms
[2015-09-30T22:14Z] INFO  23:14:38,201 MuTect - [MUTECT] Processed 26001562 reads in 713 ms
[2015-09-30T22:14Z] INFO  23:14:38,457 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:38,653 MuTect - [MUTECT] Processed 45002504 reads in 832 ms
[2015-09-30T22:14Z] INFO  23:14:38,746 MuTect - [MUTECT] Processed 39002382 reads in 703 ms
[2015-09-30T22:14Z] INFO  23:14:38,867 MuTect - [MUTECT] Processed 27001608 reads in 666 ms
[2015-09-30T22:14Z] INFO  23:14:39,339 MuTect - [MUTECT] Processed 46002627 reads in 686 ms
[2015-09-30T22:14Z] INFO  23:14:39,458 MuTect - [MUTECT] Processed 40002461 reads in 712 ms
[2015-09-30T22:14Z] INFO  23:14:39,528 MuTect - [MUTECT] Processed 28001620 reads in 661 ms
[2015-09-30T22:14Z] INFO  23:14:40,127 MuTect - [MUTECT] Processed 29001695 reads in 599 ms
[2015-09-30T22:14Z] INFO  23:14:40,154 MuTect - [MUTECT] Processed 41002531 reads in 696 ms
[2015-09-30T22:14Z] INFO  23:14:40,155 MuTect - [MUTECT] Processed 47002646 reads in 816 ms
[2015-09-30T22:14Z] INFO  23:14:40,618 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:40,771 MuTect - [MUTECT] Processed 30001721 reads in 644 ms
[2015-09-30T22:14Z] INFO  23:14:40,844 MuTect - [MUTECT] Processed 42002564 reads in 690 ms
[2015-09-30T22:14Z] INFO  23:14:40,929 MuTect - [MUTECT] Processed 48002753 reads in 774 ms
[2015-09-30T22:14Z] INFO  23:14:41,048 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:41,464 MuTect - [MUTECT] Processed 31001756 reads in 693 ms
[2015-09-30T22:14Z] INFO  23:14:41,576 MuTect - [MUTECT] Processed 43002615 reads in 732 ms
[2015-09-30T22:14Z] INFO  23:14:41,579 MuTect - [MUTECT] Processed 49002825 reads in 650 ms
[2015-09-30T22:14Z] INFO  23:14:42,150 MuTect - [MUTECT] Processed 32001878 reads in 686 ms
[2015-09-30T22:14Z] INFO  23:14:42,199 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:42,287 MuTect - [MUTECT] Processed 50002880 reads in 708 ms
[2015-09-30T22:14Z] INFO  23:14:42,319 MuTect - [MUTECT] Processed 44002675 reads in 743 ms
[2015-09-30T22:14Z] INFO  23:14:42,788 MuTect - [MUTECT] Processed 33002005 reads in 638 ms
[2015-09-30T22:14Z] INFO  23:14:42,973 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:42,980 MuTect - [MUTECT] Processed 51002963 reads in 693 ms
[2015-09-30T22:14Z] INFO  23:14:43,039 MuTect - [MUTECT] Processed 45002697 reads in 720 ms
[2015-09-30T22:14Z] INFO  23:14:43,399 MuTect - [MUTECT] Processed 34002054 reads in 611 ms
[2015-09-30T22:14Z] INFO  23:14:43,461 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:43,703 MuTect - [MUTECT] Processed 52002978 reads in 722 ms
[2015-09-30T22:14Z] INFO  23:14:43,745 MuTect - [MUTECT] Processed 46002700 reads in 706 ms
[2015-09-30T22:14Z] INFO  23:14:44,047 MuTect - [MUTECT] Processed 35002075 reads in 648 ms
[2015-09-30T22:14Z] INFO  23:14:44,415 MuTect - [MUTECT] Processed 53003012 reads in 713 ms
[2015-09-30T22:14Z] INFO  23:14:44,473 MuTect - [MUTECT] Processed 47002719 reads in 728 ms
[2015-09-30T22:14Z] INFO  23:14:44,672 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:44,685 MuTect - [MUTECT] Processed 36002119 reads in 638 ms
[2015-09-30T22:14Z] INFO  23:14:45,120 MuTect - [MUTECT] Processed 54003096 reads in 705 ms
[2015-09-30T22:14Z] INFO  23:14:45,199 MuTect - [MUTECT] Processed 48002725 reads in 726 ms
[2015-09-30T22:14Z] INFO  23:14:45,331 MuTect - [MUTECT] Processed 37002144 reads in 646 ms
[2015-09-30T22:14Z] INFO  23:14:45,576 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:45,886 MuTect - [MUTECT] Processed 55003127 reads in 766 ms
[2015-09-30T22:14Z] INFO  23:14:45,893 MuTect - [MUTECT] Processed 49002729 reads in 694 ms
[2015-09-30T22:14Z] INFO  23:14:46,025 MuTect - [MUTECT] Processed 38002226 reads in 694 ms
[2015-09-30T22:14Z] INFO  23:14:46,096 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:46,531 MuTect - [MUTECT] Processed 50002784 reads in 638 ms
[2015-09-30T22:14Z] INFO  23:14:46,550 MuTect - [MUTECT] Processed 56003289 reads in 664 ms
[2015-09-30T22:14Z] INFO  23:14:46,694 MuTect - [MUTECT] Processed 39002254 reads in 669 ms
[2015-09-30T22:14Z] INFO  23:14:46,773 ProgressMeter -      5:73045564        1.43e+06   30.0 s       21.0 s     43.4%        69.0 s    39.0 s
[2015-09-30T22:14Z] INFO  23:14:47,079 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:47,155 MuTect - [MUTECT] Processed 57003730 reads in 605 ms
[2015-09-30T22:14Z] INFO  23:14:47,201 MuTect - [MUTECT] Processed 51002794 reads in 670 ms
[2015-09-30T22:14Z] INFO  23:14:47,379 MuTect - [MUTECT] Processed 40002322 reads in 685 ms
[2015-09-30T22:14Z] INFO  23:14:47,799 MuTect - [MUTECT] Processed 58004428 reads in 644 ms
[2015-09-30T22:14Z] INFO  23:14:47,901 MuTect - [MUTECT] Processed 52002820 reads in 700 ms
[2015-09-30T22:14Z] INFO  23:14:48,038 MuTect - [MUTECT] Processed 41002369 reads in 659 ms
[2015-09-30T22:14Z] INFO  23:14:48,413 MuTect - [MUTECT] Processed 59004453 reads in 614 ms
[2015-09-30T22:14Z] INFO  23:14:48,557 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:48,565 MuTect - [MUTECT] Processed 53002837 reads in 664 ms
[2015-09-30T22:14Z] INFO  23:14:48,704 MuTect - [MUTECT] Processed 42002378 reads in 666 ms
[2015-09-30T22:14Z] INFO  23:14:49,024 MuTect - [MUTECT] Processed 60004518 reads in 611 ms
[2015-09-30T22:14Z] INFO  23:14:49,248 MuTect - [MUTECT] Processed 54002902 reads in 682 ms
[2015-09-30T22:14Z] INFO  23:14:49,370 MuTect - [MUTECT] Processed 43002390 reads in 666 ms
[2015-09-30T22:14Z] INFO  23:14:49,553 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:49,658 MuTect - [MUTECT] Processed 61005246 reads in 634 ms
[2015-09-30T22:14Z] INFO  23:14:49,904 MuTect - [MUTECT] Processed 55002910 reads in 657 ms
[2015-09-30T22:14Z] INFO  23:14:50,051 MuTect - [MUTECT] Processed 44002414 reads in 681 ms
[2015-09-30T22:14Z] INFO  23:14:50,338 MuTect - [MUTECT] Processed 62005318 reads in 680 ms
[2015-09-30T22:14Z] INFO  23:14:50,605 MuTect - [MUTECT] Processed 56002947 reads in 701 ms
[2015-09-30T22:14Z] INFO  23:14:50,748 MuTect - [MUTECT] Processed 45002456 reads in 697 ms
[2015-09-30T22:14Z] INFO  23:14:51,057 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:51,123 MuTect - [MUTECT] Processed 63005372 reads in 785 ms
[2015-09-30T22:14Z] INFO  23:14:51,370 MuTect - [MUTECT] Processed 57002974 reads in 765 ms
[2015-09-30T22:14Z] INFO  23:14:51,445 MuTect - [MUTECT] Processed 46002456 reads in 697 ms
[2015-09-30T22:14Z] INFO  23:14:51,885 MuTect - [MUTECT] Processed 64005784 reads in 762 ms
[2015-09-30T22:14Z] INFO  23:14:51,964 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:52,078 MuTect - [MUTECT] Processed 58002998 reads in 708 ms
[2015-09-30T22:14Z] INFO  23:14:52,115 MuTect - [MUTECT] Processed 47002477 reads in 670 ms
[2015-09-30T22:14Z] INFO  23:14:52,184 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:52,639 MuTect - [MUTECT] Processed 65005794 reads in 753 ms
[2015-09-30T22:14Z] INFO  23:14:52,774 MuTect - [MUTECT] Processed 59003008 reads in 696 ms
[2015-09-30T22:14Z] INFO  23:14:52,774 MuTect - [MUTECT] Processed 48002485 reads in 659 ms
[2015-09-30T22:14Z] INFO  23:14:53,370 MuTect - [MUTECT] Processed 66005854 reads in 732 ms
[2015-09-30T22:14Z] INFO  23:14:53,420 MuTect - [MUTECT] Processed 49002567 reads in 646 ms
[2015-09-30T22:14Z] INFO  23:14:53,485 MuTect - [MUTECT] Processed 60003039 reads in 711 ms
[2015-09-30T22:14Z] INFO  23:14:53,673 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:53,903 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:14Z] INFO  23:14:53,907 ProgressMeter -            done        1.77e+06   49.0 s       28.0 s    100.0%        49.0 s     0.0 s
[2015-09-30T22:14Z] INFO  23:14:53,907 ProgressMeter - Total runtime 49.96 secs, 0.83 min, 0.01 hours
[2015-09-30T22:14Z] INFO  23:14:53,973 MicroScheduler - 53379 reads were filtered out during the traversal out of approximately 803772 total reads (6.64%)
[2015-09-30T22:14Z] INFO  23:14:53,973 MicroScheduler -   -> 40302 reads (5.01% of total) failing DuplicateReadFilter
[2015-09-30T22:14Z] INFO  23:14:53,973 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:14Z] INFO  23:14:53,973 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:14Z] INFO  23:14:53,973 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:14Z] INFO  23:14:53,973 MicroScheduler -   -> 13077 reads (1.63% of total) failing UnmappedReadFilter
[2015-09-30T22:14Z] INFO  23:14:54,075 MuTect - [MUTECT] Processed 50002618 reads in 655 ms
[2015-09-30T22:14Z] INFO  23:14:54,177 MuTect - [MUTECT] Processed 61003093 reads in 692 ms
[2015-09-30T22:14Z] INFO  23:14:54,454 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:54,800 MuTect - [MUTECT] Processed 51002627 reads in 725 ms
[2015-09-30T22:14Z] INFO  23:14:54,840 MuTect - [MUTECT] Processed 62003200 reads in 663 ms
[2015-09-30T22:14Z] INFO  23:14:54,988 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:14Z] bgzip syn3-5_0_31268043-raw-mutect.vcf
[2015-09-30T22:14Z] tabix index syn3-5_0_31268043-raw-mutect.vcf.gz
[2015-09-30T22:14Z] INFO  23:14:55,451 MuTect - [MUTECT] Processed 52002644 reads in 651 ms
[2015-09-30T22:14Z] INFO  23:14:55,551 MuTect - [MUTECT] Processed 63003201 reads in 711 ms
[2015-09-30T22:14Z] INFO  23:14:56,103 MuTect - [MUTECT] Processed 53002671 reads in 652 ms
[2015-09-30T22:14Z] INFO  23:14:56,294 MuTect - [MUTECT] Processed 64003228 reads in 743 ms
[2015-09-30T22:14Z] INFO  23:14:56,383 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:56,757 MuTect - [MUTECT] Processed 54002688 reads in 654 ms
[2015-09-30T22:14Z] INFO  23:14:56,790 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:57,085 MuTect - [MUTECT] Processed 65003237 reads in 791 ms
[2015-09-30T22:14Z] MuTect: MuTect
[2015-09-30T22:14Z] INFO  23:14:57,475 MuTect - [MUTECT] Processed 55002753 reads in 718 ms
[2015-09-30T22:14Z] INFO  23:14:58,057 MuTect - [MUTECT] Processed 66003292 reads in 972 ms
[2015-09-30T22:14Z] INFO  23:14:58,158 MuTect - [MUTECT] Processed 56002767 reads in 683 ms
[2015-09-30T22:14Z] INFO  23:14:58,712 MuTect - [MUTECT] Processed 67003301 reads in 655 ms
[2015-09-30T22:14Z] INFO  23:14:58,854 MuTect - [MUTECT] Processed 57002793 reads in 696 ms
[2015-09-30T22:14Z] INFO  23:14:59,154 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:59,356 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:14Z] INFO  23:14:59,390 MuTect - [MUTECT] Processed 68003327 reads in 678 ms
[2015-09-30T22:14Z] INFO  23:14:59,557 MuTect - [MUTECT] Processed 58002812 reads in 703 ms
[2015-09-30T22:14Z] INFO  23:14:59,760 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/5/syn3-5_94277739_125696417-raw-mutect-regions.bed to be BED
[2015-09-30T22:14Z] INFO  23:14:59,817 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:59,817 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:14Z] INFO  23:14:59,817 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:14Z] INFO  23:14:59,817 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:14Z] INFO  23:14:59,821 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/5/syn3-5_94277739_125696417-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/5/tx/tmp9ICXHj/syn3-5_94277739_125696417-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:14Z] INFO  23:14:59,821 HelpFormatter - Date/Time: 2015/09/30 23:14:59
[2015-09-30T22:14Z] INFO  23:14:59,821 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:59,821 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:14Z] INFO  23:14:59,849 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:14Z] INFO  23:14:59,853 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:14Z] INFO  23:14:59,903 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:14Z] INFO  23:14:59,952 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:14Z] INFO  23:14:59,959 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:14Z] INFO  23:14:59,982 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:14Z] INFO  23:14:59,993 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:15Z] INFO  23:15:00,072 MuTect - [MUTECT] Processed 69003428 reads in 682 ms
[2015-09-30T22:15Z] INFO  23:15:00,168 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:15Z] INFO  23:15:00,226 MuTect - [MUTECT] Processed 59002832 reads in 669 ms
[2015-09-30T22:15Z] INFO  23:15:00,248 IntervalUtils - Processing 727022 bp from intervals
[2015-09-30T22:15Z] INFO  23:15:00,252 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:15Z] INFO  23:15:00,252 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:15Z] INFO  23:15:00,307 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:15Z] INFO  23:15:00,559 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:15Z] INFO  23:15:00,560 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:15Z] INFO  23:15:00,560 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:15Z] INFO  23:15:00,561 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:15Z] INFO  23:15:00,736 MuTect - [MUTECT] Processed 70003432 reads in 664 ms
[2015-09-30T22:15Z] INFO  23:15:00,900 MuTect - [MUTECT] Processed 60002888 reads in 674 ms
[2015-09-30T22:15Z] INFO  23:15:01,501 MuTect - [MUTECT] Processed 71003486 reads in 765 ms
[2015-09-30T22:15Z] INFO  23:15:01,578 MuTect - [MUTECT] Processed 61002907 reads in 678 ms
[2015-09-30T22:15Z] INFO  23:15:01,683 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:02,013 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:02,182 MuTect - [MUTECT] Processed 72003539 reads in 681 ms
[2015-09-30T22:15Z] INFO  23:15:02,266 MuTect - [MUTECT] Processed 62002957 reads in 688 ms
[2015-09-30T22:15Z] INFO  23:15:02,899 MuTect - [MUTECT] Processed 73003580 reads in 717 ms
[2015-09-30T22:15Z] INFO  23:15:02,949 MuTect - [MUTECT] Processed 63003015 reads in 683 ms
[2015-09-30T22:15Z] INFO  23:15:03,301 MuTect - [MUTECT] Processed 1000017 reads in 2690 ms
[2015-09-30T22:15Z] INFO  23:15:03,598 MuTect - [MUTECT] Processed 74003612 reads in 699 ms
[2015-09-30T22:15Z] INFO  23:15:03,651 MuTect - [MUTECT] Processed 64003046 reads in 702 ms
[2015-09-30T22:15Z] INFO  23:15:04,079 MuTect - [MUTECT] Processed 2000050 reads in 778 ms
[2015-09-30T22:15Z] INFO  23:15:04,203 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:04,284 MuTect - [MUTECT] Processed 75003666 reads in 686 ms
[2015-09-30T22:15Z] INFO  23:15:04,307 MuTect - [MUTECT] Processed 65003136 reads in 656 ms
[2015-09-30T22:15Z] INFO  23:15:04,343 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:04,837 MuTect - [MUTECT] Processed 3000088 reads in 757 ms
[2015-09-30T22:15Z] INFO  23:15:04,965 MuTect - [MUTECT] Processed 66003136 reads in 658 ms
[2015-09-30T22:15Z] INFO  23:15:05,000 MuTect - [MUTECT] Processed 76003667 reads in 716 ms
[2015-09-30T22:15Z] INFO  23:15:05,435 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:05,575 MuTect - [MUTECT] Processed 4000153 reads in 739 ms
[2015-09-30T22:15Z] INFO  23:15:05,643 MuTect - [MUTECT] Processed 67003184 reads in 678 ms
[2015-09-30T22:15Z] INFO  23:15:05,736 MuTect - [MUTECT] Processed 77003701 reads in 736 ms
[2015-09-30T22:15Z] INFO  23:15:06,334 MuTect - [MUTECT] Processed 68003192 reads in 691 ms
[2015-09-30T22:15Z] INFO  23:15:06,340 MuTect - [MUTECT] Processed 5000181 reads in 765 ms
[2015-09-30T22:15Z] INFO  23:15:06,428 MuTect - [MUTECT] Processed 78003760 reads in 691 ms
[2015-09-30T22:15Z] INFO  23:15:06,822 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:07,029 MuTect - [MUTECT] Processed 69003207 reads in 695 ms
[2015-09-30T22:15Z] INFO  23:15:07,052 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:07,098 MuTect - [MUTECT] Processed 6000254 reads in 758 ms
[2015-09-30T22:15Z] INFO  23:15:07,099 MuTect - [MUTECT] Processed 79003800 reads in 672 ms
[2015-09-30T22:15Z] INFO  23:15:07,705 MuTect - [MUTECT] Processed 70003316 reads in 676 ms
[2015-09-30T22:15Z] INFO  23:15:07,821 MuTect - [MUTECT] Processed 80003836 reads in 722 ms
[2015-09-30T22:15Z] INFO  23:15:07,847 MuTect - [MUTECT] Processed 7000320 reads in 749 ms
[2015-09-30T22:15Z] INFO  23:15:07,884 ProgressMeter -      5:62061637        3.01e+06   60.0 s       19.0 s     99.7%        60.0 s     0.0 s
[2015-09-30T22:15Z] INFO  23:15:08,001 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:15Z] INFO  23:15:08,123 ProgressMeter -            done        3.02e+06   60.0 s       19.0 s    100.0%        60.0 s     0.0 s
[2015-09-30T22:15Z] INFO  23:15:08,123 ProgressMeter - Total runtime 60.24 secs, 1.00 min, 0.02 hours
[2015-09-30T22:15Z] INFO  23:15:08,145 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:08,189 MicroScheduler - 55399 reads were filtered out during the traversal out of approximately 956550 total reads (5.79%)
[2015-09-30T22:15Z] INFO  23:15:08,190 MicroScheduler -   -> 40123 reads (4.19% of total) failing DuplicateReadFilter
[2015-09-30T22:15Z] INFO  23:15:08,190 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:15Z] INFO  23:15:08,190 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:15Z] INFO  23:15:08,190 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:15Z] INFO  23:15:08,190 MicroScheduler -   -> 15276 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:15Z] INFO  23:15:08,392 MuTect - [MUTECT] Processed 71003377 reads in 687 ms
[2015-09-30T22:15Z] INFO  23:15:08,576 MuTect - [MUTECT] Processed 8000404 reads in 729 ms
[2015-09-30T22:15Z] INFO  23:15:09,259 MuTect - [MUTECT] Processed 72003452 reads in 867 ms
[2015-09-30T22:15Z] INFO  23:15:09,301 MuTect - [MUTECT] Processed 9000466 reads in 725 ms
[2015-09-30T22:15Z] INFO  23:15:09,455 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:15Z] bgzip syn3-5_31293868_62597714-raw-mutect.vcf
[2015-09-30T22:15Z] tabix index syn3-5_31293868_62597714-raw-mutect.vcf.gz
[2015-09-30T22:15Z] INFO  23:15:09,792 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:09,978 MuTect - [MUTECT] Processed 73003537 reads in 719 ms
[2015-09-30T22:15Z] INFO  23:15:10,031 MuTect - [MUTECT] Processed 10000538 reads in 730 ms
[2015-09-30T22:15Z] INFO  23:15:10,681 MuTect - [MUTECT] Processed 74003549 reads in 703 ms
[2015-09-30T22:15Z] INFO  23:15:10,722 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:10,746 MuTect - [MUTECT] Processed 11000594 reads in 714 ms
[2015-09-30T22:15Z] INFO  23:15:11,332 MuTect - [MUTECT] Processed 75003572 reads in 651 ms
[2015-09-30T22:15Z] INFO  23:15:11,563 MuTect - [MUTECT] Processed 12000602 reads in 818 ms
[2015-09-30T22:15Z] MuTect: MuTect
[2015-09-30T22:15Z] INFO  23:15:12,040 MuTect - [MUTECT] Processed 76003626 reads in 708 ms
[2015-09-30T22:15Z] INFO  23:15:12,349 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:12,352 MuTect - [MUTECT] Processed 13000708 reads in 789 ms
[2015-09-30T22:15Z] INFO  23:15:12,766 MuTect - [MUTECT] Processed 77003665 reads in 726 ms
[2015-09-30T22:15Z] INFO  23:15:13,123 MuTect - [MUTECT] Processed 14000769 reads in 771 ms
[2015-09-30T22:15Z] INFO  23:15:13,461 MuTect - [MUTECT] Processed 78003685 reads in 695 ms
[2015-09-30T22:15Z] INFO  23:15:13,507 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:13,764 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/5/syn3-5_125759062_156781785-raw-mutect-regions.bed to be BED
[2015-09-30T22:15Z] INFO  23:15:13,818 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:15Z] INFO  23:15:13,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:15Z] INFO  23:15:13,818 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:15Z] INFO  23:15:13,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:15Z] INFO  23:15:13,822 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/5/syn3-5_125759062_156781785-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/5/tx/tmpRedfHe/syn3-5_125759062_156781785-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:15Z] INFO  23:15:13,822 HelpFormatter - Date/Time: 2015/09/30 23:15:13
[2015-09-30T22:15Z] INFO  23:15:13,822 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:15Z] INFO  23:15:13,822 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:15Z] INFO  23:15:13,850 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:15Z] INFO  23:15:13,854 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:15Z] INFO  23:15:13,895 MuTect - [MUTECT] Processed 15000818 reads in 772 ms
[2015-09-30T22:15Z] INFO  23:15:13,906 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:15Z] INFO  23:15:13,953 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:15Z] INFO  23:15:13,960 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:15Z] INFO  23:15:14,140 MuTect - [MUTECT] Processed 79003694 reads in 679 ms
[2015-09-30T22:15Z] INFO  23:15:14,237 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.28
[2015-09-30T22:15Z] INFO  23:15:14,394 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:15Z] INFO  23:15:14,572 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:15Z] INFO  23:15:14,584 MuTect - [MUTECT] Processed 16000852 reads in 689 ms
[2015-09-30T22:15Z] INFO  23:15:14,691 IntervalUtils - Processing 2012098 bp from intervals
[2015-09-30T22:15Z] INFO  23:15:14,696 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:15Z] INFO  23:15:14,696 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:15Z] INFO  23:15:14,798 MuTect - [MUTECT] Processed 80003710 reads in 658 ms
[2015-09-30T22:15Z] INFO  23:15:14,841 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:14,929 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:15Z] INFO  23:15:15,107 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:15Z] INFO  23:15:15,107 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:15Z] INFO  23:15:15,107 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:15Z] INFO  23:15:15,108 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:15Z] INFO  23:15:15,345 MuTect - [MUTECT] Processed 17000883 reads in 761 ms
[2015-09-30T22:15Z] INFO  23:15:15,447 MuTect - [MUTECT] Processed 81003765 reads in 649 ms
[2015-09-30T22:15Z] INFO  23:15:16,080 MuTect - [MUTECT] Processed 18000945 reads in 735 ms
[2015-09-30T22:15Z] INFO  23:15:16,143 MuTect - [MUTECT] Processed 82003819 reads in 696 ms
[2015-09-30T22:15Z] INFO  23:15:16,319 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:16,774 ProgressMeter -      5:90073829        2.91e+06   60.0 s       20.0 s     93.1%        64.0 s     4.0 s
[2015-09-30T22:15Z] INFO  23:15:16,828 MuTect - [MUTECT] Processed 19000946 reads in 748 ms
[2015-09-30T22:15Z] INFO  23:15:16,840 MuTect - [MUTECT] Processed 83003898 reads in 697 ms
[2015-09-30T22:15Z] INFO  23:15:17,468 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:17,495 MuTect - [MUTECT] Processed 84003981 reads in 655 ms
[2015-09-30T22:15Z] INFO  23:15:17,563 MuTect - [MUTECT] Processed 20000976 reads in 735 ms
[2015-09-30T22:15Z] INFO  23:15:17,703 MuTect - [MUTECT] Processed 1000022 reads in 2548 ms
[2015-09-30T22:15Z] INFO  23:15:18,156 MuTect - [MUTECT] Processed 85004011 reads in 660 ms
[2015-09-30T22:15Z] INFO  23:15:18,307 MuTect - [MUTECT] Processed 21000985 reads in 744 ms
[2015-09-30T22:15Z] INFO  23:15:18,813 MuTect - [MUTECT] Processed 86004048 reads in 658 ms
[2015-09-30T22:15Z] INFO  23:15:18,863 MuTect - [MUTECT] Processed 2000063 reads in 1160 ms
[2015-09-30T22:15Z] INFO  23:15:19,050 MuTect - [MUTECT] Processed 22001048 reads in 743 ms
[2015-09-30T22:15Z] INFO  23:15:19,169 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:19,456 MuTect - [MUTECT] Processed 87004089 reads in 643 ms
[2015-09-30T22:15Z] INFO  23:15:19,617 MuTect - [MUTECT] Processed 3000074 reads in 754 ms
[2015-09-30T22:15Z] INFO  23:15:19,846 MuTect - [MUTECT] Processed 23001049 reads in 796 ms
[2015-09-30T22:15Z] INFO  23:15:19,932 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:20,062 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:20,094 MuTect - [MUTECT] Processed 88004104 reads in 638 ms
[2015-09-30T22:15Z] INFO  23:15:20,179 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:15Z] INFO  23:15:20,183 ProgressMeter -            done        3.10e+06   63.0 s       20.0 s    100.0%        63.0 s     0.0 s
[2015-09-30T22:15Z] INFO  23:15:20,184 ProgressMeter - Total runtime 63.41 secs, 1.06 min, 0.02 hours
[2015-09-30T22:15Z] INFO  23:15:20,244 MicroScheduler - 55930 reads were filtered out during the traversal out of approximately 1041044 total reads (5.37%)
[2015-09-30T22:15Z] INFO  23:15:20,245 MicroScheduler -   -> 39612 reads (3.81% of total) failing DuplicateReadFilter
[2015-09-30T22:15Z] INFO  23:15:20,245 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:15Z] INFO  23:15:20,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:15Z] INFO  23:15:20,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:15Z] INFO  23:15:20,245 MicroScheduler -   -> 16318 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:15Z] INFO  23:15:20,347 MuTect - [MUTECT] Processed 4000115 reads in 730 ms
[2015-09-30T22:15Z] INFO  23:15:20,592 MuTect - [MUTECT] Processed 24001049 reads in 746 ms
[2015-09-30T22:15Z] INFO  23:15:21,071 MuTect - [MUTECT] Processed 5000148 reads in 724 ms
[2015-09-30T22:15Z] INFO  23:15:21,273 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:15Z] INFO  23:15:21,323 MuTect - [MUTECT] Processed 25001075 reads in 731 ms
[2015-09-30T22:15Z] bgzip syn3-5_63256014_94276127-raw-mutect.vcf
[2015-09-30T22:15Z] tabix index syn3-5_63256014_94276127-raw-mutect.vcf.gz
[2015-09-30T22:15Z] INFO  23:15:21,806 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:21,815 MuTect - [MUTECT] Processed 6000193 reads in 744 ms
[2015-09-30T22:15Z] INFO  23:15:22,040 MuTect - [MUTECT] Processed 26001097 reads in 717 ms
[2015-09-30T22:15Z] INFO  23:15:22,552 MuTect - [MUTECT] Processed 7000197 reads in 737 ms
[2015-09-30T22:15Z] INFO  23:15:22,790 MuTect - [MUTECT] Processed 27001101 reads in 750 ms
[2015-09-30T22:15Z] INFO  23:15:22,828 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:23,336 MuTect - [MUTECT] Processed 8000226 reads in 784 ms
[2015-09-30T22:15Z] MuTect: MuTect
[2015-09-30T22:15Z] INFO  23:15:23,528 MuTect - [MUTECT] Processed 28001169 reads in 738 ms
[2015-09-30T22:15Z] INFO  23:15:24,080 MuTect - [MUTECT] Processed 9000278 reads in 744 ms
[2015-09-30T22:15Z] INFO  23:15:24,234 MuTect - [MUTECT] Processed 29001201 reads in 706 ms
[2015-09-30T22:15Z] INFO  23:15:24,319 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:24,924 MuTect - [MUTECT] Processed 10000344 reads in 843 ms
[2015-09-30T22:15Z] INFO  23:15:24,974 MuTect - [MUTECT] Processed 30001286 reads in 740 ms
[2015-09-30T22:15Z] INFO  23:15:25,536 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/5/syn3-5_156785743_180915260-raw-mutect-regions.bed to be BED
[2015-09-30T22:15Z] INFO  23:15:25,590 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:15Z] INFO  23:15:25,590 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:15Z] INFO  23:15:25,590 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:15Z] INFO  23:15:25,590 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:15Z] INFO  23:15:25,593 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/5/syn3-5_156785743_180915260-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/5/tx/tmpiSix2g/syn3-5_156785743_180915260-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:15Z] INFO  23:15:25,594 HelpFormatter - Date/Time: 2015/09/30 23:15:25
[2015-09-30T22:15Z] INFO  23:15:25,594 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:15Z] INFO  23:15:25,594 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:15Z] INFO  23:15:25,620 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:15Z] INFO  23:15:25,624 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:15Z] INFO  23:15:25,662 MuTect - [MUTECT] Processed 11000369 reads in 739 ms
[2015-09-30T22:15Z] INFO  23:15:25,675 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:15Z] INFO  23:15:25,720 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:15Z] INFO  23:15:25,727 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:15Z] INFO  23:15:25,743 MuTect - [MUTECT] Processed 31001313 reads in 769 ms
[2015-09-30T22:15Z] INFO  23:15:25,770 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:15Z] INFO  23:15:25,774 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:25,783 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:15Z] INFO  23:15:25,952 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:15Z] INFO  23:15:26,043 IntervalUtils - Processing 1149697 bp from intervals
[2015-09-30T22:15Z] INFO  23:15:26,047 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:15Z] INFO  23:15:26,047 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:15Z] INFO  23:15:26,258 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:15Z] INFO  23:15:26,422 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:15Z] INFO  23:15:26,422 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:15Z] INFO  23:15:26,422 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:15Z] INFO  23:15:26,423 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:15Z] INFO  23:15:26,430 MuTect - [MUTECT] Processed 12000439 reads in 768 ms
[2015-09-30T22:15Z] INFO  23:15:26,465 MuTect - [MUTECT] Processed 32001361 reads in 722 ms
[2015-09-30T22:15Z] INFO  23:15:26,809 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:27,150 MuTect - [MUTECT] Processed 13000515 reads in 720 ms
[2015-09-30T22:15Z] INFO  23:15:27,170 MuTect - [MUTECT] Processed 33001361 reads in 705 ms
[2015-09-30T22:15Z] INFO  23:15:27,870 MuTect - [MUTECT] Processed 34001469 reads in 700 ms
[2015-09-30T22:15Z] INFO  23:15:27,889 MuTect - [MUTECT] Processed 14000540 reads in 738 ms
[2015-09-30T22:15Z] INFO  23:15:28,598 MuTect - [MUTECT] Processed 35001506 reads in 728 ms
[2015-09-30T22:15Z] INFO  23:15:28,622 MuTect - [MUTECT] Processed 15000593 reads in 734 ms
[2015-09-30T22:15Z] INFO  23:15:28,655 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:28,882 MuTect - [MUTECT] Processed 1000047 reads in 2412 ms
[2015-09-30T22:15Z] INFO  23:15:29,349 MuTect - [MUTECT] Processed 16000613 reads in 727 ms
[2015-09-30T22:15Z] INFO  23:15:29,362 MuTect - [MUTECT] Processed 36001535 reads in 764 ms
[2015-09-30T22:15Z] INFO  23:15:29,387 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:29,545 MuTect - [MUTECT] Processed 2000088 reads in 663 ms
[2015-09-30T22:15Z] INFO  23:15:30,066 MuTect - [MUTECT] Processed 17000620 reads in 717 ms
[2015-09-30T22:15Z] INFO  23:15:30,074 MuTect - [MUTECT] Processed 37001601 reads in 712 ms
[2015-09-30T22:15Z] INFO  23:15:30,251 MuTect - [MUTECT] Processed 3000154 reads in 706 ms
[2015-09-30T22:15Z] INFO  23:15:30,548 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:30,563 ProgressMeter -     5:115840641        1.43e+06   30.0 s       21.0 s     78.6%        38.0 s     8.0 s
[2015-09-30T22:15Z] INFO  23:15:30,786 MuTect - [MUTECT] Processed 18000633 reads in 720 ms
[2015-09-30T22:15Z] INFO  23:15:30,812 MuTect - [MUTECT] Processed 38001629 reads in 738 ms
[2015-09-30T22:15Z] INFO  23:15:30,937 MuTect - [MUTECT] Processed 4000208 reads in 686 ms
[2015-09-30T22:15Z] INFO  23:15:31,124 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:31,483 MuTect - [MUTECT] Processed 19000734 reads in 697 ms
[2015-09-30T22:15Z] INFO  23:15:31,518 MuTect - [MUTECT] Processed 39001683 reads in 706 ms
[2015-09-30T22:15Z] INFO  23:15:31,585 MuTect - [MUTECT] Processed 5000224 reads in 648 ms
[2015-09-30T22:15Z] INFO  23:15:31,916 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:32,205 MuTect - [MUTECT] Processed 20000810 reads in 722 ms
[2015-09-30T22:15Z] INFO  23:15:32,256 MuTect - [MUTECT] Processed 40001696 reads in 738 ms
[2015-09-30T22:15Z] INFO  23:15:32,302 MuTect - [MUTECT] Processed 6000227 reads in 717 ms
[2015-09-30T22:15Z] INFO  23:15:32,935 MuTect - [MUTECT] Processed 21000840 reads in 730 ms
[2015-09-30T22:15Z] INFO  23:15:32,965 MuTect - [MUTECT] Processed 41001777 reads in 709 ms
[2015-09-30T22:15Z] INFO  23:15:33,000 MuTect - [MUTECT] Processed 7000230 reads in 698 ms
[2015-09-30T22:15Z] INFO  23:15:33,002 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:33,642 MuTect - [MUTECT] Processed 22000847 reads in 707 ms
[2015-09-30T22:15Z] INFO  23:15:33,647 MuTect - [MUTECT] Processed 42001801 reads in 682 ms
[2015-09-30T22:15Z] INFO  23:15:33,706 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:33,710 MuTect - [MUTECT] Processed 8000252 reads in 710 ms
[2015-09-30T22:15Z] INFO  23:15:34,291 MuTect - [MUTECT] Processed 43001826 reads in 644 ms
[2015-09-30T22:15Z] INFO  23:15:34,379 MuTect - [MUTECT] Processed 23000902 reads in 737 ms
[2015-09-30T22:15Z] INFO  23:15:34,386 MuTect - [MUTECT] Processed 9000268 reads in 676 ms
[2015-09-30T22:15Z] INFO  23:15:34,433 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:34,960 MuTect - [MUTECT] Processed 44001888 reads in 669 ms
[2015-09-30T22:15Z] INFO  23:15:35,076 MuTect - [MUTECT] Processed 24000960 reads in 697 ms
[2015-09-30T22:15Z] INFO  23:15:35,105 MuTect - [MUTECT] Processed 10000321 reads in 719 ms
[2015-09-30T22:15Z] INFO  23:15:35,607 MuTect - [MUTECT] Processed 45001962 reads in 647 ms
[2015-09-30T22:15Z] INFO  23:15:35,660 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:35,783 MuTect - [MUTECT] Processed 25001046 reads in 707 ms
[2015-09-30T22:15Z] INFO  23:15:35,806 MuTect - [MUTECT] Processed 11000354 reads in 701 ms
[2015-09-30T22:15Z] INFO  23:15:36,291 MuTect - [MUTECT] Processed 46002037 reads in 684 ms
[2015-09-30T22:15Z] INFO  23:15:36,485 MuTect - [MUTECT] Processed 26001054 reads in 702 ms
[2015-09-30T22:15Z] INFO  23:15:36,538 MuTect - [MUTECT] Processed 12000390 reads in 731 ms
[2015-09-30T22:15Z] INFO  23:15:36,559 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:36,811 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:36,995 MuTect - [MUTECT] Processed 47002072 reads in 704 ms
[2015-09-30T22:15Z] INFO  23:15:37,177 MuTect - [MUTECT] Processed 27001146 reads in 692 ms
[2015-09-30T22:15Z] INFO  23:15:37,245 MuTect - [MUTECT] Processed 13000400 reads in 708 ms
[2015-09-30T22:15Z] INFO  23:15:37,492 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:15Z] INFO  23:15:37,612 ProgressMeter -            done        1.76e+06   37.0 s       21.0 s    100.0%        37.0 s     0.0 s
[2015-09-30T22:15Z] INFO  23:15:37,612 ProgressMeter - Total runtime 37.05 secs, 0.62 min, 0.01 hours
[2015-09-30T22:15Z] INFO  23:15:37,678 MicroScheduler - 31933 reads were filtered out during the traversal out of approximately 567532 total reads (5.63%)
[2015-09-30T22:15Z] INFO  23:15:37,679 MicroScheduler -   -> 22729 reads (4.00% of total) failing DuplicateReadFilter
[2015-09-30T22:15Z] INFO  23:15:37,679 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:15Z] INFO  23:15:37,679 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:15Z] INFO  23:15:37,679 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:15Z] INFO  23:15:37,679 MicroScheduler -   -> 9204 reads (1.62% of total) failing UnmappedReadFilter
[2015-09-30T22:15Z] INFO  23:15:37,877 MuTect - [MUTECT] Processed 28001189 reads in 699 ms
[2015-09-30T22:15Z] INFO  23:15:37,944 MuTect - [MUTECT] Processed 14000408 reads in 699 ms
[2015-09-30T22:15Z] INFO  23:15:38,149 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:38,612 MuTect - [MUTECT] Processed 29001230 reads in 736 ms
[2015-09-30T22:15Z] INFO  23:15:38,694 MuTect - [MUTECT] Processed 15000423 reads in 750 ms
[2015-09-30T22:15Z] INFO  23:15:38,932 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:15Z] bgzip syn3-5_94277739_125696417-raw-mutect.vcf
[2015-09-30T22:15Z] tabix index syn3-5_94277739_125696417-raw-mutect.vcf.gz
[2015-09-30T22:15Z] INFO  23:15:39,199 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:39,358 MuTect - [MUTECT] Processed 30001238 reads in 746 ms
[2015-09-30T22:15Z] INFO  23:15:39,446 MuTect - [MUTECT] Processed 16000451 reads in 752 ms
[2015-09-30T22:15Z] INFO  23:15:40,080 MuTect - [MUTECT] Processed 31001304 reads in 722 ms
[2015-09-30T22:15Z] INFO  23:15:40,201 MuTect - [MUTECT] Processed 17000474 reads in 755 ms
[2015-09-30T22:15Z] INFO  23:15:40,788 MuTect - [MUTECT] Processed 32001350 reads in 708 ms
[2015-09-30T22:15Z] INFO  23:15:40,934 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:40,950 MuTect - [MUTECT] Processed 18000513 reads in 749 ms
[2015-09-30T22:15Z] INFO  23:15:41,459 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:41,469 MuTect - [MUTECT] Processed 33001429 reads in 681 ms
[2015-09-30T22:15Z] MuTect: MuTect
[2015-09-30T22:15Z] INFO  23:15:41,657 MuTect - [MUTECT] Processed 19000571 reads in 707 ms
[2015-09-30T22:15Z] INFO  23:15:42,126 MuTect - [MUTECT] Processed 34001443 reads in 657 ms
[2015-09-30T22:15Z] INFO  23:15:42,298 MuTect - [MUTECT] Processed 20000632 reads in 640 ms
[2015-09-30T22:15Z] INFO  23:15:42,812 MuTect - [MUTECT] Processed 35001522 reads in 685 ms
[2015-09-30T22:15Z] INFO  23:15:42,980 MuTect - [MUTECT] Processed 21000685 reads in 683 ms
[2015-09-30T22:15Z] INFO  23:15:43,244 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:43,488 MuTect - [MUTECT] Processed 36001619 reads in 677 ms
[2015-09-30T22:15Z] INFO  23:15:43,658 MuTect - [MUTECT] Processed 22000692 reads in 678 ms
[2015-09-30T22:15Z] INFO  23:15:43,752 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/6/syn3-6_0_31080572-raw-mutect-regions.bed to be BED
[2015-09-30T22:15Z] INFO  23:15:43,805 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:15Z] INFO  23:15:43,806 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:15Z] INFO  23:15:43,806 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:15Z] INFO  23:15:43,806 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:15Z] INFO  23:15:43,809 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/6/syn3-6_0_31080572-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/6/tx/tmpnveDIK/syn3-6_0_31080572-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:15Z] INFO  23:15:43,810 HelpFormatter - Date/Time: 2015/09/30 23:15:43
[2015-09-30T22:15Z] INFO  23:15:43,810 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:15Z] INFO  23:15:43,810 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:15Z] INFO  23:15:43,836 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:15Z] INFO  23:15:43,840 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:15Z] INFO  23:15:43,889 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:15Z] INFO  23:15:43,936 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:15Z] INFO  23:15:43,944 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:15Z] INFO  23:15:44,004 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:44,007 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:15Z] INFO  23:15:44,041 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:15Z] INFO  23:15:44,176 MuTect - [MUTECT] Processed 37001633 reads in 688 ms
[2015-09-30T22:15Z] INFO  23:15:44,214 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:15Z] INFO  23:15:44,310 IntervalUtils - Processing 1374885 bp from intervals
[2015-09-30T22:15Z] INFO  23:15:44,314 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:15Z] INFO  23:15:44,315 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:15Z] INFO  23:15:44,330 MuTect - [MUTECT] Processed 23000697 reads in 672 ms
[2015-09-30T22:15Z] INFO  23:15:44,491 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:15Z] INFO  23:15:44,614 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:15Z] INFO  23:15:44,614 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:15Z] INFO  23:15:44,614 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:15Z] INFO  23:15:44,615 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:15Z] INFO  23:15:44,876 MuTect - [MUTECT] Processed 38001733 reads in 700 ms
[2015-09-30T22:15Z] INFO  23:15:44,989 MuTect - [MUTECT] Processed 24000728 reads in 659 ms
[2015-09-30T22:15Z] INFO  23:15:45,110 ProgressMeter -     5:134106329        1.32e+06   30.0 s       22.0 s     24.1%         2.1 m    94.0 s
[2015-09-30T22:15Z] INFO  23:15:45,528 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:45,589 MuTect - [MUTECT] Processed 39001749 reads in 713 ms
[2015-09-30T22:15Z] INFO  23:15:45,699 MuTect - [MUTECT] Processed 25000754 reads in 710 ms
[2015-09-30T22:15Z] INFO  23:15:46,288 MuTect - [MUTECT] Processed 40001757 reads in 699 ms
[2015-09-30T22:15Z] INFO  23:15:46,398 MuTect - [MUTECT] Processed 26000784 reads in 699 ms
[2015-09-30T22:15Z] INFO  23:15:46,615 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:47,026 MuTect - [MUTECT] Processed 41001771 reads in 738 ms
[2015-09-30T22:15Z] INFO  23:15:47,102 MuTect - [MUTECT] Processed 27000845 reads in 704 ms
[2015-09-30T22:15Z] INFO  23:15:47,114 MuTect - [MUTECT] Processed 1000100 reads in 2453 ms
[2015-09-30T22:15Z] INFO  23:15:47,725 MuTect - [MUTECT] Processed 42001849 reads in 699 ms
[2015-09-30T22:15Z] INFO  23:15:47,778 MuTect - [MUTECT] Processed 28000902 reads in 676 ms
[2015-09-30T22:15Z] INFO  23:15:47,930 MuTect - [MUTECT] Processed 2000215 reads in 816 ms
[2015-09-30T22:15Z] INFO  23:15:48,069 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:48,419 MuTect - [MUTECT] Processed 43001973 reads in 694 ms
[2015-09-30T22:15Z] INFO  23:15:48,460 MuTect - [MUTECT] Processed 29000995 reads in 682 ms
[2015-09-30T22:15Z] INFO  23:15:48,669 MuTect - [MUTECT] Processed 3000306 reads in 739 ms
[2015-09-30T22:15Z] INFO  23:15:49,021 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:49,146 MuTect - [MUTECT] Processed 44002046 reads in 727 ms
[2015-09-30T22:15Z] INFO  23:15:49,163 MuTect - [MUTECT] Processed 30001002 reads in 703 ms
[2015-09-30T22:15Z] INFO  23:15:49,202 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:49,453 MuTect - [MUTECT] Processed 4000315 reads in 784 ms
[2015-09-30T22:15Z] INFO  23:15:49,841 MuTect - [MUTECT] Processed 45002138 reads in 695 ms
[2015-09-30T22:15Z] INFO  23:15:49,862 MuTect - [MUTECT] Processed 31001036 reads in 699 ms
[2015-09-30T22:15Z] INFO  23:15:50,124 MuTect - [MUTECT] Processed 5000316 reads in 671 ms
[2015-09-30T22:15Z] INFO  23:15:50,311 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:50,539 MuTect - [MUTECT] Processed 32001150 reads in 677 ms
[2015-09-30T22:15Z] INFO  23:15:50,570 MuTect - [MUTECT] Processed 46002210 reads in 729 ms
[2015-09-30T22:15Z] INFO  23:15:50,800 MuTect - [MUTECT] Processed 6000403 reads in 676 ms
[2015-09-30T22:15Z] INFO  23:15:51,229 MuTect - [MUTECT] Processed 33001166 reads in 690 ms
[2015-09-30T22:15Z] INFO  23:15:51,277 MuTect - [MUTECT] Processed 47002259 reads in 707 ms
[2015-09-30T22:15Z] INFO  23:15:51,418 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:51,542 MuTect - [MUTECT] Processed 7000504 reads in 742 ms
[2015-09-30T22:15Z] INFO  23:15:51,613 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:51,929 MuTect - [MUTECT] Processed 34001241 reads in 700 ms
[2015-09-30T22:15Z] INFO  23:15:51,997 MuTect - [MUTECT] Processed 48002274 reads in 720 ms
[2015-09-30T22:15Z] INFO  23:15:52,231 MuTect - [MUTECT] Processed 8000567 reads in 689 ms
[2015-09-30T22:15Z] INFO  23:15:52,600 MuTect - [MUTECT] Processed 35001280 reads in 671 ms
[2015-09-30T22:15Z] INFO  23:15:52,701 MuTect - [MUTECT] Processed 49002310 reads in 704 ms
[2015-09-30T22:15Z] INFO  23:15:52,705 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:52,896 MuTect - [MUTECT] Processed 9000632 reads in 665 ms
[2015-09-30T22:15Z] INFO  23:15:53,292 MuTect - [MUTECT] Processed 36001293 reads in 691 ms
[2015-09-30T22:15Z] INFO  23:15:53,383 MuTect - [MUTECT] Processed 50002340 reads in 682 ms
[2015-09-30T22:15Z] INFO  23:15:53,633 MuTect - [MUTECT] Processed 10000640 reads in 737 ms
[2015-09-30T22:15Z] INFO  23:15:53,910 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:53,945 MuTect - [MUTECT] Processed 37001312 reads in 654 ms
[2015-09-30T22:15Z] INFO  23:15:54,120 MuTect - [MUTECT] Processed 51002402 reads in 737 ms
[2015-09-30T22:15Z] INFO  23:15:54,310 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:54,335 MuTect - [MUTECT] Processed 11000642 reads in 702 ms
[2015-09-30T22:15Z] INFO  23:15:54,624 MuTect - [MUTECT] Processed 38001415 reads in 679 ms
[2015-09-30T22:15Z] INFO  23:15:54,840 MuTect - [MUTECT] Processed 52002429 reads in 720 ms
[2015-09-30T22:15Z] INFO  23:15:55,028 MuTect - [MUTECT] Processed 12000768 reads in 693 ms
[2015-09-30T22:15Z] INFO  23:15:55,101 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:55,327 MuTect - [MUTECT] Processed 39001490 reads in 703 ms
[2015-09-30T22:15Z] INFO  23:15:55,543 MuTect - [MUTECT] Processed 53002488 reads in 703 ms
[2015-09-30T22:15Z] INFO  23:15:55,723 MuTect - [MUTECT] Processed 13000789 reads in 695 ms
[2015-09-30T22:15Z] INFO  23:15:56,024 MuTect - [MUTECT] Processed 40001558 reads in 697 ms
[2015-09-30T22:15Z] INFO  23:15:56,218 MuTect - [MUTECT] Processed 54002537 reads in 675 ms
[2015-09-30T22:15Z] INFO  23:15:56,376 MuTect - [MUTECT] Processed 14000824 reads in 653 ms
[2015-09-30T22:15Z] INFO  23:15:56,387 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:56,425 ProgressMeter -     5:172068387        1.10e+06   30.0 s       27.0 s     40.9%        73.0 s    43.0 s
[2015-09-30T22:15Z] INFO  23:15:56,733 MuTect - [MUTECT] Processed 41001613 reads in 709 ms
[2015-09-30T22:15Z] INFO  23:15:56,806 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:56,876 MuTect - [MUTECT] Processed 55002543 reads in 658 ms
[2015-09-30T22:15Z] INFO  23:15:57,034 MuTect - [MUTECT] Processed 15000869 reads in 658 ms
[2015-09-30T22:15Z] INFO  23:15:57,366 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:57,440 MuTect - [MUTECT] Processed 42001639 reads in 707 ms
[2015-09-30T22:15Z] INFO  23:15:57,549 MuTect - [MUTECT] Processed 56002612 reads in 673 ms
[2015-09-30T22:15Z] INFO  23:15:57,697 MuTect - [MUTECT] Processed 16000893 reads in 663 ms
[2015-09-30T22:15Z] INFO  23:15:58,138 MuTect - [MUTECT] Processed 43001653 reads in 697 ms
[2015-09-30T22:15Z] INFO  23:15:58,230 MuTect - [MUTECT] Processed 57002690 reads in 681 ms
[2015-09-30T22:15Z] INFO  23:15:58,371 MuTect - [MUTECT] Processed 17000916 reads in 674 ms
[2015-09-30T22:15Z] INFO  23:15:58,805 MuTect - [MUTECT] Processed 44001707 reads in 668 ms
[2015-09-30T22:15Z] INFO  23:15:58,860 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:58,920 MuTect - [MUTECT] Processed 58002729 reads in 690 ms
[2015-09-30T22:15Z] INFO  23:15:59,065 MuTect - [MUTECT] Processed 18000993 reads in 694 ms
[2015-09-30T22:15Z] INFO  23:15:59,260 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:59,455 MuTect - [MUTECT] Processed 45001778 reads in 650 ms
[2015-09-30T22:15Z] INFO  23:15:59,605 MuTect - [MUTECT] Processed 59002805 reads in 685 ms
[2015-09-30T22:15Z] INFO  23:15:59,643 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:15Z] INFO  23:15:59,790 MuTect - [MUTECT] Processed 19001084 reads in 725 ms
[2015-09-30T22:16Z] INFO  23:16:00,123 MuTect - [MUTECT] Processed 46001876 reads in 668 ms
[2015-09-30T22:16Z] INFO  23:16:00,291 MuTect - [MUTECT] Processed 60002814 reads in 686 ms
[2015-09-30T22:16Z] INFO  23:16:00,430 MuTect - [MUTECT] Processed 20001155 reads in 640 ms
[2015-09-30T22:16Z] INFO  23:16:00,796 MuTect - [MUTECT] Processed 47001930 reads in 673 ms
[2015-09-30T22:16Z] INFO  23:16:00,966 MuTect - [MUTECT] Processed 61002836 reads in 675 ms
[2015-09-30T22:16Z] INFO  23:16:01,136 MuTect - [MUTECT] Processed 21001203 reads in 706 ms
[2015-09-30T22:16Z] INFO  23:16:01,292 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:01,473 MuTect - [MUTECT] Processed 48001934 reads in 677 ms
[2015-09-30T22:16Z] INFO  23:16:01,626 MuTect - [MUTECT] Processed 62002862 reads in 660 ms
[2015-09-30T22:16Z] INFO  23:16:01,696 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:01,831 MuTect - [MUTECT] Processed 22001297 reads in 695 ms
[2015-09-30T22:16Z] INFO  23:16:02,018 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:02,134 MuTect - [MUTECT] Processed 49001999 reads in 661 ms
[2015-09-30T22:16Z] INFO  23:16:02,288 MuTect - [MUTECT] Processed 63002868 reads in 662 ms
[2015-09-30T22:16Z] INFO  23:16:02,507 MuTect - [MUTECT] Processed 23001424 reads in 676 ms
[2015-09-30T22:16Z] INFO  23:16:02,803 MuTect - [MUTECT] Processed 50002052 reads in 669 ms
[2015-09-30T22:16Z] INFO  23:16:02,958 MuTect - [MUTECT] Processed 64002924 reads in 670 ms
[2015-09-30T22:16Z] INFO  23:16:03,176 MuTect - [MUTECT] Processed 24001491 reads in 669 ms
[2015-09-30T22:16Z] INFO  23:16:03,434 MuTect - [MUTECT] Processed 51002104 reads in 631 ms
[2015-09-30T22:16Z] INFO  23:16:03,599 MuTect - [MUTECT] Processed 65002939 reads in 641 ms
[2015-09-30T22:16Z] INFO  23:16:03,600 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:03,875 MuTect - [MUTECT] Processed 25001498 reads in 699 ms
[2015-09-30T22:16Z] INFO  23:16:03,880 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:04,088 MuTect - [MUTECT] Processed 52002145 reads in 654 ms
[2015-09-30T22:16Z] INFO  23:16:04,271 MuTect - [MUTECT] Processed 66003014 reads in 672 ms
[2015-09-30T22:16Z] INFO  23:16:04,565 MuTect - [MUTECT] Processed 26001507 reads in 690 ms
[2015-09-30T22:16Z] INFO  23:16:04,728 MuTect - [MUTECT] Processed 53002187 reads in 640 ms
[2015-09-30T22:16Z] INFO  23:16:04,773 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:04,944 MuTect - [MUTECT] Processed 67003039 reads in 673 ms
[2015-09-30T22:16Z] INFO  23:16:05,232 MuTect - [MUTECT] Processed 27001510 reads in 667 ms
[2015-09-30T22:16Z] INFO  23:16:05,377 MuTect - [MUTECT] Processed 54002232 reads in 649 ms
[2015-09-30T22:16Z] INFO  23:16:05,589 MuTect - [MUTECT] Processed 68003092 reads in 645 ms
[2015-09-30T22:16Z] INFO  23:16:05,940 MuTect - [MUTECT] Processed 28001532 reads in 708 ms
[2015-09-30T22:16Z] INFO  23:16:06,029 MuTect - [MUTECT] Processed 55002256 reads in 652 ms
[2015-09-30T22:16Z] INFO  23:16:06,080 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:06,125 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:06,226 MuTect - [MUTECT] Processed 69003186 reads in 637 ms
[2015-09-30T22:16Z] INFO  23:16:06,580 MuTect - [MUTECT] Processed 29001554 reads in 640 ms
[2015-09-30T22:16Z] INFO  23:16:06,740 MuTect - [MUTECT] Processed 56002362 reads in 711 ms
[2015-09-30T22:16Z] INFO  23:16:06,871 MuTect - [MUTECT] Processed 70003271 reads in 645 ms
[2015-09-30T22:16Z] INFO  23:16:06,986 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:07,266 MuTect - [MUTECT] Processed 30001580 reads in 686 ms
[2015-09-30T22:16Z] INFO  23:16:07,397 MuTect - [MUTECT] Processed 57002380 reads in 657 ms
[2015-09-30T22:16Z] INFO  23:16:07,554 MuTect - [MUTECT] Processed 71003313 reads in 683 ms
[2015-09-30T22:16Z] INFO  23:16:08,072 MuTect - [MUTECT] Processed 31001635 reads in 806 ms
[2015-09-30T22:16Z] INFO  23:16:08,076 MuTect - [MUTECT] Processed 58002482 reads in 679 ms
[2015-09-30T22:16Z] INFO  23:16:08,245 MuTect - [MUTECT] Processed 72003369 reads in 691 ms
[2015-09-30T22:16Z] INFO  23:16:08,469 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:08,760 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:08,761 MuTect - [MUTECT] Processed 59002583 reads in 685 ms
[2015-09-30T22:16Z] INFO  23:16:08,778 MuTect - [MUTECT] Processed 32001722 reads in 706 ms
[2015-09-30T22:16Z] INFO  23:16:08,954 MuTect - [MUTECT] Processed 73003372 reads in 709 ms
[2015-09-30T22:16Z] INFO  23:16:09,106 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:09,411 MuTect - [MUTECT] Processed 60002664 reads in 650 ms
[2015-09-30T22:16Z] INFO  23:16:09,464 MuTect - [MUTECT] Processed 33001755 reads in 685 ms
[2015-09-30T22:16Z] INFO  23:16:09,634 MuTect - [MUTECT] Processed 74003400 reads in 679 ms
[2015-09-30T22:16Z] INFO  23:16:10,073 MuTect - [MUTECT] Processed 61002721 reads in 662 ms
[2015-09-30T22:16Z] INFO  23:16:10,178 MuTect - [MUTECT] Processed 34001785 reads in 715 ms
[2015-09-30T22:16Z] INFO  23:16:10,308 MuTect - [MUTECT] Processed 75003445 reads in 675 ms
[2015-09-30T22:16Z] INFO  23:16:10,732 MuTect - [MUTECT] Processed 62002762 reads in 659 ms
[2015-09-30T22:16Z] INFO  23:16:10,803 MuTect - [MUTECT] Processed 35001819 reads in 625 ms
[2015-09-30T22:16Z] INFO  23:16:10,938 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:10,954 MuTect - [MUTECT] Processed 76003468 reads in 645 ms
[2015-09-30T22:16Z] INFO  23:16:10,996 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:11,203 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:11,393 MuTect - [MUTECT] Processed 63002766 reads in 661 ms
[2015-09-30T22:16Z] INFO  23:16:11,471 MuTect - [MUTECT] Processed 36001849 reads in 668 ms
[2015-09-30T22:16Z] INFO  23:16:11,608 MuTect - [MUTECT] Processed 77003522 reads in 655 ms
[2015-09-30T22:16Z] INFO  23:16:12,044 MuTect - [MUTECT] Processed 64002770 reads in 651 ms
[2015-09-30T22:16Z] INFO  23:16:12,116 MuTect - [MUTECT] Processed 37001876 reads in 645 ms
[2015-09-30T22:16Z] INFO  23:16:12,231 MuTect - [MUTECT] Processed 78003616 reads in 623 ms
[2015-09-30T22:16Z] INFO  23:16:12,706 MuTect - [MUTECT] Processed 65002845 reads in 662 ms
[2015-09-30T22:16Z] INFO  23:16:12,791 MuTect - [MUTECT] Processed 38001890 reads in 675 ms
[2015-09-30T22:16Z] INFO  23:16:12,874 MuTect - [MUTECT] Processed 79003681 reads in 643 ms
[2015-09-30T22:16Z] INFO  23:16:13,072 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:13,335 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:13,352 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:13,362 MuTect - [MUTECT] Processed 66002882 reads in 656 ms
[2015-09-30T22:16Z] INFO  23:16:13,431 MuTect - [MUTECT] Processed 39001909 reads in 640 ms
[2015-09-30T22:16Z] INFO  23:16:13,517 MuTect - [MUTECT] Processed 80003703 reads in 643 ms
[2015-09-30T22:16Z] INFO  23:16:14,003 MuTect - [MUTECT] Processed 67002936 reads in 641 ms
[2015-09-30T22:16Z] INFO  23:16:14,070 MuTect - [MUTECT] Processed 40001913 reads in 639 ms
[2015-09-30T22:16Z] INFO  23:16:14,163 MuTect - [MUTECT] Processed 81003769 reads in 645 ms
[2015-09-30T22:16Z] INFO  23:16:14,617 ProgressMeter -      6:12122624        1.07e+06   30.0 s       27.0 s     33.6%        89.0 s    59.0 s
[2015-09-30T22:16Z] INFO  23:16:14,636 MuTect - [MUTECT] Processed 68003049 reads in 633 ms
[2015-09-30T22:16Z] INFO  23:16:14,728 MuTect - [MUTECT] Processed 41001996 reads in 658 ms
[2015-09-30T22:16Z] INFO  23:16:14,798 MuTect - [MUTECT] Processed 82003802 reads in 636 ms
[2015-09-30T22:16Z] INFO  23:16:15,111 ProgressMeter -     5:140174960        2.68e+06   60.0 s       22.0 s     47.9%         2.1 m    65.0 s
[2015-09-30T22:16Z] INFO  23:16:15,273 MuTect - [MUTECT] Processed 69003118 reads in 637 ms
[2015-09-30T22:16Z] INFO  23:16:15,367 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:15,370 MuTect - [MUTECT] Processed 42001997 reads in 642 ms
[2015-09-30T22:16Z] INFO  23:16:15,464 MuTect - [MUTECT] Processed 83003889 reads in 666 ms
[2015-09-30T22:16Z] INFO  23:16:15,472 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:15,519 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:15,913 MuTect - [MUTECT] Processed 70003210 reads in 640 ms
[2015-09-30T22:16Z] INFO  23:16:16,013 MuTect - [MUTECT] Processed 43002070 reads in 643 ms
[2015-09-30T22:16Z] INFO  23:16:16,124 MuTect - [MUTECT] Processed 84003894 reads in 660 ms
[2015-09-30T22:16Z] INFO  23:16:16,530 MuTect - [MUTECT] Processed 71003282 reads in 617 ms
[2015-09-30T22:16Z] INFO  23:16:16,669 MuTect - [MUTECT] Processed 44002089 reads in 656 ms
[2015-09-30T22:16Z] INFO  23:16:16,786 MuTect - [MUTECT] Processed 85003983 reads in 662 ms
[2015-09-30T22:16Z] INFO  23:16:17,167 MuTect - [MUTECT] Processed 72003330 reads in 637 ms
[2015-09-30T22:16Z] INFO  23:16:17,297 MuTect - [MUTECT] Processed 45002160 reads in 628 ms
[2015-09-30T22:16Z] INFO  23:16:17,431 MuTect - [MUTECT] Processed 86004029 reads in 645 ms
[2015-09-30T22:16Z] INFO  23:16:17,708 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:17,729 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:17,835 MuTect - [MUTECT] Processed 73003374 reads in 668 ms
[2015-09-30T22:16Z] INFO  23:16:17,890 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:17,950 MuTect - [MUTECT] Processed 46002224 reads in 653 ms
[2015-09-30T22:16Z] INFO  23:16:18,057 MuTect - [MUTECT] Processed 87004037 reads in 626 ms
[2015-09-30T22:16Z] INFO  23:16:18,480 MuTect - [MUTECT] Processed 74003389 reads in 645 ms
[2015-09-30T22:16Z] INFO  23:16:18,590 MuTect - [MUTECT] Processed 47002297 reads in 640 ms
[2015-09-30T22:16Z] INFO  23:16:18,687 MuTect - [MUTECT] Processed 88004135 reads in 630 ms
[2015-09-30T22:16Z] INFO  23:16:19,140 MuTect - [MUTECT] Processed 75003460 reads in 660 ms
[2015-09-30T22:16Z] INFO  23:16:19,215 MuTect - [MUTECT] Processed 48002383 reads in 625 ms
[2015-09-30T22:16Z] INFO  23:16:19,326 MuTect - [MUTECT] Processed 89004205 reads in 639 ms
[2015-09-30T22:16Z] INFO  23:16:19,827 MuTect - [MUTECT] Processed 76003463 reads in 687 ms
[2015-09-30T22:16Z] INFO  23:16:19,861 MuTect - [MUTECT] Processed 49002403 reads in 645 ms
[2015-09-30T22:16Z] INFO  23:16:19,985 MuTect - [MUTECT] Processed 90004283 reads in 659 ms
[2015-09-30T22:16Z] INFO  23:16:20,075 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:20,164 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:20,214 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:20,502 MuTect - [MUTECT] Processed 77003520 reads in 675 ms
[2015-09-30T22:16Z] INFO  23:16:20,502 MuTect - [MUTECT] Processed 50002424 reads in 642 ms
[2015-09-30T22:16Z] INFO  23:16:20,679 MuTect - [MUTECT] Processed 91004331 reads in 694 ms
[2015-09-30T22:16Z] INFO  23:16:21,123 MuTect - [MUTECT] Processed 51002424 reads in 621 ms
[2015-09-30T22:16Z] INFO  23:16:21,234 MuTect - [MUTECT] Processed 78003580 reads in 732 ms
[2015-09-30T22:16Z] INFO  23:16:21,403 MuTect - [MUTECT] Processed 92004363 reads in 724 ms
[2015-09-30T22:16Z] INFO  23:16:21,793 MuTect - [MUTECT] Processed 52002457 reads in 670 ms
[2015-09-30T22:16Z] INFO  23:16:22,083 MuTect - [MUTECT] Processed 93004438 reads in 680 ms
[2015-09-30T22:16Z] INFO  23:16:22,083 MuTect - [MUTECT] Processed 79003636 reads in 849 ms
[2015-09-30T22:16Z] INFO  23:16:22,438 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:22,486 MuTect - [MUTECT] Processed 53002533 reads in 693 ms
[2015-09-30T22:16Z] INFO  23:16:22,710 MuTect - [MUTECT] Processed 94004532 reads in 627 ms
[2015-09-30T22:16Z] INFO  23:16:22,738 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:22,747 MuTect - [MUTECT] Processed 80003697 reads in 664 ms
[2015-09-30T22:16Z] INFO  23:16:23,006 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:23,261 MuTect - [MUTECT] Processed 54002534 reads in 775 ms
[2015-09-30T22:16Z] INFO  23:16:23,337 MuTect - [MUTECT] Processed 95004535 reads in 627 ms
[2015-09-30T22:16Z] INFO  23:16:23,420 MuTect - [MUTECT] Processed 81003780 reads in 673 ms
[2015-09-30T22:16Z] INFO  23:16:23,926 MuTect - [MUTECT] Processed 55002548 reads in 665 ms
[2015-09-30T22:16Z] INFO  23:16:23,956 MuTect - [MUTECT] Processed 96004570 reads in 619 ms
[2015-09-30T22:16Z] INFO  23:16:24,123 MuTect - [MUTECT] Processed 82003899 reads in 703 ms
[2015-09-30T22:16Z] INFO  23:16:24,570 MuTect - [MUTECT] Processed 97004606 reads in 614 ms
[2015-09-30T22:16Z] INFO  23:16:24,593 MuTect - [MUTECT] Processed 56002577 reads in 666 ms
[2015-09-30T22:16Z] INFO  23:16:24,809 MuTect - [MUTECT] Processed 83003920 reads in 686 ms
[2015-09-30T22:16Z] INFO  23:16:24,940 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:25,109 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:25,187 MuTect - [MUTECT] Processed 98004606 reads in 617 ms
[2015-09-30T22:16Z] INFO  23:16:25,254 MuTect - [MUTECT] Processed 57002598 reads in 662 ms
[2015-09-30T22:16Z] INFO  23:16:25,337 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:25,516 MuTect - [MUTECT] Processed 84003938 reads in 707 ms
[2015-09-30T22:16Z] INFO  23:16:25,809 MuTect - [MUTECT] Processed 99004673 reads in 622 ms
[2015-09-30T22:16Z] INFO  23:16:25,911 MuTect - [MUTECT] Processed 58002628 reads in 657 ms
[2015-09-30T22:16Z] INFO  23:16:26,184 MuTect - [MUTECT] Processed 85004040 reads in 668 ms
[2015-09-30T22:16Z] INFO  23:16:26,426 ProgressMeter -     5:178199653        2.21e+06   60.0 s       27.0 s     77.8%        77.0 s    17.0 s
[2015-09-30T22:16Z] INFO  23:16:26,447 MuTect - [MUTECT] Processed 100004726 reads in 638 ms
[2015-09-30T22:16Z] INFO  23:16:26,585 MuTect - [MUTECT] Processed 59002679 reads in 674 ms
[2015-09-30T22:16Z] INFO  23:16:26,904 MuTect - [MUTECT] Processed 86004070 reads in 720 ms
[2015-09-30T22:16Z] INFO  23:16:27,074 MuTect - [MUTECT] Processed 101004794 reads in 627 ms
[2015-09-30T22:16Z] INFO  23:16:27,235 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:27,272 MuTect - [MUTECT] Processed 60002706 reads in 687 ms
[2015-09-30T22:16Z] INFO  23:16:27,405 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:27,564 MuTect - [MUTECT] Processed 87004127 reads in 660 ms
[2015-09-30T22:16Z] INFO  23:16:27,574 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:27,689 MuTect - [MUTECT] Processed 102004822 reads in 615 ms
[2015-09-30T22:16Z] INFO  23:16:27,910 MuTect - [MUTECT] Processed 61002784 reads in 637 ms
[2015-09-30T22:16Z] INFO  23:16:28,308 MuTect - [MUTECT] Processed 88004140 reads in 744 ms
[2015-09-30T22:16Z] INFO  23:16:28,311 MuTect - [MUTECT] Processed 103004861 reads in 622 ms
[2015-09-30T22:16Z] INFO  23:16:28,573 MuTect - [MUTECT] Processed 62002866 reads in 664 ms
[2015-09-30T22:16Z] INFO  23:16:28,963 MuTect - [MUTECT] Processed 104004871 reads in 652 ms
[2015-09-30T22:16Z] INFO  23:16:29,001 MuTect - [MUTECT] Processed 89004188 reads in 693 ms
[2015-09-30T22:16Z] INFO  23:16:29,238 MuTect - [MUTECT] Processed 63002877 reads in 665 ms
[2015-09-30T22:16Z] INFO  23:16:29,493 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:29,595 MuTect - [MUTECT] Processed 105004911 reads in 632 ms
[2015-09-30T22:16Z] INFO  23:16:29,675 MuTect - [MUTECT] Processed 90004242 reads in 674 ms
[2015-09-30T22:16Z] INFO  23:16:29,697 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:29,854 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:29,887 MuTect - [MUTECT] Processed 64002892 reads in 649 ms
[2015-09-30T22:16Z] INFO  23:16:30,240 MuTect - [MUTECT] Processed 106004991 reads in 644 ms
[2015-09-30T22:16Z] INFO  23:16:30,369 MuTect - [MUTECT] Processed 91004258 reads in 693 ms
[2015-09-30T22:16Z] INFO  23:16:30,582 MuTect - [MUTECT] Processed 65002959 reads in 695 ms
[2015-09-30T22:16Z] INFO  23:16:30,870 MuTect - [MUTECT] Processed 107005110 reads in 631 ms
[2015-09-30T22:16Z] INFO  23:16:31,087 MuTect - [MUTECT] Processed 92004289 reads in 719 ms
[2015-09-30T22:16Z] INFO  23:16:31,230 MuTect - [MUTECT] Processed 66002995 reads in 648 ms
[2015-09-30T22:16Z] INFO  23:16:31,504 MuTect - [MUTECT] Processed 108005178 reads in 634 ms
[2015-09-30T22:16Z] INFO  23:16:31,730 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:31,814 MuTect - [MUTECT] Processed 93004296 reads in 726 ms
[2015-09-30T22:16Z] INFO  23:16:31,859 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:31,867 MuTect - [MUTECT] Processed 67003070 reads in 637 ms
[2015-09-30T22:16Z] INFO  23:16:32,138 MuTect - [MUTECT] Processed 109005229 reads in 634 ms
[2015-09-30T22:16Z] INFO  23:16:32,165 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:32,528 MuTect - [MUTECT] Processed 94004342 reads in 715 ms
[2015-09-30T22:16Z] INFO  23:16:32,541 MuTect - [MUTECT] Processed 68003079 reads in 674 ms
[2015-09-30T22:16Z] INFO  23:16:32,786 MuTect - [MUTECT] Processed 110005280 reads in 648 ms
[2015-09-30T22:16Z] INFO  23:16:33,172 MuTect - [MUTECT] Processed 69003110 reads in 631 ms
[2015-09-30T22:16Z] INFO  23:16:33,176 MuTect - [MUTECT] Processed 95004417 reads in 648 ms
[2015-09-30T22:16Z] INFO  23:16:33,476 MuTect - [MUTECT] Processed 111005360 reads in 690 ms
[2015-09-30T22:16Z] INFO  23:16:33,813 MuTect - [MUTECT] Processed 96004477 reads in 637 ms
[2015-09-30T22:16Z] INFO  23:16:33,830 MuTect - [MUTECT] Processed 70003127 reads in 658 ms
[2015-09-30T22:16Z] INFO  23:16:34,056 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:34,173 MuTect - [MUTECT] Processed 112005379 reads in 697 ms
[2015-09-30T22:16Z] INFO  23:16:34,257 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:34,332 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:34,455 MuTect - [MUTECT] Processed 97004576 reads in 642 ms
[2015-09-30T22:16Z] INFO  23:16:34,491 MuTect - [MUTECT] Processed 71003158 reads in 661 ms
[2015-09-30T22:16Z] INFO  23:16:34,871 MuTect - [MUTECT] Processed 113005396 reads in 698 ms
[2015-09-30T22:16Z] INFO  23:16:35,133 MuTect - [MUTECT] Processed 72003169 reads in 642 ms
[2015-09-30T22:16Z] INFO  23:16:35,135 MuTect - [MUTECT] Processed 98004658 reads in 680 ms
[2015-09-30T22:16Z] INFO  23:16:35,576 MuTect - [MUTECT] Processed 114005482 reads in 705 ms
[2015-09-30T22:16Z] INFO  23:16:35,776 MuTect - [MUTECT] Processed 99004674 reads in 641 ms
[2015-09-30T22:16Z] INFO  23:16:35,780 MuTect - [MUTECT] Processed 73003240 reads in 647 ms
[2015-09-30T22:16Z] INFO  23:16:36,282 MuTect - [MUTECT] Processed 115005564 reads in 706 ms
[2015-09-30T22:16Z] INFO  23:16:36,423 MuTect - [MUTECT] Processed 74003244 reads in 643 ms
[2015-09-30T22:16Z] INFO  23:16:36,435 MuTect - [MUTECT] Processed 100004680 reads in 659 ms
[2015-09-30T22:16Z] INFO  23:16:36,488 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:36,574 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:36,594 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:37,015 MuTect - [MUTECT] Processed 116005637 reads in 733 ms
[2015-09-30T22:16Z] INFO  23:16:37,036 MuTect - [MUTECT] Processed 75003268 reads in 613 ms
[2015-09-30T22:16Z] INFO  23:16:37,138 MuTect - [MUTECT] Processed 101004743 reads in 702 ms
[2015-09-30T22:16Z] INFO  23:16:37,668 MuTect - [MUTECT] Processed 76003353 reads in 632 ms
[2015-09-30T22:16Z] INFO  23:16:37,747 MuTect - [MUTECT] Processed 117005711 reads in 731 ms
[2015-09-30T22:16Z] INFO  23:16:37,912 MuTect - [MUTECT] Processed 102004785 reads in 775 ms
[2015-09-30T22:16Z] INFO  23:16:38,363 MuTect - [MUTECT] Processed 77003363 reads in 695 ms
[2015-09-30T22:16Z] INFO  23:16:38,436 MuTect - [MUTECT] Processed 118005747 reads in 690 ms
[2015-09-30T22:16Z] INFO  23:16:38,594 MuTect - [MUTECT] Processed 103004879 reads in 681 ms
[2015-09-30T22:16Z] INFO  23:16:39,008 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:39,025 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:39,040 MuTect - [MUTECT] Processed 78003407 reads in 677 ms
[2015-09-30T22:16Z] INFO  23:16:39,068 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:39,143 MuTect - [MUTECT] Processed 119005769 reads in 707 ms
[2015-09-30T22:16Z] INFO  23:16:39,289 MuTect - [MUTECT] Processed 104004902 reads in 695 ms
[2015-09-30T22:16Z] INFO  23:16:39,838 MuTect - [MUTECT] Processed 120005888 reads in 695 ms
[2015-09-30T22:16Z] INFO  23:16:39,855 MuTect - [MUTECT] Processed 79003485 reads in 815 ms
[2015-09-30T22:16Z] INFO  23:16:39,998 MuTect - [MUTECT] Processed 105005003 reads in 710 ms
[2015-09-30T22:16Z] INFO  23:16:40,520 MuTect - [MUTECT] Processed 80003491 reads in 665 ms
[2015-09-30T22:16Z] INFO  23:16:40,541 MuTect - [MUTECT] Processed 121005888 reads in 702 ms
[2015-09-30T22:16Z] INFO  23:16:40,658 MuTect - [MUTECT] Processed 106005125 reads in 660 ms
[2015-09-30T22:16Z] INFO  23:16:41,079 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:41,153 MuTect - [MUTECT] Processed 81003499 reads in 633 ms
[2015-09-30T22:16Z] INFO  23:16:41,223 MuTect - [MUTECT] Processed 122005902 reads in 683 ms
[2015-09-30T22:16Z] INFO  23:16:41,295 MuTect - [MUTECT] Processed 107005207 reads in 636 ms
[2015-09-30T22:16Z] INFO  23:16:41,407 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:41,707 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:41,789 MuTect - [MUTECT] Processed 82003546 reads in 636 ms
[2015-09-30T22:16Z] INFO  23:16:41,900 MuTect - [MUTECT] Processed 123005904 reads in 677 ms
[2015-09-30T22:16Z] INFO  23:16:41,938 MuTect - [MUTECT] Processed 108005259 reads in 644 ms
[2015-09-30T22:16Z] INFO  23:16:42,459 MuTect - [MUTECT] Processed 83003615 reads in 670 ms
[2015-09-30T22:16Z] INFO  23:16:42,571 MuTect - [MUTECT] Processed 124005920 reads in 671 ms
[2015-09-30T22:16Z] INFO  23:16:42,609 MuTect - [MUTECT] Processed 109005288 reads in 671 ms
[2015-09-30T22:16Z] INFO  23:16:43,168 MuTect - [MUTECT] Processed 84003664 reads in 709 ms
[2015-09-30T22:16Z] INFO  23:16:43,247 MuTect - [MUTECT] Processed 125005927 reads in 676 ms
[2015-09-30T22:16Z] INFO  23:16:43,278 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:43,284 MuTect - [MUTECT] Processed 110005297 reads in 675 ms
[2015-09-30T22:16Z] INFO  23:16:43,833 MuTect - [MUTECT] Processed 85003786 reads in 665 ms
[2015-09-30T22:16Z] INFO  23:16:43,915 MuTect - [MUTECT] Processed 111005373 reads in 631 ms
[2015-09-30T22:16Z] INFO  23:16:44,006 MuTect - [MUTECT] Processed 126005975 reads in 759 ms
[2015-09-30T22:16Z] INFO  23:16:44,039 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:44,242 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:44,446 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:16Z] INFO  23:16:44,449 ProgressMeter -            done        2.94e+06   78.0 s       26.0 s    100.0%        78.0 s     0.0 s
[2015-09-30T22:16Z] INFO  23:16:44,449 ProgressMeter - Total runtime 78.03 secs, 1.30 min, 0.02 hours
[2015-09-30T22:16Z] INFO  23:16:44,497 MuTect - [MUTECT] Processed 86003835 reads in 664 ms
[2015-09-30T22:16Z] INFO  23:16:44,514 MicroScheduler - 88653 reads were filtered out during the traversal out of approximately 1332967 total reads (6.65%)
[2015-09-30T22:16Z] INFO  23:16:44,515 MicroScheduler -   -> 66599 reads (5.00% of total) failing DuplicateReadFilter
[2015-09-30T22:16Z] INFO  23:16:44,515 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:16Z] INFO  23:16:44,515 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:16Z] INFO  23:16:44,515 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:16Z] INFO  23:16:44,515 MicroScheduler -   -> 22054 reads (1.65% of total) failing UnmappedReadFilter
[2015-09-30T22:16Z] INFO  23:16:44,618 ProgressMeter -      6:27419924        2.33e+06   60.0 s       25.0 s     73.4%        81.0 s    21.0 s
[2015-09-30T22:16Z] INFO  23:16:44,815 MuTect - [MUTECT] Processed 127006040 reads in 809 ms
[2015-09-30T22:16Z] INFO  23:16:45,112 ProgressMeter -     5:147716259        3.96e+06   90.0 s       22.0 s     72.5%         2.1 m    34.0 s
[2015-09-30T22:16Z] INFO  23:16:45,152 MuTect - [MUTECT] Processed 87003915 reads in 655 ms
[2015-09-30T22:16Z] INFO  23:16:45,474 MuTect - [MUTECT] Processed 128006058 reads in 659 ms
[2015-09-30T22:16Z] INFO  23:16:45,660 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:16Z] bgzip syn3-5_156785743_180915260-raw-mutect.vcf
[2015-09-30T22:16Z] tabix index syn3-5_156785743_180915260-raw-mutect.vcf.gz
[2015-09-30T22:16Z] INFO  23:16:45,803 MuTect - [MUTECT] Processed 88003917 reads in 651 ms
[2015-09-30T22:16Z] INFO  23:16:46,149 MuTect - [MUTECT] Processed 129006098 reads in 675 ms
[2015-09-30T22:16Z] INFO  23:16:46,446 MuTect - [MUTECT] Processed 89003959 reads in 643 ms
[2015-09-30T22:16Z] INFO  23:16:46,618 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:46,677 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:46,833 MuTect - [MUTECT] Processed 130006147 reads in 684 ms
[2015-09-30T22:16Z] INFO  23:16:47,079 MuTect - [MUTECT] Processed 90003966 reads in 633 ms
[2015-09-30T22:16Z] INFO  23:16:47,553 MuTect - [MUTECT] Processed 131006157 reads in 720 ms
[2015-09-30T22:16Z] INFO  23:16:47,799 MuTect - [MUTECT] Processed 91004048 reads in 720 ms
[2015-09-30T22:16Z] MuTect: MuTect
[2015-09-30T22:16Z] INFO  23:16:48,263 MuTect - [MUTECT] Processed 132006253 reads in 710 ms
[2015-09-30T22:16Z] INFO  23:16:48,459 MuTect - [MUTECT] Processed 92004105 reads in 660 ms
[2015-09-30T22:16Z] INFO  23:16:48,977 MuTect - [MUTECT] Processed 133006361 reads in 714 ms
[2015-09-30T22:16Z] INFO  23:16:48,981 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:48,986 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:49,094 MuTect - [MUTECT] Processed 93004149 reads in 635 ms
[2015-09-30T22:16Z] INFO  23:16:49,659 MuTect - [MUTECT] Processed 134006400 reads in 682 ms
[2015-09-30T22:16Z] INFO  23:16:49,749 MuTect - [MUTECT] Processed 94004167 reads in 655 ms
[2015-09-30T22:16Z] INFO  23:16:50,027 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/6/syn3-6_31082315_62284583-raw-mutect-regions.bed to be BED
[2015-09-30T22:16Z] INFO  23:16:50,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:16Z] INFO  23:16:50,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:16Z] INFO  23:16:50,084 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:16Z] INFO  23:16:50,084 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:16Z] INFO  23:16:50,088 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/6/syn3-6_31082315_62284583-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/6/tx/tmpaQA208/syn3-6_31082315_62284583-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:16Z] INFO  23:16:50,088 HelpFormatter - Date/Time: 2015/09/30 23:16:50
[2015-09-30T22:16Z] INFO  23:16:50,088 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:16Z] INFO  23:16:50,088 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:16Z] INFO  23:16:50,117 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:16Z] INFO  23:16:50,121 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:16Z] INFO  23:16:50,177 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:16Z] INFO  23:16:50,227 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:16Z] INFO  23:16:50,235 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:16Z] INFO  23:16:50,285 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T22:16Z] INFO  23:16:50,311 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:16Z] INFO  23:16:50,354 MuTect - [MUTECT] Processed 135006417 reads in 695 ms
[2015-09-30T22:16Z] INFO  23:16:50,398 MuTect - [MUTECT] Processed 95004172 reads in 649 ms
[2015-09-30T22:16Z] INFO  23:16:50,489 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:16Z] INFO  23:16:50,612 IntervalUtils - Processing 2326318 bp from intervals
[2015-09-30T22:16Z] INFO  23:16:50,616 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:16Z] INFO  23:16:50,616 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:16Z] INFO  23:16:51,027 MuTect - [MUTECT] Processed 136006508 reads in 673 ms
[2015-09-30T22:16Z] INFO  23:16:51,076 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:16Z] INFO  23:16:51,084 MuTect - [MUTECT] Processed 96004199 reads in 686 ms
[2015-09-30T22:16Z] INFO  23:16:51,259 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:16Z] INFO  23:16:51,259 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:16Z] INFO  23:16:51,259 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:16Z] INFO  23:16:51,260 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:16Z] INFO  23:16:51,306 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:51,623 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:51,717 MuTect - [MUTECT] Processed 97004205 reads in 633 ms
[2015-09-30T22:16Z] INFO  23:16:51,763 MuTect - [MUTECT] Processed 137006535 reads in 735 ms
[2015-09-30T22:16Z] INFO  23:16:52,384 MuTect - [MUTECT] Processed 98004299 reads in 667 ms
[2015-09-30T22:16Z] INFO  23:16:52,464 MuTect - [MUTECT] Processed 138006547 reads in 701 ms
[2015-09-30T22:16Z] INFO  23:16:53,047 MuTect - [MUTECT] Processed 99004376 reads in 663 ms
[2015-09-30T22:16Z] INFO  23:16:53,180 MuTect - [MUTECT] Processed 139006613 reads in 717 ms
[2015-09-30T22:16Z] INFO  23:16:53,509 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:53,638 MuTect - [MUTECT] Processed 1000025 reads in 2329 ms
[2015-09-30T22:16Z] INFO  23:16:53,723 MuTect - [MUTECT] Processed 100004409 reads in 676 ms
[2015-09-30T22:16Z] INFO  23:16:53,876 MuTect - [MUTECT] Processed 140006624 reads in 696 ms
[2015-09-30T22:16Z] INFO  23:16:54,174 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:54,463 MuTect - [MUTECT] Processed 101004461 reads in 740 ms
[2015-09-30T22:16Z] INFO  23:16:54,478 MuTect - [MUTECT] Processed 2000118 reads in 841 ms
[2015-09-30T22:16Z] INFO  23:16:54,524 MuTect - [MUTECT] Processed 141006737 reads in 648 ms
[2015-09-30T22:16Z] INFO  23:16:55,172 MuTect - [MUTECT] Processed 142006737 reads in 648 ms
[2015-09-30T22:16Z] INFO  23:16:55,233 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:55,632 MuTect - [MUTECT] Processed 102004509 reads in 1169 ms
[2015-09-30T22:16Z] INFO  23:16:55,690 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:55,829 MuTect - [MUTECT] Processed 143006747 reads in 657 ms
[2015-09-30T22:16Z] INFO  23:16:55,848 MuTect - [MUTECT] Processed 3000196 reads in 1370 ms
[2015-09-30T22:16Z] INFO  23:16:56,310 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:56,490 MuTect - [MUTECT] Processed 144006780 reads in 661 ms
[2015-09-30T22:16Z] INFO  23:16:56,907 MuTect - [MUTECT] Processed 103004522 reads in 1275 ms
[2015-09-30T22:16Z] INFO  23:16:56,968 MuTect - [MUTECT] Processed 4000258 reads in 1120 ms
[2015-09-30T22:16Z] INFO  23:16:57,146 MuTect - [MUTECT] Processed 145006863 reads in 655 ms
[2015-09-30T22:16Z] INFO  23:16:57,614 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:57,701 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:57,735 MuTect - [MUTECT] Processed 5000345 reads in 767 ms
[2015-09-30T22:16Z] INFO  23:16:57,798 MuTect - [MUTECT] Processed 146006933 reads in 653 ms
[2015-09-30T22:16Z] INFO  23:16:58,049 MuTect - [MUTECT] Processed 104004599 reads in 1142 ms
[2015-09-30T22:16Z] INFO  23:16:58,419 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:58,452 MuTect - [MUTECT] Processed 6000436 reads in 716 ms
[2015-09-30T22:16Z] INFO  23:16:58,491 MuTect - [MUTECT] Processed 147006947 reads in 693 ms
[2015-09-30T22:16Z] INFO  23:16:58,779 MuTect - [MUTECT] Processed 105004657 reads in 730 ms
[2015-09-30T22:16Z] INFO  23:16:59,127 MuTect - [MUTECT] Processed 7000470 reads in 676 ms
[2015-09-30T22:16Z] INFO  23:16:59,133 MuTect - [MUTECT] Processed 148007091 reads in 642 ms
[2015-09-30T22:16Z] INFO  23:16:59,518 MuTect - [MUTECT] Processed 106004664 reads in 739 ms
[2015-09-30T22:16Z] INFO  23:16:59,770 MuTect - [MUTECT] Processed 149007153 reads in 637 ms
[2015-09-30T22:16Z] INFO  23:16:59,807 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:16Z] INFO  23:16:59,834 MuTect - [MUTECT] Processed 8000529 reads in 706 ms
[2015-09-30T22:17Z] INFO  23:17:00,222 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:00,250 MuTect - [MUTECT] Processed 107004705 reads in 732 ms
[2015-09-30T22:17Z] INFO  23:17:00,387 MuTect - [MUTECT] Processed 150007208 reads in 617 ms
[2015-09-30T22:17Z] INFO  23:17:00,430 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:00,536 MuTect - [MUTECT] Processed 9000559 reads in 703 ms
[2015-09-30T22:17Z] INFO  23:17:00,981 MuTect - [MUTECT] Processed 108004713 reads in 731 ms
[2015-09-30T22:17Z] INFO  23:17:01,024 MuTect - [MUTECT] Processed 151007241 reads in 637 ms
[2015-09-30T22:17Z] INFO  23:17:01,212 MuTect - [MUTECT] Processed 10000637 reads in 676 ms
[2015-09-30T22:17Z] INFO  23:17:01,654 MuTect - [MUTECT] Processed 109004801 reads in 673 ms
[2015-09-30T22:17Z] INFO  23:17:01,680 MuTect - [MUTECT] Processed 152007315 reads in 656 ms
[2015-09-30T22:17Z] INFO  23:17:01,914 MuTect - [MUTECT] Processed 11000731 reads in 702 ms
[2015-09-30T22:17Z] INFO  23:17:02,131 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:02,315 MuTect - [MUTECT] Processed 110004846 reads in 661 ms
[2015-09-30T22:17Z] INFO  23:17:02,319 MuTect - [MUTECT] Processed 153007400 reads in 639 ms
[2015-09-30T22:17Z] INFO  23:17:02,331 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:02,502 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:02,584 MuTect - [MUTECT] Processed 12000749 reads in 670 ms
[2015-09-30T22:17Z] INFO  23:17:02,932 MuTect - [MUTECT] Processed 154007480 reads in 613 ms
[2015-09-30T22:17Z] INFO  23:17:02,966 MuTect - [MUTECT] Processed 111004929 reads in 651 ms
[2015-09-30T22:17Z] INFO  23:17:03,242 MuTect - [MUTECT] Processed 13000812 reads in 658 ms
[2015-09-30T22:17Z] INFO  23:17:03,572 MuTect - [MUTECT] Processed 155007502 reads in 640 ms
[2015-09-30T22:17Z] INFO  23:17:03,603 MuTect - [MUTECT] Processed 112004948 reads in 637 ms
[2015-09-30T22:17Z] INFO  23:17:03,894 MuTect - [MUTECT] Processed 14000872 reads in 652 ms
[2015-09-30T22:17Z] INFO  23:17:04,224 MuTect - [MUTECT] Processed 156007521 reads in 652 ms
[2015-09-30T22:17Z] INFO  23:17:04,259 MuTect - [MUTECT] Processed 113005052 reads in 656 ms
[2015-09-30T22:17Z] INFO  23:17:04,361 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:04,492 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:04,537 MuTect - [MUTECT] Processed 15000943 reads in 643 ms
[2015-09-30T22:17Z] INFO  23:17:04,831 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:04,882 MuTect - [MUTECT] Processed 114005061 reads in 623 ms
[2015-09-30T22:17Z] INFO  23:17:04,903 MuTect - [MUTECT] Processed 157007551 reads in 679 ms
[2015-09-30T22:17Z] INFO  23:17:05,167 MuTect - [MUTECT] Processed 16000981 reads in 630 ms
[2015-09-30T22:17Z] INFO  23:17:05,498 MuTect - [MUTECT] Processed 115005105 reads in 616 ms
[2015-09-30T22:17Z] INFO  23:17:05,585 MuTect - [MUTECT] Processed 158007579 reads in 682 ms
[2015-09-30T22:17Z] INFO  23:17:05,819 MuTect - [MUTECT] Processed 17001016 reads in 652 ms
[2015-09-30T22:17Z] INFO  23:17:06,152 MuTect - [MUTECT] Processed 116005107 reads in 654 ms
[2015-09-30T22:17Z] INFO  23:17:06,255 MuTect - [MUTECT] Processed 159007690 reads in 670 ms
[2015-09-30T22:17Z] INFO  23:17:06,442 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:06,454 MuTect - [MUTECT] Processed 18001119 reads in 635 ms
[2015-09-30T22:17Z] INFO  23:17:06,458 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:06,778 MuTect - [MUTECT] Processed 117005173 reads in 626 ms
[2015-09-30T22:17Z] INFO  23:17:06,966 MuTect - [MUTECT] Processed 160007748 reads in 711 ms
[2015-09-30T22:17Z] INFO  23:17:07,082 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:07,096 MuTect - [MUTECT] Processed 19001140 reads in 642 ms
[2015-09-30T22:17Z] INFO  23:17:07,410 MuTect - [MUTECT] Processed 118005175 reads in 632 ms
[2015-09-30T22:17Z] INFO  23:17:07,677 MuTect - [MUTECT] Processed 161007806 reads in 711 ms
[2015-09-30T22:17Z] INFO  23:17:07,722 MuTect - [MUTECT] Processed 20001165 reads in 626 ms
[2015-09-30T22:17Z] INFO  23:17:08,088 MuTect - [MUTECT] Processed 119005248 reads in 678 ms
[2015-09-30T22:17Z] INFO  23:17:08,430 MuTect - [MUTECT] Processed 21001213 reads in 708 ms
[2015-09-30T22:17Z] INFO  23:17:08,455 MuTect - [MUTECT] Processed 162007886 reads in 778 ms
[2015-09-30T22:17Z] INFO  23:17:08,592 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:08,747 MuTect - [MUTECT] Processed 120005335 reads in 659 ms
[2015-09-30T22:17Z] INFO  23:17:08,959 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:09,099 MuTect - [MUTECT] Processed 22001320 reads in 669 ms
[2015-09-30T22:17Z] INFO  23:17:09,196 MuTect - [MUTECT] Processed 163007929 reads in 741 ms
[2015-09-30T22:17Z] INFO  23:17:09,245 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:09,465 MuTect - [MUTECT] Processed 121005372 reads in 718 ms
[2015-09-30T22:17Z] INFO  23:17:09,900 MuTect - [MUTECT] Processed 164008023 reads in 704 ms
[2015-09-30T22:17Z] INFO  23:17:10,197 MuTect - [MUTECT] Processed 122005492 reads in 732 ms
[2015-09-30T22:17Z] INFO  23:17:10,235 MuTect - [MUTECT] Processed 23001345 reads in 1136 ms
[2015-09-30T22:17Z] INFO  23:17:10,502 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:17Z] INFO  23:17:10,506 ProgressMeter -            done        3.27e+06   85.0 s       26.0 s    100.0%        85.0 s     0.0 s
[2015-09-30T22:17Z] INFO  23:17:10,506 ProgressMeter - Total runtime 85.89 secs, 1.43 min, 0.02 hours
[2015-09-30T22:17Z] INFO  23:17:10,567 MuTect - [MUTECT] Processed 165008090 reads in 667 ms
[2015-09-30T22:17Z] INFO  23:17:10,571 MicroScheduler - 91003 reads were filtered out during the traversal out of approximately 1444365 total reads (6.30%)
[2015-09-30T22:17Z] INFO  23:17:10,571 MicroScheduler -   -> 67440 reads (4.67% of total) failing DuplicateReadFilter
[2015-09-30T22:17Z] INFO  23:17:10,572 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:17Z] INFO  23:17:10,572 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:17Z] INFO  23:17:10,572 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:17Z] INFO  23:17:10,572 MicroScheduler -   -> 23563 reads (1.63% of total) failing UnmappedReadFilter
[2015-09-30T22:17Z] INFO  23:17:10,897 MuTect - [MUTECT] Processed 24001422 reads in 662 ms
[2015-09-30T22:17Z] INFO  23:17:11,228 MuTect - [MUTECT] Processed 166008101 reads in 661 ms
[2015-09-30T22:17Z] INFO  23:17:11,543 MuTect - [MUTECT] Processed 25001504 reads in 646 ms
[2015-09-30T22:17Z] INFO  23:17:11,550 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:17Z] INFO  23:17:11,555 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:17Z] bgzip syn3-6_0_31080572-raw-mutect.vcf
[2015-09-30T22:17Z] tabix index syn3-6_0_31080572-raw-mutect.vcf.gz
[2015-09-30T22:17Z] INFO  23:17:11,708 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:11,917 MuTect - [MUTECT] Processed 167008131 reads in 689 ms
[2015-09-30T22:17Z] INFO  23:17:12,207 MuTect - [MUTECT] Processed 26001550 reads in 664 ms
[2015-09-30T22:17Z] INFO  23:17:12,619 MuTect - [MUTECT] Processed 168008157 reads in 702 ms
[2015-09-30T22:17Z] INFO  23:17:12,829 MuTect - [MUTECT] Processed 27001601 reads in 622 ms
[2015-09-30T22:17Z] INFO  23:17:13,307 MuTect - [MUTECT] Processed 169008172 reads in 688 ms
[2015-09-30T22:17Z] INFO  23:17:13,437 MuTect - [MUTECT] Processed 28001669 reads in 608 ms
[2015-09-30T22:17Z] MuTect: MuTect
[2015-09-30T22:17Z] INFO  23:17:13,999 MuTect - [MUTECT] Processed 170008217 reads in 692 ms
[2015-09-30T22:17Z] INFO  23:17:14,028 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:14,103 MuTect - [MUTECT] Processed 29001744 reads in 666 ms
[2015-09-30T22:17Z] INFO  23:17:14,699 MuTect - [MUTECT] Processed 171008316 reads in 700 ms
[2015-09-30T22:17Z] INFO  23:17:14,715 MuTect - [MUTECT] Processed 30001851 reads in 612 ms
[2015-09-30T22:17Z] INFO  23:17:15,113 ProgressMeter -     5:153830844        5.28e+06  120.0 s       22.0 s     94.1%         2.1 m     7.0 s
[2015-09-30T22:17Z] INFO  23:17:15,365 MuTect - [MUTECT] Processed 172008328 reads in 666 ms
[2015-09-30T22:17Z] INFO  23:17:15,615 MuTect - [MUTECT] Processed 31001953 reads in 899 ms
[2015-09-30T22:17Z] INFO  23:17:15,811 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/6/syn3-6_62389878_93953543-raw-mutect-regions.bed to be BED
[2015-09-30T22:17Z] INFO  23:17:15,865 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:17Z] INFO  23:17:15,866 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:17Z] INFO  23:17:15,866 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:17Z] INFO  23:17:15,866 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:17Z] INFO  23:17:15,869 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/6/syn3-6_62389878_93953543-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/6/tx/tmpD2SccI/syn3-6_62389878_93953543-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:17Z] INFO  23:17:15,870 HelpFormatter - Date/Time: 2015/09/30 23:17:15
[2015-09-30T22:17Z] INFO  23:17:15,870 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:17Z] INFO  23:17:15,870 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:17Z] INFO  23:17:15,896 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:17Z] INFO  23:17:15,901 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:17Z] INFO  23:17:15,950 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:17Z] INFO  23:17:15,997 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:17Z] INFO  23:17:16,005 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:17Z] INFO  23:17:16,030 MuTect - [MUTECT] Processed 173008445 reads in 665 ms
[2015-09-30T22:17Z] INFO  23:17:16,045 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:17Z] INFO  23:17:16,056 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:17Z] INFO  23:17:16,229 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:17Z] INFO  23:17:16,306 MuTect - [MUTECT] Processed 32001965 reads in 692 ms
[2015-09-30T22:17Z] INFO  23:17:16,315 IntervalUtils - Processing 924860 bp from intervals
[2015-09-30T22:17Z] INFO  23:17:16,319 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:17Z] INFO  23:17:16,319 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:17Z] INFO  23:17:16,371 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:17Z] INFO  23:17:16,472 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:16,483 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:16,639 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:17Z] INFO  23:17:16,640 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:17Z] INFO  23:17:16,640 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:17Z] INFO  23:17:16,641 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:17Z] INFO  23:17:16,688 MuTect - [MUTECT] Processed 174008526 reads in 658 ms
[2015-09-30T22:17Z] INFO  23:17:16,986 MuTect - [MUTECT] Processed 33002039 reads in 680 ms
[2015-09-30T22:17Z] INFO  23:17:17,373 MuTect - [MUTECT] Processed 175008619 reads in 685 ms
[2015-09-30T22:17Z] INFO  23:17:17,666 MuTect - [MUTECT] Processed 34002040 reads in 680 ms
[2015-09-30T22:17Z] INFO  23:17:18,077 MuTect - [MUTECT] Processed 176008728 reads in 704 ms
[2015-09-30T22:17Z] INFO  23:17:18,383 MuTect - [MUTECT] Processed 35002051 reads in 717 ms
[2015-09-30T22:17Z] INFO  23:17:18,711 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:18,745 MuTect - [MUTECT] Processed 177008743 reads in 668 ms
[2015-09-30T22:17Z] INFO  23:17:19,005 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:19,071 MuTect - [MUTECT] Processed 36002070 reads in 688 ms
[2015-09-30T22:17Z] INFO  23:17:19,371 MuTect - [MUTECT] Processed 1000039 reads in 2685 ms
[2015-09-30T22:17Z] INFO  23:17:19,445 MuTect - [MUTECT] Processed 178008788 reads in 700 ms
[2015-09-30T22:17Z] INFO  23:17:19,742 MuTect - [MUTECT] Processed 37002128 reads in 671 ms
[2015-09-30T22:17Z] INFO  23:17:20,074 MuTect - [MUTECT] Processed 2000113 reads in 703 ms
[2015-09-30T22:17Z] INFO  23:17:20,164 MuTect - [MUTECT] Processed 179008825 reads in 719 ms
[2015-09-30T22:17Z] INFO  23:17:20,375 MuTect - [MUTECT] Processed 38002201 reads in 633 ms
[2015-09-30T22:17Z] INFO  23:17:20,795 MuTect - [MUTECT] Processed 3000189 reads in 720 ms
[2015-09-30T22:17Z] INFO  23:17:20,818 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:20,833 MuTect - [MUTECT] Processed 180008847 reads in 669 ms
[2015-09-30T22:17Z] INFO  23:17:21,035 MuTect - [MUTECT] Processed 39002221 reads in 660 ms
[2015-09-30T22:17Z] INFO  23:17:21,262 ProgressMeter -      6:32163979        1.08e+06   30.0 s       27.0 s     14.6%         3.4 m     2.9 m
[2015-09-30T22:17Z] INFO  23:17:21,267 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:21,360 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:21,508 MuTect - [MUTECT] Processed 181008879 reads in 675 ms
[2015-09-30T22:17Z] INFO  23:17:21,584 MuTect - [MUTECT] Processed 4000279 reads in 789 ms
[2015-09-30T22:17Z] INFO  23:17:21,682 MuTect - [MUTECT] Processed 40002272 reads in 647 ms
[2015-09-30T22:17Z] INFO  23:17:22,215 MuTect - [MUTECT] Processed 182008920 reads in 707 ms
[2015-09-30T22:17Z] INFO  23:17:22,352 MuTect - [MUTECT] Processed 41002326 reads in 670 ms
[2015-09-30T22:17Z] INFO  23:17:22,489 MuTect - [MUTECT] Processed 5000286 reads in 906 ms
[2015-09-30T22:17Z] INFO  23:17:22,633 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:17Z] INFO  23:17:22,638 ProgressMeter -            done        5.62e+06    2.1 m       22.0 s    100.0%         2.1 m     0.0 s
[2015-09-30T22:17Z] INFO  23:17:22,638 ProgressMeter - Total runtime 127.53 secs, 2.13 min, 0.04 hours
[2015-09-30T22:17Z] INFO  23:17:22,703 MicroScheduler - 137443 reads were filtered out during the traversal out of approximately 2155497 total reads (6.38%)
[2015-09-30T22:17Z] INFO  23:17:22,703 MicroScheduler -   -> 102157 reads (4.74% of total) failing DuplicateReadFilter
[2015-09-30T22:17Z] INFO  23:17:22,703 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:17Z] INFO  23:17:22,703 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:17Z] INFO  23:17:22,703 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:17Z] INFO  23:17:22,704 MicroScheduler -   -> 35286 reads (1.64% of total) failing UnmappedReadFilter
[2015-09-30T22:17Z] INFO  23:17:22,989 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:23,101 MuTect - [MUTECT] Processed 42002378 reads in 749 ms
[2015-09-30T22:17Z] INFO  23:17:23,244 MuTect - [MUTECT] Processed 6000334 reads in 755 ms
[2015-09-30T22:17Z] INFO  23:17:23,680 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:17Z] bgzip syn3-5_125759062_156781785-raw-mutect.vcf
[2015-09-30T22:17Z] tabix index syn3-5_125759062_156781785-raw-mutect.vcf.gz
[2015-09-30T22:17Z] INFO  23:17:23,896 MuTect - [MUTECT] Processed 43002403 reads in 795 ms
[2015-09-30T22:17Z] INFO  23:17:23,978 MuTect - [MUTECT] Processed 7000334 reads in 734 ms
[2015-09-30T22:17Z] INFO  23:17:24,196 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:24,666 MuTect - [MUTECT] Processed 8000344 reads in 688 ms
[2015-09-30T22:17Z] INFO  23:17:25,071 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:25,165 MuTect - [MUTECT] Processed 44002453 reads in 1269 ms
[2015-09-30T22:17Z] INFO  23:17:25,403 MuTect - [MUTECT] Processed 9000370 reads in 737 ms
[2015-09-30T22:17Z] INFO  23:17:26,105 MuTect - [MUTECT] Processed 10000405 reads in 702 ms
[2015-09-30T22:17Z] MuTect: MuTect
[2015-09-30T22:17Z] INFO  23:17:26,788 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:26,793 MuTect - [MUTECT] Processed 11000445 reads in 688 ms
[2015-09-30T22:17Z] INFO  23:17:27,139 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:27,479 MuTect - [MUTECT] Processed 12000496 reads in 686 ms
[2015-09-30T22:17Z] INFO  23:17:28,192 MuTect - [MUTECT] Processed 13000557 reads in 713 ms
[2015-09-30T22:17Z] INFO  23:17:28,311 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/6/syn3-6_93954776_124979769-raw-mutect-regions.bed to be BED
[2015-09-30T22:17Z] INFO  23:17:28,342 MuTect - [MUTECT] Processed 45002588 reads in 3177 ms
[2015-09-30T22:17Z] INFO  23:17:28,367 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:17Z] INFO  23:17:28,367 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:17Z] INFO  23:17:28,368 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:17Z] INFO  23:17:28,368 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:17Z] INFO  23:17:28,371 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/6/syn3-6_93954776_124979769-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/6/tx/tmpfBLKgT/syn3-6_93954776_124979769-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:17Z] INFO  23:17:28,371 HelpFormatter - Date/Time: 2015/09/30 23:17:28
[2015-09-30T22:17Z] INFO  23:17:28,371 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:17Z] INFO  23:17:28,371 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:17Z] INFO  23:17:28,398 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:17Z] INFO  23:17:28,402 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:17Z] INFO  23:17:28,450 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:17Z] INFO  23:17:28,497 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:17Z] INFO  23:17:28,504 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:17Z] INFO  23:17:28,567 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:17Z] INFO  23:17:28,579 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:17Z] INFO  23:17:28,752 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:17Z] INFO  23:17:28,841 IntervalUtils - Processing 964242 bp from intervals
[2015-09-30T22:17Z] INFO  23:17:28,845 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:17Z] INFO  23:17:28,845 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:17Z] INFO  23:17:28,860 MuTect - [MUTECT] Processed 14000576 reads in 668 ms
[2015-09-30T22:17Z] INFO  23:17:28,997 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:17Z] INFO  23:17:29,143 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:17Z] INFO  23:17:29,143 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:17Z] INFO  23:17:29,144 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:17Z] INFO  23:17:29,145 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:17Z] INFO  23:17:29,258 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:29,284 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:29,515 MuTect - [MUTECT] Processed 15000657 reads in 654 ms
[2015-09-30T22:17Z] INFO  23:17:30,163 MuTect - [MUTECT] Processed 16000744 reads in 649 ms
[2015-09-30T22:17Z] INFO  23:17:30,253 MuTect - [MUTECT] Processed 46002704 reads in 1911 ms
[2015-09-30T22:17Z] INFO  23:17:30,846 MuTect - [MUTECT] Processed 17000792 reads in 682 ms
[2015-09-30T22:17Z] INFO  23:17:31,069 MuTect - [MUTECT] Processed 47002759 reads in 816 ms
[2015-09-30T22:17Z] INFO  23:17:31,381 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:31,515 MuTect - [MUTECT] Processed 18000799 reads in 670 ms
[2015-09-30T22:17Z] INFO  23:17:31,572 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:31,753 MuTect - [MUTECT] Processed 1000034 reads in 2563 ms
[2015-09-30T22:17Z] INFO  23:17:31,771 MuTect - [MUTECT] Processed 48002851 reads in 702 ms
[2015-09-30T22:17Z] INFO  23:17:32,172 MuTect - [MUTECT] Processed 19000820 reads in 657 ms
[2015-09-30T22:17Z] INFO  23:17:32,467 MuTect - [MUTECT] Processed 49002856 reads in 696 ms
[2015-09-30T22:17Z] INFO  23:17:32,564 MuTect - [MUTECT] Processed 2000072 reads in 811 ms
[2015-09-30T22:17Z] INFO  23:17:32,866 MuTect - [MUTECT] Processed 20000857 reads in 694 ms
[2015-09-30T22:17Z] INFO  23:17:33,138 MuTect - [MUTECT] Processed 50002975 reads in 671 ms
[2015-09-30T22:17Z] INFO  23:17:33,333 MuTect - [MUTECT] Processed 3000145 reads in 769 ms
[2015-09-30T22:17Z] INFO  23:17:33,538 MuTect - [MUTECT] Processed 21000866 reads in 672 ms
[2015-09-30T22:17Z] INFO  23:17:33,698 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:33,797 MuTect - [MUTECT] Processed 51003060 reads in 659 ms
[2015-09-30T22:17Z] INFO  23:17:33,801 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:34,039 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:34,041 MuTect - [MUTECT] Processed 4000160 reads in 708 ms
[2015-09-30T22:17Z] INFO  23:17:34,229 MuTect - [MUTECT] Processed 22000962 reads in 691 ms
[2015-09-30T22:17Z] INFO  23:17:34,747 MuTect - [MUTECT] Processed 5000199 reads in 706 ms
[2015-09-30T22:17Z] INFO  23:17:34,842 MuTect - [MUTECT] Processed 52003094 reads in 1045 ms
[2015-09-30T22:17Z] INFO  23:17:34,864 MuTect - [MUTECT] Processed 23000987 reads in 635 ms
[2015-09-30T22:17Z] INFO  23:17:35,464 MuTect - [MUTECT] Processed 6000218 reads in 717 ms
[2015-09-30T22:17Z] INFO  23:17:35,481 MuTect - [MUTECT] Processed 24001004 reads in 617 ms
[2015-09-30T22:17Z] INFO  23:17:35,594 MuTect - [MUTECT] Processed 53003146 reads in 752 ms
[2015-09-30T22:17Z] INFO  23:17:35,872 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:36,167 MuTect - [MUTECT] Processed 25001031 reads in 686 ms
[2015-09-30T22:17Z] INFO  23:17:36,214 MuTect - [MUTECT] Processed 7000253 reads in 750 ms
[2015-09-30T22:17Z] INFO  23:17:36,265 MuTect - [MUTECT] Processed 54003150 reads in 671 ms
[2015-09-30T22:17Z] INFO  23:17:36,414 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:36,483 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:36,860 MuTect - [MUTECT] Processed 8000333 reads in 646 ms
[2015-09-30T22:17Z] INFO  23:17:36,866 MuTect - [MUTECT] Processed 26001046 reads in 699 ms
[2015-09-30T22:17Z] INFO  23:17:36,897 MuTect - [MUTECT] Processed 55003187 reads in 632 ms
[2015-09-30T22:17Z] INFO  23:17:37,515 MuTect - [MUTECT] Processed 56003254 reads in 618 ms
[2015-09-30T22:17Z] INFO  23:17:37,534 MuTect - [MUTECT] Processed 9000387 reads in 674 ms
[2015-09-30T22:17Z] INFO  23:17:37,556 MuTect - [MUTECT] Processed 27001099 reads in 690 ms
[2015-09-30T22:17Z] INFO  23:17:37,854 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:38,157 MuTect - [MUTECT] Processed 57003286 reads in 642 ms
[2015-09-30T22:17Z] INFO  23:17:38,252 MuTect - [MUTECT] Processed 10000417 reads in 718 ms
[2015-09-30T22:17Z] INFO  23:17:38,257 MuTect - [MUTECT] Processed 28001143 reads in 701 ms
[2015-09-30T22:17Z] INFO  23:17:38,854 MuTect - [MUTECT] Processed 58003414 reads in 697 ms
[2015-09-30T22:17Z] INFO  23:17:38,954 MuTect - [MUTECT] Processed 29001143 reads in 697 ms
[2015-09-30T22:17Z] INFO  23:17:38,957 MuTect - [MUTECT] Processed 11000432 reads in 705 ms
[2015-09-30T22:17Z] INFO  23:17:38,988 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:39,111 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:39,481 MuTect - [MUTECT] Processed 59003418 reads in 627 ms
[2015-09-30T22:17Z] INFO  23:17:39,646 MuTect - [MUTECT] Processed 30001201 reads in 691 ms
[2015-09-30T22:17Z] INFO  23:17:39,667 MuTect - [MUTECT] Processed 12000437 reads in 710 ms
[2015-09-30T22:17Z] INFO  23:17:39,962 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:40,148 MuTect - [MUTECT] Processed 60003454 reads in 667 ms
[2015-09-30T22:17Z] INFO  23:17:40,344 MuTect - [MUTECT] Processed 13000527 reads in 677 ms
[2015-09-30T22:17Z] INFO  23:17:40,401 MuTect - [MUTECT] Processed 31001214 reads in 756 ms
[2015-09-30T22:17Z] INFO  23:17:40,799 MuTect - [MUTECT] Processed 61003567 reads in 651 ms
[2015-09-30T22:17Z] INFO  23:17:40,997 MuTect - [MUTECT] Processed 14000590 reads in 653 ms
[2015-09-30T22:17Z] INFO  23:17:41,076 MuTect - [MUTECT] Processed 32001226 reads in 675 ms
[2015-09-30T22:17Z] INFO  23:17:41,433 MuTect - [MUTECT] Processed 62003670 reads in 634 ms
[2015-09-30T22:17Z] INFO  23:17:41,501 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:41,652 MuTect - [MUTECT] Processed 15000630 reads in 655 ms
[2015-09-30T22:17Z] INFO  23:17:41,663 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:41,757 MuTect - [MUTECT] Processed 33001303 reads in 681 ms
[2015-09-30T22:17Z] INFO  23:17:42,010 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:42,088 MuTect - [MUTECT] Processed 63003706 reads in 655 ms
[2015-09-30T22:17Z] INFO  23:17:42,303 MuTect - [MUTECT] Processed 16000657 reads in 651 ms
[2015-09-30T22:17Z] INFO  23:17:42,452 MuTect - [MUTECT] Processed 34001319 reads in 695 ms
[2015-09-30T22:17Z] INFO  23:17:42,728 MuTect - [MUTECT] Processed 64003759 reads in 640 ms
[2015-09-30T22:17Z] INFO  23:17:42,987 MuTect - [MUTECT] Processed 17000691 reads in 684 ms
[2015-09-30T22:17Z] INFO  23:17:43,109 MuTect - [MUTECT] Processed 35001337 reads in 657 ms
[2015-09-30T22:17Z] INFO  23:17:43,335 MuTect - [MUTECT] Processed 65003828 reads in 607 ms
[2015-09-30T22:17Z] INFO  23:17:43,622 MuTect - [MUTECT] Processed 18000785 reads in 635 ms
[2015-09-30T22:17Z] INFO  23:17:43,775 MuTect - [MUTECT] Processed 36001362 reads in 666 ms
[2015-09-30T22:17Z] INFO  23:17:43,859 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:43,965 MuTect - [MUTECT] Processed 66003944 reads in 630 ms
[2015-09-30T22:17Z] INFO  23:17:44,030 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:44,149 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:44,238 MuTect - [MUTECT] Processed 19000853 reads in 616 ms
[2015-09-30T22:17Z] INFO  23:17:44,472 MuTect - [MUTECT] Processed 37001391 reads in 697 ms
[2015-09-30T22:17Z] INFO  23:17:44,639 MuTect - [MUTECT] Processed 67004035 reads in 674 ms
[2015-09-30T22:17Z] INFO  23:17:44,876 MuTect - [MUTECT] Processed 20000908 reads in 638 ms
[2015-09-30T22:17Z] INFO  23:17:45,183 MuTect - [MUTECT] Processed 38001416 reads in 711 ms
[2015-09-30T22:17Z] INFO  23:17:45,297 MuTect - [MUTECT] Processed 68004146 reads in 658 ms
[2015-09-30T22:17Z] INFO  23:17:45,516 MuTect - [MUTECT] Processed 21000930 reads in 640 ms
[2015-09-30T22:17Z] INFO  23:17:45,857 MuTect - [MUTECT] Processed 39001453 reads in 674 ms
[2015-09-30T22:17Z] INFO  23:17:45,944 MuTect - [MUTECT] Processed 69004276 reads in 647 ms
[2015-09-30T22:17Z] INFO  23:17:46,090 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:46,160 MuTect - [MUTECT] Processed 22000983 reads in 644 ms
[2015-09-30T22:17Z] INFO  23:17:46,280 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:46,526 MuTect - [MUTECT] Processed 40001516 reads in 669 ms
[2015-09-30T22:17Z] INFO  23:17:46,615 MuTect - [MUTECT] Processed 70004357 reads in 671 ms
[2015-09-30T22:17Z] INFO  23:17:46,642 ProgressMeter -      6:86196760        1.65e+06   30.0 s       18.0 s     70.8%        42.0 s    12.0 s
[2015-09-30T22:17Z] INFO  23:17:46,715 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:46,767 MuTect - [MUTECT] Processed 23000988 reads in 607 ms
[2015-09-30T22:17Z] INFO  23:17:47,211 MuTect - [MUTECT] Processed 41001534 reads in 685 ms
[2015-09-30T22:17Z] INFO  23:17:47,252 MuTect - [MUTECT] Processed 71004440 reads in 637 ms
[2015-09-30T22:17Z] INFO  23:17:47,390 MuTect - [MUTECT] Processed 24001043 reads in 623 ms
[2015-09-30T22:17Z] INFO  23:17:47,868 MuTect - [MUTECT] Processed 42001610 reads in 657 ms
[2015-09-30T22:17Z] INFO  23:17:47,916 MuTect - [MUTECT] Processed 72004517 reads in 664 ms
[2015-09-30T22:17Z] INFO  23:17:48,033 MuTect - [MUTECT] Processed 25001128 reads in 643 ms
[2015-09-30T22:17Z] INFO  23:17:48,237 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:48,531 MuTect - [MUTECT] Processed 43001624 reads in 663 ms
[2015-09-30T22:17Z] INFO  23:17:48,574 MuTect - [MUTECT] Processed 73004576 reads in 658 ms
[2015-09-30T22:17Z] INFO  23:17:48,603 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:48,655 MuTect - [MUTECT] Processed 26001193 reads in 622 ms
[2015-09-30T22:17Z] INFO  23:17:49,195 MuTect - [MUTECT] Processed 44001645 reads in 664 ms
[2015-09-30T22:17Z] INFO  23:17:49,212 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:49,246 MuTect - [MUTECT] Processed 74004656 reads in 672 ms
[2015-09-30T22:17Z] INFO  23:17:49,364 MuTect - [MUTECT] Processed 27001277 reads in 709 ms
[2015-09-30T22:17Z] INFO  23:17:49,903 MuTect - [MUTECT] Processed 45001660 reads in 708 ms
[2015-09-30T22:17Z] INFO  23:17:49,911 MuTect - [MUTECT] Processed 75004681 reads in 665 ms
[2015-09-30T22:17Z] INFO  23:17:50,023 MuTect - [MUTECT] Processed 28001285 reads in 659 ms
[2015-09-30T22:17Z] INFO  23:17:50,358 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:50,529 MuTect - [MUTECT] Processed 76004691 reads in 618 ms
[2015-09-30T22:17Z] INFO  23:17:50,594 MuTect - [MUTECT] Processed 46001668 reads in 691 ms
[2015-09-30T22:17Z] INFO  23:17:50,642 MuTect - [MUTECT] Processed 29001309 reads in 619 ms
[2015-09-30T22:17Z] INFO  23:17:50,810 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:51,160 MuTect - [MUTECT] Processed 77004810 reads in 631 ms
[2015-09-30T22:17Z] INFO  23:17:51,263 ProgressMeter -      6:34737905        2.22e+06   60.0 s       27.0 s     29.4%         3.4 m     2.4 m
[2015-09-30T22:17Z] INFO  23:17:51,268 MuTect - [MUTECT] Processed 47001700 reads in 674 ms
[2015-09-30T22:17Z] INFO  23:17:51,286 MuTect - [MUTECT] Processed 30001376 reads in 644 ms
[2015-09-30T22:17Z] INFO  23:17:51,688 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:51,816 MuTect - [MUTECT] Processed 78004870 reads in 656 ms
[2015-09-30T22:17Z] INFO  23:17:51,885 MuTect - [MUTECT] Processed 31001440 reads in 599 ms
[2015-09-30T22:17Z] INFO  23:17:51,915 MuTect - [MUTECT] Processed 48001720 reads in 647 ms
[2015-09-30T22:17Z] INFO  23:17:52,451 MuTect - [MUTECT] Processed 79004882 reads in 635 ms
[2015-09-30T22:17Z] INFO  23:17:52,528 MuTect - [MUTECT] Processed 32001457 reads in 643 ms
[2015-09-30T22:17Z] INFO  23:17:52,538 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:52,562 MuTect - [MUTECT] Processed 49001767 reads in 647 ms
[2015-09-30T22:17Z] INFO  23:17:53,091 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:53,102 MuTect - [MUTECT] Processed 80004975 reads in 651 ms
[2015-09-30T22:17Z] INFO  23:17:53,213 MuTect - [MUTECT] Processed 33001527 reads in 685 ms
[2015-09-30T22:17Z] INFO  23:17:53,245 MuTect - [MUTECT] Processed 50001819 reads in 683 ms
[2015-09-30T22:17Z] INFO  23:17:53,760 MuTect - [MUTECT] Processed 81004984 reads in 658 ms
[2015-09-30T22:17Z] INFO  23:17:53,877 MuTect - [MUTECT] Processed 34001549 reads in 664 ms
[2015-09-30T22:17Z] INFO  23:17:53,886 MuTect - [MUTECT] Processed 51001876 reads in 641 ms
[2015-09-30T22:17Z] INFO  23:17:54,109 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:54,405 MuTect - [MUTECT] Processed 82005000 reads in 645 ms
[2015-09-30T22:17Z] INFO  23:17:54,509 MuTect - [MUTECT] Processed 35001559 reads in 632 ms
[2015-09-30T22:17Z] INFO  23:17:54,522 MuTect - [MUTECT] Processed 52001946 reads in 636 ms
[2015-09-30T22:17Z] INFO  23:17:54,691 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:55,029 MuTect - [MUTECT] Processed 83005092 reads in 624 ms
[2015-09-30T22:17Z] INFO  23:17:55,145 MuTect - [MUTECT] Processed 36001566 reads in 636 ms
[2015-09-30T22:17Z] INFO  23:17:55,167 MuTect - [MUTECT] Processed 53002045 reads in 645 ms
[2015-09-30T22:17Z] INFO  23:17:55,538 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:55,669 MuTect - [MUTECT] Processed 84005132 reads in 640 ms
[2015-09-30T22:17Z] INFO  23:17:55,785 MuTect - [MUTECT] Processed 37001649 reads in 640 ms
[2015-09-30T22:17Z] INFO  23:17:55,820 MuTect - [MUTECT] Processed 54002104 reads in 653 ms
[2015-09-30T22:17Z] INFO  23:17:56,306 MuTect - [MUTECT] Processed 85005195 reads in 637 ms
[2015-09-30T22:17Z] INFO  23:17:56,384 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:56,434 MuTect - [MUTECT] Processed 38001657 reads in 649 ms
[2015-09-30T22:17Z] INFO  23:17:56,451 MuTect - [MUTECT] Processed 55002122 reads in 630 ms
[2015-09-30T22:17Z] INFO  23:17:56,814 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:56,981 MuTect - [MUTECT] Processed 86005196 reads in 675 ms
[2015-09-30T22:17Z] INFO  23:17:57,095 MuTect - [MUTECT] Processed 56002157 reads in 645 ms
[2015-09-30T22:17Z] INFO  23:17:57,121 MuTect - [MUTECT] Processed 39001679 reads in 687 ms
[2015-09-30T22:17Z] INFO  23:17:57,641 MuTect - [MUTECT] Processed 87005223 reads in 660 ms
[2015-09-30T22:17Z] INFO  23:17:57,741 MuTect - [MUTECT] Processed 57002159 reads in 646 ms
[2015-09-30T22:17Z] INFO  23:17:57,759 MuTect - [MUTECT] Processed 40001697 reads in 638 ms
[2015-09-30T22:17Z] INFO  23:17:57,846 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:58,269 MuTect - [MUTECT] Processed 88005254 reads in 628 ms
[2015-09-30T22:17Z] INFO  23:17:58,384 MuTect - [MUTECT] Processed 41001724 reads in 625 ms
[2015-09-30T22:17Z] INFO  23:17:58,394 MuTect - [MUTECT] Processed 58002159 reads in 653 ms
[2015-09-30T22:17Z] INFO  23:17:58,676 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:58,897 MuTect - [MUTECT] Processed 89005324 reads in 628 ms
[2015-09-30T22:17Z] INFO  23:17:59,002 MuTect - [MUTECT] Processed 42001734 reads in 618 ms
[2015-09-30T22:17Z] INFO  23:17:59,016 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:17Z] INFO  23:17:59,035 MuTect - [MUTECT] Processed 59002231 reads in 641 ms
[2015-09-30T22:17Z] INFO  23:17:59,146 ProgressMeter -     6:111922201        1.36e+06   30.0 s       22.0 s     62.2%        48.0 s    18.0 s
[2015-09-30T22:17Z] INFO  23:17:59,543 MuTect - [MUTECT] Processed 90005563 reads in 646 ms
[2015-09-30T22:17Z] INFO  23:17:59,639 MuTect - [MUTECT] Processed 43001771 reads in 637 ms
[2015-09-30T22:17Z] INFO  23:17:59,695 MuTect - [MUTECT] Processed 60002288 reads in 660 ms
[2015-09-30T22:18Z] INFO  23:18:00,068 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:00,072 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:18Z] INFO  23:18:00,075 ProgressMeter -            done        2.44e+06   43.0 s       17.0 s    100.0%        43.0 s     0.0 s
[2015-09-30T22:18Z] INFO  23:18:00,076 ProgressMeter - Total runtime 43.44 secs, 0.72 min, 0.01 hours
[2015-09-30T22:18Z] INFO  23:18:00,139 MicroScheduler - 40116 reads were filtered out during the traversal out of approximately 717507 total reads (5.59%)
[2015-09-30T22:18Z] INFO  23:18:00,139 MicroScheduler -   -> 28672 reads (4.00% of total) failing DuplicateReadFilter
[2015-09-30T22:18Z] INFO  23:18:00,139 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:18Z] INFO  23:18:00,139 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:18Z] INFO  23:18:00,139 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:18Z] INFO  23:18:00,139 MicroScheduler -   -> 11444 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:18Z] INFO  23:18:00,172 MuTect - [MUTECT] Processed 91005579 reads in 629 ms
[2015-09-30T22:18Z] INFO  23:18:00,301 MuTect - [MUTECT] Processed 44001814 reads in 662 ms
[2015-09-30T22:18Z] INFO  23:18:00,810 MuTect - [MUTECT] Processed 92005671 reads in 638 ms
[2015-09-30T22:18Z] INFO  23:18:00,959 MuTect - [MUTECT] Processed 45001855 reads in 658 ms
[2015-09-30T22:18Z] INFO  23:18:01,144 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:01,332 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:18Z] bgzip syn3-6_62389878_93953543-raw-mutect.vcf
[2015-09-30T22:18Z] tabix index syn3-6_62389878_93953543-raw-mutect.vcf.gz
[2015-09-30T22:18Z] INFO  23:18:01,472 MuTect - [MUTECT] Processed 93005699 reads in 662 ms
[2015-09-30T22:18Z] INFO  23:18:01,638 MuTect - [MUTECT] Processed 46001968 reads in 679 ms
[2015-09-30T22:18Z] INFO  23:18:02,151 MuTect - [MUTECT] Processed 94005739 reads in 679 ms
[2015-09-30T22:18Z] INFO  23:18:02,295 MuTect - [MUTECT] Processed 47001978 reads in 656 ms
[2015-09-30T22:18Z] INFO  23:18:02,432 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:02,777 MuTect - [MUTECT] Processed 95005873 reads in 626 ms
[2015-09-30T22:18Z] INFO  23:18:02,999 MuTect - [MUTECT] Processed 48002005 reads in 705 ms
[2015-09-30T22:18Z] INFO  23:18:03,379 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:03,398 MuTect - [MUTECT] Processed 96005967 reads in 621 ms
[2015-09-30T22:18Z] MuTect: MuTect
[2015-09-30T22:18Z] INFO  23:18:03,619 MuTect - [MUTECT] Processed 49002013 reads in 619 ms
[2015-09-30T22:18Z] INFO  23:18:04,064 MuTect - [MUTECT] Processed 97006009 reads in 666 ms
[2015-09-30T22:18Z] INFO  23:18:04,264 MuTect - [MUTECT] Processed 50002112 reads in 646 ms
[2015-09-30T22:18Z] INFO  23:18:04,712 MuTect - [MUTECT] Processed 98006020 reads in 648 ms
[2015-09-30T22:18Z] INFO  23:18:04,868 MuTect - [MUTECT] Processed 51002186 reads in 604 ms
[2015-09-30T22:18Z] INFO  23:18:04,885 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:05,417 MuTect - [MUTECT] Processed 99006095 reads in 705 ms
[2015-09-30T22:18Z] INFO  23:18:05,471 MuTect - [MUTECT] Processed 52002193 reads in 603 ms
[2015-09-30T22:18Z] INFO  23:18:05,731 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/6/syn3-6_125064552_156268261-raw-mutect-regions.bed to be BED
[2015-09-30T22:18Z] INFO  23:18:05,749 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:05,785 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:18Z] INFO  23:18:05,785 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:18Z] INFO  23:18:05,785 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:18Z] INFO  23:18:05,785 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:18Z] INFO  23:18:05,789 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/6/syn3-6_125064552_156268261-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/6/tx/tmp98BDXe/syn3-6_125064552_156268261-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:18Z] INFO  23:18:05,789 HelpFormatter - Date/Time: 2015/09/30 23:18:05
[2015-09-30T22:18Z] INFO  23:18:05,789 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:18Z] INFO  23:18:05,789 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:18Z] INFO  23:18:05,815 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:18Z] INFO  23:18:05,820 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:18Z] INFO  23:18:05,868 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:18Z] INFO  23:18:05,915 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:18Z] INFO  23:18:05,922 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:18Z] INFO  23:18:05,944 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:18Z] INFO  23:18:05,955 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:18Z] INFO  23:18:06,101 MuTect - [MUTECT] Processed 100006140 reads in 684 ms
[2015-09-30T22:18Z] INFO  23:18:06,126 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:18Z] INFO  23:18:06,129 MuTect - [MUTECT] Processed 53002254 reads in 658 ms
[2015-09-30T22:18Z] INFO  23:18:06,227 IntervalUtils - Processing 1262148 bp from intervals
[2015-09-30T22:18Z] INFO  23:18:06,231 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:18Z] INFO  23:18:06,231 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:18Z] INFO  23:18:06,397 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:18Z] INFO  23:18:06,565 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:18Z] INFO  23:18:06,566 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:18Z] INFO  23:18:06,566 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:18Z] INFO  23:18:06,567 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:18Z] INFO  23:18:06,770 MuTect - [MUTECT] Processed 54002271 reads in 641 ms
[2015-09-30T22:18Z] INFO  23:18:06,785 MuTect - [MUTECT] Processed 101006254 reads in 684 ms
[2015-09-30T22:18Z] INFO  23:18:07,191 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:07,446 MuTect - [MUTECT] Processed 55002320 reads in 676 ms
[2015-09-30T22:18Z] INFO  23:18:07,513 MuTect - [MUTECT] Processed 102006348 reads in 727 ms
[2015-09-30T22:18Z] INFO  23:18:08,030 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:08,109 MuTect - [MUTECT] Processed 56002349 reads in 663 ms
[2015-09-30T22:18Z] INFO  23:18:08,233 MuTect - [MUTECT] Processed 103006375 reads in 721 ms
[2015-09-30T22:18Z] INFO  23:18:08,800 MuTect - [MUTECT] Processed 57002375 reads in 691 ms
[2015-09-30T22:18Z] INFO  23:18:08,910 MuTect - [MUTECT] Processed 104006422 reads in 677 ms
[2015-09-30T22:18Z] INFO  23:18:09,127 MuTect - [MUTECT] Processed 1000083 reads in 2514 ms
[2015-09-30T22:18Z] INFO  23:18:09,500 MuTect - [MUTECT] Processed 58002434 reads in 700 ms
[2015-09-30T22:18Z] INFO  23:18:09,618 MuTect - [MUTECT] Processed 105006480 reads in 708 ms
[2015-09-30T22:18Z] INFO  23:18:09,662 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:09,966 MuTect - [MUTECT] Processed 2000196 reads in 839 ms
[2015-09-30T22:18Z] INFO  23:18:10,186 MuTect - [MUTECT] Processed 59002477 reads in 686 ms
[2015-09-30T22:18Z] INFO  23:18:10,269 MuTect - [MUTECT] Processed 106006600 reads in 651 ms
[2015-09-30T22:18Z] INFO  23:18:10,297 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:10,753 MuTect - [MUTECT] Processed 3000220 reads in 787 ms
[2015-09-30T22:18Z] INFO  23:18:10,803 MuTect - [MUTECT] Processed 60002497 reads in 617 ms
[2015-09-30T22:18Z] INFO  23:18:10,907 MuTect - [MUTECT] Processed 107006744 reads in 638 ms
[2015-09-30T22:18Z] INFO  23:18:11,282 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:11,440 MuTect - [MUTECT] Processed 61002534 reads in 637 ms
[2015-09-30T22:18Z] INFO  23:18:11,552 MuTect - [MUTECT] Processed 108006815 reads in 645 ms
[2015-09-30T22:18Z] INFO  23:18:11,965 MuTect - [MUTECT] Processed 4000248 reads in 1212 ms
[2015-09-30T22:18Z] INFO  23:18:12,182 MuTect - [MUTECT] Processed 109006886 reads in 630 ms
[2015-09-30T22:18Z] INFO  23:18:12,366 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:12,413 MuTect - [MUTECT] Processed 62002548 reads in 973 ms
[2015-09-30T22:18Z] INFO  23:18:12,481 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:12,674 MuTect - [MUTECT] Processed 5000250 reads in 709 ms
[2015-09-30T22:18Z] INFO  23:18:12,823 MuTect - [MUTECT] Processed 110006982 reads in 641 ms
[2015-09-30T22:18Z] INFO  23:18:13,072 MuTect - [MUTECT] Processed 63002608 reads in 659 ms
[2015-09-30T22:18Z] INFO  23:18:13,372 MuTect - [MUTECT] Processed 6000283 reads in 698 ms
[2015-09-30T22:18Z] INFO  23:18:13,451 MuTect - [MUTECT] Processed 111007056 reads in 628 ms
[2015-09-30T22:18Z] INFO  23:18:13,722 MuTect - [MUTECT] Processed 64002649 reads in 650 ms
[2015-09-30T22:18Z] INFO  23:18:14,088 MuTect - [MUTECT] Processed 7000300 reads in 716 ms
[2015-09-30T22:18Z] INFO  23:18:14,094 MuTect - [MUTECT] Processed 112007163 reads in 643 ms
[2015-09-30T22:18Z] INFO  23:18:14,370 MuTect - [MUTECT] Processed 65002674 reads in 648 ms
[2015-09-30T22:18Z] INFO  23:18:14,472 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:14,532 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:14,733 MuTect - [MUTECT] Processed 113007253 reads in 639 ms
[2015-09-30T22:18Z] INFO  23:18:14,798 MuTect - [MUTECT] Processed 8000326 reads in 710 ms
[2015-09-30T22:18Z] INFO  23:18:14,920 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:15,067 MuTect - [MUTECT] Processed 66002676 reads in 697 ms
[2015-09-30T22:18Z] INFO  23:18:15,255 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:18Z] INFO  23:18:15,370 MuTect - [MUTECT] Processed 114007269 reads in 637 ms
[2015-09-30T22:18Z] INFO  23:18:15,560 MuTect - [MUTECT] Processed 9000334 reads in 762 ms
[2015-09-30T22:18Z] INFO  23:18:16,001 MuTect - [MUTECT] Processed 115007317 reads in 631 ms
[2015-09-30T22:18Z] INFO  23:18:16,681 MuTect - [MUTECT] Processed 116007383 reads in 680 ms
[2015-09-30T22:18Z] INFO  23:18:16,883 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:17,343 MuTect - [MUTECT] Processed 117007392 reads in 662 ms
[2015-09-30T22:18Z] INFO  23:18:18,010 MuTect - [MUTECT] Processed 118007436 reads in 667 ms
[2015-09-30T22:18Z] INFO  23:18:18,675 MuTect - [MUTECT] Processed 119007469 reads in 665 ms
[2015-09-30T22:18Z] INFO  23:18:19,353 MuTect - [MUTECT] Processed 120007494 reads in 677 ms
[2015-09-30T22:18Z] INFO  23:18:19,414 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:19,972 MuTect - [MUTECT] Processed 121007553 reads in 620 ms
[2015-09-30T22:18Z] INFO  23:18:20,118 ProgressMeter -            done        2.30e+06   50.0 s       22.0 s    100.0%        50.0 s     0.0 s
[2015-09-30T22:18Z] INFO  23:18:20,118 ProgressMeter - Total runtime 50.97 secs, 0.85 min, 0.01 hours
[2015-09-30T22:18Z] INFO  23:18:20,184 MicroScheduler - 44634 reads were filtered out during the traversal out of approximately 789436 total reads (5.65%)
[2015-09-30T22:18Z] INFO  23:18:20,185 MicroScheduler -   -> 32264 reads (4.09% of total) failing DuplicateReadFilter
[2015-09-30T22:18Z] INFO  23:18:20,185 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:18Z] INFO  23:18:20,185 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:18Z] INFO  23:18:20,185 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:18Z] INFO  23:18:20,185 MicroScheduler -   -> 12370 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:18Z] INFO  23:18:20,625 MuTect - [MUTECT] Processed 122007659 reads in 653 ms
[2015-09-30T22:18Z] INFO  23:18:20,756 MuTect - [MUTECT] Processed 10000334 reads in 5196 ms
[2015-09-30T22:18Z] INFO  23:18:21,262 MuTect - [MUTECT] Processed 123007700 reads in 637 ms
[2015-09-30T22:18Z] INFO  23:18:21,264 ProgressMeter -      6:39602754        3.62e+06   90.0 s       24.0 s     49.5%         3.0 m    91.0 s
[2015-09-30T22:18Z] INFO  23:18:21,299 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:18Z] bgzip syn3-6_93954776_124979769-raw-mutect.vcf
[2015-09-30T22:18Z] tabix index syn3-6_93954776_124979769-raw-mutect.vcf.gz
[2015-09-30T22:18Z] INFO  23:18:21,453 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:21,494 MuTect - [MUTECT] Processed 11000336 reads in 738 ms
[2015-09-30T22:18Z] INFO  23:18:21,542 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:21,937 MuTect - [MUTECT] Processed 124007750 reads in 675 ms
[2015-09-30T22:18Z] INFO  23:18:22,239 MuTect - [MUTECT] Processed 12000341 reads in 744 ms
[2015-09-30T22:18Z] INFO  23:18:22,588 MuTect - [MUTECT] Processed 125007761 reads in 651 ms
[2015-09-30T22:18Z] INFO  23:18:22,980 MuTect - [MUTECT] Processed 13000367 reads in 742 ms
[2015-09-30T22:18Z] INFO  23:18:23,243 MuTect - [MUTECT] Processed 126007863 reads in 655 ms
[2015-09-30T22:18Z] MuTect: MuTect
[2015-09-30T22:18Z] INFO  23:18:23,682 MuTect - [MUTECT] Processed 14000454 reads in 701 ms
[2015-09-30T22:18Z] INFO  23:18:23,735 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:23,910 MuTect - [MUTECT] Processed 127007863 reads in 667 ms
[2015-09-30T22:18Z] INFO  23:18:24,131 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:24,415 MuTect - [MUTECT] Processed 15000482 reads in 734 ms
[2015-09-30T22:18Z] INFO  23:18:24,578 MuTect - [MUTECT] Processed 128007971 reads in 668 ms
[2015-09-30T22:18Z] INFO  23:18:25,110 MuTect - [MUTECT] Processed 16000487 reads in 695 ms
[2015-09-30T22:18Z] INFO  23:18:25,201 MuTect - [MUTECT] Processed 129007996 reads in 623 ms
[2015-09-30T22:18Z] INFO  23:18:25,513 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/6/syn3-6_156275378_171115067-raw-mutect-regions.bed to be BED
[2015-09-30T22:18Z] INFO  23:18:25,567 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:18Z] INFO  23:18:25,568 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:18Z] INFO  23:18:25,568 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:18Z] INFO  23:18:25,568 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:18Z] INFO  23:18:25,571 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/6/syn3-6_156275378_171115067-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/6/tx/tmpGJWgAM/syn3-6_156275378_171115067-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:18Z] INFO  23:18:25,571 HelpFormatter - Date/Time: 2015/09/30 23:18:25
[2015-09-30T22:18Z] INFO  23:18:25,572 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:18Z] INFO  23:18:25,572 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:18Z] INFO  23:18:25,598 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:18Z] INFO  23:18:25,602 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:18Z] INFO  23:18:25,653 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:18Z] INFO  23:18:25,700 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:18Z] INFO  23:18:25,707 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:18Z] INFO  23:18:25,769 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:18Z] INFO  23:18:25,789 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:18Z] INFO  23:18:25,815 MuTect - [MUTECT] Processed 17000537 reads in 705 ms
[2015-09-30T22:18Z] INFO  23:18:25,836 MuTect - [MUTECT] Processed 130008070 reads in 635 ms
[2015-09-30T22:18Z] INFO  23:18:25,961 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:18Z] INFO  23:18:26,039 IntervalUtils - Processing 630229 bp from intervals
[2015-09-30T22:18Z] INFO  23:18:26,042 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:18Z] INFO  23:18:26,043 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:18Z] INFO  23:18:26,045 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:26,094 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:18Z] INFO  23:18:26,318 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:18Z] INFO  23:18:26,318 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:18Z] INFO  23:18:26,318 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:18Z] INFO  23:18:26,319 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:18Z] INFO  23:18:26,502 MuTect - [MUTECT] Processed 18000549 reads in 687 ms
[2015-09-30T22:18Z] INFO  23:18:26,515 MuTect - [MUTECT] Processed 131008164 reads in 679 ms
[2015-09-30T22:18Z] INFO  23:18:27,196 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:27,241 MuTect - [MUTECT] Processed 19000577 reads in 738 ms
[2015-09-30T22:18Z] INFO  23:18:27,251 MuTect - [MUTECT] Processed 132008191 reads in 736 ms
[2015-09-30T22:18Z] INFO  23:18:27,921 MuTect - [MUTECT] Processed 133008280 reads in 670 ms
[2015-09-30T22:18Z] INFO  23:18:27,933 MuTect - [MUTECT] Processed 20000623 reads in 693 ms
[2015-09-30T22:18Z] INFO  23:18:28,236 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:28,566 MuTect - [MUTECT] Processed 134008308 reads in 645 ms
[2015-09-30T22:18Z] INFO  23:18:28,645 MuTect - [MUTECT] Processed 21000670 reads in 712 ms
[2015-09-30T22:18Z] INFO  23:18:28,812 MuTect - [MUTECT] Processed 1000021 reads in 2448 ms
[2015-09-30T22:18Z] INFO  23:18:29,202 MuTect - [MUTECT] Processed 135008392 reads in 636 ms
[2015-09-30T22:18Z] INFO  23:18:29,381 MuTect - [MUTECT] Processed 22000682 reads in 736 ms
[2015-09-30T22:18Z] INFO  23:18:29,491 MuTect - [MUTECT] Processed 2000067 reads in 679 ms
[2015-09-30T22:18Z] INFO  23:18:29,814 MuTect - [MUTECT] Processed 136008441 reads in 612 ms
[2015-09-30T22:18Z] INFO  23:18:29,844 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:30,092 MuTect - [MUTECT] Processed 23000698 reads in 711 ms
[2015-09-30T22:18Z] INFO  23:18:30,188 MuTect - [MUTECT] Processed 3000070 reads in 697 ms
[2015-09-30T22:18Z] INFO  23:18:30,264 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:30,445 MuTect - [MUTECT] Processed 137008492 reads in 630 ms
[2015-09-30T22:18Z] INFO  23:18:30,610 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:30,795 MuTect - [MUTECT] Processed 24000740 reads in 703 ms
[2015-09-30T22:18Z] INFO  23:18:30,853 MuTect - [MUTECT] Processed 4000080 reads in 665 ms
[2015-09-30T22:18Z] INFO  23:18:31,141 MuTect - [MUTECT] Processed 138008530 reads in 697 ms
[2015-09-30T22:18Z] INFO  23:18:31,472 MuTect - [MUTECT] Processed 25000795 reads in 677 ms
[2015-09-30T22:18Z] INFO  23:18:31,510 MuTect - [MUTECT] Processed 5000128 reads in 657 ms
[2015-09-30T22:18Z] INFO  23:18:31,751 MuTect - [MUTECT] Processed 139008589 reads in 610 ms
[2015-09-30T22:18Z] INFO  23:18:32,141 MuTect - [MUTECT] Processed 26000811 reads in 669 ms
[2015-09-30T22:18Z] INFO  23:18:32,247 MuTect - [MUTECT] Processed 6000134 reads in 737 ms
[2015-09-30T22:18Z] INFO  23:18:32,259 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:32,394 MuTect - [MUTECT] Processed 140008655 reads in 643 ms
[2015-09-30T22:18Z] INFO  23:18:32,487 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:32,837 MuTect - [MUTECT] Processed 27000863 reads in 696 ms
[2015-09-30T22:18Z] INFO  23:18:33,029 MuTect - [MUTECT] Processed 7000142 reads in 782 ms
[2015-09-30T22:18Z] INFO  23:18:33,068 MuTect - [MUTECT] Processed 141008736 reads in 674 ms
[2015-09-30T22:18Z] INFO  23:18:33,120 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:33,506 MuTect - [MUTECT] Processed 28000914 reads in 669 ms
[2015-09-30T22:18Z] INFO  23:18:33,734 MuTect - [MUTECT] Processed 8000199 reads in 705 ms
[2015-09-30T22:18Z] INFO  23:18:33,776 MuTect - [MUTECT] Processed 142008756 reads in 708 ms
[2015-09-30T22:18Z] INFO  23:18:34,166 MuTect - [MUTECT] Processed 29000950 reads in 660 ms
[2015-09-30T22:18Z] INFO  23:18:34,395 MuTect - [MUTECT] Processed 9000290 reads in 661 ms
[2015-09-30T22:18Z] INFO  23:18:34,436 MuTect - [MUTECT] Processed 143008785 reads in 660 ms
[2015-09-30T22:18Z] INFO  23:18:34,771 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:34,839 MuTect - [MUTECT] Processed 30001021 reads in 673 ms
[2015-09-30T22:18Z] INFO  23:18:34,901 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:35,047 MuTect - [MUTECT] Processed 10000320 reads in 652 ms
[2015-09-30T22:18Z] INFO  23:18:35,122 MuTect - [MUTECT] Processed 144008799 reads in 686 ms
[2015-09-30T22:18Z] INFO  23:18:35,359 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:35,523 MuTect - [MUTECT] Processed 31001027 reads in 684 ms
[2015-09-30T22:18Z] INFO  23:18:35,719 MuTect - [MUTECT] Processed 11000392 reads in 672 ms
[2015-09-30T22:18Z] INFO  23:18:35,836 MuTect - [MUTECT] Processed 145008846 reads in 714 ms
[2015-09-30T22:18Z] INFO  23:18:36,210 MuTect - [MUTECT] Processed 32001109 reads in 687 ms
[2015-09-30T22:18Z] INFO  23:18:36,416 MuTect - [MUTECT] Processed 12000453 reads in 697 ms
[2015-09-30T22:18Z] INFO  23:18:36,530 MuTect - [MUTECT] Processed 146008898 reads in 694 ms
[2015-09-30T22:18Z] INFO  23:18:36,570 ProgressMeter -     6:136871701        1.17e+06   30.0 s       25.0 s     37.9%        79.0 s    49.0 s
[2015-09-30T22:18Z] INFO  23:18:36,831 MuTect - [MUTECT] Processed 33001179 reads in 621 ms
[2015-09-30T22:18Z] INFO  23:18:37,113 MuTect - [MUTECT] Processed 13000457 reads in 697 ms
[2015-09-30T22:18Z] INFO  23:18:37,119 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:37,199 MuTect - [MUTECT] Processed 147008903 reads in 669 ms
[2015-09-30T22:18Z] INFO  23:18:37,441 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:37,462 MuTect - [MUTECT] Processed 34001181 reads in 631 ms
[2015-09-30T22:18Z] INFO  23:18:37,507 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:37,772 MuTect - [MUTECT] Processed 14000544 reads in 659 ms
[2015-09-30T22:18Z] INFO  23:18:37,907 MuTect - [MUTECT] Processed 148008931 reads in 708 ms
[2015-09-30T22:18Z] INFO  23:18:38,107 MuTect - [MUTECT] Processed 35001233 reads in 645 ms
[2015-09-30T22:18Z] INFO  23:18:38,559 MuTect - [MUTECT] Processed 15000572 reads in 787 ms
[2015-09-30T22:18Z] INFO  23:18:38,624 MuTect - [MUTECT] Processed 149009021 reads in 717 ms
[2015-09-30T22:18Z] INFO  23:18:38,778 MuTect - [MUTECT] Processed 36001234 reads in 671 ms
[2015-09-30T22:18Z] INFO  23:18:39,225 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:39,279 MuTect - [MUTECT] Processed 16000667 reads in 720 ms
[2015-09-30T22:18Z] INFO  23:18:39,336 MuTect - [MUTECT] Processed 150009129 reads in 712 ms
[2015-09-30T22:18Z] INFO  23:18:39,424 MuTect - [MUTECT] Processed 37001234 reads in 646 ms
[2015-09-30T22:18Z] INFO  23:18:39,808 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:39,971 MuTect - [MUTECT] Processed 17000765 reads in 692 ms
[2015-09-30T22:18Z] INFO  23:18:39,982 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:40,006 MuTect - [MUTECT] Processed 151009134 reads in 670 ms
[2015-09-30T22:18Z] INFO  23:18:40,056 MuTect - [MUTECT] Processed 38001333 reads in 632 ms
[2015-09-30T22:18Z] INFO  23:18:40,673 MuTect - [MUTECT] Processed 18000805 reads in 702 ms
[2015-09-30T22:18Z] INFO  23:18:40,677 MuTect - [MUTECT] Processed 39001360 reads in 621 ms
[2015-09-30T22:18Z] INFO  23:18:40,689 MuTect - [MUTECT] Processed 152009213 reads in 683 ms
[2015-09-30T22:18Z] INFO  23:18:41,282 MuTect - [MUTECT] Processed 40001375 reads in 605 ms
[2015-09-30T22:18Z] INFO  23:18:41,341 MuTect - [MUTECT] Processed 153009249 reads in 652 ms
[2015-09-30T22:18Z] INFO  23:18:41,352 MuTect - [MUTECT] Processed 19000858 reads in 679 ms
[2015-09-30T22:18Z] INFO  23:18:41,494 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:41,906 MuTect - [MUTECT] Processed 41001411 reads in 624 ms
[2015-09-30T22:18Z] INFO  23:18:41,990 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:42,021 MuTect - [MUTECT] Processed 154009281 reads in 680 ms
[2015-09-30T22:18Z] INFO  23:18:42,036 MuTect - [MUTECT] Processed 20000957 reads in 684 ms
[2015-09-30T22:18Z] INFO  23:18:42,375 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:42,551 MuTect - [MUTECT] Processed 42001436 reads in 645 ms
[2015-09-30T22:18Z] INFO  23:18:42,687 MuTect - [MUTECT] Processed 155009344 reads in 666 ms
[2015-09-30T22:18Z] INFO  23:18:42,698 MuTect - [MUTECT] Processed 21000999 reads in 662 ms
[2015-09-30T22:18Z] INFO  23:18:43,193 MuTect - [MUTECT] Processed 43001447 reads in 642 ms
[2015-09-30T22:18Z] INFO  23:18:43,354 MuTect - [MUTECT] Processed 156009444 reads in 667 ms
[2015-09-30T22:18Z] INFO  23:18:43,374 MuTect - [MUTECT] Processed 22001044 reads in 676 ms
[2015-09-30T22:18Z] INFO  23:18:43,810 MuTect - [MUTECT] Processed 44001456 reads in 617 ms
[2015-09-30T22:18Z] INFO  23:18:43,944 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:44,012 MuTect - [MUTECT] Processed 157009451 reads in 658 ms
[2015-09-30T22:18Z] INFO  23:18:44,090 MuTect - [MUTECT] Processed 23001060 reads in 716 ms
[2015-09-30T22:18Z] INFO  23:18:44,250 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:44,423 MuTect - [MUTECT] Processed 45001468 reads in 613 ms
[2015-09-30T22:18Z] INFO  23:18:44,668 MuTect - [MUTECT] Processed 158009515 reads in 656 ms
[2015-09-30T22:18Z] INFO  23:18:44,750 MuTect - [MUTECT] Processed 24001062 reads in 660 ms
[2015-09-30T22:18Z] INFO  23:18:44,946 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:45,110 MuTect - [MUTECT] Processed 46001514 reads in 687 ms
[2015-09-30T22:18Z] INFO  23:18:45,348 MuTect - [MUTECT] Processed 159009538 reads in 680 ms
[2015-09-30T22:18Z] INFO  23:18:45,393 MuTect - [MUTECT] Processed 25001104 reads in 643 ms
[2015-09-30T22:18Z] INFO  23:18:45,790 MuTect - [MUTECT] Processed 47001544 reads in 680 ms
[2015-09-30T22:18Z] INFO  23:18:46,015 MuTect - [MUTECT] Processed 160009613 reads in 667 ms
[2015-09-30T22:18Z] INFO  23:18:46,057 MuTect - [MUTECT] Processed 26001137 reads in 664 ms
[2015-09-30T22:18Z] INFO  23:18:46,404 MuTect - [MUTECT] Processed 48001564 reads in 614 ms
[2015-09-30T22:18Z] INFO  23:18:46,451 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:46,531 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:46,667 MuTect - [MUTECT] Processed 27001393 reads in 610 ms
[2015-09-30T22:18Z] INFO  23:18:46,714 MuTect - [MUTECT] Processed 161009645 reads in 699 ms
[2015-09-30T22:18Z] INFO  23:18:47,044 MuTect - [MUTECT] Processed 49001566 reads in 640 ms
[2015-09-30T22:18Z] INFO  23:18:47,270 MuTect - [MUTECT] Processed 28001779 reads in 603 ms
[2015-09-30T22:18Z] INFO  23:18:47,353 MuTect - [MUTECT] Processed 162009722 reads in 639 ms
[2015-09-30T22:18Z] INFO  23:18:47,739 MuTect - [MUTECT] Processed 50001627 reads in 695 ms
[2015-09-30T22:18Z] INFO  23:18:47,969 MuTect - [MUTECT] Processed 29002008 reads in 699 ms
[2015-09-30T22:18Z] INFO  23:18:48,014 MuTect - [MUTECT] Processed 163009767 reads in 661 ms
[2015-09-30T22:18Z] INFO  23:18:48,409 MuTect - [MUTECT] Processed 51001662 reads in 670 ms
[2015-09-30T22:18Z] INFO  23:18:48,547 MuTect - [MUTECT] Processed 30002112 reads in 578 ms
[2015-09-30T22:18Z] INFO  23:18:48,636 MuTect - [MUTECT] Processed 164009782 reads in 622 ms
[2015-09-30T22:18Z] INFO  23:18:48,666 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:48,899 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:49,057 MuTect - [MUTECT] Processed 52001737 reads in 648 ms
[2015-09-30T22:18Z] INFO  23:18:49,178 MuTect - [MUTECT] Processed 31002137 reads in 631 ms
[2015-09-30T22:18Z] INFO  23:18:49,262 MuTect - [MUTECT] Processed 165009913 reads in 626 ms
[2015-09-30T22:18Z] INFO  23:18:49,384 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:49,740 MuTect - [MUTECT] Processed 53001748 reads in 683 ms
[2015-09-30T22:18Z] INFO  23:18:49,793 MuTect - [MUTECT] Processed 32002193 reads in 615 ms
[2015-09-30T22:18Z] INFO  23:18:49,885 MuTect - [MUTECT] Processed 166009927 reads in 623 ms
[2015-09-30T22:18Z] INFO  23:18:50,419 MuTect - [MUTECT] Processed 54001825 reads in 679 ms
[2015-09-30T22:18Z] INFO  23:18:50,421 MuTect - [MUTECT] Processed 33002234 reads in 628 ms
[2015-09-30T22:18Z] INFO  23:18:50,506 MuTect - [MUTECT] Processed 167010058 reads in 621 ms
[2015-09-30T22:18Z] INFO  23:18:50,655 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:51,080 MuTect - [MUTECT] Processed 34002262 reads in 659 ms
[2015-09-30T22:18Z] INFO  23:18:51,100 MuTect - [MUTECT] Processed 55001878 reads in 681 ms
[2015-09-30T22:18Z] INFO  23:18:51,128 MuTect - [MUTECT] Processed 168010102 reads in 622 ms
[2015-09-30T22:18Z] INFO  23:18:51,265 ProgressMeter -      6:43501631        5.10e+06  120.0 s       23.0 s     68.0%         2.9 m    56.0 s
[2015-09-30T22:18Z] INFO  23:18:51,376 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:51,770 MuTect - [MUTECT] Processed 56001926 reads in 670 ms
[2015-09-30T22:18Z] INFO  23:18:51,773 MuTect - [MUTECT] Processed 169010164 reads in 645 ms
[2015-09-30T22:18Z] INFO  23:18:51,777 MuTect - [MUTECT] Processed 35002287 reads in 697 ms
[2015-09-30T22:18Z] INFO  23:18:51,930 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:52,395 MuTect - [MUTECT] Processed 170010221 reads in 622 ms
[2015-09-30T22:18Z] INFO  23:18:52,415 MuTect - [MUTECT] Processed 57001958 reads in 644 ms
[2015-09-30T22:18Z] INFO  23:18:52,435 MuTect - [MUTECT] Processed 36002343 reads in 658 ms
[2015-09-30T22:18Z] INFO  23:18:52,984 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:53,018 MuTect - [MUTECT] Processed 171010280 reads in 623 ms
[2015-09-30T22:18Z] INFO  23:18:53,061 MuTect - [MUTECT] Processed 58002070 reads in 647 ms
[2015-09-30T22:18Z] INFO  23:18:53,096 MuTect - [MUTECT] Processed 37002437 reads in 661 ms
[2015-09-30T22:18Z] INFO  23:18:53,686 MuTect - [MUTECT] Processed 172010351 reads in 668 ms
[2015-09-30T22:18Z] INFO  23:18:53,723 MuTect - [MUTECT] Processed 59002128 reads in 662 ms
[2015-09-30T22:18Z] INFO  23:18:53,743 MuTect - [MUTECT] Processed 38002545 reads in 647 ms
[2015-09-30T22:18Z] INFO  23:18:53,897 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:54,337 MuTect - [MUTECT] Processed 173010408 reads in 651 ms
[2015-09-30T22:18Z] INFO  23:18:54,387 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:54,404 MuTect - [MUTECT] Processed 60002215 reads in 681 ms
[2015-09-30T22:18Z] INFO  23:18:54,423 MuTect - [MUTECT] Processed 39002547 reads in 680 ms
[2015-09-30T22:18Z] INFO  23:18:54,964 MuTect - [MUTECT] Processed 174010510 reads in 627 ms
[2015-09-30T22:18Z] INFO  23:18:55,044 MuTect - [MUTECT] Processed 61002245 reads in 640 ms
[2015-09-30T22:18Z] INFO  23:18:55,073 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:55,108 MuTect - [MUTECT] Processed 40002578 reads in 685 ms
[2015-09-30T22:18Z] INFO  23:18:55,580 MuTect - [MUTECT] Processed 175010540 reads in 615 ms
[2015-09-30T22:18Z] INFO  23:18:55,691 MuTect - [MUTECT] Processed 62002303 reads in 647 ms
[2015-09-30T22:18Z] INFO  23:18:55,777 MuTect - [MUTECT] Processed 41002612 reads in 669 ms
[2015-09-30T22:18Z] INFO  23:18:56,176 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:56,250 MuTect - [MUTECT] Processed 176010623 reads in 671 ms
[2015-09-30T22:18Z] INFO  23:18:56,315 MuTect - [MUTECT] Processed 63002370 reads in 624 ms
[2015-09-30T22:18Z] INFO  23:18:56,321 ProgressMeter -     6:167411050        1.18e+06   30.0 s       25.0 s     69.7%        43.0 s    13.0 s
[2015-09-30T22:18Z] INFO  23:18:56,698 MuTect - [MUTECT] Processed 42002623 reads in 921 ms
[2015-09-30T22:18Z] INFO  23:18:56,858 MuTect - [MUTECT] Processed 177010698 reads in 608 ms
[2015-09-30T22:18Z] INFO  23:18:56,943 MuTect - [MUTECT] Processed 64002447 reads in 628 ms
[2015-09-30T22:18Z] INFO  23:18:56,965 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:57,191 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:57,370 MuTect - [MUTECT] Processed 43002636 reads in 672 ms
[2015-09-30T22:18Z] INFO  23:18:57,472 MuTect - [MUTECT] Processed 178010732 reads in 614 ms
[2015-09-30T22:18Z] INFO  23:18:57,563 MuTect - [MUTECT] Processed 65002523 reads in 620 ms
[2015-09-30T22:18Z] INFO  23:18:58,134 MuTect - [MUTECT] Processed 44002683 reads in 764 ms
[2015-09-30T22:18Z] INFO  23:18:58,144 MuTect - [MUTECT] Processed 179010800 reads in 672 ms
[2015-09-30T22:18Z] INFO  23:18:58,187 MuTect - [MUTECT] Processed 66002581 reads in 624 ms
[2015-09-30T22:18Z] INFO  23:18:58,565 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:58,777 MuTect - [MUTECT] Processed 180010827 reads in 633 ms
[2015-09-30T22:18Z] INFO  23:18:58,822 MuTect - [MUTECT] Processed 67002601 reads in 635 ms
[2015-09-30T22:18Z] INFO  23:18:58,859 MuTect - [MUTECT] Processed 45002694 reads in 725 ms
[2015-09-30T22:18Z] INFO  23:18:59,179 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:59,410 MuTect - [MUTECT] Processed 181010858 reads in 633 ms
[2015-09-30T22:18Z] INFO  23:18:59,449 MuTect - [MUTECT] Processed 68002678 reads in 627 ms
[2015-09-30T22:18Z] INFO  23:18:59,465 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:18Z] INFO  23:18:59,602 MuTect - [MUTECT] Processed 46002694 reads in 743 ms
[2015-09-30T22:19Z] INFO  23:19:00,072 MuTect - [MUTECT] Processed 182010941 reads in 662 ms
[2015-09-30T22:19Z] INFO  23:19:00,149 MuTect - [MUTECT] Processed 69002784 reads in 700 ms
[2015-09-30T22:19Z] INFO  23:19:00,283 MuTect - [MUTECT] Processed 47002698 reads in 681 ms
[2015-09-30T22:19Z] INFO  23:19:00,719 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:00,740 MuTect - [MUTECT] Processed 183010993 reads in 668 ms
[2015-09-30T22:19Z] INFO  23:19:00,839 MuTect - [MUTECT] Processed 70002855 reads in 690 ms
[2015-09-30T22:19Z] INFO  23:19:01,020 MuTect - [MUTECT] Processed 48002728 reads in 737 ms
[2015-09-30T22:19Z] INFO  23:19:01,362 MuTect - [MUTECT] Processed 184011030 reads in 622 ms
[2015-09-30T22:19Z] INFO  23:19:01,512 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:01,529 MuTect - [MUTECT] Processed 71002860 reads in 690 ms
[2015-09-30T22:19Z] INFO  23:19:01,777 MuTect - [MUTECT] Processed 49002770 reads in 757 ms
[2015-09-30T22:19Z] INFO  23:19:01,879 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:02,025 MuTect - [MUTECT] Processed 185011049 reads in 663 ms
[2015-09-30T22:19Z] INFO  23:19:02,187 MuTect - [MUTECT] Processed 72002877 reads in 658 ms
[2015-09-30T22:19Z] INFO  23:19:02,464 MuTect - [MUTECT] Processed 50002779 reads in 687 ms
[2015-09-30T22:19Z] INFO  23:19:02,701 MuTect - [MUTECT] Processed 186011089 reads in 676 ms
[2015-09-30T22:19Z] INFO  23:19:02,875 MuTect - [MUTECT] Processed 73002934 reads in 688 ms
[2015-09-30T22:19Z] INFO  23:19:03,043 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:03,209 MuTect - [MUTECT] Processed 51002781 reads in 745 ms
[2015-09-30T22:19Z] INFO  23:19:03,340 MuTect - [MUTECT] Processed 187011132 reads in 639 ms
[2015-09-30T22:19Z] INFO  23:19:03,596 MuTect - [MUTECT] Processed 74002982 reads in 721 ms
[2015-09-30T22:19Z] INFO  23:19:03,920 MuTect - [MUTECT] Processed 52002786 reads in 711 ms
[2015-09-30T22:19Z] INFO  23:19:04,020 MuTect - [MUTECT] Processed 188011170 reads in 680 ms
[2015-09-30T22:19Z] INFO  23:19:04,033 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:04,168 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:04,250 MuTect - [MUTECT] Processed 75003049 reads in 654 ms
[2015-09-30T22:19Z] INFO  23:19:04,571 MuTect - [MUTECT] Processed 53002795 reads in 651 ms
[2015-09-30T22:19Z] INFO  23:19:04,755 MuTect - [MUTECT] Processed 189011175 reads in 735 ms
[2015-09-30T22:19Z] INFO  23:19:04,896 MuTect - [MUTECT] Processed 76003095 reads in 646 ms
[2015-09-30T22:19Z] INFO  23:19:05,261 MuTect - [MUTECT] Processed 54002874 reads in 690 ms
[2015-09-30T22:19Z] INFO  23:19:05,366 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:05,448 MuTect - [MUTECT] Processed 190011217 reads in 693 ms
[2015-09-30T22:19Z] INFO  23:19:05,553 MuTect - [MUTECT] Processed 77003135 reads in 657 ms
[2015-09-30T22:19Z] INFO  23:19:05,935 MuTect - [MUTECT] Processed 55002948 reads in 674 ms
[2015-09-30T22:19Z] INFO  23:19:06,129 MuTect - [MUTECT] Processed 191011221 reads in 681 ms
[2015-09-30T22:19Z] INFO  23:19:06,246 MuTect - [MUTECT] Processed 78003155 reads in 693 ms
[2015-09-30T22:19Z] INFO  23:19:06,335 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:06,402 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:06,571 ProgressMeter -     6:152473169        2.53e+06   60.0 s       23.0 s     85.5%        70.0 s    10.0 s
[2015-09-30T22:19Z] INFO  23:19:06,613 MuTect - [MUTECT] Processed 56003020 reads in 677 ms
[2015-09-30T22:19Z] INFO  23:19:06,863 MuTect - [MUTECT] Processed 192011238 reads in 734 ms
[2015-09-30T22:19Z] INFO  23:19:06,968 MuTect - [MUTECT] Processed 79003186 reads in 722 ms
[2015-09-30T22:19Z] INFO  23:19:07,296 MuTect - [MUTECT] Processed 57003118 reads in 684 ms
[2015-09-30T22:19Z] INFO  23:19:07,573 MuTect - [MUTECT] Processed 193011306 reads in 710 ms
[2015-09-30T22:19Z] INFO  23:19:07,801 MuTect - [MUTECT] Processed 80003250 reads in 833 ms
[2015-09-30T22:19Z] INFO  23:19:07,862 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:07,982 MuTect - [MUTECT] Processed 58003176 reads in 686 ms
[2015-09-30T22:19Z] INFO  23:19:08,292 MuTect - [MUTECT] Processed 194011309 reads in 719 ms
[2015-09-30T22:19Z] INFO  23:19:08,516 MuTect - [MUTECT] Processed 81003359 reads in 715 ms
[2015-09-30T22:19Z] INFO  23:19:08,668 MuTect - [MUTECT] Processed 59003262 reads in 686 ms
[2015-09-30T22:19Z] INFO  23:19:08,750 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:08,809 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:19Z] INFO  23:19:08,956 ProgressMeter -            done        1.72e+06   42.0 s       24.0 s    100.0%        42.0 s     0.0 s
[2015-09-30T22:19Z] INFO  23:19:08,956 ProgressMeter - Total runtime 42.64 secs, 0.71 min, 0.01 hours
[2015-09-30T22:19Z] INFO  23:19:09,015 MuTect - [MUTECT] Processed 195011331 reads in 723 ms
[2015-09-30T22:19Z] INFO  23:19:09,026 MicroScheduler - 45570 reads were filtered out during the traversal out of approximately 716017 total reads (6.36%)
[2015-09-30T22:19Z] INFO  23:19:09,026 MicroScheduler -   -> 33922 reads (4.74% of total) failing DuplicateReadFilter
[2015-09-30T22:19Z] INFO  23:19:09,026 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:19Z] INFO  23:19:09,027 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:19Z] INFO  23:19:09,027 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:19Z] INFO  23:19:09,027 MicroScheduler -   -> 11648 reads (1.63% of total) failing UnmappedReadFilter
[2015-09-30T22:19Z] INFO  23:19:09,241 MuTect - [MUTECT] Processed 82003359 reads in 725 ms
[2015-09-30T22:19Z] INFO  23:19:09,733 MuTect - [MUTECT] Processed 196011378 reads in 718 ms
[2015-09-30T22:19Z] INFO  23:19:09,947 MuTect - [MUTECT] Processed 83003396 reads in 706 ms
[2015-09-30T22:19Z] INFO  23:19:10,298 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:19Z] INFO  23:19:10,300 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:10,414 MuTect - [MUTECT] Processed 197011430 reads in 681 ms
[2015-09-30T22:19Z] INFO  23:19:10,566 MuTect - [MUTECT] Processed 84003447 reads in 619 ms
[2015-09-30T22:19Z] INFO  23:19:11,083 MuTect - [MUTECT] Processed 198011434 reads in 669 ms
[2015-09-30T22:19Z] INFO  23:19:11,146 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:11,204 MuTect - [MUTECT] Processed 85003489 reads in 638 ms
[2015-09-30T22:19Z] INFO  23:19:11,761 MuTect - [MUTECT] Processed 199011481 reads in 678 ms
[2015-09-30T22:19Z] INFO  23:19:11,868 MuTect - [MUTECT] Processed 86003539 reads in 664 ms
[2015-09-30T22:19Z] INFO  23:19:12,453 MuTect - [MUTECT] Processed 200011490 reads in 692 ms
[2015-09-30T22:19Z] bgzip syn3-6_156275378_171115067-raw-mutect.vcf
[2015-09-30T22:19Z] INFO  23:19:12,717 MuTect - [MUTECT] Processed 87003595 reads in 849 ms
[2015-09-30T22:19Z] INFO  23:19:13,007 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:19Z] tabix index syn3-6_156275378_171115067-raw-mutect.vcf.gz
[2015-09-30T22:19Z] INFO  23:19:13,102 MuTect - [MUTECT] Processed 201011547 reads in 649 ms
[2015-09-30T22:19Z] INFO  23:19:13,352 MuTect - [MUTECT] Processed 88003701 reads in 635 ms
[2015-09-30T22:19Z] INFO  23:19:13,605 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:13,767 MuTect - [MUTECT] Processed 202011566 reads in 665 ms
[2015-09-30T22:19Z] INFO  23:19:13,987 MuTect - [MUTECT] Processed 89003774 reads in 635 ms
[2015-09-30T22:19Z] INFO  23:19:14,449 MuTect - [MUTECT] Processed 203011582 reads in 682 ms
[2015-09-30T22:19Z] INFO  23:19:14,605 MuTect - [MUTECT] Processed 90003867 reads in 617 ms
[2015-09-30T22:19Z] INFO  23:19:15,110 MuTect - [MUTECT] Processed 204011597 reads in 661 ms
[2015-09-30T22:19Z] INFO  23:19:15,254 MuTect - [MUTECT] Processed 91003938 reads in 650 ms
[2015-09-30T22:19Z] INFO  23:19:15,300 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:15,784 MuTect - [MUTECT] Processed 205011688 reads in 674 ms
[2015-09-30T22:19Z] MuTect: MuTect
[2015-09-30T22:19Z] INFO  23:19:15,912 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:19Z] INFO  23:19:15,916 ProgressMeter -            done        3.06e+06   69.0 s       22.0 s    100.0%        69.0 s     0.0 s
[2015-09-30T22:19Z] INFO  23:19:15,916 ProgressMeter - Total runtime 69.35 secs, 1.16 min, 0.02 hours
[2015-09-30T22:19Z] INFO  23:19:15,919 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:15,983 MicroScheduler - 63093 reads were filtered out during the traversal out of approximately 1097400 total reads (5.75%)
[2015-09-30T22:19Z] INFO  23:19:15,983 MicroScheduler -   -> 45869 reads (4.18% of total) failing DuplicateReadFilter
[2015-09-30T22:19Z] INFO  23:19:15,984 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:19Z] INFO  23:19:15,984 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:19Z] INFO  23:19:15,984 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:19Z] INFO  23:19:15,984 MicroScheduler -   -> 17224 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:19Z] INFO  23:19:16,488 MuTect - [MUTECT] Processed 206011708 reads in 704 ms
[2015-09-30T22:19Z] INFO  23:19:16,967 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:19Z] bgzip syn3-6_125064552_156268261-raw-mutect.vcf
[2015-09-30T22:19Z] tabix index syn3-6_125064552_156268261-raw-mutect.vcf.gz
[2015-09-30T22:19Z] INFO  23:19:17,228 MuTect - [MUTECT] Processed 207011777 reads in 740 ms
[2015-09-30T22:19Z] INFO  23:19:17,963 MuTect - [MUTECT] Processed 208011817 reads in 735 ms
[2015-09-30T22:19Z] INFO  23:19:18,208 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/7/syn3-7_0_31019109-raw-mutect-regions.bed to be BED
[2015-09-30T22:19Z] INFO  23:19:18,265 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:19Z] INFO  23:19:18,265 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:19Z] INFO  23:19:18,265 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:19Z] INFO  23:19:18,265 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:19Z] INFO  23:19:18,269 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/7/syn3-7_0_31019109-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/7/tx/tmptaTHDO/syn3-7_0_31019109-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:19Z] INFO  23:19:18,269 HelpFormatter - Date/Time: 2015/09/30 23:19:18
[2015-09-30T22:19Z] INFO  23:19:18,269 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:19Z] INFO  23:19:18,269 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:19Z] INFO  23:19:18,297 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:19Z] INFO  23:19:18,302 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:19Z] INFO  23:19:18,308 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:18,353 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:19Z] INFO  23:19:18,403 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:19Z] INFO  23:19:18,411 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:19Z] INFO  23:19:18,452 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:19Z] INFO  23:19:18,463 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:19Z] INFO  23:19:18,633 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:19Z] INFO  23:19:18,652 MuTect - [MUTECT] Processed 209011828 reads in 689 ms
[2015-09-30T22:19Z] INFO  23:19:18,737 IntervalUtils - Processing 1428141 bp from intervals
[2015-09-30T22:19Z] INFO  23:19:18,741 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:19Z] INFO  23:19:18,741 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:19Z] INFO  23:19:18,912 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:19Z] INFO  23:19:19,076 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:19Z] INFO  23:19:19,077 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:19Z] INFO  23:19:19,077 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:19Z] INFO  23:19:19,078 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:19Z] INFO  23:19:19,345 MuTect - [MUTECT] Processed 210011882 reads in 693 ms
[2015-09-30T22:19Z] MuTect: MuTect
[2015-09-30T22:19Z] INFO  23:19:20,035 MuTect - [MUTECT] Processed 211011939 reads in 690 ms
[2015-09-30T22:19Z] INFO  23:19:20,727 MuTect - [MUTECT] Processed 212012005 reads in 692 ms
[2015-09-30T22:19Z] INFO  23:19:20,924 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:21,266 ProgressMeter -      6:54001965        6.57e+06    2.5 m       22.0 s     91.4%         2.7 m    14.0 s
[2015-09-30T22:19Z] INFO  23:19:21,412 MuTect - [MUTECT] Processed 1000082 reads in 2286 ms
[2015-09-30T22:19Z] INFO  23:19:21,431 MuTect - [MUTECT] Processed 213012023 reads in 704 ms
[2015-09-30T22:19Z] INFO  23:19:21,788 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/7/syn3-7_31022897_62585293-raw-mutect-regions.bed to be BED
[2015-09-30T22:19Z] INFO  23:19:21,846 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:19Z] INFO  23:19:21,846 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:19Z] INFO  23:19:21,846 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:19Z] INFO  23:19:21,846 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:19Z] INFO  23:19:21,850 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/7/syn3-7_31022897_62585293-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/7/tx/tmpbSiI2M/syn3-7_31022897_62585293-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:19Z] INFO  23:19:21,850 HelpFormatter - Date/Time: 2015/09/30 23:19:21
[2015-09-30T22:19Z] INFO  23:19:21,850 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:19Z] INFO  23:19:21,850 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:19Z] INFO  23:19:21,878 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:19Z] INFO  23:19:21,883 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:19Z] INFO  23:19:21,940 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:19Z] INFO  23:19:21,989 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:19Z] INFO  23:19:21,996 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:19Z] INFO  23:19:22,020 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:19Z] INFO  23:19:22,031 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:19Z] INFO  23:19:22,166 MuTect - [MUTECT] Processed 214012030 reads in 735 ms
[2015-09-30T22:19Z] INFO  23:19:22,176 MuTect - [MUTECT] Processed 2000116 reads in 765 ms
[2015-09-30T22:19Z] INFO  23:19:22,213 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:19Z] INFO  23:19:22,306 IntervalUtils - Processing 1035831 bp from intervals
[2015-09-30T22:19Z] INFO  23:19:22,310 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:19Z] INFO  23:19:22,310 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:19Z] INFO  23:19:22,631 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:19Z] INFO  23:19:22,792 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:19Z] INFO  23:19:22,792 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:19Z] INFO  23:19:22,792 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:19Z] INFO  23:19:22,793 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:19Z] INFO  23:19:22,913 MuTect - [MUTECT] Processed 215012121 reads in 747 ms
[2015-09-30T22:19Z] INFO  23:19:22,944 MuTect - [MUTECT] Processed 3000163 reads in 768 ms
[2015-09-30T22:19Z] INFO  23:19:23,258 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:23,646 MuTect - [MUTECT] Processed 216012145 reads in 733 ms
[2015-09-30T22:19Z] INFO  23:19:23,710 MuTect - [MUTECT] Processed 4000216 reads in 766 ms
[2015-09-30T22:19Z] INFO  23:19:23,788 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:24,323 MuTect - [MUTECT] Processed 217012193 reads in 677 ms
[2015-09-30T22:19Z] INFO  23:19:24,468 MuTect - [MUTECT] Processed 5000235 reads in 758 ms
[2015-09-30T22:19Z] INFO  23:19:24,969 MuTect - [MUTECT] Processed 1000008 reads in 2127 ms
[2015-09-30T22:19Z] INFO  23:19:25,012 MuTect - [MUTECT] Processed 218012252 reads in 689 ms
[2015-09-30T22:19Z] INFO  23:19:25,226 MuTect - [MUTECT] Processed 6000256 reads in 758 ms
[2015-09-30T22:19Z] INFO  23:19:25,697 MuTect - [MUTECT] Processed 219012286 reads in 685 ms
[2015-09-30T22:19Z] INFO  23:19:25,740 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:25,918 MuTect - [MUTECT] Processed 7000336 reads in 692 ms
[2015-09-30T22:19Z] INFO  23:19:26,066 MuTect - [MUTECT] Processed 2000079 reads in 1097 ms
[2015-09-30T22:19Z] INFO  23:19:26,346 MuTect - [MUTECT] Processed 220012307 reads in 649 ms
[2015-09-30T22:19Z] INFO  23:19:26,442 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:26,726 MuTect - [MUTECT] Processed 8000430 reads in 807 ms
[2015-09-30T22:19Z] INFO  23:19:26,948 MuTect - [MUTECT] Processed 3000112 reads in 882 ms
[2015-09-30T22:19Z] INFO  23:19:27,011 MuTect - [MUTECT] Processed 221012382 reads in 665 ms
[2015-09-30T22:19Z] INFO  23:19:27,347 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:27,431 MuTect - [MUTECT] Processed 9000451 reads in 706 ms
[2015-09-30T22:19Z] INFO  23:19:27,696 MuTect - [MUTECT] Processed 222012411 reads in 685 ms
[2015-09-30T22:19Z] INFO  23:19:27,723 MuTect - [MUTECT] Processed 4000221 reads in 775 ms
[2015-09-30T22:19Z] INFO  23:19:27,771 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:28,123 MuTect - [MUTECT] Processed 10000473 reads in 692 ms
[2015-09-30T22:19Z] INFO  23:19:28,367 MuTect - [MUTECT] Processed 223012447 reads in 671 ms
[2015-09-30T22:19Z] INFO  23:19:28,525 MuTect - [MUTECT] Processed 5000239 reads in 802 ms
[2015-09-30T22:19Z] INFO  23:19:28,989 MuTect - [MUTECT] Processed 11000588 reads in 866 ms
[2015-09-30T22:19Z] INFO  23:19:29,041 MuTect - [MUTECT] Processed 224012502 reads in 674 ms
[2015-09-30T22:19Z] INFO  23:19:29,365 MuTect - [MUTECT] Processed 6000258 reads in 840 ms
[2015-09-30T22:19Z] INFO  23:19:29,396 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:29,694 MuTect - [MUTECT] Processed 12000669 reads in 705 ms
[2015-09-30T22:19Z] INFO  23:19:29,868 MuTect - [MUTECT] Processed 225012547 reads in 827 ms
[2015-09-30T22:19Z] INFO  23:19:30,044 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:30,120 MuTect - [MUTECT] Processed 7000268 reads in 755 ms
[2015-09-30T22:19Z] INFO  23:19:30,265 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:30,300 MuTect - [MUTECT] Processed 13000720 reads in 606 ms
[2015-09-30T22:19Z] INFO  23:19:30,892 MuTect - [MUTECT] Processed 8000312 reads in 772 ms
[2015-09-30T22:19Z] INFO  23:19:31,055 MuTect - [MUTECT] Processed 226012592 reads in 1187 ms
[2015-09-30T22:19Z] INFO  23:19:31,149 MuTect - [MUTECT] Processed 14000852 reads in 849 ms
[2015-09-30T22:19Z] INFO  23:19:31,421 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:19Z] INFO  23:19:31,468 ProgressMeter -            done        7.10e+06    2.7 m       22.0 s    100.0%         2.7 m     0.0 s
[2015-09-30T22:19Z] INFO  23:19:31,468 ProgressMeter - Total runtime 160.21 secs, 2.67 min, 0.04 hours
[2015-09-30T22:19Z] INFO  23:19:31,535 MicroScheduler - 173951 reads were filtered out during the traversal out of approximately 2662262 total reads (6.53%)
[2015-09-30T22:19Z] INFO  23:19:31,535 MicroScheduler -   -> 130108 reads (4.89% of total) failing DuplicateReadFilter
[2015-09-30T22:19Z] INFO  23:19:31,535 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:19Z] INFO  23:19:31,535 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:19Z] INFO  23:19:31,535 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:19Z] INFO  23:19:31,535 MicroScheduler -   -> 43843 reads (1.65% of total) failing UnmappedReadFilter
[2015-09-30T22:19Z] INFO  23:19:31,631 MuTect - [MUTECT] Processed 9000425 reads in 739 ms
[2015-09-30T22:19Z] INFO  23:19:31,799 MuTect - [MUTECT] Processed 15000923 reads in 649 ms
[2015-09-30T22:19Z] INFO  23:19:32,331 MuTect - [MUTECT] Processed 10000446 reads in 700 ms
[2015-09-30T22:19Z] INFO  23:19:32,441 MuTect - [MUTECT] Processed 16000972 reads in 643 ms
[2015-09-30T22:19Z] INFO  23:19:32,534 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:19Z] INFO  23:19:32,554 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:19Z] bgzip syn3-6_31082315_62284583-raw-mutect.vcf
[2015-09-30T22:19Z] INFO  23:19:32,619 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:19Z] tabix index syn3-6_31082315_62284583-raw-mutect.vcf.gz
[2015-09-30T22:19Z] INFO  23:19:33,077 MuTect - [MUTECT] Processed 17000997 reads in 636 ms
[2015-09-30T22:19Z] INFO  23:19:33,111 MuTect - [MUTECT] Processed 11000483 reads in 780 ms
[2015-09-30T22:19Z] INFO  23:19:33,742 MuTect - [MUTECT] Processed 18001059 reads in 665 ms
[2015-09-30T22:19Z] INFO  23:19:33,882 MuTect - [MUTECT] Processed 12000544 reads in 771 ms
[2015-09-30T22:19Z] INFO  23:19:34,426 MuTect - [MUTECT] Processed 19001096 reads in 683 ms
[2015-09-30T22:19Z] INFO  23:19:34,676 MuTect - [MUTECT] Processed 13000565 reads in 794 ms
[2015-09-30T22:19Z] INFO  23:19:34,724 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:19Z] MuTect: MuTect
[2015-09-30T22:19Z] INFO  23:19:35,094 MuTect - [MUTECT] Processed 20001177 reads in 669 ms
[2015-09-30T22:19Z] INFO  23:19:35,350 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:35,412 MuTect - [MUTECT] Processed 14000605 reads in 736 ms
[2015-09-30T22:19Z] INFO  23:19:35,783 MuTect - [MUTECT] Processed 21001190 reads in 689 ms
[2015-09-30T22:19Z] INFO  23:19:36,146 MuTect - [MUTECT] Processed 15000616 reads in 734 ms
[2015-09-30T22:19Z] INFO  23:19:36,506 MuTect - [MUTECT] Processed 22001317 reads in 723 ms
[2015-09-30T22:19Z] INFO  23:19:36,866 MuTect - [MUTECT] Processed 16000660 reads in 720 ms
[2015-09-30T22:19Z] INFO  23:19:36,869 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:36,951 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/7/syn3-7_62708318_93925745-raw-mutect-regions.bed to be BED
[2015-09-30T22:19Z] INFO  23:19:37,009 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:19Z] INFO  23:19:37,009 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:19Z] INFO  23:19:37,009 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:19Z] INFO  23:19:37,009 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:19Z] INFO  23:19:37,013 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/7/syn3-7_62708318_93925745-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/7/tx/tmpEmuHeC/syn3-7_62708318_93925745-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:19Z] INFO  23:19:37,013 HelpFormatter - Date/Time: 2015/09/30 23:19:37
[2015-09-30T22:19Z] INFO  23:19:37,013 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:19Z] INFO  23:19:37,013 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:19Z] INFO  23:19:37,041 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:19Z] INFO  23:19:37,046 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:19Z] INFO  23:19:37,102 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:19Z] INFO  23:19:37,151 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:19Z] INFO  23:19:37,159 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:19Z] INFO  23:19:37,182 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:19Z] INFO  23:19:37,194 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:19Z] INFO  23:19:37,196 MuTect - [MUTECT] Processed 23001340 reads in 690 ms
[2015-09-30T22:19Z] INFO  23:19:37,373 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:19Z] INFO  23:19:37,480 IntervalUtils - Processing 1466050 bp from intervals
[2015-09-30T22:19Z] INFO  23:19:37,484 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:19Z] INFO  23:19:37,485 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:19Z] INFO  23:19:37,612 MuTect - [MUTECT] Processed 17000679 reads in 746 ms
[2015-09-30T22:19Z] INFO  23:19:37,649 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:19Z] INFO  23:19:37,859 MuTect - [MUTECT] Processed 24001412 reads in 663 ms
[2015-09-30T22:19Z] INFO  23:19:37,869 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:19Z] INFO  23:19:37,869 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:19Z] INFO  23:19:37,870 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:19Z] INFO  23:19:37,871 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:19Z] INFO  23:19:37,965 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:38,325 MuTect - [MUTECT] Processed 18000685 reads in 713 ms
[2015-09-30T22:19Z] INFO  23:19:38,469 MuTect - [MUTECT] Processed 25001481 reads in 610 ms
[2015-09-30T22:19Z] INFO  23:19:38,928 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:39,084 MuTect - [MUTECT] Processed 26001497 reads in 615 ms
[2015-09-30T22:19Z] INFO  23:19:39,116 MuTect - [MUTECT] Processed 19000791 reads in 791 ms
[2015-09-30T22:19Z] INFO  23:19:39,775 MuTect - [MUTECT] Processed 27001539 reads in 691 ms
[2015-09-30T22:19Z] INFO  23:19:39,853 MuTect - [MUTECT] Processed 20000792 reads in 737 ms
[2015-09-30T22:19Z] INFO  23:19:40,528 MuTect - [MUTECT] Processed 28001650 reads in 753 ms
[2015-09-30T22:19Z] INFO  23:19:40,540 MuTect - [MUTECT] Processed 1000122 reads in 2621 ms
[2015-09-30T22:19Z] INFO  23:19:40,613 MuTect - [MUTECT] Processed 21000915 reads in 759 ms
[2015-09-30T22:19Z] INFO  23:19:40,618 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:41,171 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:41,202 MuTect - [MUTECT] Processed 29001705 reads in 674 ms
[2015-09-30T22:19Z] INFO  23:19:41,349 MuTect - [MUTECT] Processed 22000959 reads in 737 ms
[2015-09-30T22:19Z] INFO  23:19:41,485 MuTect - [MUTECT] Processed 2000215 reads in 945 ms
[2015-09-30T22:19Z] INFO  23:19:41,914 MuTect - [MUTECT] Processed 30001790 reads in 712 ms
[2015-09-30T22:19Z] INFO  23:19:42,098 MuTect - [MUTECT] Processed 23001053 reads in 749 ms
[2015-09-30T22:19Z] INFO  23:19:42,426 MuTect - [MUTECT] Processed 3000407 reads in 940 ms
[2015-09-30T22:19Z] INFO  23:19:42,656 MuTect - [MUTECT] Processed 31001804 reads in 742 ms
[2015-09-30T22:19Z] INFO  23:19:42,784 MuTect - [MUTECT] Processed 24001134 reads in 686 ms
[2015-09-30T22:19Z] INFO  23:19:43,052 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:43,318 MuTect - [MUTECT] Processed 32001820 reads in 662 ms
[2015-09-30T22:19Z] INFO  23:19:43,442 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:43,490 MuTect - [MUTECT] Processed 25001184 reads in 706 ms
[2015-09-30T22:19Z] INFO  23:19:43,511 MuTect - [MUTECT] Processed 4000534 reads in 1086 ms
[2015-09-30T22:19Z] INFO  23:19:43,747 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:44,006 MuTect - [MUTECT] Processed 33001919 reads in 688 ms
[2015-09-30T22:19Z] INFO  23:19:44,180 MuTect - [MUTECT] Processed 26001205 reads in 690 ms
[2015-09-30T22:19Z] INFO  23:19:44,250 MuTect - [MUTECT] Processed 5000636 reads in 739 ms
[2015-09-30T22:19Z] INFO  23:19:44,754 MuTect - [MUTECT] Processed 34002007 reads in 748 ms
[2015-09-30T22:19Z] INFO  23:19:44,838 MuTect - [MUTECT] Processed 27001288 reads in 658 ms
[2015-09-30T22:19Z] INFO  23:19:45,321 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:45,449 MuTect - [MUTECT] Processed 28001296 reads in 611 ms
[2015-09-30T22:19Z] INFO  23:19:45,798 MuTect - [MUTECT] Processed 35002028 reads in 1044 ms
[2015-09-30T22:19Z] INFO  23:19:46,102 MuTect - [MUTECT] Processed 6000674 reads in 1852 ms
[2015-09-30T22:19Z] INFO  23:19:46,109 MuTect - [MUTECT] Processed 29001382 reads in 660 ms
[2015-09-30T22:19Z] INFO  23:19:46,233 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:46,478 MuTect - [MUTECT] Processed 36002162 reads in 680 ms
[2015-09-30T22:19Z] INFO  23:19:46,786 MuTect - [MUTECT] Processed 30001484 reads in 677 ms
[2015-09-30T22:19Z] INFO  23:19:46,865 MuTect - [MUTECT] Processed 7000701 reads in 763 ms
[2015-09-30T22:19Z] INFO  23:19:47,164 MuTect - [MUTECT] Processed 37002262 reads in 686 ms
[2015-09-30T22:19Z] INFO  23:19:47,311 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:47,480 MuTect - [MUTECT] Processed 31001521 reads in 694 ms
[2015-09-30T22:19Z] INFO  23:19:47,567 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:47,694 MuTect - [MUTECT] Processed 8000765 reads in 829 ms
[2015-09-30T22:19Z] INFO  23:19:47,835 MuTect - [MUTECT] Processed 38002326 reads in 671 ms
[2015-09-30T22:19Z] INFO  23:19:48,164 MuTect - [MUTECT] Processed 32001597 reads in 684 ms
[2015-09-30T22:19Z] INFO  23:19:48,410 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:48,501 MuTect - [MUTECT] Processed 39002352 reads in 666 ms
[2015-09-30T22:19Z] INFO  23:19:48,516 MuTect - [MUTECT] Processed 9000786 reads in 822 ms
[2015-09-30T22:19Z] INFO  23:19:48,849 MuTect - [MUTECT] Processed 33001675 reads in 685 ms
[2015-09-30T22:19Z] INFO  23:19:49,163 MuTect - [MUTECT] Processed 40002438 reads in 662 ms
[2015-09-30T22:19Z] INFO  23:19:49,470 MuTect - [MUTECT] Processed 10000854 reads in 954 ms
[2015-09-30T22:19Z] INFO  23:19:49,550 MuTect - [MUTECT] Processed 34001693 reads in 701 ms
[2015-09-30T22:19Z] INFO  23:19:49,835 MuTect - [MUTECT] Processed 41002585 reads in 672 ms
[2015-09-30T22:19Z] INFO  23:19:49,930 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:50,215 MuTect - [MUTECT] Processed 11000924 reads in 745 ms
[2015-09-30T22:19Z] INFO  23:19:50,267 MuTect - [MUTECT] Processed 35001735 reads in 717 ms
[2015-09-30T22:19Z] INFO  23:19:50,361 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:50,473 MuTect - [MUTECT] Processed 42002637 reads in 638 ms
[2015-09-30T22:19Z] INFO  23:19:50,668 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:50,951 MuTect - [MUTECT] Processed 36001793 reads in 684 ms
[2015-09-30T22:19Z] INFO  23:19:51,058 MuTect - [MUTECT] Processed 12000931 reads in 842 ms
[2015-09-30T22:19Z] INFO  23:19:51,158 MuTect - [MUTECT] Processed 43002680 reads in 685 ms
[2015-09-30T22:19Z] INFO  23:19:51,667 MuTect - [MUTECT] Processed 37001801 reads in 716 ms
[2015-09-30T22:19Z] INFO  23:19:51,811 MuTect - [MUTECT] Processed 13000967 reads in 754 ms
[2015-09-30T22:19Z] INFO  23:19:51,852 MuTect - [MUTECT] Processed 44002788 reads in 694 ms
[2015-09-30T22:19Z] INFO  23:19:52,399 MuTect - [MUTECT] Processed 38001806 reads in 732 ms
[2015-09-30T22:19Z] INFO  23:19:52,535 MuTect - [MUTECT] Processed 14000983 reads in 724 ms
[2015-09-30T22:19Z] INFO  23:19:52,537 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:52,572 MuTect - [MUTECT] Processed 45002906 reads in 720 ms
[2015-09-30T22:19Z] INFO  23:19:52,747 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:52,795 ProgressMeter -      7:44078140        1.09e+06   30.0 s       27.0 s     46.7%        64.0 s    34.0 s
[2015-09-30T22:19Z] INFO  23:19:52,882 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:53,103 MuTect - [MUTECT] Processed 39001854 reads in 704 ms
[2015-09-30T22:19Z] INFO  23:19:53,247 MuTect - [MUTECT] Processed 15001097 reads in 712 ms
[2015-09-30T22:19Z] INFO  23:19:53,310 MuTect - [MUTECT] Processed 46002906 reads in 738 ms
[2015-09-30T22:19Z] INFO  23:19:53,764 MuTect - [MUTECT] Processed 40001876 reads in 661 ms
[2015-09-30T22:19Z] INFO  23:19:53,953 MuTect - [MUTECT] Processed 16001100 reads in 706 ms
[2015-09-30T22:19Z] INFO  23:19:53,979 MuTect - [MUTECT] Processed 47003015 reads in 669 ms
[2015-09-30T22:19Z] INFO  23:19:54,407 MuTect - [MUTECT] Processed 41002013 reads in 643 ms
[2015-09-30T22:19Z] INFO  23:19:54,613 MuTect - [MUTECT] Processed 17001174 reads in 660 ms
[2015-09-30T22:19Z] INFO  23:19:54,647 MuTect - [MUTECT] Processed 48003050 reads in 668 ms
[2015-09-30T22:19Z] INFO  23:19:54,829 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:54,944 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:55,011 MuTect - [MUTECT] Processed 42002032 reads in 604 ms
[2015-09-30T22:19Z] INFO  23:19:55,180 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:55,277 MuTect - [MUTECT] Processed 18001245 reads in 664 ms
[2015-09-30T22:19Z] INFO  23:19:55,375 MuTect - [MUTECT] Processed 49003070 reads in 728 ms
[2015-09-30T22:19Z] INFO  23:19:55,643 MuTect - [MUTECT] Processed 43002057 reads in 632 ms
[2015-09-30T22:19Z] INFO  23:19:55,979 MuTect - [MUTECT] Processed 19001247 reads in 702 ms
[2015-09-30T22:19Z] INFO  23:19:56,049 MuTect - [MUTECT] Processed 50003096 reads in 674 ms
[2015-09-30T22:19Z] INFO  23:19:56,300 MuTect - [MUTECT] Processed 44002074 reads in 657 ms
[2015-09-30T22:19Z] INFO  23:19:56,663 MuTect - [MUTECT] Processed 20001279 reads in 684 ms
[2015-09-30T22:19Z] INFO  23:19:56,743 MuTect - [MUTECT] Processed 51003128 reads in 694 ms
[2015-09-30T22:19Z] INFO  23:19:56,972 MuTect - [MUTECT] Processed 45002104 reads in 672 ms
[2015-09-30T22:19Z] INFO  23:19:57,009 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:57,408 MuTect - [MUTECT] Processed 21001352 reads in 745 ms
[2015-09-30T22:19Z] INFO  23:19:57,490 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:57,512 MuTect - [MUTECT] Processed 52003205 reads in 769 ms
[2015-09-30T22:19Z] INFO  23:19:57,555 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:57,656 MuTect - [MUTECT] Processed 46002147 reads in 684 ms
[2015-09-30T22:19Z] INFO  23:19:58,100 MuTect - [MUTECT] Processed 22001397 reads in 692 ms
[2015-09-30T22:19Z] INFO  23:19:58,235 MuTect - [MUTECT] Processed 53003228 reads in 723 ms
[2015-09-30T22:19Z] INFO  23:19:58,314 MuTect - [MUTECT] Processed 47002210 reads in 658 ms
[2015-09-30T22:19Z] INFO  23:19:58,847 MuTect - [MUTECT] Processed 23001492 reads in 746 ms
[2015-09-30T22:19Z] INFO  23:19:58,918 MuTect - [MUTECT] Processed 48002302 reads in 604 ms
[2015-09-30T22:19Z] INFO  23:19:58,921 MuTect - [MUTECT] Processed 54003237 reads in 686 ms
[2015-09-30T22:19Z] INFO  23:19:59,024 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:19Z] INFO  23:19:59,079 ProgressMeter -       7:6022487        1.36e+06   40.0 s       29.0 s     32.9%         2.0 m    81.0 s
[2015-09-30T22:19Z] INFO  23:19:59,554 MuTect - [MUTECT] Processed 24001509 reads in 708 ms
[2015-09-30T22:19Z] INFO  23:19:59,564 MuTect - [MUTECT] Processed 49002350 reads in 646 ms
[2015-09-30T22:19Z] INFO  23:19:59,663 MuTect - [MUTECT] Processed 55003252 reads in 742 ms
[2015-09-30T22:20Z] INFO  23:20:00,022 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:00,246 MuTect - [MUTECT] Processed 50002374 reads in 682 ms
[2015-09-30T22:20Z] INFO  23:20:00,258 MuTect - [MUTECT] Processed 25001565 reads in 704 ms
[2015-09-30T22:20Z] INFO  23:20:00,343 MuTect - [MUTECT] Processed 56003267 reads in 680 ms
[2015-09-30T22:20Z] INFO  23:20:00,421 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:00,915 MuTect - [MUTECT] Processed 51002380 reads in 669 ms
[2015-09-30T22:20Z] INFO  23:20:00,959 MuTect - [MUTECT] Processed 26001575 reads in 701 ms
[2015-09-30T22:20Z] INFO  23:20:01,032 MuTect - [MUTECT] Processed 57003345 reads in 689 ms
[2015-09-30T22:20Z] INFO  23:20:01,193 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:01,557 MuTect - [MUTECT] Processed 52002521 reads in 642 ms
[2015-09-30T22:20Z] INFO  23:20:01,602 MuTect - [MUTECT] Processed 27001668 reads in 643 ms
[2015-09-30T22:20Z] INFO  23:20:01,670 MuTect - [MUTECT] Processed 58003363 reads in 638 ms
[2015-09-30T22:20Z] INFO  23:20:02,240 MuTect - [MUTECT] Processed 53002533 reads in 683 ms
[2015-09-30T22:20Z] INFO  23:20:02,266 MuTect - [MUTECT] Processed 28001767 reads in 664 ms
[2015-09-30T22:20Z] INFO  23:20:02,325 MuTect - [MUTECT] Processed 59003393 reads in 655 ms
[2015-09-30T22:20Z] INFO  23:20:02,850 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:02,874 MuTect - [MUTECT] Processed 54002652 reads in 634 ms
[2015-09-30T22:20Z] INFO  23:20:02,893 MuTect - [MUTECT] Processed 29001909 reads in 627 ms
[2015-09-30T22:20Z] INFO  23:20:02,974 MuTect - [MUTECT] Processed 60003432 reads in 649 ms
[2015-09-30T22:20Z] INFO  23:20:03,361 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:03,505 MuTect - [MUTECT] Processed 30001922 reads in 612 ms
[2015-09-30T22:20Z] INFO  23:20:03,507 MuTect - [MUTECT] Processed 55002708 reads in 633 ms
[2015-09-30T22:20Z] INFO  23:20:03,650 MuTect - [MUTECT] Processed 61003441 reads in 676 ms
[2015-09-30T22:20Z] INFO  23:20:04,091 MuTect - [MUTECT] Processed 31001951 reads in 586 ms
[2015-09-30T22:20Z] INFO  23:20:04,169 MuTect - [MUTECT] Processed 56002780 reads in 662 ms
[2015-09-30T22:20Z] INFO  23:20:04,292 MuTect - [MUTECT] Processed 62003444 reads in 642 ms
[2015-09-30T22:20Z] INFO  23:20:04,699 MuTect - [MUTECT] Processed 32001983 reads in 608 ms
[2015-09-30T22:20Z] INFO  23:20:04,869 MuTect - [MUTECT] Processed 57002830 reads in 700 ms
[2015-09-30T22:20Z] INFO  23:20:04,920 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:04,936 MuTect - [MUTECT] Processed 63003517 reads in 644 ms
[2015-09-30T22:20Z] INFO  23:20:05,115 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:05,328 MuTect - [MUTECT] Processed 33001994 reads in 629 ms
[2015-09-30T22:20Z] INFO  23:20:05,519 MuTect - [MUTECT] Processed 58002862 reads in 650 ms
[2015-09-30T22:20Z] INFO  23:20:05,569 MuTect - [MUTECT] Processed 64003537 reads in 633 ms
[2015-09-30T22:20Z] INFO  23:20:05,579 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:05,971 MuTect - [MUTECT] Processed 34002001 reads in 643 ms
[2015-09-30T22:20Z] INFO  23:20:06,232 MuTect - [MUTECT] Processed 59002882 reads in 713 ms
[2015-09-30T22:20Z] INFO  23:20:06,233 MuTect - [MUTECT] Processed 65003548 reads in 664 ms
[2015-09-30T22:20Z] INFO  23:20:06,622 MuTect - [MUTECT] Processed 35002142 reads in 651 ms
[2015-09-30T22:20Z] INFO  23:20:06,883 MuTect - [MUTECT] Processed 60002883 reads in 650 ms
[2015-09-30T22:20Z] INFO  23:20:06,918 MuTect - [MUTECT] Processed 66003604 reads in 685 ms
[2015-09-30T22:20Z] INFO  23:20:07,283 MuTect - [MUTECT] Processed 36002217 reads in 661 ms
[2015-09-30T22:20Z] INFO  23:20:07,578 MuTect - [MUTECT] Processed 61002970 reads in 696 ms
[2015-09-30T22:20Z] INFO  23:20:07,659 MuTect - [MUTECT] Processed 67003637 reads in 741 ms
[2015-09-30T22:20Z] INFO  23:20:07,712 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:07,872 ProgressMeter -      7:72891476        9.71e+05   30.0 s       30.0 s     26.9%       111.0 s    81.0 s
[2015-09-30T22:20Z] INFO  23:20:07,952 MuTect - [MUTECT] Processed 37002237 reads in 669 ms
[2015-09-30T22:20Z] INFO  23:20:07,974 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:08,069 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:08,275 MuTect - [MUTECT] Processed 62002983 reads in 697 ms
[2015-09-30T22:20Z] INFO  23:20:08,387 MuTect - [MUTECT] Processed 68003645 reads in 728 ms
[2015-09-30T22:20Z] INFO  23:20:08,647 MuTect - [MUTECT] Processed 38002280 reads in 695 ms
[2015-09-30T22:20Z] INFO  23:20:08,961 MuTect - [MUTECT] Processed 63003068 reads in 686 ms
[2015-09-30T22:20Z] INFO  23:20:09,100 MuTect - [MUTECT] Processed 69003728 reads in 713 ms
[2015-09-30T22:20Z] INFO  23:20:09,342 MuTect - [MUTECT] Processed 39002323 reads in 695 ms
[2015-09-30T22:20Z] INFO  23:20:09,665 MuTect - [MUTECT] Processed 64003134 reads in 704 ms
[2015-09-30T22:20Z] INFO  23:20:09,867 MuTect - [MUTECT] Processed 70003760 reads in 767 ms
[2015-09-30T22:20Z] INFO  23:20:10,012 MuTect - [MUTECT] Processed 40002393 reads in 670 ms
[2015-09-30T22:20Z] INFO  23:20:10,046 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:10,254 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:10,395 MuTect - [MUTECT] Processed 65003168 reads in 730 ms
[2015-09-30T22:20Z] INFO  23:20:10,837 MuTect - [MUTECT] Processed 41002456 reads in 825 ms
[2015-09-30T22:20Z] INFO  23:20:10,923 MuTect - [MUTECT] Processed 71003797 reads in 1056 ms
[2015-09-30T22:20Z] INFO  23:20:11,078 MuTect - [MUTECT] Processed 66003177 reads in 683 ms
[2015-09-30T22:20Z] INFO  23:20:11,159 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:11,486 MuTect - [MUTECT] Processed 42002515 reads in 649 ms
[2015-09-30T22:20Z] INFO  23:20:11,589 MuTect - [MUTECT] Processed 72003809 reads in 666 ms
[2015-09-30T22:20Z] INFO  23:20:11,821 MuTect - [MUTECT] Processed 67003218 reads in 743 ms
[2015-09-30T22:20Z] INFO  23:20:12,163 MuTect - [MUTECT] Processed 43002609 reads in 676 ms
[2015-09-30T22:20Z] INFO  23:20:12,262 MuTect - [MUTECT] Processed 73003842 reads in 673 ms
[2015-09-30T22:20Z] INFO  23:20:12,416 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:12,516 MuTect - [MUTECT] Processed 68003262 reads in 695 ms
[2015-09-30T22:20Z] INFO  23:20:12,771 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:12,866 MuTect - [MUTECT] Processed 44002681 reads in 704 ms
[2015-09-30T22:20Z] INFO  23:20:12,903 MuTect - [MUTECT] Processed 74003845 reads in 641 ms
[2015-09-30T22:20Z] INFO  23:20:13,281 MuTect - [MUTECT] Processed 69003304 reads in 765 ms
[2015-09-30T22:20Z] INFO  23:20:13,643 MuTect - [MUTECT] Processed 75003846 reads in 740 ms
[2015-09-30T22:20Z] INFO  23:20:13,659 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:13,714 MuTect - [MUTECT] Processed 45002727 reads in 848 ms
[2015-09-30T22:20Z] INFO  23:20:14,027 MuTect - [MUTECT] Processed 70003322 reads in 746 ms
[2015-09-30T22:20Z] INFO  23:20:14,353 MuTect - [MUTECT] Processed 76003901 reads in 710 ms
[2015-09-30T22:20Z] INFO  23:20:14,461 MuTect - [MUTECT] Processed 46002747 reads in 747 ms
[2015-09-30T22:20Z] INFO  23:20:14,700 MuTect - [MUTECT] Processed 71003356 reads in 673 ms
[2015-09-30T22:20Z] INFO  23:20:14,893 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:15,020 MuTect - [MUTECT] Processed 77003937 reads in 666 ms
[2015-09-30T22:20Z] INFO  23:20:15,098 MuTect - [MUTECT] Processed 47002815 reads in 637 ms
[2015-09-30T22:20Z] INFO  23:20:15,390 MuTect - [MUTECT] Processed 72003362 reads in 690 ms
[2015-09-30T22:20Z] INFO  23:20:15,465 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:15,741 MuTect - [MUTECT] Processed 78003997 reads in 722 ms
[2015-09-30T22:20Z] INFO  23:20:15,757 MuTect - [MUTECT] Processed 48002922 reads in 659 ms
[2015-09-30T22:20Z] INFO  23:20:16,089 MuTect - [MUTECT] Processed 73003375 reads in 699 ms
[2015-09-30T22:20Z] INFO  23:20:16,158 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:16,439 MuTect - [MUTECT] Processed 49002996 reads in 682 ms
[2015-09-30T22:20Z] INFO  23:20:16,492 MuTect - [MUTECT] Processed 79004010 reads in 751 ms
[2015-09-30T22:20Z] INFO  23:20:16,814 MuTect - [MUTECT] Processed 74003384 reads in 725 ms
[2015-09-30T22:20Z] INFO  23:20:17,121 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:17,139 MuTect - [MUTECT] Processed 50003029 reads in 700 ms
[2015-09-30T22:20Z] INFO  23:20:17,256 MuTect - [MUTECT] Processed 80004059 reads in 764 ms
[2015-09-30T22:20Z] INFO  23:20:17,528 MuTect - [MUTECT] Processed 75003391 reads in 714 ms
[2015-09-30T22:20Z] INFO  23:20:17,807 MuTect - [MUTECT] Processed 51003138 reads in 668 ms
[2015-09-30T22:20Z] INFO  23:20:17,880 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:17,957 MuTect - [MUTECT] Processed 81004089 reads in 700 ms
[2015-09-30T22:20Z] INFO  23:20:18,246 MuTect - [MUTECT] Processed 76003503 reads in 718 ms
[2015-09-30T22:20Z] INFO  23:20:18,481 MuTect - [MUTECT] Processed 52003213 reads in 674 ms
[2015-09-30T22:20Z] INFO  23:20:18,718 MuTect - [MUTECT] Processed 82004107 reads in 762 ms
[2015-09-30T22:20Z] INFO  23:20:18,753 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:18,951 MuTect - [MUTECT] Processed 77003605 reads in 705 ms
[2015-09-30T22:20Z] INFO  23:20:19,114 MuTect - [MUTECT] Processed 53003255 reads in 633 ms
[2015-09-30T22:20Z] INFO  23:20:19,405 MuTect - [MUTECT] Processed 83004164 reads in 687 ms
[2015-09-30T22:20Z] INFO  23:20:19,654 MuTect - [MUTECT] Processed 78003687 reads in 703 ms
[2015-09-30T22:20Z] INFO  23:20:19,739 MuTect - [MUTECT] Processed 54003350 reads in 625 ms
[2015-09-30T22:20Z] INFO  23:20:20,068 MuTect - [MUTECT] Processed 84004178 reads in 663 ms
[2015-09-30T22:20Z] INFO  23:20:20,355 MuTect - [MUTECT] Processed 55003438 reads in 616 ms
[2015-09-30T22:20Z] INFO  23:20:20,372 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:20,390 MuTect - [MUTECT] Processed 79003740 reads in 736 ms
[2015-09-30T22:20Z] INFO  23:20:20,475 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:20,708 MuTect - [MUTECT] Processed 85004185 reads in 640 ms
[2015-09-30T22:20Z] INFO  23:20:20,994 MuTect - [MUTECT] Processed 56003442 reads in 639 ms
[2015-09-30T22:20Z] INFO  23:20:21,187 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:21,296 MuTect - [MUTECT] Processed 80003798 reads in 906 ms
[2015-09-30T22:20Z] INFO  23:20:21,364 MuTect - [MUTECT] Processed 86004226 reads in 656 ms
[2015-09-30T22:20Z] INFO  23:20:21,616 MuTect - [MUTECT] Processed 57003472 reads in 622 ms
[2015-09-30T22:20Z] INFO  23:20:21,978 MuTect - [MUTECT] Processed 81003911 reads in 682 ms
[2015-09-30T22:20Z] INFO  23:20:22,053 MuTect - [MUTECT] Processed 87004247 reads in 689 ms
[2015-09-30T22:20Z] INFO  23:20:22,262 MuTect - [MUTECT] Processed 58003643 reads in 646 ms
[2015-09-30T22:20Z] INFO  23:20:22,636 MuTect - [MUTECT] Processed 82003919 reads in 658 ms
[2015-09-30T22:20Z] INFO  23:20:22,769 MuTect - [MUTECT] Processed 88004312 reads in 716 ms
[2015-09-30T22:20Z] INFO  23:20:22,796 ProgressMeter -      7:55249277        2.23e+06   60.0 s       26.0 s     88.7%        67.0 s     7.0 s
[2015-09-30T22:20Z] INFO  23:20:22,922 MuTect - [MUTECT] Processed 59003719 reads in 660 ms
[2015-09-30T22:20Z] INFO  23:20:23,034 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:23,285 MuTect - [MUTECT] Processed 83003930 reads in 649 ms
[2015-09-30T22:20Z] INFO  23:20:23,439 MuTect - [MUTECT] Processed 89004344 reads in 670 ms
[2015-09-30T22:20Z] INFO  23:20:23,543 MuTect - [MUTECT] Processed 60003801 reads in 621 ms
[2015-09-30T22:20Z] INFO  23:20:23,653 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:23,950 MuTect - [MUTECT] Processed 84003931 reads in 665 ms
[2015-09-30T22:20Z] INFO  23:20:24,134 MuTect - [MUTECT] Processed 90004379 reads in 695 ms
[2015-09-30T22:20Z] INFO  23:20:24,162 MuTect - [MUTECT] Processed 61003827 reads in 619 ms
[2015-09-30T22:20Z] INFO  23:20:24,623 MuTect - [MUTECT] Processed 85003997 reads in 673 ms
[2015-09-30T22:20Z] INFO  23:20:24,778 MuTect - [MUTECT] Processed 62003835 reads in 616 ms
[2015-09-30T22:20Z] INFO  23:20:24,842 MuTect - [MUTECT] Processed 91004396 reads in 708 ms
[2015-09-30T22:20Z] INFO  23:20:25,293 MuTect - [MUTECT] Processed 86004039 reads in 670 ms
[2015-09-30T22:20Z] INFO  23:20:25,325 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:25,382 MuTect - [MUTECT] Processed 63003903 reads in 604 ms
[2015-09-30T22:20Z] INFO  23:20:25,564 MuTect - [MUTECT] Processed 92004471 reads in 722 ms
[2015-09-30T22:20Z] INFO  23:20:26,009 MuTect - [MUTECT] Processed 64003977 reads in 627 ms
[2015-09-30T22:20Z] INFO  23:20:26,092 MuTect - [MUTECT] Processed 87004107 reads in 799 ms
[2015-09-30T22:20Z] INFO  23:20:26,214 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:26,263 MuTect - [MUTECT] Processed 93004541 reads in 699 ms
[2015-09-30T22:20Z] INFO  23:20:26,677 MuTect - [MUTECT] Processed 65004043 reads in 668 ms
[2015-09-30T22:20Z] INFO  23:20:26,747 MuTect - [MUTECT] Processed 88004161 reads in 655 ms
[2015-09-30T22:20Z] INFO  23:20:26,952 MuTect - [MUTECT] Processed 94004639 reads in 689 ms
[2015-09-30T22:20Z] INFO  23:20:27,369 MuTect - [MUTECT] Processed 66004111 reads in 692 ms
[2015-09-30T22:20Z] INFO  23:20:27,389 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:27,416 MuTect - [MUTECT] Processed 89004163 reads in 669 ms
[2015-09-30T22:20Z] INFO  23:20:27,474 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:27,636 MuTect - [MUTECT] Processed 95004723 reads in 684 ms
[2015-09-30T22:20Z] INFO  23:20:28,098 MuTect - [MUTECT] Processed 67004209 reads in 729 ms
[2015-09-30T22:20Z] INFO  23:20:28,370 MuTect - [MUTECT] Processed 90004168 reads in 954 ms
[2015-09-30T22:20Z] INFO  23:20:28,388 MuTect - [MUTECT] Processed 96004728 reads in 752 ms
[2015-09-30T22:20Z] INFO  23:20:28,789 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:28,807 MuTect - [MUTECT] Processed 68004290 reads in 709 ms
[2015-09-30T22:20Z] INFO  23:20:29,080 ProgressMeter -      7:22985368        2.80e+06   70.0 s       24.0 s     73.4%        95.0 s    25.0 s
[2015-09-30T22:20Z] INFO  23:20:29,089 MuTect - [MUTECT] Processed 97004731 reads in 701 ms
[2015-09-30T22:20Z] INFO  23:20:29,143 MuTect - [MUTECT] Processed 91004220 reads in 773 ms
[2015-09-30T22:20Z] INFO  23:20:29,467 MuTect - [MUTECT] Processed 69004391 reads in 660 ms
[2015-09-30T22:20Z] INFO  23:20:29,597 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:29,773 MuTect - [MUTECT] Processed 98004769 reads in 684 ms
[2015-09-30T22:20Z] INFO  23:20:29,871 MuTect - [MUTECT] Processed 92004254 reads in 728 ms
[2015-09-30T22:20Z] INFO  23:20:30,152 MuTect - [MUTECT] Processed 70004402 reads in 685 ms
[2015-09-30T22:20Z] INFO  23:20:30,242 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:30,418 MuTect - [MUTECT] Processed 99004780 reads in 645 ms
[2015-09-30T22:20Z] INFO  23:20:30,801 MuTect - [MUTECT] Processed 93004297 reads in 930 ms
[2015-09-30T22:20Z] INFO  23:20:30,859 MuTect - [MUTECT] Processed 71004526 reads in 707 ms
[2015-09-30T22:20Z] INFO  23:20:31,040 MuTect - [MUTECT] Processed 100004845 reads in 622 ms
[2015-09-30T22:20Z] INFO  23:20:31,175 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:31,421 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:20Z] INFO  23:20:31,425 ProgressMeter -            done        2.52e+06   68.0 s       27.0 s    100.0%        68.0 s     0.0 s
[2015-09-30T22:20Z] INFO  23:20:31,425 ProgressMeter - Total runtime 68.63 secs, 1.14 min, 0.02 hours
[2015-09-30T22:20Z] INFO  23:20:31,489 MicroScheduler - 71549 reads were filtered out during the traversal out of approximately 1124353 total reads (6.36%)
[2015-09-30T22:20Z] INFO  23:20:31,490 MicroScheduler -   -> 53623 reads (4.77% of total) failing DuplicateReadFilter
[2015-09-30T22:20Z] INFO  23:20:31,490 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:20Z] INFO  23:20:31,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:20Z] INFO  23:20:31,490 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:20Z] INFO  23:20:31,490 MicroScheduler -   -> 17926 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:20Z] INFO  23:20:31,564 MuTect - [MUTECT] Processed 72004645 reads in 705 ms
[2015-09-30T22:20Z] INFO  23:20:31,675 MuTect - [MUTECT] Processed 101004930 reads in 635 ms
[2015-09-30T22:20Z] INFO  23:20:31,979 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:32,264 MuTect - [MUTECT] Processed 73004754 reads in 700 ms
[2015-09-30T22:20Z] INFO  23:20:32,356 MuTect - [MUTECT] Processed 102004945 reads in 681 ms
[2015-09-30T22:20Z] INFO  23:20:32,485 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:20Z] bgzip syn3-7_31022897_62585293-raw-mutect.vcf
[2015-09-30T22:20Z] tabix index syn3-7_31022897_62585293-raw-mutect.vcf.gz
[2015-09-30T22:20Z] INFO  23:20:32,917 MuTect - [MUTECT] Processed 74004811 reads in 653 ms
[2015-09-30T22:20Z] INFO  23:20:33,073 MuTect - [MUTECT] Processed 103005000 reads in 717 ms
[2015-09-30T22:20Z] INFO  23:20:33,536 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:33,621 MuTect - [MUTECT] Processed 75004867 reads in 704 ms
[2015-09-30T22:20Z] INFO  23:20:33,754 MuTect - [MUTECT] Processed 104005079 reads in 681 ms
[2015-09-30T22:20Z] INFO  23:20:34,336 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:34,359 MuTect - [MUTECT] Processed 76005004 reads in 738 ms
[2015-09-30T22:20Z] INFO  23:20:34,421 MuTect - [MUTECT] Processed 105005079 reads in 667 ms
[2015-09-30T22:20Z] MuTect: MuTect
[2015-09-30T22:20Z] INFO  23:20:35,123 MuTect - [MUTECT] Processed 106005130 reads in 702 ms
[2015-09-30T22:20Z] INFO  23:20:35,129 MuTect - [MUTECT] Processed 77005104 reads in 770 ms
[2015-09-30T22:20Z] INFO  23:20:35,772 MuTect - [MUTECT] Processed 107005158 reads in 649 ms
[2015-09-30T22:20Z] INFO  23:20:35,887 MuTect - [MUTECT] Processed 78005126 reads in 758 ms
[2015-09-30T22:20Z] INFO  23:20:36,105 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:36,418 MuTect - [MUTECT] Processed 108005200 reads in 646 ms
[2015-09-30T22:20Z] INFO  23:20:36,680 MuTect - [MUTECT] Processed 79005159 reads in 793 ms
[2015-09-30T22:20Z] INFO  23:20:37,056 MuTect - [MUTECT] Processed 109005314 reads in 638 ms
[2015-09-30T22:20Z] INFO  23:20:37,172 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/7/syn3-7_94024041_125680568-raw-mutect-regions.bed to be BED
[2015-09-30T22:20Z] INFO  23:20:37,228 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:20Z] INFO  23:20:37,228 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:20Z] INFO  23:20:37,228 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:20Z] INFO  23:20:37,228 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:20Z] INFO  23:20:37,232 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/7/syn3-7_94024041_125680568-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/7/tx/tmpIwnSfh/syn3-7_94024041_125680568-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:20Z] INFO  23:20:37,232 HelpFormatter - Date/Time: 2015/09/30 23:20:37
[2015-09-30T22:20Z] INFO  23:20:37,232 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:20Z] INFO  23:20:37,232 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:20Z] INFO  23:20:37,260 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:20Z] INFO  23:20:37,264 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:20Z] INFO  23:20:37,314 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:20Z] INFO  23:20:37,361 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:20Z] INFO  23:20:37,369 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:20Z] INFO  23:20:37,391 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:20Z] INFO  23:20:37,403 MuTect - [MUTECT] Processed 80005188 reads in 722 ms
[2015-09-30T22:20Z] INFO  23:20:37,403 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:20Z] INFO  23:20:37,571 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:37,582 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:20Z] INFO  23:20:37,715 MuTect - [MUTECT] Processed 110005378 reads in 659 ms
[2015-09-30T22:20Z] INFO  23:20:37,715 IntervalUtils - Processing 1767772 bp from intervals
[2015-09-30T22:20Z] INFO  23:20:37,719 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:20Z] INFO  23:20:37,719 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:20Z] INFO  23:20:37,873 ProgressMeter -      7:76682511        2.36e+06   60.0 s       25.0 s     56.7%       105.0 s    45.0 s
[2015-09-30T22:20Z] INFO  23:20:37,892 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:20Z] INFO  23:20:38,108 MuTect - [MUTECT] Processed 81005211 reads in 706 ms
[2015-09-30T22:20Z] INFO  23:20:38,110 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:20Z] INFO  23:20:38,110 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:20Z] INFO  23:20:38,111 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:20Z] INFO  23:20:38,112 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:20Z] INFO  23:20:38,357 MuTect - [MUTECT] Processed 111005427 reads in 642 ms
[2015-09-30T22:20Z] INFO  23:20:38,537 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:38,854 MuTect - [MUTECT] Processed 82005299 reads in 746 ms
[2015-09-30T22:20Z] INFO  23:20:39,029 MuTect - [MUTECT] Processed 112005480 reads in 672 ms
[2015-09-30T22:20Z] INFO  23:20:39,582 MuTect - [MUTECT] Processed 83005331 reads in 728 ms
[2015-09-30T22:20Z] INFO  23:20:39,836 MuTect - [MUTECT] Processed 113005505 reads in 807 ms
[2015-09-30T22:20Z] INFO  23:20:40,304 MuTect - [MUTECT] Processed 84005371 reads in 722 ms
[2015-09-30T22:20Z] INFO  23:20:40,314 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:40,518 MuTect - [MUTECT] Processed 114005518 reads in 682 ms
[2015-09-30T22:20Z] INFO  23:20:40,567 MuTect - [MUTECT] Processed 1000061 reads in 2410 ms
[2015-09-30T22:20Z] INFO  23:20:41,054 MuTect - [MUTECT] Processed 85005418 reads in 750 ms
[2015-09-30T22:20Z] INFO  23:20:41,077 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:41,199 MuTect - [MUTECT] Processed 115005520 reads in 681 ms
[2015-09-30T22:20Z] INFO  23:20:41,487 MuTect - [MUTECT] Processed 2000099 reads in 920 ms
[2015-09-30T22:20Z] INFO  23:20:41,779 MuTect - [MUTECT] Processed 86005447 reads in 725 ms
[2015-09-30T22:20Z] INFO  23:20:41,848 MuTect - [MUTECT] Processed 116005529 reads in 649 ms
[2015-09-30T22:20Z] INFO  23:20:42,194 MuTect - [MUTECT] Processed 3000138 reads in 707 ms
[2015-09-30T22:20Z] INFO  23:20:42,492 MuTect - [MUTECT] Processed 87005517 reads in 713 ms
[2015-09-30T22:20Z] INFO  23:20:42,503 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:42,526 MuTect - [MUTECT] Processed 117005577 reads in 678 ms
[2015-09-30T22:20Z] INFO  23:20:42,849 MuTect - [MUTECT] Processed 4000173 reads in 655 ms
[2015-09-30T22:20Z] INFO  23:20:42,985 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:43,191 MuTect - [MUTECT] Processed 118005583 reads in 665 ms
[2015-09-30T22:20Z] INFO  23:20:43,230 MuTect - [MUTECT] Processed 88005543 reads in 738 ms
[2015-09-30T22:20Z] INFO  23:20:43,510 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:43,532 MuTect - [MUTECT] Processed 5000255 reads in 683 ms
[2015-09-30T22:20Z] INFO  23:20:43,863 MuTect - [MUTECT] Processed 119005593 reads in 672 ms
[2015-09-30T22:20Z] INFO  23:20:43,997 MuTect - [MUTECT] Processed 89005577 reads in 767 ms
[2015-09-30T22:20Z] INFO  23:20:44,509 MuTect - [MUTECT] Processed 120005615 reads in 646 ms
[2015-09-30T22:20Z] INFO  23:20:44,534 MuTect - [MUTECT] Processed 6000258 reads in 1002 ms
[2015-09-30T22:20Z] INFO  23:20:44,739 MuTect - [MUTECT] Processed 90005596 reads in 742 ms
[2015-09-30T22:20Z] INFO  23:20:45,152 MuTect - [MUTECT] Processed 121005661 reads in 643 ms
[2015-09-30T22:20Z] INFO  23:20:45,333 MuTect - [MUTECT] Processed 7000293 reads in 798 ms
[2015-09-30T22:20Z] INFO  23:20:45,497 MuTect - [MUTECT] Processed 91005603 reads in 758 ms
[2015-09-30T22:20Z] INFO  23:20:45,542 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:45,693 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:45,733 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:45,757 MuTect - [MUTECT] Processed 122005675 reads in 605 ms
[2015-09-30T22:20Z] INFO  23:20:46,042 MuTect - [MUTECT] Processed 8000344 reads in 710 ms
[2015-09-30T22:20Z] INFO  23:20:46,265 MuTect - [MUTECT] Processed 92005651 reads in 768 ms
[2015-09-30T22:20Z] INFO  23:20:46,415 MuTect - [MUTECT] Processed 123005755 reads in 658 ms
[2015-09-30T22:20Z] INFO  23:20:46,723 MuTect - [MUTECT] Processed 9000378 reads in 681 ms
[2015-09-30T22:20Z] INFO  23:20:46,900 MuTect - [MUTECT] Processed 93005715 reads in 635 ms
[2015-09-30T22:20Z] INFO  23:20:47,090 MuTect - [MUTECT] Processed 124005803 reads in 675 ms
[2015-09-30T22:20Z] INFO  23:20:47,446 MuTect - [MUTECT] Processed 10000467 reads in 723 ms
[2015-09-30T22:20Z] INFO  23:20:47,617 MuTect - [MUTECT] Processed 94005726 reads in 717 ms
[2015-09-30T22:20Z] INFO  23:20:47,735 MuTect - [MUTECT] Processed 125005881 reads in 645 ms
[2015-09-30T22:20Z] INFO  23:20:47,967 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:48,227 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:48,331 MuTect - [MUTECT] Processed 11000562 reads in 885 ms
[2015-09-30T22:20Z] INFO  23:20:48,346 MuTect - [MUTECT] Processed 95005730 reads in 729 ms
[2015-09-30T22:20Z] INFO  23:20:48,428 MuTect - [MUTECT] Processed 126005898 reads in 693 ms
[2015-09-30T22:20Z] INFO  23:20:48,500 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:48,998 MuTect - [MUTECT] Processed 12000620 reads in 667 ms
[2015-09-30T22:20Z] INFO  23:20:49,031 MuTect - [MUTECT] Processed 96005770 reads in 684 ms
[2015-09-30T22:20Z] INFO  23:20:49,079 MuTect - [MUTECT] Processed 127006020 reads in 651 ms
[2015-09-30T22:20Z] INFO  23:20:49,664 MuTect - [MUTECT] Processed 13000627 reads in 666 ms
[2015-09-30T22:20Z] INFO  23:20:49,700 MuTect - [MUTECT] Processed 97005826 reads in 670 ms
[2015-09-30T22:20Z] INFO  23:20:49,731 MuTect - [MUTECT] Processed 128006064 reads in 652 ms
[2015-09-30T22:20Z] INFO  23:20:49,788 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:20Z] INFO  23:20:49,790 ProgressMeter -            done        3.73e+06   90.0 s       24.0 s    100.0%        90.0 s     0.0 s
[2015-09-30T22:20Z] INFO  23:20:49,790 ProgressMeter - Total runtime 90.71 secs, 1.51 min, 0.03 hours
[2015-09-30T22:20Z] INFO  23:20:49,857 MicroScheduler - 100332 reads were filtered out during the traversal out of approximately 1539689 total reads (6.52%)
[2015-09-30T22:20Z] INFO  23:20:49,857 MicroScheduler -   -> 75190 reads (4.88% of total) failing DuplicateReadFilter
[2015-09-30T22:20Z] INFO  23:20:49,857 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:20Z] INFO  23:20:49,857 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:20Z] INFO  23:20:49,857 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:20Z] INFO  23:20:49,857 MicroScheduler -   -> 25142 reads (1.63% of total) failing UnmappedReadFilter
[2015-09-30T22:20Z] INFO  23:20:50,328 MuTect - [MUTECT] Processed 14000673 reads in 663 ms
[2015-09-30T22:20Z] INFO  23:20:50,378 MuTect - [MUTECT] Processed 98005830 reads in 678 ms
[2015-09-30T22:20Z] INFO  23:20:50,475 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:50,832 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:20Z] bgzip syn3-7_0_31019109-raw-mutect.vcf
[2015-09-30T22:20Z] tabix index syn3-7_0_31019109-raw-mutect.vcf.gz
[2015-09-30T22:20Z] INFO  23:20:50,961 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:51,020 MuTect - [MUTECT] Processed 15000749 reads in 693 ms
[2015-09-30T22:20Z] INFO  23:20:51,080 MuTect - [MUTECT] Processed 99005880 reads in 702 ms
[2015-09-30T22:20Z] INFO  23:20:51,684 MuTect - [MUTECT] Processed 16000768 reads in 664 ms
[2015-09-30T22:20Z] INFO  23:20:51,768 MuTect - [MUTECT] Processed 100005965 reads in 688 ms
[2015-09-30T22:20Z] INFO  23:20:52,370 MuTect - [MUTECT] Processed 17000795 reads in 685 ms
[2015-09-30T22:20Z] INFO  23:20:52,464 MuTect - [MUTECT] Processed 101006029 reads in 696 ms
[2015-09-30T22:20Z] INFO  23:20:52,911 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:53,027 MuTect - [MUTECT] Processed 18000801 reads in 658 ms
[2015-09-30T22:20Z] MuTect: MuTect
[2015-09-30T22:20Z] INFO  23:20:53,186 MuTect - [MUTECT] Processed 102006033 reads in 722 ms
[2015-09-30T22:20Z] INFO  23:20:53,621 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:53,700 MuTect - [MUTECT] Processed 19000813 reads in 673 ms
[2015-09-30T22:20Z] INFO  23:20:53,884 MuTect - [MUTECT] Processed 103006033 reads in 698 ms
[2015-09-30T22:20Z] INFO  23:20:54,356 MuTect - [MUTECT] Processed 20000908 reads in 656 ms
[2015-09-30T22:20Z] INFO  23:20:54,582 MuTect - [MUTECT] Processed 104006033 reads in 698 ms
[2015-09-30T22:20Z] INFO  23:20:54,986 MuTect - [MUTECT] Processed 21000994 reads in 630 ms
[2015-09-30T22:20Z] INFO  23:20:55,029 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/7/syn3-7_126078434_157151579-raw-mutect-regions.bed to be BED
[2015-09-30T22:20Z] INFO  23:20:55,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:20Z] INFO  23:20:55,085 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:20Z] INFO  23:20:55,085 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:20Z] INFO  23:20:55,085 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:20Z] INFO  23:20:55,088 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/7/syn3-7_126078434_157151579-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/7/tx/tmpSdy09X/syn3-7_126078434_157151579-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:20Z] INFO  23:20:55,088 HelpFormatter - Date/Time: 2015/09/30 23:20:55
[2015-09-30T22:20Z] INFO  23:20:55,088 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:20Z] INFO  23:20:55,089 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:20Z] INFO  23:20:55,116 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:20Z] INFO  23:20:55,120 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:20Z] INFO  23:20:55,172 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:20Z] INFO  23:20:55,220 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:20Z] INFO  23:20:55,228 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:20Z] INFO  23:20:55,255 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:55,261 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T22:20Z] INFO  23:20:55,279 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:20Z] INFO  23:20:55,312 MuTect - [MUTECT] Processed 105006052 reads in 730 ms
[2015-09-30T22:20Z] INFO  23:20:55,457 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:20Z] INFO  23:20:55,573 IntervalUtils - Processing 1895508 bp from intervals
[2015-09-30T22:20Z] INFO  23:20:55,577 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:20Z] INFO  23:20:55,577 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:20Z] INFO  23:20:55,642 MuTect - [MUTECT] Processed 22001067 reads in 656 ms
[2015-09-30T22:20Z] INFO  23:20:55,858 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:20Z] INFO  23:20:56,028 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:20Z] INFO  23:20:56,028 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:20Z] INFO  23:20:56,029 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:20Z] INFO  23:20:56,030 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:20Z] INFO  23:20:56,070 MuTect - [MUTECT] Processed 106006060 reads in 758 ms
[2015-09-30T22:20Z] INFO  23:20:56,292 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:56,341 MuTect - [MUTECT] Processed 23001126 reads in 699 ms
[2015-09-30T22:20Z] INFO  23:20:56,819 MuTect - [MUTECT] Processed 107006065 reads in 749 ms
[2015-09-30T22:20Z] INFO  23:20:57,009 MuTect - [MUTECT] Processed 24001198 reads in 668 ms
[2015-09-30T22:20Z] INFO  23:20:57,501 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:57,576 MuTect - [MUTECT] Processed 108006147 reads in 757 ms
[2015-09-30T22:20Z] INFO  23:20:57,659 MuTect - [MUTECT] Processed 25001249 reads in 650 ms
[2015-09-30T22:20Z] INFO  23:20:58,291 MuTect - [MUTECT] Processed 109006152 reads in 715 ms
[2015-09-30T22:20Z] INFO  23:20:58,303 MuTect - [MUTECT] Processed 26001253 reads in 644 ms
[2015-09-30T22:20Z] INFO  23:20:58,469 MuTect - [MUTECT] Processed 1000057 reads in 2393 ms
[2015-09-30T22:20Z] INFO  23:20:58,962 MuTect - [MUTECT] Processed 27001290 reads in 659 ms
[2015-09-30T22:20Z] INFO  23:20:59,032 MuTect - [MUTECT] Processed 110006153 reads in 741 ms
[2015-09-30T22:20Z] INFO  23:20:59,167 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:59,248 MuTect - [MUTECT] Processed 2000060 reads in 778 ms
[2015-09-30T22:20Z] INFO  23:20:59,599 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:20Z] INFO  23:20:59,600 MuTect - [MUTECT] Processed 28001337 reads in 638 ms
[2015-09-30T22:20Z] INFO  23:20:59,758 MuTect - [MUTECT] Processed 111006219 reads in 726 ms
[2015-09-30T22:20Z] INFO  23:20:59,950 MuTect - [MUTECT] Processed 3000070 reads in 702 ms
[2015-09-30T22:21Z] INFO  23:21:00,201 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:00,241 MuTect - [MUTECT] Processed 29001337 reads in 641 ms
[2015-09-30T22:21Z] INFO  23:21:00,485 MuTect - [MUTECT] Processed 112006248 reads in 727 ms
[2015-09-30T22:21Z] INFO  23:21:00,633 MuTect - [MUTECT] Processed 4000144 reads in 684 ms
[2015-09-30T22:21Z] INFO  23:21:00,871 MuTect - [MUTECT] Processed 30001393 reads in 630 ms
[2015-09-30T22:21Z] INFO  23:21:01,187 MuTect - [MUTECT] Processed 113006280 reads in 702 ms
[2015-09-30T22:21Z] INFO  23:21:01,304 MuTect - [MUTECT] Processed 5000210 reads in 671 ms
[2015-09-30T22:21Z] INFO  23:21:01,497 MuTect - [MUTECT] Processed 31001407 reads in 626 ms
[2015-09-30T22:21Z] INFO  23:21:01,837 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:01,841 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:01,867 MuTect - [MUTECT] Processed 114006338 reads in 680 ms
[2015-09-30T22:21Z] INFO  23:21:01,981 MuTect - [MUTECT] Processed 6000229 reads in 677 ms
[2015-09-30T22:21Z] INFO  23:21:02,140 MuTect - [MUTECT] Processed 32001525 reads in 643 ms
[2015-09-30T22:21Z] INFO  23:21:02,549 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:02,565 MuTect - [MUTECT] Processed 115006365 reads in 698 ms
[2015-09-30T22:21Z] INFO  23:21:02,658 MuTect - [MUTECT] Processed 7000284 reads in 677 ms
[2015-09-30T22:21Z] INFO  23:21:02,790 MuTect - [MUTECT] Processed 33001610 reads in 650 ms
[2015-09-30T22:21Z] INFO  23:21:03,276 MuTect - [MUTECT] Processed 116006446 reads in 711 ms
[2015-09-30T22:21Z] INFO  23:21:03,299 MuTect - [MUTECT] Processed 8000347 reads in 641 ms
[2015-09-30T22:21Z] INFO  23:21:03,461 MuTect - [MUTECT] Processed 34001627 reads in 671 ms
[2015-09-30T22:21Z] INFO  23:21:03,956 MuTect - [MUTECT] Processed 117006459 reads in 680 ms
[2015-09-30T22:21Z] INFO  23:21:03,971 MuTect - [MUTECT] Processed 9000392 reads in 672 ms
[2015-09-30T22:21Z] INFO  23:21:04,070 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:04,102 MuTect - [MUTECT] Processed 35001675 reads in 641 ms
[2015-09-30T22:21Z] INFO  23:21:04,607 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:04,635 MuTect - [MUTECT] Processed 118006495 reads in 679 ms
[2015-09-30T22:21Z] INFO  23:21:04,672 MuTect - [MUTECT] Processed 10000476 reads in 701 ms
[2015-09-30T22:21Z] INFO  23:21:04,762 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:04,783 MuTect - [MUTECT] Processed 36001801 reads in 681 ms
[2015-09-30T22:21Z] INFO  23:21:05,340 MuTect - [MUTECT] Processed 119006565 reads in 705 ms
[2015-09-30T22:21Z] INFO  23:21:05,368 MuTect - [MUTECT] Processed 11000570 reads in 696 ms
[2015-09-30T22:21Z] INFO  23:21:05,455 MuTect - [MUTECT] Processed 37001827 reads in 672 ms
[2015-09-30T22:21Z] INFO  23:21:05,965 MuTect - [MUTECT] Processed 12000651 reads in 597 ms
[2015-09-30T22:21Z] INFO  23:21:05,993 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:21Z] INFO  23:21:05,997 ProgressMeter -            done        3.91e+06   88.0 s       22.0 s    100.0%        88.0 s     0.0 s
[2015-09-30T22:21Z] INFO  23:21:05,997 ProgressMeter - Total runtime 88.13 secs, 1.47 min, 0.02 hours
[2015-09-30T22:21Z] INFO  23:21:06,061 MicroScheduler - 83934 reads were filtered out during the traversal out of approximately 1432007 total reads (5.86%)
[2015-09-30T22:21Z] INFO  23:21:06,062 MicroScheduler -   -> 60760 reads (4.24% of total) failing DuplicateReadFilter
[2015-09-30T22:21Z] INFO  23:21:06,062 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:21Z] INFO  23:21:06,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:21Z] INFO  23:21:06,062 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:21Z] INFO  23:21:06,062 MicroScheduler -   -> 23174 reads (1.62% of total) failing UnmappedReadFilter
[2015-09-30T22:21Z] INFO  23:21:06,116 MuTect - [MUTECT] Processed 38001944 reads in 661 ms
[2015-09-30T22:21Z] INFO  23:21:06,458 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:06,558 MuTect - [MUTECT] Processed 13000729 reads in 593 ms
[2015-09-30T22:21Z] INFO  23:21:06,734 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:06,800 MuTect - [MUTECT] Processed 39001986 reads in 684 ms
[2015-09-30T22:21Z] INFO  23:21:07,068 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:21Z] bgzip syn3-7_62708318_93925745-raw-mutect.vcf
[2015-09-30T22:21Z] INFO  23:21:07,163 MuTect - [MUTECT] Processed 14000811 reads in 605 ms
[2015-09-30T22:21Z] tabix index syn3-7_62708318_93925745-raw-mutect.vcf.gz
[2015-09-30T22:21Z] INFO  23:21:07,461 MuTect - [MUTECT] Processed 40002029 reads in 661 ms
[2015-09-30T22:21Z] INFO  23:21:07,798 MuTect - [MUTECT] Processed 15000906 reads in 635 ms
[2015-09-30T22:21Z] INFO  23:21:08,113 ProgressMeter -      7:99726167        1.40e+06   30.0 s       21.0 s     25.6%       117.0 s    87.0 s
[2015-09-30T22:21Z] INFO  23:21:08,129 MuTect - [MUTECT] Processed 41002032 reads in 668 ms
[2015-09-30T22:21Z] INFO  23:21:08,449 MuTect - [MUTECT] Processed 16000933 reads in 651 ms
[2015-09-30T22:21Z] INFO  23:21:08,557 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:08,781 MuTect - [MUTECT] Processed 42002086 reads in 652 ms
[2015-09-30T22:21Z] INFO  23:21:08,783 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:09,085 MuTect - [MUTECT] Processed 17000989 reads in 636 ms
[2015-09-30T22:21Z] INFO  23:21:09,489 MuTect - [MUTECT] Processed 43002096 reads in 708 ms
[2015-09-30T22:21Z] INFO  23:21:09,733 MuTect - [MUTECT] Processed 18001106 reads in 648 ms
[2015-09-30T22:21Z] INFO  23:21:10,209 MuTect - [MUTECT] Processed 44002150 reads in 720 ms
[2015-09-30T22:21Z] INFO  23:21:10,390 MuTect - [MUTECT] Processed 19001140 reads in 657 ms
[2015-09-30T22:21Z] INFO  23:21:10,827 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:10,861 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:11,006 MuTect - [MUTECT] Processed 45002195 reads in 797 ms
[2015-09-30T22:21Z] INFO  23:21:11,053 MuTect - [MUTECT] Processed 20001235 reads in 663 ms
[2015-09-30T22:21Z] INFO  23:21:11,670 MuTect - [MUTECT] Processed 46002212 reads in 664 ms
[2015-09-30T22:21Z] INFO  23:21:11,734 MuTect - [MUTECT] Processed 21001356 reads in 681 ms
[2015-09-30T22:21Z] MuTect: MuTect
[2015-09-30T22:21Z] INFO  23:21:12,316 MuTect - [MUTECT] Processed 47002245 reads in 646 ms
[2015-09-30T22:21Z] INFO  23:21:12,397 MuTect - [MUTECT] Processed 22001374 reads in 663 ms
[2015-09-30T22:21Z] INFO  23:21:12,980 MuTect - [MUTECT] Processed 48002309 reads in 664 ms
[2015-09-30T22:21Z] INFO  23:21:13,029 MuTect - [MUTECT] Processed 23001386 reads in 632 ms
[2015-09-30T22:21Z] INFO  23:21:13,235 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:13,381 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:13,656 MuTect - [MUTECT] Processed 49002409 reads in 676 ms
[2015-09-30T22:21Z] INFO  23:21:13,695 MuTect - [MUTECT] Processed 24001461 reads in 666 ms
[2015-09-30T22:21Z] INFO  23:21:14,332 MuTect - [MUTECT] Processed 50002463 reads in 676 ms
[2015-09-30T22:21Z] INFO  23:21:14,376 MuTect - [MUTECT] Processed 25001461 reads in 681 ms
[2015-09-30T22:21Z] INFO  23:21:14,584 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/7/syn3-7_157155595_159138663-raw-mutect-regions.bed to be BED
[2015-09-30T22:21Z] INFO  23:21:14,637 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:21Z] INFO  23:21:14,638 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:21Z] INFO  23:21:14,638 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:21Z] INFO  23:21:14,638 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:21Z] INFO  23:21:14,641 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/7/syn3-7_157155595_159138663-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/7/tx/tmpJl3WlC/syn3-7_157155595_159138663-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:21Z] INFO  23:21:14,642 HelpFormatter - Date/Time: 2015/09/30 23:21:14
[2015-09-30T22:21Z] INFO  23:21:14,642 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:21Z] INFO  23:21:14,642 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:21Z] INFO  23:21:14,668 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:21Z] INFO  23:21:14,672 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:21Z] INFO  23:21:14,719 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:21Z] INFO  23:21:14,767 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:21Z] INFO  23:21:14,774 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:21Z] INFO  23:21:14,797 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:21Z] INFO  23:21:14,807 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:21Z] INFO  23:21:14,974 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:21Z] INFO  23:21:14,997 MuTect - [MUTECT] Processed 51002475 reads in 665 ms
[2015-09-30T22:21Z] INFO  23:21:15,006 MuTect - [MUTECT] Processed 26001539 reads in 630 ms
[2015-09-30T22:21Z] INFO  23:21:15,028 IntervalUtils - Processing 103094 bp from intervals
[2015-09-30T22:21Z] INFO  23:21:15,032 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:21Z] INFO  23:21:15,032 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:21Z] INFO  23:21:15,083 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:21Z] INFO  23:21:15,273 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:21Z] INFO  23:21:15,273 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:21Z] INFO  23:21:15,273 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:21Z] INFO  23:21:15,274 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:21Z] INFO  23:21:15,410 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:15,641 MuTect - [MUTECT] Processed 27001596 reads in 634 ms
[2015-09-30T22:21Z] INFO  23:21:15,643 MuTect - [MUTECT] Processed 52002581 reads in 646 ms
[2015-09-30T22:21Z] INFO  23:21:15,718 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:16,278 MuTect - [MUTECT] Processed 28001656 reads in 638 ms
[2015-09-30T22:21Z] INFO  23:21:16,309 MuTect - [MUTECT] Processed 53002666 reads in 666 ms
[2015-09-30T22:21Z] INFO  23:21:16,932 MuTect - [MUTECT] Processed 29001682 reads in 654 ms
[2015-09-30T22:21Z] INFO  23:21:16,963 MuTect - [MUTECT] Processed 54002700 reads in 654 ms
[2015-09-30T22:21Z] INFO  23:21:17,545 MuTect - [MUTECT] Processed 30001800 reads in 613 ms
[2015-09-30T22:21Z] INFO  23:21:17,562 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:17,618 MuTect - [MUTECT] Processed 55002718 reads in 655 ms
[2015-09-30T22:21Z] INFO  23:21:17,904 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:18,175 MuTect - [MUTECT] Processed 31001813 reads in 630 ms
[2015-09-30T22:21Z] INFO  23:21:18,274 MuTect - [MUTECT] Processed 56002785 reads in 656 ms
[2015-09-30T22:21Z] INFO  23:21:18,450 MuTect - [MUTECT] Processed 1000110 reads in 3026 ms
[2015-09-30T22:21Z] INFO  23:21:18,774 MuTect - [MUTECT] Processed 32001878 reads in 599 ms
[2015-09-30T22:21Z] INFO  23:21:18,939 MuTect - [MUTECT] Processed 57002866 reads in 665 ms
[2015-09-30T22:21Z] INFO  23:21:19,260 MuTect - [MUTECT] Processed 2000138 reads in 810 ms
[2015-09-30T22:21Z] INFO  23:21:19,406 MuTect - [MUTECT] Processed 33001908 reads in 632 ms
[2015-09-30T22:21Z] INFO  23:21:19,604 MuTect - [MUTECT] Processed 58002895 reads in 665 ms
[2015-09-30T22:21Z] INFO  23:21:19,856 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:19,961 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:20,022 MuTect - [MUTECT] Processed 34001941 reads in 616 ms
[2015-09-30T22:21Z] INFO  23:21:20,070 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:20,193 MuTect - [MUTECT] Processed 3000161 reads in 933 ms
[2015-09-30T22:21Z] INFO  23:21:20,271 MuTect - [MUTECT] Processed 59002998 reads in 667 ms
[2015-09-30T22:21Z] INFO  23:21:20,643 MuTect - [MUTECT] Processed 35002023 reads in 621 ms
[2015-09-30T22:21Z] INFO  23:21:20,975 MuTect - [MUTECT] Processed 60003080 reads in 704 ms
[2015-09-30T22:21Z] INFO  23:21:21,068 MuTect - [MUTECT] Processed 4000172 reads in 875 ms
[2015-09-30T22:21Z] INFO  23:21:21,264 MuTect - [MUTECT] Processed 36002124 reads in 621 ms
[2015-09-30T22:21Z] INFO  23:21:21,651 MuTect - [MUTECT] Processed 61003111 reads in 676 ms
[2015-09-30T22:21Z] INFO  23:21:21,887 MuTect - [MUTECT] Processed 5000203 reads in 819 ms
[2015-09-30T22:21Z] INFO  23:21:21,914 MuTect - [MUTECT] Processed 37002178 reads in 650 ms
[2015-09-30T22:21Z] INFO  23:21:21,986 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:22,011 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:22,319 MuTect - [MUTECT] Processed 62003123 reads in 668 ms
[2015-09-30T22:21Z] INFO  23:21:22,452 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:22,568 MuTect - [MUTECT] Processed 38002275 reads in 654 ms
[2015-09-30T22:21Z] INFO  23:21:22,796 MuTect - [MUTECT] Processed 6000213 reads in 909 ms
[2015-09-30T22:21Z] INFO  23:21:22,972 MuTect - [MUTECT] Processed 63003160 reads in 653 ms
[2015-09-30T22:21Z] INFO  23:21:23,216 MuTect - [MUTECT] Processed 39002337 reads in 648 ms
[2015-09-30T22:21Z] INFO  23:21:23,504 MuTect - [MUTECT] Processed 7000266 reads in 708 ms
[2015-09-30T22:21Z] INFO  23:21:23,615 MuTect - [MUTECT] Processed 64003278 reads in 643 ms
[2015-09-30T22:21Z] INFO  23:21:23,892 MuTect - [MUTECT] Processed 40002364 reads in 676 ms
[2015-09-30T22:21Z] INFO  23:21:24,199 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:24,240 MuTect - [MUTECT] Processed 8000334 reads in 736 ms
[2015-09-30T22:21Z] INFO  23:21:24,537 MuTect - [MUTECT] Processed 65003454 reads in 922 ms
[2015-09-30T22:21Z] INFO  23:21:24,547 MuTect - [MUTECT] Processed 41002387 reads in 655 ms
[2015-09-30T22:21Z] INFO  23:21:24,708 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:24,753 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:24,946 MuTect - [MUTECT] Processed 9000429 reads in 706 ms
[2015-09-30T22:21Z] INFO  23:21:25,191 MuTect - [MUTECT] Processed 42002417 reads in 644 ms
[2015-09-30T22:21Z] INFO  23:21:25,608 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:21Z] INFO  23:21:25,613 ProgressMeter -            done        2.55e+05   10.0 s       40.0 s     99.9%        10.0 s     0.0 s
[2015-09-30T22:21Z] INFO  23:21:25,613 ProgressMeter - Total runtime 10.34 secs, 0.17 min, 0.00 hours
[2015-09-30T22:21Z] INFO  23:21:25,678 MicroScheduler - 7867 reads were filtered out during the traversal out of approximately 122364 total reads (6.43%)
[2015-09-30T22:21Z] INFO  23:21:25,678 MicroScheduler -   -> 5887 reads (4.81% of total) failing DuplicateReadFilter
[2015-09-30T22:21Z] INFO  23:21:25,678 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:21Z] INFO  23:21:25,678 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:21Z] INFO  23:21:25,678 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:21Z] INFO  23:21:25,679 MicroScheduler -   -> 1980 reads (1.62% of total) failing UnmappedReadFilter
[2015-09-30T22:21Z] INFO  23:21:25,886 MuTect - [MUTECT] Processed 43002457 reads in 695 ms
[2015-09-30T22:21Z] INFO  23:21:26,031 ProgressMeter -     7:133894439        1.26e+06   30.0 s       23.0 s     24.1%         2.1 m    94.0 s
[2015-09-30T22:21Z] INFO  23:21:26,523 MuTect - [MUTECT] Processed 44002461 reads in 637 ms
[2015-09-30T22:21Z] INFO  23:21:26,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:21Z] bgzip syn3-7_157155595_159138663-raw-mutect.vcf
[2015-09-30T22:21Z] tabix index syn3-7_157155595_159138663-raw-mutect.vcf.gz
[2015-09-30T22:21Z] INFO  23:21:27,052 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:27,183 MuTect - [MUTECT] Processed 45002505 reads in 660 ms
[2015-09-30T22:21Z] INFO  23:21:27,885 MuTect - [MUTECT] Processed 46002574 reads in 702 ms
[2015-09-30T22:21Z] INFO  23:21:28,536 MuTect - [MUTECT] Processed 47002592 reads in 651 ms
[2015-09-30T22:21Z] MuTect: MuTect
[2015-09-30T22:21Z] INFO  23:21:29,259 MuTect - [MUTECT] Processed 48002621 reads in 723 ms
[2015-09-30T22:21Z] INFO  23:21:29,464 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:29,920 MuTect - [MUTECT] Processed 49002686 reads in 661 ms
[2015-09-30T22:21Z] INFO  23:21:30,553 MuTect - [MUTECT] Processed 50002743 reads in 633 ms
[2015-09-30T22:21Z] INFO  23:21:30,956 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/8/syn3-8_0_31024990-raw-mutect-regions.bed to be BED
[2015-09-30T22:21Z] INFO  23:21:31,011 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:21Z] INFO  23:21:31,011 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:21Z] INFO  23:21:31,011 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:21Z] INFO  23:21:31,012 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:21Z] INFO  23:21:31,015 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/8/syn3-8_0_31024990-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/8/tx/tmpBjFXGm/syn3-8_0_31024990-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:21Z] INFO  23:21:31,015 HelpFormatter - Date/Time: 2015/09/30 23:21:31
[2015-09-30T22:21Z] INFO  23:21:31,015 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:21Z] INFO  23:21:31,015 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:21Z] INFO  23:21:31,042 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:21Z] INFO  23:21:31,046 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:21Z] INFO  23:21:31,154 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:21Z] INFO  23:21:31,201 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:21Z] INFO  23:21:31,208 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:21Z] INFO  23:21:31,225 MuTect - [MUTECT] Processed 51002821 reads in 672 ms
[2015-09-30T22:21Z] INFO  23:21:31,261 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T22:21Z] INFO  23:21:31,293 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:21Z] INFO  23:21:31,468 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:21Z] INFO  23:21:31,571 IntervalUtils - Processing 1421167 bp from intervals
[2015-09-30T22:21Z] INFO  23:21:31,575 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:21Z] INFO  23:21:31,575 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:21Z] INFO  23:21:31,635 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:31,722 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:21Z] INFO  23:21:31,858 MuTect - [MUTECT] Processed 52002917 reads in 633 ms
[2015-09-30T22:21Z] INFO  23:21:31,870 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:21Z] INFO  23:21:31,870 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:21Z] INFO  23:21:31,870 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:21Z] INFO  23:21:31,871 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:21Z] INFO  23:21:32,494 MuTect - [MUTECT] Processed 53002928 reads in 636 ms
[2015-09-30T22:21Z] INFO  23:21:33,140 MuTect - [MUTECT] Processed 54002963 reads in 646 ms
[2015-09-30T22:21Z] INFO  23:21:33,796 MuTect - [MUTECT] Processed 55003014 reads in 656 ms
[2015-09-30T22:21Z] INFO  23:21:33,929 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:34,340 MuTect - [MUTECT] Processed 1000000 reads in 2422 ms
[2015-09-30T22:21Z] INFO  23:21:34,420 MuTect - [MUTECT] Processed 56003016 reads in 624 ms
[2015-09-30T22:21Z] INFO  23:21:35,005 MuTect - [MUTECT] Processed 57003030 reads in 585 ms
[2015-09-30T22:21Z] INFO  23:21:35,162 MuTect - [MUTECT] Processed 2000075 reads in 823 ms
[2015-09-30T22:21Z] INFO  23:21:35,693 MuTect - [MUTECT] Processed 58003088 reads in 688 ms
[2015-09-30T22:21Z] INFO  23:21:35,950 MuTect - [MUTECT] Processed 3000158 reads in 788 ms
[2015-09-30T22:21Z] INFO  23:21:36,059 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:36,134 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:36,332 MuTect - [MUTECT] Processed 59003126 reads in 639 ms
[2015-09-30T22:21Z] INFO  23:21:36,646 MuTect - [MUTECT] Processed 4000211 reads in 696 ms
[2015-09-30T22:21Z] INFO  23:21:36,972 MuTect - [MUTECT] Processed 60003166 reads in 640 ms
[2015-09-30T22:21Z] INFO  23:21:37,403 MuTect - [MUTECT] Processed 5000304 reads in 757 ms
[2015-09-30T22:21Z] INFO  23:21:37,644 MuTect - [MUTECT] Processed 61003191 reads in 672 ms
[2015-09-30T22:21Z] INFO  23:21:38,114 ProgressMeter -     7:100550811        2.15e+06   60.0 s       27.0 s     37.9%         2.6 m    98.0 s
[2015-09-30T22:21Z] INFO  23:21:38,140 MuTect - [MUTECT] Processed 6000353 reads in 737 ms
[2015-09-30T22:21Z] INFO  23:21:38,304 MuTect - [MUTECT] Processed 62003215 reads in 660 ms
[2015-09-30T22:21Z] INFO  23:21:38,378 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:38,665 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:38,880 MuTect - [MUTECT] Processed 7000357 reads in 740 ms
[2015-09-30T22:21Z] INFO  23:21:38,918 MuTect - [MUTECT] Processed 63003293 reads in 614 ms
[2015-09-30T22:21Z] INFO  23:21:39,546 MuTect - [MUTECT] Processed 64003298 reads in 627 ms
[2015-09-30T22:21Z] INFO  23:21:39,729 MuTect - [MUTECT] Processed 8000391 reads in 848 ms
[2015-09-30T22:21Z] INFO  23:21:40,224 MuTect - [MUTECT] Processed 65003370 reads in 679 ms
[2015-09-30T22:21Z] INFO  23:21:40,531 MuTect - [MUTECT] Processed 9000447 reads in 803 ms
[2015-09-30T22:21Z] INFO  23:21:40,562 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:40,908 MuTect - [MUTECT] Processed 66003373 reads in 684 ms
[2015-09-30T22:21Z] INFO  23:21:41,283 MuTect - [MUTECT] Processed 10000486 reads in 752 ms
[2015-09-30T22:21Z] INFO  23:21:41,384 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:41,523 MuTect - [MUTECT] Processed 67003373 reads in 615 ms
[2015-09-30T22:21Z] INFO  23:21:42,052 MuTect - [MUTECT] Processed 11000491 reads in 769 ms
[2015-09-30T22:21Z] INFO  23:21:42,126 MuTect - [MUTECT] Processed 68003473 reads in 603 ms
[2015-09-30T22:21Z] INFO  23:21:42,737 MuTect - [MUTECT] Processed 69003480 reads in 611 ms
[2015-09-30T22:21Z] INFO  23:21:42,824 MuTect - [MUTECT] Processed 12000497 reads in 772 ms
[2015-09-30T22:21Z] INFO  23:21:42,897 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:43,256 MuTect - [MUTECT] Processed 66004991 reads in 18719 ms
[2015-09-30T22:21Z] INFO  23:21:43,364 MuTect - [MUTECT] Processed 70003511 reads in 627 ms
[2015-09-30T22:21Z] INFO  23:21:43,534 MuTect - [MUTECT] Processed 13000517 reads in 710 ms
[2015-09-30T22:21Z] INFO  23:21:43,754 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:44,006 MuTect - [MUTECT] Processed 71003587 reads in 642 ms
[2015-09-30T22:21Z] INFO  23:21:44,239 MuTect - [MUTECT] Processed 14000574 reads in 705 ms
[2015-09-30T22:21Z] INFO  23:21:44,630 MuTect - [MUTECT] Processed 72003591 reads in 624 ms
[2015-09-30T22:21Z] INFO  23:21:44,923 MuTect - [MUTECT] Processed 15000709 reads in 684 ms
[2015-09-30T22:21Z] INFO  23:21:45,022 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:45,257 MuTect - [MUTECT] Processed 73003598 reads in 627 ms
[2015-09-30T22:21Z] INFO  23:21:45,592 MuTect - [MUTECT] Processed 16000756 reads in 669 ms
[2015-09-30T22:21Z] INFO  23:21:45,876 MuTect - [MUTECT] Processed 74003657 reads in 619 ms
[2015-09-30T22:21Z] INFO  23:21:46,268 MuTect - [MUTECT] Processed 17000860 reads in 676 ms
[2015-09-30T22:21Z] INFO  23:21:46,539 MuTect - [MUTECT] Processed 75003693 reads in 663 ms
[2015-09-30T22:21Z] INFO  23:21:46,971 MuTect - [MUTECT] Processed 18000879 reads in 703 ms
[2015-09-30T22:21Z] INFO  23:21:47,196 MuTect - [MUTECT] Processed 76003778 reads in 657 ms
[2015-09-30T22:21Z] INFO  23:21:47,223 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:47,382 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:47,689 MuTect - [MUTECT] Processed 19001043 reads in 718 ms
[2015-09-30T22:21Z] INFO  23:21:47,856 MuTect - [MUTECT] Processed 77003810 reads in 660 ms
[2015-09-30T22:21Z] INFO  23:21:48,380 MuTect - [MUTECT] Processed 20001128 reads in 691 ms
[2015-09-30T22:21Z] INFO  23:21:48,540 MuTect - [MUTECT] Processed 78003817 reads in 684 ms
[2015-09-30T22:21Z] INFO  23:21:48,983 MuTect - [MUTECT] Processed 21001154 reads in 603 ms
[2015-09-30T22:21Z] INFO  23:21:49,170 MuTect - [MUTECT] Processed 79003822 reads in 630 ms
[2015-09-30T22:21Z] INFO  23:21:49,558 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:49,656 MuTect - [MUTECT] Processed 22001283 reads in 673 ms
[2015-09-30T22:21Z] INFO  23:21:49,801 MuTect - [MUTECT] Processed 80003893 reads in 631 ms
[2015-09-30T22:21Z] INFO  23:21:50,323 MuTect - [MUTECT] Processed 23001303 reads in 667 ms
[2015-09-30T22:21Z] INFO  23:21:50,462 MuTect - [MUTECT] Processed 81003933 reads in 661 ms
[2015-09-30T22:21Z] INFO  23:21:51,041 MuTect - [MUTECT] Processed 24001435 reads in 718 ms
[2015-09-30T22:21Z] INFO  23:21:51,165 MuTect - [MUTECT] Processed 82004012 reads in 703 ms
[2015-09-30T22:21Z] INFO  23:21:51,836 MuTect - [MUTECT] Processed 83004060 reads in 671 ms
[2015-09-30T22:21Z] INFO  23:21:51,842 MuTect - [MUTECT] Processed 25001453 reads in 801 ms
[2015-09-30T22:21Z] INFO  23:21:52,019 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:52,541 MuTect - [MUTECT] Processed 26001456 reads in 699 ms
[2015-09-30T22:21Z] INFO  23:21:52,555 MuTect - [MUTECT] Processed 84004111 reads in 719 ms
[2015-09-30T22:21Z] INFO  23:21:52,615 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:53,245 MuTect - [MUTECT] Processed 27001530 reads in 704 ms
[2015-09-30T22:21Z] INFO  23:21:53,253 MuTect - [MUTECT] Processed 85004127 reads in 698 ms
[2015-09-30T22:21Z] INFO  23:21:53,907 MuTect - [MUTECT] Processed 86004216 reads in 654 ms
[2015-09-30T22:21Z] INFO  23:21:53,988 MuTect - [MUTECT] Processed 28001568 reads in 743 ms
[2015-09-30T22:21Z] INFO  23:21:54,376 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:54,579 MuTect - [MUTECT] Processed 87004256 reads in 672 ms
[2015-09-30T22:21Z] INFO  23:21:54,693 MuTect - [MUTECT] Processed 29001584 reads in 705 ms
[2015-09-30T22:21Z] INFO  23:21:55,246 MuTect - [MUTECT] Processed 88004338 reads in 667 ms
[2015-09-30T22:21Z] INFO  23:21:55,265 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:55,462 MuTect - [MUTECT] Processed 30001597 reads in 769 ms
[2015-09-30T22:21Z] INFO  23:21:55,837 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:55,920 MuTect - [MUTECT] Processed 89004377 reads in 674 ms
[2015-09-30T22:21Z] INFO  23:21:56,032 ProgressMeter -     7:142028300        2.78e+06   60.0 s       21.0 s     52.8%       113.0 s    53.0 s
[2015-09-30T22:21Z] INFO  23:21:56,162 MuTect - [MUTECT] Processed 31001678 reads in 700 ms
[2015-09-30T22:21Z] INFO  23:21:56,659 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:56,917 MuTect - [MUTECT] Processed 32001701 reads in 755 ms
[2015-09-30T22:21Z] INFO  23:21:57,251 MuTect - [MUTECT] Processed 90004421 reads in 1331 ms
[2015-09-30T22:21Z] INFO  23:21:57,592 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:57,613 MuTect - [MUTECT] Processed 33001760 reads in 696 ms
[2015-09-30T22:21Z] INFO  23:21:58,401 MuTect - [MUTECT] Processed 34001799 reads in 788 ms
[2015-09-30T22:21Z] INFO  23:21:58,761 MuTect - [MUTECT] Processed 91004577 reads in 1510 ms
[2015-09-30T22:21Z] INFO  23:21:59,051 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:21Z] INFO  23:21:59,120 MuTect - [MUTECT] Processed 35001813 reads in 719 ms
[2015-09-30T22:21Z] INFO  23:21:59,811 MuTect - [MUTECT] Processed 36001849 reads in 691 ms
[2015-09-30T22:22Z] INFO  23:22:00,000 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:00,300 MuTect - [MUTECT] Processed 92004622 reads in 1539 ms
[2015-09-30T22:22Z] INFO  23:22:00,530 MuTect - [MUTECT] Processed 37001942 reads in 719 ms
[2015-09-30T22:22Z] INFO  23:22:01,117 MuTect - [MUTECT] Processed 93004652 reads in 817 ms
[2015-09-30T22:22Z] INFO  23:22:01,245 MuTect - [MUTECT] Processed 38001959 reads in 715 ms
[2015-09-30T22:22Z] INFO  23:22:01,272 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:01,873 ProgressMeter -      8:11985687        9.82e+05   30.0 s       30.0 s     30.8%        97.0 s    67.0 s
[2015-09-30T22:22Z] INFO  23:22:01,963 MuTect - [MUTECT] Processed 39002010 reads in 718 ms
[2015-09-30T22:22Z] INFO  23:22:02,417 MuTect - [MUTECT] Processed 94004818 reads in 1300 ms
[2015-09-30T22:22Z] INFO  23:22:02,419 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:02,698 MuTect - [MUTECT] Processed 40002020 reads in 735 ms
[2015-09-30T22:22Z] INFO  23:22:03,057 MuTect - [MUTECT] Processed 95004854 reads in 640 ms
[2015-09-30T22:22Z] INFO  23:22:03,221 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:03,414 MuTect - [MUTECT] Processed 41002126 reads in 716 ms
[2015-09-30T22:22Z] INFO  23:22:03,632 MuTect - [MUTECT] Processed 96004922 reads in 575 ms
[2015-09-30T22:22Z] INFO  23:22:04,097 MuTect - [MUTECT] Processed 42002152 reads in 683 ms
[2015-09-30T22:22Z] INFO  23:22:04,233 MuTect - [MUTECT] Processed 97005058 reads in 601 ms
[2015-09-30T22:22Z] INFO  23:22:04,837 MuTect - [MUTECT] Processed 98005060 reads in 604 ms
[2015-09-30T22:22Z] INFO  23:22:04,936 MuTect - [MUTECT] Processed 43002219 reads in 839 ms
[2015-09-30T22:22Z] INFO  23:22:05,183 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:05,439 MuTect - [MUTECT] Processed 99005139 reads in 602 ms
[2015-09-30T22:22Z] INFO  23:22:05,605 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:05,749 MuTect - [MUTECT] Processed 44002279 reads in 813 ms
[2015-09-30T22:22Z] INFO  23:22:06,023 MuTect - [MUTECT] Processed 100005212 reads in 584 ms
[2015-09-30T22:22Z] INFO  23:22:06,453 MuTect - [MUTECT] Processed 45002282 reads in 704 ms
[2015-09-30T22:22Z] INFO  23:22:06,605 MuTect - [MUTECT] Processed 101005325 reads in 582 ms
[2015-09-30T22:22Z] INFO  23:22:07,124 MuTect - [MUTECT] Processed 46002319 reads in 671 ms
[2015-09-30T22:22Z] INFO  23:22:07,199 MuTect - [MUTECT] Processed 102005365 reads in 594 ms
[2015-09-30T22:22Z] INFO  23:22:07,253 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:07,791 MuTect - [MUTECT] Processed 103005394 reads in 592 ms
[2015-09-30T22:22Z] INFO  23:22:07,825 MuTect - [MUTECT] Processed 47002325 reads in 701 ms
[2015-09-30T22:22Z] INFO  23:22:08,026 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:08,390 MuTect - [MUTECT] Processed 104005490 reads in 599 ms
[2015-09-30T22:22Z] INFO  23:22:08,532 MuTect - [MUTECT] Processed 48002355 reads in 707 ms
[2015-09-30T22:22Z] INFO  23:22:09,019 MuTect - [MUTECT] Processed 105005524 reads in 629 ms
[2015-09-30T22:22Z] INFO  23:22:09,295 MuTect - [MUTECT] Processed 67005584 reads in 26039 ms
[2015-09-30T22:22Z] INFO  23:22:09,315 MuTect - [MUTECT] Processed 49002397 reads in 783 ms
[2015-09-30T22:22Z] INFO  23:22:09,648 MuTect - [MUTECT] Processed 106005575 reads in 629 ms
[2015-09-30T22:22Z] INFO  23:22:10,175 MuTect - [MUTECT] Processed 50002462 reads in 860 ms
[2015-09-30T22:22Z] INFO  23:22:10,259 MuTect - [MUTECT] Processed 107005715 reads in 611 ms
[2015-09-30T22:22Z] INFO  23:22:10,284 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:10,866 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:10,898 MuTect - [MUTECT] Processed 51002511 reads in 723 ms
[2015-09-30T22:22Z] INFO  23:22:10,904 MuTect - [MUTECT] Processed 108005865 reads in 645 ms
[2015-09-30T22:22Z] INFO  23:22:11,483 MuTect - [MUTECT] Processed 109005966 reads in 579 ms
[2015-09-30T22:22Z] INFO  23:22:11,581 MuTect - [MUTECT] Processed 52002543 reads in 683 ms
[2015-09-30T22:22Z] INFO  23:22:12,097 MuTect - [MUTECT] Processed 110006145 reads in 614 ms
[2015-09-30T22:22Z] INFO  23:22:12,288 MuTect - [MUTECT] Processed 53002566 reads in 707 ms
[2015-09-30T22:22Z] INFO  23:22:12,687 MuTect - [MUTECT] Processed 111006256 reads in 590 ms
[2015-09-30T22:22Z] INFO  23:22:12,984 MuTect - [MUTECT] Processed 54002630 reads in 696 ms
[2015-09-30T22:22Z] INFO  23:22:13,268 MuTect - [MUTECT] Processed 112006269 reads in 581 ms
[2015-09-30T22:22Z] INFO  23:22:13,843 MuTect - [MUTECT] Processed 113006448 reads in 575 ms
[2015-09-30T22:22Z] INFO  23:22:14,063 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:14,376 MuTect - [MUTECT] Processed 55002644 reads in 1392 ms
[2015-09-30T22:22Z] INFO  23:22:14,422 MuTect - [MUTECT] Processed 114006636 reads in 579 ms
[2015-09-30T22:22Z] INFO  23:22:15,653 MuTect - [MUTECT] Processed 115006734 reads in 1231 ms
[2015-09-30T22:22Z] INFO  23:22:16,020 MuTect - [MUTECT] Processed 56002693 reads in 1644 ms
[2015-09-30T22:22Z] INFO  23:22:16,268 MuTect - [MUTECT] Processed 116006987 reads in 615 ms
[2015-09-30T22:22Z] INFO  23:22:16,457 MuTect - [MUTECT] Processed 68005713 reads in 7162 ms
[2015-09-30T22:22Z] INFO  23:22:16,851 MuTect - [MUTECT] Processed 117007021 reads in 583 ms
[2015-09-30T22:22Z] INFO  23:22:16,883 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:17,114 MuTect - [MUTECT] Processed 57002736 reads in 1094 ms
[2015-09-30T22:22Z] INFO  23:22:17,270 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:17,481 MuTect - [MUTECT] Processed 118007134 reads in 630 ms
[2015-09-30T22:22Z] INFO  23:22:17,828 MuTect - [MUTECT] Processed 58002752 reads in 714 ms
[2015-09-30T22:22Z] INFO  23:22:17,837 MuTect - [MUTECT] Processed 69005729 reads in 1380 ms
[2015-09-30T22:22Z] INFO  23:22:17,935 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:18,115 ProgressMeter -     7:100635683        2.18e+06  100.0 s       45.0 s     38.6%         4.3 m     2.7 m
[2015-09-30T22:22Z] INFO  23:22:18,132 MuTect - [MUTECT] Processed 119007147 reads in 651 ms
[2015-09-30T22:22Z] INFO  23:22:18,536 MuTect - [MUTECT] Processed 70006079 reads in 699 ms
[2015-09-30T22:22Z] INFO  23:22:18,549 MuTect - [MUTECT] Processed 59002810 reads in 721 ms
[2015-09-30T22:22Z] INFO  23:22:18,804 MuTect - [MUTECT] Processed 120007183 reads in 672 ms
[2015-09-30T22:22Z] INFO  23:22:19,231 MuTect - [MUTECT] Processed 71006337 reads in 695 ms
[2015-09-30T22:22Z] INFO  23:22:19,261 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:19,277 MuTect - [MUTECT] Processed 60002855 reads in 728 ms
[2015-09-30T22:22Z] INFO  23:22:19,486 MuTect - [MUTECT] Processed 121007222 reads in 682 ms
[2015-09-30T22:22Z] INFO  23:22:19,958 MuTect - [MUTECT] Processed 61002858 reads in 681 ms
[2015-09-30T22:22Z] INFO  23:22:19,973 MuTect - [MUTECT] Processed 72006600 reads in 742 ms
[2015-09-30T22:22Z] INFO  23:22:20,137 MuTect - [MUTECT] Processed 122007281 reads in 651 ms
[2015-09-30T22:22Z] INFO  23:22:20,403 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:20,596 MuTect - [MUTECT] Processed 62002918 reads in 638 ms
[2015-09-30T22:22Z] INFO  23:22:20,639 MuTect - [MUTECT] Processed 73006944 reads in 665 ms
[2015-09-30T22:22Z] INFO  23:22:20,782 MuTect - [MUTECT] Processed 123007366 reads in 645 ms
[2015-09-30T22:22Z] INFO  23:22:21,250 MuTect - [MUTECT] Processed 63002920 reads in 654 ms
[2015-09-30T22:22Z] INFO  23:22:21,358 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:21,368 MuTect - [MUTECT] Processed 74006980 reads in 730 ms
[2015-09-30T22:22Z] INFO  23:22:21,440 MuTect - [MUTECT] Processed 124007407 reads in 658 ms
[2015-09-30T22:22Z] INFO  23:22:21,593 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:21,904 MuTect - [MUTECT] Processed 64002975 reads in 654 ms
[2015-09-30T22:22Z] INFO  23:22:22,021 MuTect - [MUTECT] Processed 75007063 reads in 653 ms
[2015-09-30T22:22Z] INFO  23:22:22,082 MuTect - [MUTECT] Processed 125007419 reads in 642 ms
[2015-09-30T22:22Z] INFO  23:22:22,558 MuTect - [MUTECT] Processed 65002984 reads in 654 ms
[2015-09-30T22:22Z] INFO  23:22:22,597 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:22,684 MuTect - [MUTECT] Processed 76007099 reads in 663 ms
[2015-09-30T22:22Z] INFO  23:22:22,814 MuTect - [MUTECT] Processed 126007444 reads in 732 ms
[2015-09-30T22:22Z] INFO  23:22:23,241 MuTect - [MUTECT] Processed 66003074 reads in 683 ms
[2015-09-30T22:22Z] INFO  23:22:23,326 MuTect - [MUTECT] Processed 77007100 reads in 642 ms
[2015-09-30T22:22Z] INFO  23:22:23,472 MuTect - [MUTECT] Processed 127007559 reads in 658 ms
[2015-09-30T22:22Z] INFO  23:22:23,501 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:23,807 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:23,897 MuTect - [MUTECT] Processed 67003175 reads in 656 ms
[2015-09-30T22:22Z] INFO  23:22:23,983 MuTect - [MUTECT] Processed 78007152 reads in 657 ms
[2015-09-30T22:22Z] INFO  23:22:24,142 MuTect - [MUTECT] Processed 128007607 reads in 670 ms
[2015-09-30T22:22Z] INFO  23:22:24,536 MuTect - [MUTECT] Processed 68003211 reads in 639 ms
[2015-09-30T22:22Z] INFO  23:22:24,622 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:24,629 MuTect - [MUTECT] Processed 79007225 reads in 646 ms
[2015-09-30T22:22Z] INFO  23:22:24,776 MuTect - [MUTECT] Processed 129007639 reads in 634 ms
[2015-09-30T22:22Z] INFO  23:22:25,146 MuTect - [MUTECT] Processed 69003246 reads in 610 ms
[2015-09-30T22:22Z] INFO  23:22:25,309 MuTect - [MUTECT] Processed 80007324 reads in 680 ms
[2015-09-30T22:22Z] INFO  23:22:25,469 MuTect - [MUTECT] Processed 130007710 reads in 693 ms
[2015-09-30T22:22Z] INFO  23:22:25,644 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:25,765 MuTect - [MUTECT] Processed 70003285 reads in 618 ms
[2015-09-30T22:22Z] INFO  23:22:25,922 MuTect - [MUTECT] Processed 81007414 reads in 613 ms
[2015-09-30T22:22Z] INFO  23:22:25,939 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:26,033 ProgressMeter -     7:149427697        3.68e+06   90.0 s       24.0 s     73.0%         2.1 m    33.0 s
[2015-09-30T22:22Z] INFO  23:22:26,107 MuTect - [MUTECT] Processed 131007746 reads in 638 ms
[2015-09-30T22:22Z] INFO  23:22:26,393 MuTect - [MUTECT] Processed 71003349 reads in 629 ms
[2015-09-30T22:22Z] INFO  23:22:26,586 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:26,618 MuTect - [MUTECT] Processed 82007494 reads in 696 ms
[2015-09-30T22:22Z] INFO  23:22:26,722 MuTect - [MUTECT] Processed 132007752 reads in 615 ms
[2015-09-30T22:22Z] INFO  23:22:27,029 MuTect - [MUTECT] Processed 72003381 reads in 636 ms
[2015-09-30T22:22Z] INFO  23:22:27,291 MuTect - [MUTECT] Processed 83007603 reads in 673 ms
[2015-09-30T22:22Z] INFO  23:22:27,327 MuTect - [MUTECT] Processed 133007836 reads in 605 ms
[2015-09-30T22:22Z] INFO  23:22:27,671 MuTect - [MUTECT] Processed 73003476 reads in 641 ms
[2015-09-30T22:22Z] INFO  23:22:27,911 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:27,936 MuTect - [MUTECT] Processed 134007845 reads in 609 ms
[2015-09-30T22:22Z] INFO  23:22:27,973 MuTect - [MUTECT] Processed 84007603 reads in 682 ms
[2015-09-30T22:22Z] INFO  23:22:28,037 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:28,287 MuTect - [MUTECT] Processed 74003515 reads in 617 ms
[2015-09-30T22:22Z] INFO  23:22:28,573 MuTect - [MUTECT] Processed 135007891 reads in 637 ms
[2015-09-30T22:22Z] INFO  23:22:28,615 MuTect - [MUTECT] Processed 85007625 reads in 642 ms
[2015-09-30T22:22Z] INFO  23:22:28,812 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:28,942 MuTect - [MUTECT] Processed 75003569 reads in 655 ms
[2015-09-30T22:22Z] INFO  23:22:29,241 MuTect - [MUTECT] Processed 136007944 reads in 667 ms
[2015-09-30T22:22Z] INFO  23:22:29,248 MuTect - [MUTECT] Processed 86007638 reads in 633 ms
[2015-09-30T22:22Z] INFO  23:22:29,581 MuTect - [MUTECT] Processed 76003605 reads in 639 ms
[2015-09-30T22:22Z] INFO  23:22:29,898 MuTect - [MUTECT] Processed 87007992 reads in 650 ms
[2015-09-30T22:22Z] INFO  23:22:29,916 MuTect - [MUTECT] Processed 137007974 reads in 676 ms
[2015-09-30T22:22Z] INFO  23:22:30,189 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:30,221 MuTect - [MUTECT] Processed 77003609 reads in 640 ms
[2015-09-30T22:22Z] INFO  23:22:30,502 MuTect - [MUTECT] Processed 88007995 reads in 604 ms
[2015-09-30T22:22Z] INFO  23:22:30,563 MuTect - [MUTECT] Processed 138008020 reads in 647 ms
[2015-09-30T22:22Z] INFO  23:22:30,638 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:30,878 MuTect - [MUTECT] Processed 78003698 reads in 657 ms
[2015-09-30T22:22Z] INFO  23:22:31,070 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:31,140 MuTect - [MUTECT] Processed 89008061 reads in 638 ms
[2015-09-30T22:22Z] INFO  23:22:31,205 MuTect - [MUTECT] Processed 139008038 reads in 642 ms
[2015-09-30T22:22Z] INFO  23:22:31,521 MuTect - [MUTECT] Processed 79003814 reads in 643 ms
[2015-09-30T22:22Z] INFO  23:22:31,776 MuTect - [MUTECT] Processed 90008176 reads in 636 ms
[2015-09-30T22:22Z] INFO  23:22:31,874 ProgressMeter -      8:22473396        2.35e+06   60.0 s       25.0 s     63.5%        94.0 s    34.0 s
[2015-09-30T22:22Z] INFO  23:22:31,910 MuTect - [MUTECT] Processed 140008051 reads in 705 ms
[2015-09-30T22:22Z] INFO  23:22:32,210 MuTect - [MUTECT] Processed 80003918 reads in 689 ms
[2015-09-30T22:22Z] INFO  23:22:32,413 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:32,438 MuTect - [MUTECT] Processed 91008445 reads in 662 ms
[2015-09-30T22:22Z] INFO  23:22:32,513 MuTect - [MUTECT] Processed 141008152 reads in 603 ms
[2015-09-30T22:22Z] INFO  23:22:32,893 MuTect - [MUTECT] Processed 81003952 reads in 683 ms
[2015-09-30T22:22Z] INFO  23:22:33,088 MuTect - [MUTECT] Processed 92008639 reads in 650 ms
[2015-09-30T22:22Z] INFO  23:22:33,118 MuTect - [MUTECT] Processed 142008191 reads in 605 ms
[2015-09-30T22:22Z] INFO  23:22:33,202 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:33,610 MuTect - [MUTECT] Processed 82004054 reads in 717 ms
[2015-09-30T22:22Z] INFO  23:22:33,742 MuTect - [MUTECT] Processed 93008752 reads in 654 ms
[2015-09-30T22:22Z] INFO  23:22:33,744 MuTect - [MUTECT] Processed 143008195 reads in 626 ms
[2015-09-30T22:22Z] INFO  23:22:34,343 MuTect - [MUTECT] Processed 94008825 reads in 601 ms
[2015-09-30T22:22Z] INFO  23:22:34,344 MuTect - [MUTECT] Processed 83004060 reads in 734 ms
[2015-09-30T22:22Z] INFO  23:22:34,394 MuTect - [MUTECT] Processed 144008292 reads in 650 ms
[2015-09-30T22:22Z] INFO  23:22:34,579 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:34,973 MuTect - [MUTECT] Processed 95009129 reads in 630 ms
[2015-09-30T22:22Z] INFO  23:22:35,046 MuTect - [MUTECT] Processed 145008383 reads in 652 ms
[2015-09-30T22:22Z] INFO  23:22:35,241 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:35,451 MuTect - [MUTECT] Processed 84004172 reads in 1107 ms
[2015-09-30T22:22Z] INFO  23:22:35,451 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:35,571 MuTect - [MUTECT] Processed 96009249 reads in 598 ms
[2015-09-30T22:22Z] INFO  23:22:35,685 MuTect - [MUTECT] Processed 146008468 reads in 639 ms
[2015-09-30T22:22Z] INFO  23:22:36,287 MuTect - [MUTECT] Processed 97009300 reads in 716 ms
[2015-09-30T22:22Z] INFO  23:22:36,291 MuTect - [MUTECT] Processed 147008488 reads in 606 ms
[2015-09-30T22:22Z] INFO  23:22:36,586 MuTect - [MUTECT] Processed 85004205 reads in 1135 ms
[2015-09-30T22:22Z] INFO  23:22:36,626 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:36,883 MuTect - [MUTECT] Processed 148008549 reads in 592 ms
[2015-09-30T22:22Z] INFO  23:22:36,927 MuTect - [MUTECT] Processed 98009345 reads in 640 ms
[2015-09-30T22:22Z] INFO  23:22:37,323 MuTect - [MUTECT] Processed 86004237 reads in 736 ms
[2015-09-30T22:22Z] INFO  23:22:37,480 MuTect - [MUTECT] Processed 149008610 reads in 597 ms
[2015-09-30T22:22Z] INFO  23:22:37,561 MuTect - [MUTECT] Processed 99009640 reads in 634 ms
[2015-09-30T22:22Z] INFO  23:22:37,627 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:38,007 MuTect - [MUTECT] Processed 87004241 reads in 685 ms
[2015-09-30T22:22Z] INFO  23:22:38,065 MuTect - [MUTECT] Processed 150008651 reads in 585 ms
[2015-09-30T22:22Z] INFO  23:22:38,212 MuTect - [MUTECT] Processed 100009719 reads in 651 ms
[2015-09-30T22:22Z] INFO  23:22:38,584 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:38,666 MuTect - [MUTECT] Processed 88004284 reads in 659 ms
[2015-09-30T22:22Z] INFO  23:22:38,674 MuTect - [MUTECT] Processed 151008696 reads in 609 ms
[2015-09-30T22:22Z] INFO  23:22:38,845 MuTect - [MUTECT] Processed 101010003 reads in 632 ms
[2015-09-30T22:22Z] INFO  23:22:39,271 MuTect - [MUTECT] Processed 152008814 reads in 597 ms
[2015-09-30T22:22Z] INFO  23:22:39,318 MuTect - [MUTECT] Processed 89004324 reads in 652 ms
[2015-09-30T22:22Z] INFO  23:22:39,469 MuTect - [MUTECT] Processed 102010021 reads in 625 ms
[2015-09-30T22:22Z] INFO  23:22:39,812 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:39,864 MuTect - [MUTECT] Processed 153008953 reads in 593 ms
[2015-09-30T22:22Z] INFO  23:22:39,985 MuTect - [MUTECT] Processed 90004366 reads in 667 ms
[2015-09-30T22:22Z] INFO  23:22:40,099 MuTect - [MUTECT] Processed 103010092 reads in 630 ms
[2015-09-30T22:22Z] INFO  23:22:40,461 MuTect - [MUTECT] Processed 154008992 reads in 597 ms
[2015-09-30T22:22Z] INFO  23:22:40,534 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:40,667 MuTect - [MUTECT] Processed 91004463 reads in 682 ms
[2015-09-30T22:22Z] INFO  23:22:40,739 MuTect - [MUTECT] Processed 104010256 reads in 640 ms
[2015-09-30T22:22Z] INFO  23:22:41,050 MuTect - [MUTECT] Processed 155009104 reads in 589 ms
[2015-09-30T22:22Z] INFO  23:22:41,361 MuTect - [MUTECT] Processed 92004463 reads in 694 ms
[2015-09-30T22:22Z] INFO  23:22:41,541 MuTect - [MUTECT] Processed 105010323 reads in 802 ms
[2015-09-30T22:22Z] INFO  23:22:41,650 MuTect - [MUTECT] Processed 156009128 reads in 600 ms
[2015-09-30T22:22Z] INFO  23:22:42,030 MuTect - [MUTECT] Processed 93004483 reads in 669 ms
[2015-09-30T22:22Z] INFO  23:22:42,170 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:42,189 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:42,231 MuTect - [MUTECT] Processed 106010325 reads in 690 ms
[2015-09-30T22:22Z] INFO  23:22:42,247 MuTect - [MUTECT] Processed 157009214 reads in 597 ms
[2015-09-30T22:22Z] INFO  23:22:42,597 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:42,674 MuTect - [MUTECT] Processed 94004562 reads in 644 ms
[2015-09-30T22:22Z] INFO  23:22:42,840 MuTect - [MUTECT] Processed 158009299 reads in 593 ms
[2015-09-30T22:22Z] INFO  23:22:43,075 MuTect - [MUTECT] Processed 107010341 reads in 844 ms
[2015-09-30T22:22Z] INFO  23:22:43,349 MuTect - [MUTECT] Processed 95004631 reads in 675 ms
[2015-09-30T22:22Z] INFO  23:22:43,479 MuTect - [MUTECT] Processed 159009315 reads in 639 ms
[2015-09-30T22:22Z] INFO  23:22:43,765 MuTect - [MUTECT] Processed 108010412 reads in 690 ms
[2015-09-30T22:22Z] INFO  23:22:44,044 MuTect - [MUTECT] Processed 96004687 reads in 695 ms
[2015-09-30T22:22Z] INFO  23:22:44,099 MuTect - [MUTECT] Processed 160009385 reads in 620 ms
[2015-09-30T22:22Z] INFO  23:22:44,403 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:44,446 MuTect - [MUTECT] Processed 109010420 reads in 681 ms
[2015-09-30T22:22Z] INFO  23:22:44,684 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:44,716 MuTect - [MUTECT] Processed 97004710 reads in 671 ms
[2015-09-30T22:22Z] INFO  23:22:44,733 MuTect - [MUTECT] Processed 161009385 reads in 634 ms
[2015-09-30T22:22Z] INFO  23:22:44,789 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:45,141 MuTect - [MUTECT] Processed 110010519 reads in 695 ms
[2015-09-30T22:22Z] INFO  23:22:45,348 MuTect - [MUTECT] Processed 162009431 reads in 615 ms
[2015-09-30T22:22Z] INFO  23:22:45,399 MuTect - [MUTECT] Processed 98004735 reads in 684 ms
[2015-09-30T22:22Z] INFO  23:22:45,881 MuTect - [MUTECT] Processed 111010546 reads in 740 ms
[2015-09-30T22:22Z] INFO  23:22:45,983 MuTect - [MUTECT] Processed 163009545 reads in 635 ms
[2015-09-30T22:22Z] INFO  23:22:46,044 MuTect - [MUTECT] Processed 99004793 reads in 645 ms
[2015-09-30T22:22Z] INFO  23:22:46,592 MuTect - [MUTECT] Processed 112010582 reads in 711 ms
[2015-09-30T22:22Z] INFO  23:22:46,603 MuTect - [MUTECT] Processed 164009593 reads in 620 ms
[2015-09-30T22:22Z] INFO  23:22:46,670 MuTect - [MUTECT] Processed 100004844 reads in 626 ms
[2015-09-30T22:22Z] INFO  23:22:46,896 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:46,908 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:47,214 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:47,278 MuTect - [MUTECT] Processed 165009722 reads in 675 ms
[2015-09-30T22:22Z] INFO  23:22:47,282 MuTect - [MUTECT] Processed 113010620 reads in 690 ms
[2015-09-30T22:22Z] INFO  23:22:47,324 MuTect - [MUTECT] Processed 101004959 reads in 654 ms
[2015-09-30T22:22Z] INFO  23:22:47,900 MuTect - [MUTECT] Processed 166009759 reads in 622 ms
[2015-09-30T22:22Z] INFO  23:22:48,008 MuTect - [MUTECT] Processed 102005047 reads in 684 ms
[2015-09-30T22:22Z] INFO  23:22:48,013 MuTect - [MUTECT] Processed 114010679 reads in 731 ms
[2015-09-30T22:22Z] INFO  23:22:48,481 MuTect - [MUTECT] Processed 167009799 reads in 581 ms
[2015-09-30T22:22Z] INFO  23:22:48,647 MuTect - [MUTECT] Processed 103005099 reads in 639 ms
[2015-09-30T22:22Z] INFO  23:22:48,724 MuTect - [MUTECT] Processed 115010697 reads in 711 ms
[2015-09-30T22:22Z] INFO  23:22:48,875 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:49,069 MuTect - [MUTECT] Processed 168009836 reads in 587 ms
[2015-09-30T22:22Z] INFO  23:22:49,088 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:49,306 MuTect - [MUTECT] Processed 104005207 reads in 659 ms
[2015-09-30T22:22Z] INFO  23:22:49,396 MuTect - [MUTECT] Processed 116010711 reads in 672 ms
[2015-09-30T22:22Z] INFO  23:22:49,716 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:49,845 MuTect - [MUTECT] Processed 169009958 reads in 777 ms
[2015-09-30T22:22Z] INFO  23:22:49,973 MuTect - [MUTECT] Processed 105005268 reads in 667 ms
[2015-09-30T22:22Z] INFO  23:22:50,104 MuTect - [MUTECT] Processed 117010773 reads in 708 ms
[2015-09-30T22:22Z] INFO  23:22:50,552 MuTect - [MUTECT] Processed 170010020 reads in 707 ms
[2015-09-30T22:22Z] INFO  23:22:50,626 MuTect - [MUTECT] Processed 106005300 reads in 653 ms
[2015-09-30T22:22Z] INFO  23:22:50,785 MuTect - [MUTECT] Processed 118010809 reads in 681 ms
[2015-09-30T22:22Z] INFO  23:22:51,245 MuTect - [MUTECT] Processed 171010050 reads in 693 ms
[2015-09-30T22:22Z] INFO  23:22:51,246 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:51,275 MuTect - [MUTECT] Processed 107005367 reads in 649 ms
[2015-09-30T22:22Z] INFO  23:22:51,309 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:51,458 MuTect - [MUTECT] Processed 119010901 reads in 673 ms
[2015-09-30T22:22Z] INFO  23:22:51,926 MuTect - [MUTECT] Processed 172010084 reads in 681 ms
[2015-09-30T22:22Z] INFO  23:22:51,933 MuTect - [MUTECT] Processed 108005451 reads in 658 ms
[2015-09-30T22:22Z] INFO  23:22:52,062 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:52,129 MuTect - [MUTECT] Processed 120010927 reads in 671 ms
[2015-09-30T22:22Z] INFO  23:22:52,577 MuTect - [MUTECT] Processed 109005491 reads in 643 ms
[2015-09-30T22:22Z] INFO  23:22:52,581 MuTect - [MUTECT] Processed 173010138 reads in 655 ms
[2015-09-30T22:22Z] INFO  23:22:52,801 MuTect - [MUTECT] Processed 121010927 reads in 672 ms
[2015-09-30T22:22Z] INFO  23:22:53,184 MuTect - [MUTECT] Processed 174010190 reads in 603 ms
[2015-09-30T22:22Z] INFO  23:22:53,296 MuTect - [MUTECT] Processed 110005557 reads in 720 ms
[2015-09-30T22:22Z] INFO  23:22:53,419 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:53,509 MuTect - [MUTECT] Processed 122010985 reads in 707 ms
[2015-09-30T22:22Z] INFO  23:22:53,655 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:53,783 MuTect - [MUTECT] Processed 175010200 reads in 599 ms
[2015-09-30T22:22Z] INFO  23:22:53,991 MuTect - [MUTECT] Processed 111005597 reads in 695 ms
[2015-09-30T22:22Z] INFO  23:22:54,177 MuTect - [MUTECT] Processed 123010991 reads in 669 ms
[2015-09-30T22:22Z] INFO  23:22:54,393 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:54,424 MuTect - [MUTECT] Processed 176010287 reads in 641 ms
[2015-09-30T22:22Z] INFO  23:22:54,636 MuTect - [MUTECT] Processed 112005682 reads in 645 ms
[2015-09-30T22:22Z] INFO  23:22:54,883 MuTect - [MUTECT] Processed 124011024 reads in 706 ms
[2015-09-30T22:22Z] INFO  23:22:55,065 MuTect - [MUTECT] Processed 177010385 reads in 641 ms
[2015-09-30T22:22Z] INFO  23:22:55,290 MuTect - [MUTECT] Processed 113005747 reads in 654 ms
[2015-09-30T22:22Z] INFO  23:22:55,605 MuTect - [MUTECT] Processed 125011058 reads in 722 ms
[2015-09-30T22:22Z] INFO  23:22:55,658 MuTect - [MUTECT] Processed 178010408 reads in 593 ms
[2015-09-30T22:22Z] INFO  23:22:55,742 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:55,930 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:55,953 MuTect - [MUTECT] Processed 114005807 reads in 663 ms
[2015-09-30T22:22Z] INFO  23:22:56,034 ProgressMeter -     7:155664221        5.06e+06  120.0 s       23.0 s     97.0%         2.1 m     3.0 s
[2015-09-30T22:22Z] INFO  23:22:56,325 MuTect - [MUTECT] Processed 179010566 reads in 667 ms
[2015-09-30T22:22Z] INFO  23:22:56,331 MuTect - [MUTECT] Processed 126011069 reads in 726 ms
[2015-09-30T22:22Z] INFO  23:22:56,581 MuTect - [MUTECT] Processed 115005837 reads in 628 ms
[2015-09-30T22:22Z] INFO  23:22:56,911 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:56,933 MuTect - [MUTECT] Processed 180010587 reads in 608 ms
[2015-09-30T22:22Z] INFO  23:22:57,012 MuTect - [MUTECT] Processed 127011111 reads in 681 ms
[2015-09-30T22:22Z] INFO  23:22:57,254 MuTect - [MUTECT] Processed 116005859 reads in 673 ms
[2015-09-30T22:22Z] INFO  23:22:57,557 MuTect - [MUTECT] Processed 181010626 reads in 624 ms
[2015-09-30T22:22Z] INFO  23:22:57,706 MuTect - [MUTECT] Processed 128011139 reads in 694 ms
[2015-09-30T22:22Z] INFO  23:22:57,894 MuTect - [MUTECT] Processed 117005953 reads in 640 ms
[2015-09-30T22:22Z] INFO  23:22:58,055 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:58,116 ProgressMeter -     7:107533696        3.83e+06    2.3 m       36.0 s     70.4%         3.3 m    58.0 s
[2015-09-30T22:22Z] INFO  23:22:58,192 MuTect - [MUTECT] Processed 182010666 reads in 635 ms
[2015-09-30T22:22Z] INFO  23:22:58,268 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:58,395 MuTect - [MUTECT] Processed 129011189 reads in 689 ms
[2015-09-30T22:22Z] INFO  23:22:58,540 MuTect - [MUTECT] Processed 118005954 reads in 646 ms
[2015-09-30T22:22Z] INFO  23:22:58,847 MuTect - [MUTECT] Processed 183010763 reads in 655 ms
[2015-09-30T22:22Z] INFO  23:22:59,016 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:22Z] INFO  23:22:59,021 ProgressMeter -            done        5.20e+06    2.0 m       23.0 s    100.0%         2.0 m     0.0 s
[2015-09-30T22:22Z] INFO  23:22:59,021 ProgressMeter - Total runtime 122.99 secs, 2.05 min, 0.03 hours
[2015-09-30T22:22Z] INFO  23:22:59,087 MicroScheduler - 142280 reads were filtered out during the traversal out of approximately 2174395 total reads (6.54%)
[2015-09-30T22:22Z] INFO  23:22:59,087 MicroScheduler -   -> 105515 reads (4.85% of total) failing DuplicateReadFilter
[2015-09-30T22:22Z] INFO  23:22:59,087 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:22Z] INFO  23:22:59,088 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:22Z] INFO  23:22:59,088 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:22Z] INFO  23:22:59,088 MicroScheduler -   -> 36765 reads (1.69% of total) failing UnmappedReadFilter
[2015-09-30T22:22Z] INFO  23:22:59,104 MuTect - [MUTECT] Processed 130011225 reads in 708 ms
[2015-09-30T22:22Z] INFO  23:22:59,199 MuTect - [MUTECT] Processed 119006055 reads in 659 ms
[2015-09-30T22:22Z] INFO  23:22:59,624 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:22Z] INFO  23:22:59,785 MuTect - [MUTECT] Processed 131011263 reads in 682 ms
[2015-09-30T22:22Z] INFO  23:22:59,890 MuTect - [MUTECT] Processed 120006082 reads in 691 ms
[2015-09-30T22:23Z] INFO  23:23:00,130 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:23Z] bgzip syn3-7_126078434_157151579-raw-mutect.vcf
[2015-09-30T22:23Z] tabix index syn3-7_126078434_157151579-raw-mutect.vcf.gz
[2015-09-30T22:23Z] INFO  23:23:00,471 MuTect - [MUTECT] Processed 132011318 reads in 686 ms
[2015-09-30T22:23Z] INFO  23:23:00,563 MuTect - [MUTECT] Processed 121006168 reads in 673 ms
[2015-09-30T22:23Z] INFO  23:23:00,879 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:01,202 MuTect - [MUTECT] Processed 133011367 reads in 731 ms
[2015-09-30T22:23Z] INFO  23:23:01,233 MuTect - [MUTECT] Processed 122006178 reads in 670 ms
[2015-09-30T22:23Z] INFO  23:23:01,875 ProgressMeter -      8:30608779        3.65e+06   90.0 s       24.0 s     96.6%        93.0 s     3.0 s
[2015-09-30T22:23Z] INFO  23:23:01,907 MuTect - [MUTECT] Processed 123006186 reads in 674 ms
[2015-09-30T22:23Z] INFO  23:23:01,939 MuTect - [MUTECT] Processed 134011424 reads in 737 ms
[2015-09-30T22:23Z] INFO  23:23:02,142 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:23Z] MuTect: MuTect
[2015-09-30T22:23Z] INFO  23:23:02,563 MuTect - [MUTECT] Processed 124006193 reads in 656 ms
[2015-09-30T22:23Z] INFO  23:23:02,642 MuTect - [MUTECT] Processed 135011462 reads in 703 ms
[2015-09-30T22:23Z] INFO  23:23:03,226 MuTect - [MUTECT] Processed 125006200 reads in 663 ms
[2015-09-30T22:23Z] INFO  23:23:03,340 MuTect - [MUTECT] Processed 136011470 reads in 698 ms
[2015-09-30T22:23Z] INFO  23:23:03,453 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:03,846 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:23Z] INFO  23:23:03,849 ProgressMeter -            done        3.78e+06   91.0 s       24.0 s    100.0%        91.0 s     0.0 s
[2015-09-30T22:23Z] INFO  23:23:03,849 ProgressMeter - Total runtime 91.98 secs, 1.53 min, 0.03 hours
[2015-09-30T22:23Z] INFO  23:23:03,916 MicroScheduler - 93807 reads were filtered out during the traversal out of approximately 1511664 total reads (6.21%)
[2015-09-30T22:23Z] INFO  23:23:03,916 MicroScheduler -   -> 69523 reads (4.60% of total) failing DuplicateReadFilter
[2015-09-30T22:23Z] INFO  23:23:03,917 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:23Z] INFO  23:23:03,917 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:23Z] INFO  23:23:03,917 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:23Z] INFO  23:23:03,917 MicroScheduler -   -> 24284 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:23Z] INFO  23:23:04,033 MuTect - [MUTECT] Processed 137011512 reads in 693 ms
[2015-09-30T22:23Z] INFO  23:23:04,711 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:04,725 MuTect - [MUTECT] Processed 138011547 reads in 692 ms
[2015-09-30T22:23Z] INFO  23:23:04,786 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/8/syn3-8_31030285_62213090-raw-mutect-regions.bed to be BED
[2015-09-30T22:23Z] INFO  23:23:04,841 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:04,842 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:23Z] INFO  23:23:04,842 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:23Z] INFO  23:23:04,842 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:23Z] INFO  23:23:04,845 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/8/syn3-8_31030285_62213090-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/8/tx/tmpq2WpTS/syn3-8_31030285_62213090-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:23Z] INFO  23:23:04,845 HelpFormatter - Date/Time: 2015/09/30 23:23:04
[2015-09-30T22:23Z] INFO  23:23:04,845 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:04,846 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:04,872 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:23Z] INFO  23:23:04,877 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:23Z] INFO  23:23:04,925 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:23Z] INFO  23:23:04,951 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:23Z] INFO  23:23:04,975 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:23Z] INFO  23:23:04,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:23Z] bgzip syn3-8_0_31024990-raw-mutect.vcf
[2015-09-30T22:23Z] INFO  23:23:05,008 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:23Z] INFO  23:23:05,020 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:23Z] tabix index syn3-8_0_31024990-raw-mutect.vcf.gz
[2015-09-30T22:23Z] INFO  23:23:05,198 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:23Z] INFO  23:23:05,290 IntervalUtils - Processing 902318 bp from intervals
[2015-09-30T22:23Z] INFO  23:23:05,294 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:23Z] INFO  23:23:05,294 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:23Z] INFO  23:23:05,348 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:23Z] INFO  23:23:05,442 MuTect - [MUTECT] Processed 139011635 reads in 717 ms
[2015-09-30T22:23Z] INFO  23:23:05,577 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:23Z] INFO  23:23:05,577 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:23Z] INFO  23:23:05,578 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:23Z] INFO  23:23:05,579 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:23Z] INFO  23:23:06,128 MuTect - [MUTECT] Processed 140011637 reads in 686 ms
[2015-09-30T22:23Z] INFO  23:23:06,804 MuTect - [MUTECT] Processed 141011659 reads in 676 ms
[2015-09-30T22:23Z] MuTect: MuTect
[2015-09-30T22:23Z] INFO  23:23:07,482 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:07,514 MuTect - [MUTECT] Processed 142011698 reads in 710 ms
[2015-09-30T22:23Z] INFO  23:23:07,968 MuTect - [MUTECT] Processed 1000037 reads in 2343 ms
[2015-09-30T22:23Z] INFO  23:23:08,217 MuTect - [MUTECT] Processed 143011700 reads in 703 ms
[2015-09-30T22:23Z] INFO  23:23:08,830 MuTect - [MUTECT] Processed 2000090 reads in 861 ms
[2015-09-30T22:23Z] INFO  23:23:08,940 MuTect - [MUTECT] Processed 144011768 reads in 723 ms
[2015-09-30T22:23Z] INFO  23:23:09,477 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/8/syn3-8_62288979_93648031-raw-mutect-regions.bed to be BED
[2015-09-30T22:23Z] INFO  23:23:09,535 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:09,535 MuTect - [MUTECT] Processed 3000146 reads in 706 ms
[2015-09-30T22:23Z] INFO  23:23:09,535 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:23Z] INFO  23:23:09,536 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:23Z] INFO  23:23:09,536 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:23Z] INFO  23:23:09,539 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/8/syn3-8_62288979_93648031-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/8/tx/tmpPj6OJc/syn3-8_62288979_93648031-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:23Z] INFO  23:23:09,539 HelpFormatter - Date/Time: 2015/09/30 23:23:09
[2015-09-30T22:23Z] INFO  23:23:09,539 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:09,540 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:09,634 MuTect - [MUTECT] Processed 145011777 reads in 694 ms
[2015-09-30T22:23Z] INFO  23:23:09,707 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:23Z] INFO  23:23:09,782 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:23Z] INFO  23:23:09,833 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:23Z] INFO  23:23:09,907 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:09,930 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:23Z] INFO  23:23:09,937 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:23Z] INFO  23:23:09,996 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:10,108 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17
[2015-09-30T22:23Z] INFO  23:23:10,215 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:23Z] INFO  23:23:10,264 MuTect - [MUTECT] Processed 4000157 reads in 729 ms
[2015-09-30T22:23Z] INFO  23:23:10,315 MuTect - [MUTECT] Processed 146011786 reads in 681 ms
[2015-09-30T22:23Z] INFO  23:23:10,528 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:23Z] INFO  23:23:10,759 IntervalUtils - Processing 820076 bp from intervals
[2015-09-30T22:23Z] INFO  23:23:10,763 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:23Z] INFO  23:23:10,763 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:23Z] INFO  23:23:10,818 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:23Z] INFO  23:23:11,013 MuTect - [MUTECT] Processed 147011864 reads in 698 ms
[2015-09-30T22:23Z] INFO  23:23:11,103 MuTect - [MUTECT] Processed 5000192 reads in 839 ms
[2015-09-30T22:23Z] INFO  23:23:11,549 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:23Z] INFO  23:23:11,549 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:23Z] INFO  23:23:11,549 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:23Z] INFO  23:23:11,550 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:23Z] INFO  23:23:11,671 MuTect - [MUTECT] Processed 148011877 reads in 658 ms
[2015-09-30T22:23Z] INFO  23:23:11,802 MuTect - [MUTECT] Processed 6000203 reads in 699 ms
[2015-09-30T22:23Z] INFO  23:23:12,358 MuTect - [MUTECT] Processed 149011899 reads in 687 ms
[2015-09-30T22:23Z] INFO  23:23:12,374 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:12,436 MuTect - [MUTECT] Processed 7000233 reads in 634 ms
[2015-09-30T22:23Z] INFO  23:23:12,489 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:13,032 MuTect - [MUTECT] Processed 150011956 reads in 674 ms
[2015-09-30T22:23Z] INFO  23:23:13,084 MuTect - [MUTECT] Processed 8000258 reads in 648 ms
[2015-09-30T22:23Z] INFO  23:23:13,655 MuTect - [MUTECT] Processed 151011978 reads in 623 ms
[2015-09-30T22:23Z] INFO  23:23:13,750 MuTect - [MUTECT] Processed 9000316 reads in 666 ms
[2015-09-30T22:23Z] INFO  23:23:14,318 MuTect - [MUTECT] Processed 152012012 reads in 663 ms
[2015-09-30T22:23Z] INFO  23:23:14,406 MuTect - [MUTECT] Processed 10000345 reads in 656 ms
[2015-09-30T22:23Z] INFO  23:23:14,583 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:14,780 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:14,949 MuTect - [MUTECT] Processed 1000047 reads in 3353 ms
[2015-09-30T22:23Z] INFO  23:23:14,972 MuTect - [MUTECT] Processed 153012038 reads in 653 ms
[2015-09-30T22:23Z] INFO  23:23:15,110 MuTect - [MUTECT] Processed 11000443 reads in 704 ms
[2015-09-30T22:23Z] INFO  23:23:15,656 MuTect - [MUTECT] Processed 154012064 reads in 685 ms
[2015-09-30T22:23Z] INFO  23:23:15,743 MuTect - [MUTECT] Processed 12000501 reads in 633 ms
[2015-09-30T22:23Z] INFO  23:23:15,784 MuTect - [MUTECT] Processed 2000118 reads in 835 ms
[2015-09-30T22:23Z] INFO  23:23:16,327 MuTect - [MUTECT] Processed 155012089 reads in 671 ms
[2015-09-30T22:23Z] INFO  23:23:16,380 MuTect - [MUTECT] Processed 13000538 reads in 637 ms
[2015-09-30T22:23Z] INFO  23:23:16,713 MuTect - [MUTECT] Processed 3000126 reads in 929 ms
[2015-09-30T22:23Z] INFO  23:23:16,849 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:16,964 MuTect - [MUTECT] Processed 156012169 reads in 637 ms
[2015-09-30T22:23Z] INFO  23:23:17,010 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:17,027 MuTect - [MUTECT] Processed 14000564 reads in 647 ms
[2015-09-30T22:23Z] INFO  23:23:17,192 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:17,389 MuTect - [MUTECT] Processed 4000208 reads in 676 ms
[2015-09-30T22:23Z] INFO  23:23:17,604 MuTect - [MUTECT] Processed 157012230 reads in 640 ms
[2015-09-30T22:23Z] INFO  23:23:17,663 MuTect - [MUTECT] Processed 15000668 reads in 636 ms
[2015-09-30T22:23Z] INFO  23:23:18,112 MuTect - [MUTECT] Processed 5000231 reads in 723 ms
[2015-09-30T22:23Z] INFO  23:23:18,248 MuTect - [MUTECT] Processed 158012295 reads in 644 ms
[2015-09-30T22:23Z] INFO  23:23:18,287 MuTect - [MUTECT] Processed 16000697 reads in 624 ms
[2015-09-30T22:23Z] INFO  23:23:18,799 MuTect - [MUTECT] Processed 6000283 reads in 687 ms
[2015-09-30T22:23Z] INFO  23:23:18,914 MuTect - [MUTECT] Processed 159012350 reads in 666 ms
[2015-09-30T22:23Z] INFO  23:23:18,923 MuTect - [MUTECT] Processed 17000702 reads in 635 ms
[2015-09-30T22:23Z] INFO  23:23:19,274 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:19,468 MuTect - [MUTECT] Processed 7000286 reads in 669 ms
[2015-09-30T22:23Z] INFO  23:23:19,536 MuTect - [MUTECT] Processed 18000734 reads in 614 ms
[2015-09-30T22:23Z] INFO  23:23:19,606 MuTect - [MUTECT] Processed 160012352 reads in 692 ms
[2015-09-30T22:23Z] INFO  23:23:19,626 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:19,635 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:20,156 MuTect - [MUTECT] Processed 8000295 reads in 688 ms
[2015-09-30T22:23Z] INFO  23:23:20,189 MuTect - [MUTECT] Processed 19000779 reads in 653 ms
[2015-09-30T22:23Z] INFO  23:23:20,298 MuTect - [MUTECT] Processed 161012423 reads in 692 ms
[2015-09-30T22:23Z] INFO  23:23:20,814 MuTect - [MUTECT] Processed 20000786 reads in 624 ms
[2015-09-30T22:23Z] INFO  23:23:20,850 MuTect - [MUTECT] Processed 9000338 reads in 694 ms
[2015-09-30T22:23Z] INFO  23:23:20,965 MuTect - [MUTECT] Processed 162012491 reads in 667 ms
[2015-09-30T22:23Z] INFO  23:23:21,369 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:21,463 MuTect - [MUTECT] Processed 21000896 reads in 650 ms
[2015-09-30T22:23Z] INFO  23:23:21,542 MuTect - [MUTECT] Processed 10000390 reads in 692 ms
[2015-09-30T22:23Z] INFO  23:23:21,639 MuTect - [MUTECT] Processed 163012550 reads in 674 ms
[2015-09-30T22:23Z] INFO  23:23:22,132 MuTect - [MUTECT] Processed 22000900 reads in 669 ms
[2015-09-30T22:23Z] INFO  23:23:22,132 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:22,241 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:22,247 MuTect - [MUTECT] Processed 11000436 reads in 705 ms
[2015-09-30T22:23Z] INFO  23:23:22,295 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:23Z] INFO  23:23:22,297 ProgressMeter -            done        5.07e+06    2.7 m       32.0 s    100.0%         2.7 m     0.0 s
[2015-09-30T22:23Z] INFO  23:23:22,298 ProgressMeter - Total runtime 164.19 secs, 2.74 min, 0.05 hours
[2015-09-30T22:23Z] INFO  23:23:22,362 MicroScheduler - 131561 reads were filtered out during the traversal out of approximately 1961897 total reads (6.71%)
[2015-09-30T22:23Z] INFO  23:23:22,362 MicroScheduler -   -> 96053 reads (4.90% of total) failing DuplicateReadFilter
[2015-09-30T22:23Z] INFO  23:23:22,363 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:23Z] INFO  23:23:22,363 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:23Z] INFO  23:23:22,363 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:23Z] INFO  23:23:22,363 MicroScheduler -   -> 35508 reads (1.81% of total) failing UnmappedReadFilter
[2015-09-30T22:23Z] INFO  23:23:22,824 MuTect - [MUTECT] Processed 23000904 reads in 692 ms
[2015-09-30T22:23Z] INFO  23:23:22,979 MuTect - [MUTECT] Processed 12000476 reads in 732 ms
[2015-09-30T22:23Z] INFO  23:23:23,538 MuTect - [MUTECT] Processed 24000929 reads in 714 ms
[2015-09-30T22:23Z] INFO  23:23:23,658 MuTect - [MUTECT] Processed 13000523 reads in 679 ms
[2015-09-30T22:23Z] INFO  23:23:23,873 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:24,289 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:23Z] INFO  23:23:24,321 MuTect - [MUTECT] Processed 25000978 reads in 783 ms
[2015-09-30T22:23Z] bgzip syn3-7_94024041_125680568-raw-mutect.vcf
[2015-09-30T22:23Z] INFO  23:23:24,349 MuTect - [MUTECT] Processed 14000579 reads in 691 ms
[2015-09-30T22:23Z] tabix index syn3-7_94024041_125680568-raw-mutect.vcf.gz
[2015-09-30T22:23Z] INFO  23:23:25,002 MuTect - [MUTECT] Processed 26001056 reads in 681 ms
[2015-09-30T22:23Z] INFO  23:23:25,031 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:25,174 MuTect - [MUTECT] Processed 15000628 reads in 825 ms
[2015-09-30T22:23Z] INFO  23:23:25,669 MuTect - [MUTECT] Processed 27001120 reads in 667 ms
[2015-09-30T22:23Z] INFO  23:23:25,952 MuTect - [MUTECT] Processed 16000638 reads in 778 ms
[2015-09-30T22:23Z] INFO  23:23:26,344 MuTect - [MUTECT] Processed 28001143 reads in 675 ms
[2015-09-30T22:23Z] INFO  23:23:26,383 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:23Z] MuTect: MuTect
[2015-09-30T22:23Z] INFO  23:23:26,679 MuTect - [MUTECT] Processed 17000689 reads in 727 ms
[2015-09-30T22:23Z] INFO  23:23:26,963 MuTect - [MUTECT] Processed 29001193 reads in 619 ms
[2015-09-30T22:23Z] INFO  23:23:27,348 MuTect - [MUTECT] Processed 18000730 reads in 669 ms
[2015-09-30T22:23Z] INFO  23:23:27,591 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:27,605 MuTect - [MUTECT] Processed 30001316 reads in 642 ms
[2015-09-30T22:23Z] INFO  23:23:28,014 MuTect - [MUTECT] Processed 19000735 reads in 666 ms
[2015-09-30T22:23Z] INFO  23:23:28,221 MuTect - [MUTECT] Processed 31001383 reads in 616 ms
[2015-09-30T22:23Z] INFO  23:23:28,558 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:28,636 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/8/syn3-8_93896832_124968568-raw-mutect-regions.bed to be BED
[2015-09-30T22:23Z] INFO  23:23:28,681 MuTect - [MUTECT] Processed 20000752 reads in 667 ms
[2015-09-30T22:23Z] INFO  23:23:28,690 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:28,691 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:23Z] INFO  23:23:28,691 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:23Z] INFO  23:23:28,691 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:23Z] INFO  23:23:28,695 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/8/syn3-8_93896832_124968568-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/8/tx/tmpQsIT6T/syn3-8_93896832_124968568-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:23Z] INFO  23:23:28,695 HelpFormatter - Date/Time: 2015/09/30 23:23:28
[2015-09-30T22:23Z] INFO  23:23:28,695 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:28,695 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:28,723 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:23Z] INFO  23:23:28,727 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:23Z] INFO  23:23:28,777 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:23Z] INFO  23:23:28,825 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:23Z] INFO  23:23:28,832 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:23Z] INFO  23:23:28,855 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:23Z] INFO  23:23:28,866 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:23Z] INFO  23:23:28,899 MuTect - [MUTECT] Processed 32001476 reads in 678 ms
[2015-09-30T22:23Z] INFO  23:23:29,042 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:23Z] INFO  23:23:29,134 IntervalUtils - Processing 1023564 bp from intervals
[2015-09-30T22:23Z] INFO  23:23:29,138 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:23Z] INFO  23:23:29,139 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:23Z] INFO  23:23:29,401 MuTect - [MUTECT] Processed 21000793 reads in 720 ms
[2015-09-30T22:23Z] INFO  23:23:29,519 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:23Z] INFO  23:23:29,573 MuTect - [MUTECT] Processed 33001498 reads in 674 ms
[2015-09-30T22:23Z] INFO  23:23:29,664 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:23Z] INFO  23:23:29,664 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:23Z] INFO  23:23:29,664 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:23Z] INFO  23:23:29,665 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:23Z] INFO  23:23:29,991 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:30,091 MuTect - [MUTECT] Processed 22000852 reads in 690 ms
[2015-09-30T22:23Z] INFO  23:23:30,215 MuTect - [MUTECT] Processed 34001519 reads in 642 ms
[2015-09-30T22:23Z] INFO  23:23:30,850 MuTect - [MUTECT] Processed 35001568 reads in 635 ms
[2015-09-30T22:23Z] INFO  23:23:30,855 MuTect - [MUTECT] Processed 23000855 reads in 764 ms
[2015-09-30T22:23Z] INFO  23:23:30,962 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:31,480 MuTect - [MUTECT] Processed 36001571 reads in 630 ms
[2015-09-30T22:23Z] INFO  23:23:31,598 MuTect - [MUTECT] Processed 24000936 reads in 743 ms
[2015-09-30T22:23Z] INFO  23:23:32,108 MuTect - [MUTECT] Processed 37001633 reads in 628 ms
[2015-09-30T22:23Z] INFO  23:23:32,315 MuTect - [MUTECT] Processed 1000011 reads in 2601 ms
[2015-09-30T22:23Z] INFO  23:23:32,321 MuTect - [MUTECT] Processed 25001001 reads in 723 ms
[2015-09-30T22:23Z] INFO  23:23:32,573 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:32,755 MuTect - [MUTECT] Processed 38001692 reads in 646 ms
[2015-09-30T22:23Z] INFO  23:23:32,985 MuTect - [MUTECT] Processed 26001032 reads in 664 ms
[2015-09-30T22:23Z] INFO  23:23:33,042 MuTect - [MUTECT] Processed 2000019 reads in 728 ms
[2015-09-30T22:23Z] INFO  23:23:33,264 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:33,382 MuTect - [MUTECT] Processed 39001736 reads in 628 ms
[2015-09-30T22:23Z] INFO  23:23:33,681 MuTect - [MUTECT] Processed 27001032 reads in 696 ms
[2015-09-30T22:23Z] INFO  23:23:33,794 MuTect - [MUTECT] Processed 3000091 reads in 752 ms
[2015-09-30T22:23Z] INFO  23:23:34,047 MuTect - [MUTECT] Processed 40001797 reads in 665 ms
[2015-09-30T22:23Z] INFO  23:23:34,367 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:34,415 MuTect - [MUTECT] Processed 28001047 reads in 734 ms
[2015-09-30T22:23Z] INFO  23:23:34,540 MuTect - [MUTECT] Processed 4000129 reads in 746 ms
[2015-09-30T22:23Z] INFO  23:23:34,686 MuTect - [MUTECT] Processed 41001803 reads in 639 ms
[2015-09-30T22:23Z] INFO  23:23:35,113 MuTect - [MUTECT] Processed 29001069 reads in 698 ms
[2015-09-30T22:23Z] INFO  23:23:35,204 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:35,313 MuTect - [MUTECT] Processed 42001865 reads in 627 ms
[2015-09-30T22:23Z] INFO  23:23:35,325 MuTect - [MUTECT] Processed 5000172 reads in 785 ms
[2015-09-30T22:23Z] INFO  23:23:35,560 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:35,580 ProgressMeter -      8:43028962        1.39e+06   30.0 s       21.0 s     57.0%        52.0 s    22.0 s
[2015-09-30T22:23Z] INFO  23:23:35,819 MuTect - [MUTECT] Processed 30001124 reads in 706 ms
[2015-09-30T22:23Z] INFO  23:23:35,923 MuTect - [MUTECT] Processed 43001954 reads in 610 ms
[2015-09-30T22:23Z] INFO  23:23:36,090 MuTect - [MUTECT] Processed 6000214 reads in 765 ms
[2015-09-30T22:23Z] INFO  23:23:36,471 MuTect - [MUTECT] Processed 31001136 reads in 651 ms
[2015-09-30T22:23Z] INFO  23:23:36,602 MuTect - [MUTECT] Processed 44001973 reads in 679 ms
[2015-09-30T22:23Z] INFO  23:23:36,844 MuTect - [MUTECT] Processed 7000276 reads in 753 ms
[2015-09-30T22:23Z] INFO  23:23:37,146 MuTect - [MUTECT] Processed 32001181 reads in 676 ms
[2015-09-30T22:23Z] INFO  23:23:37,196 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:37,199 MuTect - [MUTECT] Processed 45002075 reads in 597 ms
[2015-09-30T22:23Z] INFO  23:23:37,631 MuTect - [MUTECT] Processed 8000308 reads in 788 ms
[2015-09-30T22:23Z] INFO  23:23:37,782 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:37,807 MuTect - [MUTECT] Processed 46002135 reads in 608 ms
[2015-09-30T22:23Z] INFO  23:23:37,814 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:37,836 MuTect - [MUTECT] Processed 33001245 reads in 690 ms
[2015-09-30T22:23Z] INFO  23:23:38,363 MuTect - [MUTECT] Processed 9000379 reads in 732 ms
[2015-09-30T22:23Z] INFO  23:23:38,406 MuTect - [MUTECT] Processed 47002191 reads in 598 ms
[2015-09-30T22:23Z] INFO  23:23:38,538 MuTect - [MUTECT] Processed 34001283 reads in 702 ms
[2015-09-30T22:23Z] INFO  23:23:39,003 MuTect - [MUTECT] Processed 48002207 reads in 598 ms
[2015-09-30T22:23Z] INFO  23:23:39,108 MuTect - [MUTECT] Processed 10000426 reads in 745 ms
[2015-09-30T22:23Z] INFO  23:23:39,208 MuTect - [MUTECT] Processed 35001305 reads in 670 ms
[2015-09-30T22:23Z] INFO  23:23:39,604 MuTect - [MUTECT] Processed 49002296 reads in 601 ms
[2015-09-30T22:23Z] INFO  23:23:39,767 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:39,835 MuTect - [MUTECT] Processed 11000447 reads in 727 ms
[2015-09-30T22:23Z] INFO  23:23:39,891 MuTect - [MUTECT] Processed 36001314 reads in 683 ms
[2015-09-30T22:23Z] INFO  23:23:40,128 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:40,262 MuTect - [MUTECT] Processed 50002328 reads in 657 ms
[2015-09-30T22:23Z] INFO  23:23:40,307 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:40,583 MuTect - [MUTECT] Processed 12000522 reads in 748 ms
[2015-09-30T22:23Z] INFO  23:23:40,594 MuTect - [MUTECT] Processed 37001333 reads in 703 ms
[2015-09-30T22:23Z] INFO  23:23:40,982 MuTect - [MUTECT] Processed 51002348 reads in 721 ms
[2015-09-30T22:23Z] INFO  23:23:41,296 MuTect - [MUTECT] Processed 38001355 reads in 702 ms
[2015-09-30T22:23Z] INFO  23:23:41,297 MuTect - [MUTECT] Processed 13000595 reads in 714 ms
[2015-09-30T22:23Z] INFO  23:23:41,552 ProgressMeter -      8:85208104        1.24e+06   30.0 s       24.0 s     68.6%        43.0 s    13.0 s
[2015-09-30T22:23Z] INFO  23:23:41,641 MuTect - [MUTECT] Processed 52002351 reads in 659 ms
[2015-09-30T22:23Z] INFO  23:23:42,027 MuTect - [MUTECT] Processed 39001365 reads in 731 ms
[2015-09-30T22:23Z] INFO  23:23:42,059 MuTect - [MUTECT] Processed 14000596 reads in 762 ms
[2015-09-30T22:23Z] INFO  23:23:42,381 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:42,381 MuTect - [MUTECT] Processed 53002370 reads in 740 ms
[2015-09-30T22:23Z] INFO  23:23:42,571 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:42,730 MuTect - [MUTECT] Processed 40001407 reads in 703 ms
[2015-09-30T22:23Z] INFO  23:23:42,788 MuTect - [MUTECT] Processed 15000614 reads in 729 ms
[2015-09-30T22:23Z] INFO  23:23:43,005 MuTect - [MUTECT] Processed 54002403 reads in 624 ms
[2015-09-30T22:23Z] INFO  23:23:43,073 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:43,443 MuTect - [MUTECT] Processed 41001504 reads in 713 ms
[2015-09-30T22:23Z] INFO  23:23:43,519 MuTect - [MUTECT] Processed 16000633 reads in 731 ms
[2015-09-30T22:23Z] INFO  23:23:43,642 MuTect - [MUTECT] Processed 55002495 reads in 637 ms
[2015-09-30T22:23Z] INFO  23:23:44,077 MuTect - [MUTECT] Processed 42002385 reads in 634 ms
[2015-09-30T22:23Z] INFO  23:23:44,259 MuTect - [MUTECT] Processed 56002509 reads in 617 ms
[2015-09-30T22:23Z] INFO  23:23:44,279 MuTect - [MUTECT] Processed 17000674 reads in 760 ms
[2015-09-30T22:23Z] INFO  23:23:44,775 MuTect - [MUTECT] Processed 43002576 reads in 698 ms
[2015-09-30T22:23Z] INFO  23:23:44,879 MuTect - [MUTECT] Processed 57002538 reads in 620 ms
[2015-09-30T22:23Z] INFO  23:23:44,930 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:44,957 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:44,996 MuTect - [MUTECT] Processed 18000709 reads in 717 ms
[2015-09-30T22:23Z] INFO  23:23:45,421 MuTect - [MUTECT] Processed 44002747 reads in 646 ms
[2015-09-30T22:23Z] INFO  23:23:45,505 MuTect - [MUTECT] Processed 58002641 reads in 626 ms
[2015-09-30T22:23Z] INFO  23:23:45,697 MuTect - [MUTECT] Processed 19000715 reads in 701 ms
[2015-09-30T22:23Z] INFO  23:23:46,166 MuTect - [MUTECT] Processed 59002645 reads in 661 ms
[2015-09-30T22:23Z] INFO  23:23:46,219 MuTect - [MUTECT] Processed 45002938 reads in 798 ms
[2015-09-30T22:23Z] INFO  23:23:46,415 MuTect - [MUTECT] Processed 20000732 reads in 718 ms
[2015-09-30T22:23Z] INFO  23:23:46,833 MuTect - [MUTECT] Processed 60002646 reads in 667 ms
[2015-09-30T22:23Z] INFO  23:23:46,956 MuTect - [MUTECT] Processed 46003758 reads in 737 ms
[2015-09-30T22:23Z] INFO  23:23:47,067 MuTect - [MUTECT] Processed 21000773 reads in 652 ms
[2015-09-30T22:23Z] INFO  23:23:47,222 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:47,500 MuTect - [MUTECT] Processed 61002661 reads in 667 ms
[2015-09-30T22:23Z] INFO  23:23:47,610 MuTect - [MUTECT] Processed 47004392 reads in 654 ms
[2015-09-30T22:23Z] INFO  23:23:47,700 MuTect - [MUTECT] Processed 22000829 reads in 633 ms
[2015-09-30T22:23Z] INFO  23:23:47,757 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:48,130 MuTect - [MUTECT] Processed 62002692 reads in 630 ms
[2015-09-30T22:23Z] INFO  23:23:48,204 MuTect - [MUTECT] Processed 48004929 reads in 594 ms
[2015-09-30T22:23Z] INFO  23:23:48,345 MuTect - [MUTECT] Processed 23000833 reads in 645 ms
[2015-09-30T22:23Z] INFO  23:23:48,781 MuTect - [MUTECT] Processed 49005462 reads in 577 ms
[2015-09-30T22:23Z] INFO  23:23:48,788 MuTect - [MUTECT] Processed 63002695 reads in 658 ms
[2015-09-30T22:23Z] INFO  23:23:49,047 MuTect - [MUTECT] Processed 24000903 reads in 702 ms
[2015-09-30T22:23Z] INFO  23:23:49,349 MuTect - [MUTECT] Processed 50005639 reads in 568 ms
[2015-09-30T22:23Z] INFO  23:23:49,431 MuTect - [MUTECT] Processed 64002737 reads in 643 ms
[2015-09-30T22:23Z] INFO  23:23:49,508 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:49,730 MuTect - [MUTECT] Processed 25000905 reads in 683 ms
[2015-09-30T22:23Z] INFO  23:23:49,946 MuTect - [MUTECT] Processed 51006557 reads in 597 ms
[2015-09-30T22:23Z] INFO  23:23:50,057 MuTect - [MUTECT] Processed 65002753 reads in 626 ms
[2015-09-30T22:23Z] INFO  23:23:50,353 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:50,419 MuTect - [MUTECT] Processed 26000905 reads in 689 ms
[2015-09-30T22:23Z] INFO  23:23:50,487 MuTect - [MUTECT] Processed 52007103 reads in 541 ms
[2015-09-30T22:23Z] INFO  23:23:50,703 MuTect - [MUTECT] Processed 66002776 reads in 646 ms
[2015-09-30T22:23Z] INFO  23:23:51,057 MuTect - [MUTECT] Processed 53007341 reads in 570 ms
[2015-09-30T22:23Z] INFO  23:23:51,223 MuTect - [MUTECT] Processed 27000906 reads in 804 ms
[2015-09-30T22:23Z] INFO  23:23:51,357 MuTect - [MUTECT] Processed 67002835 reads in 653 ms
[2015-09-30T22:23Z] INFO  23:23:51,630 MuTect - [MUTECT] Processed 54007640 reads in 573 ms
[2015-09-30T22:23Z] INFO  23:23:51,903 MuTect - [MUTECT] Processed 28000944 reads in 680 ms
[2015-09-30T22:23Z] INFO  23:23:51,923 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:52,032 MuTect - [MUTECT] Processed 68002859 reads in 676 ms
[2015-09-30T22:23Z] INFO  23:23:52,198 MuTect - [MUTECT] Processed 55007816 reads in 568 ms
[2015-09-30T22:23Z] INFO  23:23:52,582 MuTect - [MUTECT] Processed 29001023 reads in 679 ms
[2015-09-30T22:23Z] INFO  23:23:52,635 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:52,674 MuTect - [MUTECT] Processed 69002859 reads in 642 ms
[2015-09-30T22:23Z] INFO  23:23:52,779 MuTect - [MUTECT] Processed 56008173 reads in 581 ms
[2015-09-30T22:23Z] INFO  23:23:53,259 MuTect - [MUTECT] Processed 30001097 reads in 677 ms
[2015-09-30T22:23Z] INFO  23:23:53,281 MuTect - [MUTECT] Processed 70002983 reads in 607 ms
[2015-09-30T22:23Z] INFO  23:23:53,333 MuTect - [MUTECT] Processed 57008608 reads in 554 ms
[2015-09-30T22:23Z] INFO  23:23:53,552 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:23Z] INFO  23:23:53,554 ProgressMeter -            done        2.36e+06   47.0 s       20.0 s    100.0%        47.0 s     0.0 s
[2015-09-30T22:23Z] INFO  23:23:53,554 ProgressMeter - Total runtime 47.98 secs, 0.80 min, 0.01 hours
[2015-09-30T22:23Z] INFO  23:23:53,618 MicroScheduler - 50666 reads were filtered out during the traversal out of approximately 842349 total reads (6.01%)
[2015-09-30T22:23Z] INFO  23:23:53,618 MicroScheduler -   -> 37462 reads (4.45% of total) failing DuplicateReadFilter
[2015-09-30T22:23Z] INFO  23:23:53,618 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:23Z] INFO  23:23:53,619 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:23Z] INFO  23:23:53,619 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:23Z] INFO  23:23:53,619 MicroScheduler -   -> 13204 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:23Z] INFO  23:23:53,954 MuTect - [MUTECT] Processed 31001128 reads in 695 ms
[2015-09-30T22:23Z] INFO  23:23:54,080 MuTect - [MUTECT] Processed 58009374 reads in 747 ms
[2015-09-30T22:23Z] INFO  23:23:54,626 MuTect - [MUTECT] Processed 32001140 reads in 672 ms
[2015-09-30T22:23Z] INFO  23:23:54,641 MuTect - [MUTECT] Processed 59009472 reads in 561 ms
[2015-09-30T22:23Z] INFO  23:23:54,651 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:23Z] bgzip syn3-8_31030285_62213090-raw-mutect.vcf
[2015-09-30T22:23Z] tabix index syn3-8_31030285_62213090-raw-mutect.vcf.gz
[2015-09-30T22:23Z] INFO  23:23:55,200 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:55,236 MuTect - [MUTECT] Processed 60010512 reads in 595 ms
[2015-09-30T22:23Z] INFO  23:23:55,302 MuTect - [MUTECT] Processed 33001155 reads in 676 ms
[2015-09-30T22:23Z] INFO  23:23:55,832 MuTect - [MUTECT] Processed 61010696 reads in 596 ms
[2015-09-30T22:23Z] INFO  23:23:56,010 MuTect - [MUTECT] Processed 34001190 reads in 708 ms
[2015-09-30T22:23Z] INFO  23:23:56,430 MuTect - [MUTECT] Processed 62010831 reads in 598 ms
[2015-09-30T22:23Z] INFO  23:23:56,730 MuTect - [MUTECT] Processed 35001241 reads in 720 ms
[2015-09-30T22:23Z] INFO  23:23:57,009 MuTect - [MUTECT] Processed 63011298 reads in 579 ms
[2015-09-30T22:23Z] MuTect: MuTect
[2015-09-30T22:23Z] INFO  23:23:57,436 MuTect - [MUTECT] Processed 36001274 reads in 705 ms
[2015-09-30T22:23Z] INFO  23:23:57,608 MuTect - [MUTECT] Processed 64011719 reads in 599 ms
[2015-09-30T22:23Z] INFO  23:23:57,998 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:23Z] INFO  23:23:58,153 MuTect - [MUTECT] Processed 37001295 reads in 718 ms
[2015-09-30T22:23Z] INFO  23:23:58,189 MuTect - [MUTECT] Processed 65012796 reads in 581 ms
[2015-09-30T22:23Z] INFO  23:23:58,763 MuTect - [MUTECT] Processed 66012825 reads in 574 ms
[2015-09-30T22:23Z] INFO  23:23:58,829 MuTect - [MUTECT] Processed 38001356 reads in 676 ms
[2015-09-30T22:23Z] INFO  23:23:58,990 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/8/syn3-8_124975213_146364022-raw-mutect-regions.bed to be BED
[2015-09-30T22:23Z] INFO  23:23:59,044 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:59,045 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:23Z] INFO  23:23:59,045 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:23Z] INFO  23:23:59,045 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:23Z] INFO  23:23:59,049 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/8/syn3-8_124975213_146364022-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/8/tx/tmpXlftXg/syn3-8_124975213_146364022-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:23Z] INFO  23:23:59,049 HelpFormatter - Date/Time: 2015/09/30 23:23:59
[2015-09-30T22:23Z] INFO  23:23:59,049 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:59,049 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:23Z] INFO  23:23:59,076 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:23Z] INFO  23:23:59,080 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:23Z] INFO  23:23:59,130 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:23Z] INFO  23:23:59,176 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:23Z] INFO  23:23:59,183 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:23Z] INFO  23:23:59,206 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:23Z] INFO  23:23:59,217 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:23Z] INFO  23:23:59,349 MuTect - [MUTECT] Processed 67013120 reads in 586 ms
[2015-09-30T22:23Z] INFO  23:23:59,397 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:23Z] INFO  23:23:59,479 IntervalUtils - Processing 951635 bp from intervals
[2015-09-30T22:23Z] INFO  23:23:59,483 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:23Z] INFO  23:23:59,483 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:23Z] INFO  23:23:59,534 MuTect - [MUTECT] Processed 39001439 reads in 705 ms
[2015-09-30T22:23Z] INFO  23:23:59,535 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:23Z] INFO  23:23:59,667 ProgressMeter -     8:106811334        1.37e+06   30.0 s       21.0 s     54.3%        55.0 s    25.0 s
[2015-09-30T22:23Z] INFO  23:23:59,775 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:23Z] INFO  23:23:59,775 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:23Z] INFO  23:23:59,775 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:23Z] INFO  23:23:59,776 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:23Z] INFO  23:23:59,931 MuTect - [MUTECT] Processed 68013141 reads in 582 ms
[2015-09-30T22:24Z] INFO  23:24:00,209 MuTect - [MUTECT] Processed 40001483 reads in 675 ms
[2015-09-30T22:24Z] INFO  23:24:00,511 MuTect - [MUTECT] Processed 69013171 reads in 580 ms
[2015-09-30T22:24Z] INFO  23:24:00,649 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:00,941 MuTect - [MUTECT] Processed 41001483 reads in 732 ms
[2015-09-30T22:24Z] INFO  23:24:01,126 MuTect - [MUTECT] Processed 70013643 reads in 615 ms
[2015-09-30T22:24Z] INFO  23:24:01,634 MuTect - [MUTECT] Processed 42001554 reads in 693 ms
[2015-09-30T22:24Z] INFO  23:24:01,737 MuTect - [MUTECT] Processed 71014228 reads in 611 ms
[2015-09-30T22:24Z] INFO  23:24:02,238 MuTect - [MUTECT] Processed 1000088 reads in 2398 ms
[2015-09-30T22:24Z] INFO  23:24:02,337 MuTect - [MUTECT] Processed 43001615 reads in 703 ms
[2015-09-30T22:24Z] INFO  23:24:02,380 MuTect - [MUTECT] Processed 72014287 reads in 643 ms
[2015-09-30T22:24Z] INFO  23:24:02,970 MuTect - [MUTECT] Processed 2000129 reads in 732 ms
[2015-09-30T22:24Z] INFO  23:24:03,040 MuTect - [MUTECT] Processed 44001624 reads in 703 ms
[2015-09-30T22:24Z] INFO  23:24:03,155 MuTect - [MUTECT] Processed 73014319 reads in 775 ms
[2015-09-30T22:24Z] INFO  23:24:03,300 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:03,551 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:03,694 MuTect - [MUTECT] Processed 3000177 reads in 724 ms
[2015-09-30T22:24Z] INFO  23:24:03,728 MuTect - [MUTECT] Processed 45001650 reads in 688 ms
[2015-09-30T22:24Z] INFO  23:24:03,934 MuTect - [MUTECT] Processed 74014344 reads in 779 ms
[2015-09-30T22:24Z] INFO  23:24:04,076 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:04,407 MuTect - [MUTECT] Processed 46001663 reads in 679 ms
[2015-09-30T22:24Z] INFO  23:24:04,430 MuTect - [MUTECT] Processed 4000230 reads in 736 ms
[2015-09-30T22:24Z] INFO  23:24:04,641 MuTect - [MUTECT] Processed 75014390 reads in 707 ms
[2015-09-30T22:24Z] INFO  23:24:05,063 MuTect - [MUTECT] Processed 47001748 reads in 656 ms
[2015-09-30T22:24Z] INFO  23:24:05,147 MuTect - [MUTECT] Processed 5000334 reads in 717 ms
[2015-09-30T22:24Z] INFO  23:24:05,370 MuTect - [MUTECT] Processed 76014394 reads in 729 ms
[2015-09-30T22:24Z] INFO  23:24:05,744 MuTect - [MUTECT] Processed 48001758 reads in 681 ms
[2015-09-30T22:24Z] INFO  23:24:05,844 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:05,864 MuTect - [MUTECT] Processed 6000369 reads in 717 ms
[2015-09-30T22:24Z] INFO  23:24:06,087 MuTect - [MUTECT] Processed 77014396 reads in 717 ms
[2015-09-30T22:24Z] INFO  23:24:06,238 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:06,453 MuTect - [MUTECT] Processed 49001758 reads in 709 ms
[2015-09-30T22:24Z] INFO  23:24:06,517 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:06,617 MuTect - [MUTECT] Processed 7000369 reads in 753 ms
[2015-09-30T22:24Z] INFO  23:24:06,779 MuTect - [MUTECT] Processed 78014455 reads in 692 ms
[2015-09-30T22:24Z] INFO  23:24:07,143 MuTect - [MUTECT] Processed 50001792 reads in 690 ms
[2015-09-30T22:24Z] INFO  23:24:07,406 MuTect - [MUTECT] Processed 8000409 reads in 789 ms
[2015-09-30T22:24Z] INFO  23:24:07,478 MuTect - [MUTECT] Processed 79014464 reads in 699 ms
[2015-09-30T22:24Z] INFO  23:24:07,811 MuTect - [MUTECT] Processed 51001844 reads in 668 ms
[2015-09-30T22:24Z] INFO  23:24:08,193 MuTect - [MUTECT] Processed 80014475 reads in 715 ms
[2015-09-30T22:24Z] INFO  23:24:08,351 MuTect - [MUTECT] Processed 9001440 reads in 945 ms
[2015-09-30T22:24Z] INFO  23:24:08,389 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:08,489 MuTect - [MUTECT] Processed 52001889 reads in 678 ms
[2015-09-30T22:24Z] INFO  23:24:08,828 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:08,861 MuTect - [MUTECT] Processed 81014483 reads in 668 ms
[2015-09-30T22:24Z] INFO  23:24:09,175 MuTect - [MUTECT] Processed 53001968 reads in 686 ms
[2015-09-30T22:24Z] INFO  23:24:09,265 MuTect - [MUTECT] Processed 10004223 reads in 914 ms
[2015-09-30T22:24Z] INFO  23:24:09,521 MuTect - [MUTECT] Processed 82014487 reads in 660 ms
[2015-09-30T22:24Z] INFO  23:24:09,731 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:24Z] INFO  23:24:09,733 ProgressMeter -            done        1.80e+06   58.0 s       32.0 s    100.0%        58.0 s     0.0 s
[2015-09-30T22:24Z] INFO  23:24:09,733 ProgressMeter - Total runtime 58.18 secs, 0.97 min, 0.02 hours
[2015-09-30T22:24Z] INFO  23:24:09,798 MicroScheduler - 59302 reads were filtered out during the traversal out of approximately 959318 total reads (6.18%)
[2015-09-30T22:24Z] INFO  23:24:09,798 MicroScheduler -   -> 43251 reads (4.51% of total) failing DuplicateReadFilter
[2015-09-30T22:24Z] INFO  23:24:09,798 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:24Z] INFO  23:24:09,798 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:24Z] INFO  23:24:09,798 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:24Z] INFO  23:24:09,799 MicroScheduler -   -> 16051 reads (1.67% of total) failing UnmappedReadFilter
[2015-09-30T22:24Z] INFO  23:24:09,860 MuTect - [MUTECT] Processed 54001982 reads in 685 ms
[2015-09-30T22:24Z] INFO  23:24:09,890 MuTect - [MUTECT] Processed 11005219 reads in 625 ms
[2015-09-30T22:24Z] INFO  23:24:10,545 MuTect - [MUTECT] Processed 55001983 reads in 685 ms
[2015-09-30T22:24Z] INFO  23:24:10,606 MuTect - [MUTECT] Processed 12005998 reads in 716 ms
[2015-09-30T22:24Z] INFO  23:24:10,807 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:11,055 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:24Z] INFO  23:24:11,264 MuTect - [MUTECT] Processed 13007775 reads in 658 ms
[2015-09-30T22:24Z] INFO  23:24:11,274 MuTect - [MUTECT] Processed 56002015 reads in 729 ms
[2015-09-30T22:24Z] INFO  23:24:11,899 MuTect - [MUTECT] Processed 14010241 reads in 635 ms
[2015-09-30T22:24Z] INFO  23:24:11,981 MuTect - [MUTECT] Processed 57002047 reads in 707 ms
[2015-09-30T22:24Z] bgzip syn3-8_62288979_93648031-raw-mutect.vcf
[2015-09-30T22:24Z] INFO  23:24:12,671 MuTect - [MUTECT] Processed 58002155 reads in 690 ms
[2015-09-30T22:24Z] INFO  23:24:13,285 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:13,368 MuTect - [MUTECT] Processed 59002232 reads in 697 ms
[2015-09-30T22:24Z] INFO  23:24:13,416 MuTect - [MUTECT] Processed 15010336 reads in 1517 ms
[2015-09-30T22:24Z] tabix index syn3-8_62288979_93648031-raw-mutect.vcf.gz
[2015-09-30T22:24Z] INFO  23:24:13,904 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:14,053 MuTect - [MUTECT] Processed 60002252 reads in 685 ms
[2015-09-30T22:24Z] INFO  23:24:14,093 MuTect - [MUTECT] Processed 16010382 reads in 677 ms
[2015-09-30T22:24Z] INFO  23:24:14,737 MuTect - [MUTECT] Processed 17010409 reads in 643 ms
[2015-09-30T22:24Z] INFO  23:24:14,755 MuTect - [MUTECT] Processed 61002276 reads in 702 ms
[2015-09-30T22:24Z] INFO  23:24:15,422 MuTect - [MUTECT] Processed 18010447 reads in 686 ms
[2015-09-30T22:24Z] INFO  23:24:15,429 MuTect - [MUTECT] Processed 62002342 reads in 674 ms
[2015-09-30T22:24Z] INFO  23:24:15,719 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:16,095 MuTect - [MUTECT] Processed 63002414 reads in 666 ms
[2015-09-30T22:24Z] INFO  23:24:16,122 MuTect - [MUTECT] Processed 19010475 reads in 700 ms
[2015-09-30T22:24Z] INFO  23:24:16,268 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:24Z] MuTect: MuTect
[2015-09-30T22:24Z] INFO  23:24:16,757 MuTect - [MUTECT] Processed 64002504 reads in 662 ms
[2015-09-30T22:24Z] INFO  23:24:16,827 MuTect - [MUTECT] Processed 20010491 reads in 705 ms
[2015-09-30T22:24Z] INFO  23:24:17,395 MuTect - [MUTECT] Processed 65002585 reads in 638 ms
[2015-09-30T22:24Z] INFO  23:24:17,491 MuTect - [MUTECT] Processed 21010540 reads in 664 ms
[2015-09-30T22:24Z] INFO  23:24:18,048 MuTect - [MUTECT] Processed 66002598 reads in 653 ms
[2015-09-30T22:24Z] INFO  23:24:18,156 MuTect - [MUTECT] Processed 22010595 reads in 665 ms
[2015-09-30T22:24Z] INFO  23:24:18,157 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:18,634 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/9/syn3-9_0_32405837-raw-mutect-regions.bed to be BED
[2015-09-30T22:24Z] INFO  23:24:18,680 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:18,688 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:24Z] INFO  23:24:18,689 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:24Z] INFO  23:24:18,689 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:24Z] INFO  23:24:18,689 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:24Z] INFO  23:24:18,692 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/9/syn3-9_0_32405837-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/9/tx/tmpH75t1N/syn3-9_0_32405837-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:24Z] INFO  23:24:18,693 HelpFormatter - Date/Time: 2015/09/30 23:24:18
[2015-09-30T22:24Z] INFO  23:24:18,693 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:24Z] INFO  23:24:18,693 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:24Z] INFO  23:24:18,714 MuTect - [MUTECT] Processed 67002603 reads in 666 ms
[2015-09-30T22:24Z] INFO  23:24:18,720 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:24Z] INFO  23:24:18,725 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:24Z] INFO  23:24:18,774 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:24Z] INFO  23:24:18,822 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:24Z] INFO  23:24:18,829 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:24Z] INFO  23:24:18,851 MuTect - [MUTECT] Processed 23010607 reads in 695 ms
[2015-09-30T22:24Z] INFO  23:24:18,867 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:24Z] INFO  23:24:18,890 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:24Z] INFO  23:24:19,060 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:24Z] INFO  23:24:19,145 IntervalUtils - Processing 859116 bp from intervals
[2015-09-30T22:24Z] INFO  23:24:19,149 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:24Z] INFO  23:24:19,149 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:24Z] INFO  23:24:19,201 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:24Z] INFO  23:24:19,390 MuTect - [MUTECT] Processed 68002629 reads in 676 ms
[2015-09-30T22:24Z] INFO  23:24:19,436 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:24Z] INFO  23:24:19,437 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:24Z] INFO  23:24:19,437 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:24Z] INFO  23:24:19,438 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:24Z] INFO  23:24:19,543 MuTect - [MUTECT] Processed 24010621 reads in 692 ms
[2015-09-30T22:24Z] INFO  23:24:20,090 MuTect - [MUTECT] Processed 69002683 reads in 700 ms
[2015-09-30T22:24Z] INFO  23:24:20,226 MuTect - [MUTECT] Processed 25010649 reads in 683 ms
[2015-09-30T22:24Z] INFO  23:24:20,294 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:24Z] INFO  23:24:20,297 ProgressMeter -            done        2.55e+06   50.0 s       19.0 s    100.0%        50.0 s     0.0 s
[2015-09-30T22:24Z] INFO  23:24:20,297 ProgressMeter - Total runtime 50.63 secs, 0.84 min, 0.01 hours
[2015-09-30T22:24Z] INFO  23:24:20,364 MicroScheduler - 47073 reads were filtered out during the traversal out of approximately 828531 total reads (5.68%)
[2015-09-30T22:24Z] INFO  23:24:20,364 MicroScheduler -   -> 33768 reads (4.08% of total) failing DuplicateReadFilter
[2015-09-30T22:24Z] INFO  23:24:20,364 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:24Z] INFO  23:24:20,365 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:24Z] INFO  23:24:20,365 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:24Z] INFO  23:24:20,365 MicroScheduler -   -> 13305 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:24Z] INFO  23:24:20,932 MuTect - [MUTECT] Processed 26010720 reads in 706 ms
[2015-09-30T22:24Z] INFO  23:24:21,174 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:21,387 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:24Z] bgzip syn3-8_93896832_124968568-raw-mutect.vcf
[2015-09-30T22:24Z] tabix index syn3-8_93896832_124968568-raw-mutect.vcf.gz
[2015-09-30T22:24Z] INFO  23:24:21,652 MuTect - [MUTECT] Processed 1000050 reads in 2168 ms
[2015-09-30T22:24Z] INFO  23:24:21,713 MuTect - [MUTECT] Processed 27010775 reads in 781 ms
[2015-09-30T22:24Z] INFO  23:24:22,389 MuTect - [MUTECT] Processed 28010856 reads in 676 ms
[2015-09-30T22:24Z] INFO  23:24:22,625 MuTect - [MUTECT] Processed 2000097 reads in 973 ms
[2015-09-30T22:24Z] INFO  23:24:23,077 MuTect - [MUTECT] Processed 29010922 reads in 688 ms
[2015-09-30T22:24Z] INFO  23:24:23,362 MuTect - [MUTECT] Processed 3000211 reads in 737 ms
[2015-09-30T22:24Z] INFO  23:24:23,459 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:24Z] MuTect: MuTect
[2015-09-30T22:24Z] INFO  23:24:23,771 MuTect - [MUTECT] Processed 30010923 reads in 694 ms
[2015-09-30T22:24Z] INFO  23:24:24,148 MuTect - [MUTECT] Processed 4000311 reads in 786 ms
[2015-09-30T22:24Z] INFO  23:24:24,260 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:24,454 MuTect - [MUTECT] Processed 31010950 reads in 682 ms
[2015-09-30T22:24Z] INFO  23:24:24,920 MuTect - [MUTECT] Processed 5000374 reads in 772 ms
[2015-09-30T22:24Z] INFO  23:24:25,120 MuTect - [MUTECT] Processed 32011008 reads in 667 ms
[2015-09-30T22:24Z] INFO  23:24:25,646 MuTect - [MUTECT] Processed 6000417 reads in 726 ms
[2015-09-30T22:24Z] INFO  23:24:25,708 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/9/syn3-9_32406980_65488652-raw-mutect-regions.bed to be BED
[2015-09-30T22:24Z] INFO  23:24:25,762 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:25,764 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:24Z] INFO  23:24:25,764 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:24Z] INFO  23:24:25,764 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:24Z] INFO  23:24:25,764 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:24Z] INFO  23:24:25,768 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/9/syn3-9_32406980_65488652-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/9/tx/tmpjQbXNc/syn3-9_32406980_65488652-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:24Z] INFO  23:24:25,768 HelpFormatter - Date/Time: 2015/09/30 23:24:25
[2015-09-30T22:24Z] INFO  23:24:25,768 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:24Z] INFO  23:24:25,768 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:24Z] INFO  23:24:25,797 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:24Z] INFO  23:24:25,801 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:24Z] INFO  23:24:25,809 MuTect - [MUTECT] Processed 33011105 reads in 689 ms
[2015-09-30T22:24Z] INFO  23:24:25,855 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:24Z] INFO  23:24:25,904 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:24Z] INFO  23:24:25,911 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:24Z] INFO  23:24:25,934 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:24Z] INFO  23:24:25,945 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:24Z] INFO  23:24:26,120 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:24Z] INFO  23:24:26,202 IntervalUtils - Processing 906990 bp from intervals
[2015-09-30T22:24Z] INFO  23:24:26,206 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:24Z] INFO  23:24:26,206 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:24Z] INFO  23:24:26,260 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:24Z] INFO  23:24:26,357 MuTect - [MUTECT] Processed 7000445 reads in 711 ms
[2015-09-30T22:24Z] INFO  23:24:26,490 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:24Z] INFO  23:24:26,491 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:24Z] INFO  23:24:26,491 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:24Z] INFO  23:24:26,492 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:24Z] INFO  23:24:26,499 MuTect - [MUTECT] Processed 34011114 reads in 690 ms
[2015-09-30T22:24Z] INFO  23:24:26,802 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:27,069 MuTect - [MUTECT] Processed 8000499 reads in 712 ms
[2015-09-30T22:24Z] INFO  23:24:27,185 MuTect - [MUTECT] Processed 35011115 reads in 686 ms
[2015-09-30T22:24Z] INFO  23:24:27,802 MuTect - [MUTECT] Processed 9000552 reads in 732 ms
[2015-09-30T22:24Z] INFO  23:24:27,863 MuTect - [MUTECT] Processed 36011194 reads in 677 ms
[2015-09-30T22:24Z] INFO  23:24:28,106 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:28,488 MuTect - [MUTECT] Processed 10000582 reads in 687 ms
[2015-09-30T22:24Z] INFO  23:24:28,553 MuTect - [MUTECT] Processed 37011246 reads in 691 ms
[2015-09-30T22:24Z] INFO  23:24:28,860 MuTect - [MUTECT] Processed 1000006 reads in 2321 ms
[2015-09-30T22:24Z] INFO  23:24:29,187 MuTect - [MUTECT] Processed 11000641 reads in 699 ms
[2015-09-30T22:24Z] INFO  23:24:29,196 MuTect - [MUTECT] Processed 38011295 reads in 643 ms
[2015-09-30T22:24Z] INFO  23:24:29,342 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:29,705 MuTect - [MUTECT] Processed 2000071 reads in 845 ms
[2015-09-30T22:24Z] INFO  23:24:29,777 ProgressMeter -     8:140922185        9.64e+05   30.0 s       31.0 s     40.5%        74.0 s    44.0 s
[2015-09-30T22:24Z] INFO  23:24:29,878 MuTect - [MUTECT] Processed 12000689 reads in 691 ms
[2015-09-30T22:24Z] INFO  23:24:30,056 MuTect - [MUTECT] Processed 39011343 reads in 860 ms
[2015-09-30T22:24Z] INFO  23:24:30,230 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:30,434 MuTect - [MUTECT] Processed 3000089 reads in 729 ms
[2015-09-30T22:24Z] INFO  23:24:30,555 MuTect - [MUTECT] Processed 13000753 reads in 677 ms
[2015-09-30T22:24Z] INFO  23:24:30,681 MuTect - [MUTECT] Processed 40011454 reads in 624 ms
[2015-09-30T22:24Z] INFO  23:24:30,936 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:31,141 MuTect - [MUTECT] Processed 4000092 reads in 707 ms
[2015-09-30T22:24Z] INFO  23:24:31,244 MuTect - [MUTECT] Processed 14000774 reads in 689 ms
[2015-09-30T22:24Z] INFO  23:24:31,307 MuTect - [MUTECT] Processed 41011497 reads in 627 ms
[2015-09-30T22:24Z] INFO  23:24:31,875 MuTect - [MUTECT] Processed 5000153 reads in 734 ms
[2015-09-30T22:24Z] INFO  23:24:31,918 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:31,939 MuTect - [MUTECT] Processed 15000887 reads in 695 ms
[2015-09-30T22:24Z] INFO  23:24:31,956 MuTect - [MUTECT] Processed 42011562 reads in 649 ms
[2015-09-30T22:24Z] INFO  23:24:32,499 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:32,572 MuTect - [MUTECT] Processed 43011616 reads in 616 ms
[2015-09-30T22:24Z] INFO  23:24:32,592 MuTect - [MUTECT] Processed 6000170 reads in 717 ms
[2015-09-30T22:24Z] INFO  23:24:32,652 MuTect - [MUTECT] Processed 16000912 reads in 713 ms
[2015-09-30T22:24Z] INFO  23:24:33,220 MuTect - [MUTECT] Processed 44011733 reads in 648 ms
[2015-09-30T22:24Z] INFO  23:24:33,265 MuTect - [MUTECT] Processed 7000202 reads in 673 ms
[2015-09-30T22:24Z] INFO  23:24:33,376 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:33,385 MuTect - [MUTECT] Processed 17000996 reads in 733 ms
[2015-09-30T22:24Z] INFO  23:24:33,868 MuTect - [MUTECT] Processed 45011754 reads in 648 ms
[2015-09-30T22:24Z] INFO  23:24:33,928 MuTect - [MUTECT] Processed 8000232 reads in 663 ms
[2015-09-30T22:24Z] INFO  23:24:34,108 MuTect - [MUTECT] Processed 18001034 reads in 723 ms
[2015-09-30T22:24Z] INFO  23:24:34,518 MuTect - [MUTECT] Processed 46011887 reads in 650 ms
[2015-09-30T22:24Z] INFO  23:24:34,567 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:34,596 MuTect - [MUTECT] Processed 9000245 reads in 668 ms
[2015-09-30T22:24Z] INFO  23:24:34,743 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:34,780 MuTect - [MUTECT] Processed 19001073 reads in 672 ms
[2015-09-30T22:24Z] INFO  23:24:35,194 MuTect - [MUTECT] Processed 47011909 reads in 676 ms
[2015-09-30T22:24Z] INFO  23:24:35,483 MuTect - [MUTECT] Processed 20001105 reads in 703 ms
[2015-09-30T22:24Z] INFO  23:24:35,718 MuTect - [MUTECT] Processed 10000332 reads in 1122 ms
[2015-09-30T22:24Z] INFO  23:24:35,863 MuTect - [MUTECT] Processed 48012017 reads in 669 ms
[2015-09-30T22:24Z] INFO  23:24:35,920 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:36,200 MuTect - [MUTECT] Processed 21001108 reads in 717 ms
[2015-09-30T22:24Z] INFO  23:24:36,345 MuTect - [MUTECT] Processed 11000357 reads in 627 ms
[2015-09-30T22:24Z] INFO  23:24:36,557 MuTect - [MUTECT] Processed 49012033 reads in 694 ms
[2015-09-30T22:24Z] INFO  23:24:36,772 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:36,889 MuTect - [MUTECT] Processed 22001168 reads in 689 ms
[2015-09-30T22:24Z] INFO  23:24:37,037 MuTect - [MUTECT] Processed 12000408 reads in 692 ms
[2015-09-30T22:24Z] INFO  23:24:37,311 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:37,320 MuTect - [MUTECT] Processed 50012149 reads in 763 ms
[2015-09-30T22:24Z] INFO  23:24:37,579 MuTect - [MUTECT] Processed 23001220 reads in 690 ms
[2015-09-30T22:24Z] INFO  23:24:37,725 MuTect - [MUTECT] Processed 13000449 reads in 688 ms
[2015-09-30T22:24Z] INFO  23:24:38,041 MuTect - [MUTECT] Processed 51012191 reads in 721 ms
[2015-09-30T22:24Z] INFO  23:24:38,150 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:38,264 MuTect - [MUTECT] Processed 24001293 reads in 685 ms
[2015-09-30T22:24Z] INFO  23:24:38,668 MuTect - [MUTECT] Processed 52012249 reads in 627 ms
[2015-09-30T22:24Z] INFO  23:24:38,919 MuTect - [MUTECT] Processed 25001345 reads in 655 ms
[2015-09-30T22:24Z] INFO  23:24:39,062 MuTect - [MUTECT] Processed 14000596 reads in 1337 ms
[2015-09-30T22:24Z] INFO  23:24:39,164 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:39,434 MuTect - [MUTECT] Processed 53012360 reads in 766 ms
[2015-09-30T22:24Z] INFO  23:24:39,574 MuTect - [MUTECT] Processed 26001373 reads in 654 ms
[2015-09-30T22:24Z] INFO  23:24:39,641 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:39,792 MuTect - [MUTECT] Processed 15000643 reads in 730 ms
[2015-09-30T22:24Z] INFO  23:24:40,078 MuTect - [MUTECT] Processed 54012463 reads in 644 ms
[2015-09-30T22:24Z] INFO  23:24:40,264 MuTect - [MUTECT] Processed 27001475 reads in 691 ms
[2015-09-30T22:24Z] INFO  23:24:40,547 MuTect - [MUTECT] Processed 16000699 reads in 755 ms
[2015-09-30T22:24Z] INFO  23:24:40,839 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:40,921 MuTect - [MUTECT] Processed 55012533 reads in 843 ms
[2015-09-30T22:24Z] INFO  23:24:40,986 MuTect - [MUTECT] Processed 28001511 reads in 722 ms
[2015-09-30T22:24Z] INFO  23:24:41,434 MuTect - [MUTECT] Processed 17000769 reads in 887 ms
[2015-09-30T22:24Z] INFO  23:24:41,495 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:41,577 MuTect - [MUTECT] Processed 56012604 reads in 656 ms
[2015-09-30T22:24Z] INFO  23:24:41,783 MuTect - [MUTECT] Processed 29001528 reads in 797 ms
[2015-09-30T22:24Z] INFO  23:24:42,073 MuTect - [MUTECT] Processed 18000792 reads in 639 ms
[2015-09-30T22:24Z] INFO  23:24:42,196 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:42,323 MuTect - [MUTECT] Processed 57012698 reads in 746 ms
[2015-09-30T22:24Z] INFO  23:24:42,517 MuTect - [MUTECT] Processed 30001584 reads in 734 ms
[2015-09-30T22:24Z] INFO  23:24:42,735 MuTect - [MUTECT] Processed 19000855 reads in 662 ms
[2015-09-30T22:24Z] INFO  23:24:43,051 MuTect - [MUTECT] Processed 58012704 reads in 728 ms
[2015-09-30T22:24Z] INFO  23:24:43,144 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:43,228 MuTect - [MUTECT] Processed 31001648 reads in 711 ms
[2015-09-30T22:24Z] INFO  23:24:43,375 MuTect - [MUTECT] Processed 20000950 reads in 639 ms
[2015-09-30T22:24Z] INFO  23:24:43,614 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:43,717 MuTect - [MUTECT] Processed 59012810 reads in 666 ms
[2015-09-30T22:24Z] INFO  23:24:43,943 MuTect - [MUTECT] Processed 32001698 reads in 715 ms
[2015-09-30T22:24Z] INFO  23:24:44,036 MuTect - [MUTECT] Processed 21000979 reads in 662 ms
[2015-09-30T22:24Z] INFO  23:24:44,406 MuTect - [MUTECT] Processed 60012856 reads in 689 ms
[2015-09-30T22:24Z] INFO  23:24:44,659 MuTect - [MUTECT] Processed 33001789 reads in 716 ms
[2015-09-30T22:24Z] INFO  23:24:44,705 MuTect - [MUTECT] Processed 22001076 reads in 669 ms
[2015-09-30T22:24Z] INFO  23:24:44,855 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:45,116 MuTect - [MUTECT] Processed 61012901 reads in 710 ms
[2015-09-30T22:24Z] INFO  23:24:45,320 MuTect - [MUTECT] Processed 34001800 reads in 661 ms
[2015-09-30T22:24Z] INFO  23:24:45,363 MuTect - [MUTECT] Processed 23001107 reads in 658 ms
[2015-09-30T22:24Z] INFO  23:24:45,390 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:45,739 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:45,748 MuTect - [MUTECT] Processed 62012923 reads in 632 ms
[2015-09-30T22:24Z] INFO  23:24:46,017 MuTect - [MUTECT] Processed 35001863 reads in 697 ms
[2015-09-30T22:24Z] INFO  23:24:46,025 MuTect - [MUTECT] Processed 24001135 reads in 662 ms
[2015-09-30T22:24Z] INFO  23:24:46,390 MuTect - [MUTECT] Processed 63012994 reads in 642 ms
[2015-09-30T22:24Z] INFO  23:24:46,670 MuTect - [MUTECT] Processed 25001209 reads in 645 ms
[2015-09-30T22:24Z] INFO  23:24:46,700 MuTect - [MUTECT] Processed 36001925 reads in 683 ms
[2015-09-30T22:24Z] INFO  23:24:47,062 MuTect - [MUTECT] Processed 64013002 reads in 671 ms
[2015-09-30T22:24Z] INFO  23:24:47,303 MuTect - [MUTECT] Processed 26001268 reads in 633 ms
[2015-09-30T22:24Z] INFO  23:24:47,305 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:47,381 MuTect - [MUTECT] Processed 37002009 reads in 681 ms
[2015-09-30T22:24Z] INFO  23:24:47,548 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:47,705 MuTect - [MUTECT] Processed 65013054 reads in 644 ms
[2015-09-30T22:24Z] INFO  23:24:47,864 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:47,971 MuTect - [MUTECT] Processed 27001387 reads in 668 ms
[2015-09-30T22:24Z] INFO  23:24:48,096 MuTect - [MUTECT] Processed 38002018 reads in 715 ms
[2015-09-30T22:24Z] INFO  23:24:48,332 MuTect - [MUTECT] Processed 66013151 reads in 627 ms
[2015-09-30T22:24Z] INFO  23:24:48,656 MuTect - [MUTECT] Processed 28001408 reads in 685 ms
[2015-09-30T22:24Z] INFO  23:24:48,820 MuTect - [MUTECT] Processed 39002060 reads in 724 ms
[2015-09-30T22:24Z] INFO  23:24:49,059 MuTect - [MUTECT] Processed 67013182 reads in 727 ms
[2015-09-30T22:24Z] INFO  23:24:49,290 MuTect - [MUTECT] Processed 29001469 reads in 634 ms
[2015-09-30T22:24Z] INFO  23:24:49,440 ProgressMeter -      9:15729805        1.34e+06   30.0 s       22.0 s     61.7%        48.0 s    18.0 s
[2015-09-30T22:24Z] INFO  23:24:49,518 MuTect - [MUTECT] Processed 40002075 reads in 698 ms
[2015-09-30T22:24Z] INFO  23:24:49,702 MuTect - [MUTECT] Processed 68013214 reads in 643 ms
[2015-09-30T22:24Z] INFO  23:24:49,913 MuTect - [MUTECT] Processed 30001499 reads in 623 ms
[2015-09-30T22:24Z] INFO  23:24:49,947 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:50,031 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:50,138 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:50,233 MuTect - [MUTECT] Processed 41002118 reads in 715 ms
[2015-09-30T22:24Z] INFO  23:24:50,343 MuTect - [MUTECT] Processed 69013298 reads in 641 ms
[2015-09-30T22:24Z] INFO  23:24:50,518 MuTect - [MUTECT] Processed 31001557 reads in 605 ms
[2015-09-30T22:24Z] INFO  23:24:50,880 MuTect - [MUTECT] Processed 42002125 reads in 647 ms
[2015-09-30T22:24Z] INFO  23:24:51,008 MuTect - [MUTECT] Processed 70013358 reads in 665 ms
[2015-09-30T22:24Z] INFO  23:24:51,119 MuTect - [MUTECT] Processed 32001687 reads in 601 ms
[2015-09-30T22:24Z] INFO  23:24:51,616 MuTect - [MUTECT] Processed 43002149 reads in 736 ms
[2015-09-30T22:24Z] INFO  23:24:51,648 MuTect - [MUTECT] Processed 71013393 reads in 640 ms
[2015-09-30T22:24Z] INFO  23:24:51,755 MuTect - [MUTECT] Processed 33001719 reads in 636 ms
[2015-09-30T22:24Z] INFO  23:24:52,196 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:52,273 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:52,295 MuTect - [MUTECT] Processed 72013460 reads in 647 ms
[2015-09-30T22:24Z] INFO  23:24:52,305 MuTect - [MUTECT] Processed 44002154 reads in 689 ms
[2015-09-30T22:24Z] INFO  23:24:52,372 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:52,391 MuTect - [MUTECT] Processed 34001838 reads in 636 ms
[2015-09-30T22:24Z] INFO  23:24:52,965 MuTect - [MUTECT] Processed 73013517 reads in 670 ms
[2015-09-30T22:24Z] INFO  23:24:53,019 MuTect - [MUTECT] Processed 45002216 reads in 714 ms
[2015-09-30T22:24Z] INFO  23:24:53,026 MuTect - [MUTECT] Processed 35001878 reads in 635 ms
[2015-09-30T22:24Z] INFO  23:24:53,638 MuTect - [MUTECT] Processed 36001972 reads in 612 ms
[2015-09-30T22:24Z] INFO  23:24:53,692 MuTect - [MUTECT] Processed 46002337 reads in 673 ms
[2015-09-30T22:24Z] INFO  23:24:53,700 MuTect - [MUTECT] Processed 74013613 reads in 735 ms
[2015-09-30T22:24Z] INFO  23:24:54,270 MuTect - [MUTECT] Processed 37002080 reads in 631 ms
[2015-09-30T22:24Z] INFO  23:24:54,329 MuTect - [MUTECT] Processed 47002341 reads in 637 ms
[2015-09-30T22:24Z] INFO  23:24:54,338 MuTect - [MUTECT] Processed 75013617 reads in 638 ms
[2015-09-30T22:24Z] INFO  23:24:54,560 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:54,657 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:54,729 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:54,871 MuTect - [MUTECT] Processed 38002194 reads in 602 ms
[2015-09-30T22:24Z] INFO  23:24:54,949 MuTect - [MUTECT] Processed 76013715 reads in 611 ms
[2015-09-30T22:24Z] INFO  23:24:54,977 MuTect - [MUTECT] Processed 48002354 reads in 648 ms
[2015-09-30T22:24Z] INFO  23:24:55,465 MuTect - [MUTECT] Processed 39002267 reads in 594 ms
[2015-09-30T22:24Z] INFO  23:24:55,576 MuTect - [MUTECT] Processed 77013814 reads in 627 ms
[2015-09-30T22:24Z] INFO  23:24:55,642 MuTect - [MUTECT] Processed 49002408 reads in 665 ms
[2015-09-30T22:24Z] INFO  23:24:56,100 MuTect - [MUTECT] Processed 40002397 reads in 635 ms
[2015-09-30T22:24Z] INFO  23:24:56,205 MuTect - [MUTECT] Processed 78013928 reads in 629 ms
[2015-09-30T22:24Z] INFO  23:24:56,294 MuTect - [MUTECT] Processed 50002451 reads in 652 ms
[2015-09-30T22:24Z] INFO  23:24:56,493 ProgressMeter -      9:35677521        1.10e+06   30.0 s       27.0 s     45.3%        66.0 s    36.0 s
[2015-09-30T22:24Z] INFO  23:24:56,649 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:56,722 MuTect - [MUTECT] Processed 41002428 reads in 622 ms
[2015-09-30T22:24Z] INFO  23:24:56,835 MuTect - [MUTECT] Processed 79014018 reads in 630 ms
[2015-09-30T22:24Z] INFO  23:24:56,927 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:56,943 MuTect - [MUTECT] Processed 51002513 reads in 649 ms
[2015-09-30T22:24Z] INFO  23:24:57,148 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:57,326 MuTect - [MUTECT] Processed 42002529 reads in 604 ms
[2015-09-30T22:24Z] INFO  23:24:57,454 MuTect - [MUTECT] Processed 80014040 reads in 619 ms
[2015-09-30T22:24Z] INFO  23:24:57,626 MuTect - [MUTECT] Processed 52002544 reads in 682 ms
[2015-09-30T22:24Z] INFO  23:24:57,928 MuTect - [MUTECT] Processed 43002545 reads in 602 ms
[2015-09-30T22:24Z] INFO  23:24:58,070 MuTect - [MUTECT] Processed 81014133 reads in 616 ms
[2015-09-30T22:24Z] INFO  23:24:58,293 MuTect - [MUTECT] Processed 53002572 reads in 668 ms
[2015-09-30T22:24Z] INFO  23:24:58,520 MuTect - [MUTECT] Processed 44002591 reads in 592 ms
[2015-09-30T22:24Z] INFO  23:24:58,670 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:58,684 MuTect - [MUTECT] Processed 82014222 reads in 614 ms
[2015-09-30T22:24Z] INFO  23:24:58,958 MuTect - [MUTECT] Processed 54002644 reads in 665 ms
[2015-09-30T22:24Z] INFO  23:24:59,053 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:59,115 MuTect - [MUTECT] Processed 45002634 reads in 595 ms
[2015-09-30T22:24Z] INFO  23:24:59,311 MuTect - [MUTECT] Processed 83014297 reads in 627 ms
[2015-09-30T22:24Z] INFO  23:24:59,515 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:24Z] INFO  23:24:59,583 MuTect - [MUTECT] Processed 55002653 reads in 625 ms
[2015-09-30T22:24Z] INFO  23:24:59,710 MuTect - [MUTECT] Processed 46002639 reads in 595 ms
[2015-09-30T22:24Z] INFO  23:24:59,778 ProgressMeter -     8:145163341        1.94e+06   60.0 s       30.0 s     79.2%        75.0 s    15.0 s
[2015-09-30T22:24Z] INFO  23:24:59,957 MuTect - [MUTECT] Processed 84014411 reads in 646 ms
[2015-09-30T22:25Z] INFO  23:25:00,255 MuTect - [MUTECT] Processed 56002730 reads in 672 ms
[2015-09-30T22:25Z] INFO  23:25:00,364 MuTect - [MUTECT] Processed 47002687 reads in 654 ms
[2015-09-30T22:25Z] INFO  23:25:00,568 MuTect - [MUTECT] Processed 85014495 reads in 611 ms
[2015-09-30T22:25Z] INFO  23:25:00,746 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:00,943 MuTect - [MUTECT] Processed 57002748 reads in 688 ms
[2015-09-30T22:25Z] INFO  23:25:00,994 MuTect - [MUTECT] Processed 48002810 reads in 630 ms
[2015-09-30T22:25Z] INFO  23:25:01,022 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:01,192 MuTect - [MUTECT] Processed 86014568 reads in 624 ms
[2015-09-30T22:25Z] INFO  23:25:01,635 MuTect - [MUTECT] Processed 49002849 reads in 641 ms
[2015-09-30T22:25Z] INFO  23:25:01,643 MuTect - [MUTECT] Processed 58002755 reads in 700 ms
[2015-09-30T22:25Z] INFO  23:25:01,717 MuTect - [MUTECT] Processed 87014629 reads in 525 ms
[2015-09-30T22:25Z] INFO  23:25:02,034 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:02,242 MuTect - [MUTECT] Processed 88014681 reads in 525 ms
[2015-09-30T22:25Z] INFO  23:25:02,285 MuTect - [MUTECT] Processed 50002973 reads in 650 ms
[2015-09-30T22:25Z] INFO  23:25:02,375 MuTect - [MUTECT] Processed 59002774 reads in 732 ms
[2015-09-30T22:25Z] INFO  23:25:02,791 MuTect - [MUTECT] Processed 89014753 reads in 549 ms
[2015-09-30T22:25Z] INFO  23:25:02,975 MuTect - [MUTECT] Processed 51003056 reads in 690 ms
[2015-09-30T22:25Z] INFO  23:25:03,041 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:03,186 MuTect - [MUTECT] Processed 60002816 reads in 811 ms
[2015-09-30T22:25Z] INFO  23:25:03,390 MuTect - [MUTECT] Processed 90014855 reads in 599 ms
[2015-09-30T22:25Z] INFO  23:25:03,650 MuTect - [MUTECT] Processed 52003101 reads in 675 ms
[2015-09-30T22:25Z] INFO  23:25:03,906 MuTect - [MUTECT] Processed 61002879 reads in 720 ms
[2015-09-30T22:25Z] INFO  23:25:04,003 MuTect - [MUTECT] Processed 91014865 reads in 613 ms
[2015-09-30T22:25Z] INFO  23:25:04,291 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:04,325 MuTect - [MUTECT] Processed 53003193 reads in 675 ms
[2015-09-30T22:25Z] INFO  23:25:04,593 MuTect - [MUTECT] Processed 92014909 reads in 590 ms
[2015-09-30T22:25Z] INFO  23:25:04,631 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:04,647 MuTect - [MUTECT] Processed 62002959 reads in 741 ms
[2015-09-30T22:25Z] INFO  23:25:04,997 MuTect - [MUTECT] Processed 54003255 reads in 672 ms
[2015-09-30T22:25Z] INFO  23:25:05,198 MuTect - [MUTECT] Processed 93014993 reads in 605 ms
[2015-09-30T22:25Z] INFO  23:25:05,354 MuTect - [MUTECT] Processed 63002987 reads in 707 ms
[2015-09-30T22:25Z] INFO  23:25:05,500 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:05,675 MuTect - [MUTECT] Processed 55003310 reads in 678 ms
[2015-09-30T22:25Z] INFO  23:25:05,750 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:25Z] INFO  23:25:05,754 ProgressMeter -            done        2.05e+06   46.0 s       22.0 s    100.0%        46.0 s     0.0 s
[2015-09-30T22:25Z] INFO  23:25:05,754 ProgressMeter - Total runtime 46.32 secs, 0.77 min, 0.01 hours
[2015-09-30T22:25Z] INFO  23:25:05,787 MuTect - [MUTECT] Processed 94015042 reads in 589 ms
[2015-09-30T22:25Z] INFO  23:25:05,819 MicroScheduler - 44090 reads were filtered out during the traversal out of approximately 758565 total reads (5.81%)
[2015-09-30T22:25Z] INFO  23:25:05,820 MicroScheduler -   -> 32108 reads (4.23% of total) failing DuplicateReadFilter
[2015-09-30T22:25Z] INFO  23:25:05,820 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:25Z] INFO  23:25:05,820 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:25Z] INFO  23:25:05,820 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:25Z] INFO  23:25:05,820 MicroScheduler -   -> 11982 reads (1.58% of total) failing UnmappedReadFilter
[2015-09-30T22:25Z] INFO  23:25:06,154 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:06,416 MuTect - [MUTECT] Processed 95015159 reads in 629 ms
[2015-09-30T22:25Z] INFO  23:25:06,419 MuTect - [MUTECT] Processed 56003363 reads in 744 ms
[2015-09-30T22:25Z] INFO  23:25:06,845 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:25Z] bgzip syn3-9_0_32405837-raw-mutect.vcf
[2015-09-30T22:25Z] tabix index syn3-9_0_32405837-raw-mutect.vcf.gz
[2015-09-30T22:25Z] INFO  23:25:07,060 MuTect - [MUTECT] Processed 96015189 reads in 644 ms
[2015-09-30T22:25Z] INFO  23:25:07,572 MuTect - [MUTECT] Processed 57003383 reads in 1153 ms
[2015-09-30T22:25Z] INFO  23:25:07,696 MuTect - [MUTECT] Processed 97015289 reads in 635 ms
[2015-09-30T22:25Z] INFO  23:25:08,221 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:08,255 MuTect - [MUTECT] Processed 58003414 reads in 683 ms
[2015-09-30T22:25Z] INFO  23:25:08,279 MuTect - [MUTECT] Processed 98015392 reads in 584 ms
[2015-09-30T22:25Z] INFO  23:25:08,580 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:08,888 MuTect - [MUTECT] Processed 99015436 reads in 609 ms
[2015-09-30T22:25Z] INFO  23:25:08,927 MuTect - [MUTECT] Processed 59003437 reads in 672 ms
[2015-09-30T22:25Z] MuTect: MuTect
[2015-09-30T22:25Z] INFO  23:25:09,529 MuTect - [MUTECT] Processed 100015541 reads in 641 ms
[2015-09-30T22:25Z] INFO  23:25:09,596 MuTect - [MUTECT] Processed 60003504 reads in 669 ms
[2015-09-30T22:25Z] INFO  23:25:10,160 MuTect - [MUTECT] Processed 101015646 reads in 631 ms
[2015-09-30T22:25Z] INFO  23:25:10,302 MuTect - [MUTECT] Processed 61003557 reads in 706 ms
[2015-09-30T22:25Z] INFO  23:25:10,330 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:10,772 MuTect - [MUTECT] Processed 102015710 reads in 612 ms
[2015-09-30T22:25Z] INFO  23:25:10,915 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:10,998 MuTect - [MUTECT] Processed 62003622 reads in 696 ms
[2015-09-30T22:25Z] INFO  23:25:11,373 MuTect - [MUTECT] Processed 103015817 reads in 601 ms
[2015-09-30T22:25Z] INFO  23:25:11,611 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/9/syn3-9_65505265_96581951-raw-mutect-regions.bed to be BED
[2015-09-30T22:25Z] INFO  23:25:11,668 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:25Z] INFO  23:25:11,668 MuTect - [MUTECT] Processed 63003636 reads in 670 ms
[2015-09-30T22:25Z] INFO  23:25:11,668 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:25Z] INFO  23:25:11,669 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:25Z] INFO  23:25:11,669 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:25Z] INFO  23:25:11,672 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/9/syn3-9_65505265_96581951-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/9/tx/tmpRmh1Yc/syn3-9_65505265_96581951-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:25Z] INFO  23:25:11,672 HelpFormatter - Date/Time: 2015/09/30 23:25:11
[2015-09-30T22:25Z] INFO  23:25:11,672 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:25Z] INFO  23:25:11,672 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:25Z] INFO  23:25:11,700 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:25Z] INFO  23:25:11,705 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:25Z] INFO  23:25:11,756 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:25Z] INFO  23:25:11,806 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:25Z] INFO  23:25:11,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:25Z] INFO  23:25:11,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:25Z] INFO  23:25:11,848 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:25Z] INFO  23:25:12,013 MuTect - [MUTECT] Processed 104015928 reads in 640 ms
[2015-09-30T22:25Z] INFO  23:25:12,024 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:25Z] INFO  23:25:12,119 IntervalUtils - Processing 1183943 bp from intervals
[2015-09-30T22:25Z] INFO  23:25:12,123 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:25Z] INFO  23:25:12,123 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:25Z] INFO  23:25:12,286 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:25Z] INFO  23:25:12,342 MuTect - [MUTECT] Processed 64003674 reads in 674 ms
[2015-09-30T22:25Z] INFO  23:25:12,572 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:12,666 MuTect - [MUTECT] Processed 105015990 reads in 653 ms
[2015-09-30T22:25Z] INFO  23:25:13,012 MuTect - [MUTECT] Processed 65003726 reads in 670 ms
[2015-09-30T22:25Z] INFO  23:25:13,168 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:25Z] INFO  23:25:13,171 ProgressMeter -            done        2.48e+06   73.0 s       29.0 s    100.0%        73.0 s     0.0 s
[2015-09-30T22:25Z] INFO  23:25:13,171 ProgressMeter - Total runtime 73.40 secs, 1.22 min, 0.02 hours
[2015-09-30T22:25Z] INFO  23:25:13,235 MicroScheduler - 89659 reads were filtered out during the traversal out of approximately 1254163 total reads (7.15%)
[2015-09-30T22:25Z] INFO  23:25:13,235 MicroScheduler -   -> 67522 reads (5.38% of total) failing DuplicateReadFilter
[2015-09-30T22:25Z] INFO  23:25:13,235 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:25Z] INFO  23:25:13,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:25Z] INFO  23:25:13,235 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:25Z] INFO  23:25:13,235 MicroScheduler -   -> 22137 reads (1.77% of total) failing UnmappedReadFilter
[2015-09-30T22:25Z] INFO  23:25:13,305 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:13,573 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:25Z] INFO  23:25:13,573 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:25Z] INFO  23:25:13,574 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:25Z] INFO  23:25:13,575 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:25Z] INFO  23:25:13,787 MuTect - [MUTECT] Processed 66003726 reads in 775 ms
[2015-09-30T22:25Z] INFO  23:25:14,247 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:25Z] bgzip syn3-8_124975213_146364022-raw-mutect.vcf
[2015-09-30T22:25Z] tabix index syn3-8_124975213_146364022-raw-mutect.vcf.gz
[2015-09-30T22:25Z] INFO  23:25:14,511 MuTect - [MUTECT] Processed 67003758 reads in 724 ms
[2015-09-30T22:25Z] INFO  23:25:15,153 MuTect - [MUTECT] Processed 68003771 reads in 642 ms
[2015-09-30T22:25Z] INFO  23:25:15,856 MuTect - [MUTECT] Processed 69003785 reads in 703 ms
[2015-09-30T22:25Z] MuTect: MuTect
[2015-09-30T22:25Z] INFO  23:25:16,550 MuTect - [MUTECT] Processed 70003852 reads in 694 ms
[2015-09-30T22:25Z] INFO  23:25:16,603 MuTect - [MUTECT] Processed 1000114 reads in 2874 ms
[2015-09-30T22:25Z] INFO  23:25:17,200 MuTect - [MUTECT] Processed 71003883 reads in 649 ms
[2015-09-30T22:25Z] INFO  23:25:17,923 MuTect - [MUTECT] Processed 72003909 reads in 724 ms
[2015-09-30T22:25Z] INFO  23:25:18,038 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:18,612 MuTect - [MUTECT] Processed 73003949 reads in 689 ms
[2015-09-30T22:25Z] INFO  23:25:18,656 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/9/syn3-9_96714155_127734373-raw-mutect-regions.bed to be BED
[2015-09-30T22:25Z] INFO  23:25:18,709 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:25Z] INFO  23:25:18,710 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:25Z] INFO  23:25:18,710 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:25Z] INFO  23:25:18,710 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:25Z] INFO  23:25:18,714 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/9/syn3-9_96714155_127734373-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/9/tx/tmp_h_y3e/syn3-9_96714155_127734373-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:25Z] INFO  23:25:18,714 HelpFormatter - Date/Time: 2015/09/30 23:25:18
[2015-09-30T22:25Z] INFO  23:25:18,714 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:25Z] INFO  23:25:18,714 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:25Z] INFO  23:25:18,741 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:25Z] INFO  23:25:18,745 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:25Z] INFO  23:25:18,796 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:25Z] INFO  23:25:18,844 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:25Z] INFO  23:25:18,852 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:25Z] INFO  23:25:19,234 MuTect - [MUTECT] Processed 74004030 reads in 622 ms
[2015-09-30T22:25Z] INFO  23:25:19,318 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.47
[2015-09-30T22:25Z] INFO  23:25:19,402 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:25Z] INFO  23:25:19,571 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:25Z] INFO  23:25:19,680 IntervalUtils - Processing 1674397 bp from intervals
[2015-09-30T22:25Z] INFO  23:25:19,684 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:25Z] INFO  23:25:19,684 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:25Z] INFO  23:25:19,832 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:25Z] INFO  23:25:19,902 MuTect - [MUTECT] Processed 75004180 reads in 668 ms
[2015-09-30T22:25Z] INFO  23:25:19,979 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:25Z] INFO  23:25:19,979 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:25Z] INFO  23:25:19,979 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:25Z] INFO  23:25:19,980 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:25Z] INFO  23:25:20,584 MuTect - [MUTECT] Processed 76004202 reads in 682 ms
[2015-09-30T22:25Z] INFO  23:25:21,294 MuTect - [MUTECT] Processed 77004222 reads in 710 ms
[2015-09-30T22:25Z] INFO  23:25:21,817 MuTect - [MUTECT] Processed 2000228 reads in 5213 ms
[2015-09-30T22:25Z] INFO  23:25:22,079 MuTect - [MUTECT] Processed 78004239 reads in 785 ms
[2015-09-30T22:25Z] INFO  23:25:22,317 MuTect - [MUTECT] Processed 1000076 reads in 2290 ms
[2015-09-30T22:25Z] INFO  23:25:22,903 MuTect - [MUTECT] Processed 79004276 reads in 824 ms
[2015-09-30T22:25Z] INFO  23:25:23,021 MuTect - [MUTECT] Processed 2000110 reads in 704 ms
[2015-09-30T22:25Z] INFO  23:25:23,211 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:23,754 MuTect - [MUTECT] Processed 3000192 reads in 733 ms
[2015-09-30T22:25Z] INFO  23:25:23,851 MuTect - [MUTECT] Processed 80004343 reads in 948 ms
[2015-09-30T22:25Z] INFO  23:25:24,156 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:24,430 MuTect - [MUTECT] Processed 4000240 reads in 676 ms
[2015-09-30T22:25Z] INFO  23:25:24,652 MuTect - [MUTECT] Processed 3000383 reads in 2836 ms
[2015-09-30T22:25Z] INFO  23:25:25,096 MuTect - [MUTECT] Processed 81004543 reads in 1245 ms
[2015-09-30T22:25Z] INFO  23:25:25,121 MuTect - [MUTECT] Processed 5000334 reads in 691 ms
[2015-09-30T22:25Z] INFO  23:25:25,537 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:25,616 MuTect - [MUTECT] Processed 4000441 reads in 964 ms
[2015-09-30T22:25Z] INFO  23:25:25,852 MuTect - [MUTECT] Processed 6000375 reads in 731 ms
[2015-09-30T22:25Z] INFO  23:25:25,985 MuTect - [MUTECT] Processed 82004554 reads in 889 ms
[2015-09-30T22:25Z] INFO  23:25:26,153 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:26,322 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:25Z] INFO  23:25:26,325 ProgressMeter -            done        2.28e+06   59.0 s       26.0 s    100.0%        59.0 s     0.0 s
[2015-09-30T22:25Z] INFO  23:25:26,325 ProgressMeter - Total runtime 59.83 secs, 1.00 min, 0.02 hours
[2015-09-30T22:25Z] INFO  23:25:26,388 MicroScheduler - 59566 reads were filtered out during the traversal out of approximately 965275 total reads (6.17%)
[2015-09-30T22:25Z] INFO  23:25:26,388 MicroScheduler -   -> 43863 reads (4.54% of total) failing DuplicateReadFilter
[2015-09-30T22:25Z] INFO  23:25:26,389 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:25Z] INFO  23:25:26,389 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:25Z] INFO  23:25:26,389 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:25Z] INFO  23:25:26,389 MicroScheduler -   -> 15703 reads (1.63% of total) failing UnmappedReadFilter
[2015-09-30T22:25Z] INFO  23:25:26,448 MuTect - [MUTECT] Processed 5000448 reads in 832 ms
[2015-09-30T22:25Z] INFO  23:25:26,461 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:26,582 MuTect - [MUTECT] Processed 7000416 reads in 730 ms
[2015-09-30T22:25Z] INFO  23:25:27,244 MuTect - [MUTECT] Processed 8000430 reads in 662 ms
[2015-09-30T22:25Z] INFO  23:25:27,297 MuTect - [MUTECT] Processed 6000494 reads in 849 ms
[2015-09-30T22:25Z] INFO  23:25:27,401 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:25Z] bgzip syn3-9_32406980_65488652-raw-mutect.vcf
[2015-09-30T22:25Z] tabix index syn3-9_32406980_65488652-raw-mutect.vcf.gz
[2015-09-30T22:25Z] INFO  23:25:27,914 MuTect - [MUTECT] Processed 9000437 reads in 670 ms
[2015-09-30T22:25Z] INFO  23:25:28,391 MuTect - [MUTECT] Processed 7000662 reads in 1094 ms
[2015-09-30T22:25Z] INFO  23:25:28,600 MuTect - [MUTECT] Processed 10000482 reads in 686 ms
[2015-09-30T22:25Z] INFO  23:25:28,972 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:29,276 MuTect - [MUTECT] Processed 11000515 reads in 676 ms
[2015-09-30T22:25Z] INFO  23:25:29,709 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:25Z] MuTect: MuTect
[2015-09-30T22:25Z] INFO  23:25:29,831 MuTect - [MUTECT] Processed 8000678 reads in 1440 ms
[2015-09-30T22:25Z] INFO  23:25:29,940 MuTect - [MUTECT] Processed 12000515 reads in 664 ms
[2015-09-30T22:25Z] INFO  23:25:30,620 MuTect - [MUTECT] Processed 13000539 reads in 680 ms
[2015-09-30T22:25Z] INFO  23:25:30,956 MuTect - [MUTECT] Processed 9000905 reads in 1125 ms
[2015-09-30T22:25Z] INFO  23:25:31,305 MuTect - [MUTECT] Processed 14000540 reads in 685 ms
[2015-09-30T22:25Z] INFO  23:25:31,508 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:31,968 MuTect - [MUTECT] Processed 15000565 reads in 663 ms
[2015-09-30T22:25Z] INFO  23:25:31,969 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/9/syn3-9_127737328_141213431-raw-mutect-regions.bed to be BED
[2015-09-30T22:25Z] INFO  23:25:32,023 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:25Z] INFO  23:25:32,024 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:25Z] INFO  23:25:32,024 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:25Z] INFO  23:25:32,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:25Z] INFO  23:25:32,027 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/9/syn3-9_127737328_141213431-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/9/tx/tmpuvVhET/syn3-9_127737328_141213431-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:25Z] INFO  23:25:32,028 HelpFormatter - Date/Time: 2015/09/30 23:25:32
[2015-09-30T22:25Z] INFO  23:25:32,028 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:25Z] INFO  23:25:32,028 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:25Z] INFO  23:25:32,055 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:25Z] INFO  23:25:32,059 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:25Z] INFO  23:25:32,107 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:25Z] INFO  23:25:32,154 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:25Z] INFO  23:25:32,161 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:25Z] INFO  23:25:32,184 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:25Z] INFO  23:25:32,195 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:25Z] INFO  23:25:32,371 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:25Z] INFO  23:25:32,481 IntervalUtils - Processing 1771848 bp from intervals
[2015-09-30T22:25Z] INFO  23:25:32,485 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:25Z] INFO  23:25:32,485 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:25Z] INFO  23:25:32,636 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:25Z] INFO  23:25:32,672 MuTect - [MUTECT] Processed 16000588 reads in 704 ms
[2015-09-30T22:25Z] INFO  23:25:32,880 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:25Z] INFO  23:25:32,880 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:25Z] INFO  23:25:32,880 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:25Z] INFO  23:25:32,881 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:25Z] INFO  23:25:33,406 MuTect - [MUTECT] Processed 17000628 reads in 734 ms
[2015-09-30T22:25Z] INFO  23:25:33,925 MuTect - [MUTECT] Processed 10000960 reads in 2968 ms
[2015-09-30T22:25Z] INFO  23:25:34,027 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:34,078 MuTect - [MUTECT] Processed 18000642 reads in 672 ms
[2015-09-30T22:25Z] INFO  23:25:34,753 MuTect - [MUTECT] Processed 19000643 reads in 675 ms
[2015-09-30T22:25Z] INFO  23:25:35,374 MuTect - [MUTECT] Processed 1000053 reads in 2426 ms
[2015-09-30T22:25Z] INFO  23:25:35,454 MuTect - [MUTECT] Processed 20000688 reads in 701 ms
[2015-09-30T22:25Z] INFO  23:25:36,070 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:36,117 MuTect - [MUTECT] Processed 21000691 reads in 663 ms
[2015-09-30T22:25Z] INFO  23:25:36,199 MuTect - [MUTECT] Processed 2000158 reads in 826 ms
[2015-09-30T22:25Z] INFO  23:25:36,263 MuTect - [MUTECT] Processed 11000979 reads in 2339 ms
[2015-09-30T22:25Z] INFO  23:25:36,442 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:36,753 MuTect - [MUTECT] Processed 22000699 reads in 636 ms
[2015-09-30T22:25Z] INFO  23:25:36,872 MuTect - [MUTECT] Processed 3000195 reads in 673 ms
[2015-09-30T22:25Z] INFO  23:25:37,337 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:37,406 MuTect - [MUTECT] Processed 23000710 reads in 653 ms
[2015-09-30T22:25Z] INFO  23:25:37,534 MuTect - [MUTECT] Processed 4000244 reads in 662 ms
[2015-09-30T22:25Z] INFO  23:25:37,636 MuTect - [MUTECT] Processed 12001012 reads in 1373 ms
[2015-09-30T22:25Z] INFO  23:25:38,076 MuTect - [MUTECT] Processed 24000777 reads in 670 ms
[2015-09-30T22:25Z] INFO  23:25:38,196 MuTect - [MUTECT] Processed 5000309 reads in 662 ms
[2015-09-30T22:25Z] INFO  23:25:38,305 MuTect - [MUTECT] Processed 13001012 reads in 669 ms
[2015-09-30T22:25Z] INFO  23:25:38,823 MuTect - [MUTECT] Processed 25000779 reads in 747 ms
[2015-09-30T22:25Z] INFO  23:25:38,905 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:38,936 MuTect - [MUTECT] Processed 6000330 reads in 739 ms
[2015-09-30T22:25Z] INFO  23:25:39,063 MuTect - [MUTECT] Processed 14001058 reads in 758 ms
[2015-09-30T22:25Z] INFO  23:25:39,462 MuTect - [MUTECT] Processed 26000827 reads in 639 ms
[2015-09-30T22:25Z] INFO  23:25:39,650 MuTect - [MUTECT] Processed 7000340 reads in 714 ms
[2015-09-30T22:25Z] INFO  23:25:39,806 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:39,851 MuTect - [MUTECT] Processed 15001218 reads in 788 ms
[2015-09-30T22:25Z] INFO  23:25:40,151 MuTect - [MUTECT] Processed 27000847 reads in 689 ms
[2015-09-30T22:25Z] INFO  23:25:40,264 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:40,308 MuTect - [MUTECT] Processed 8000438 reads in 659 ms
[2015-09-30T22:25Z] INFO  23:25:40,841 MuTect - [MUTECT] Processed 16001226 reads in 990 ms
[2015-09-30T22:25Z] INFO  23:25:40,857 MuTect - [MUTECT] Processed 28000872 reads in 706 ms
[2015-09-30T22:25Z] INFO  23:25:40,954 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:40,964 MuTect - [MUTECT] Processed 9000531 reads in 656 ms
[2015-09-30T22:25Z] INFO  23:25:41,541 MuTect - [MUTECT] Processed 17001327 reads in 700 ms
[2015-09-30T22:25Z] INFO  23:25:41,588 MuTect - [MUTECT] Processed 29000897 reads in 731 ms
[2015-09-30T22:25Z] INFO  23:25:41,650 MuTect - [MUTECT] Processed 10000581 reads in 686 ms
[2015-09-30T22:25Z] INFO  23:25:42,203 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:42,278 MuTect - [MUTECT] Processed 30000968 reads in 690 ms
[2015-09-30T22:25Z] INFO  23:25:42,298 MuTect - [MUTECT] Processed 18001396 reads in 757 ms
[2015-09-30T22:25Z] INFO  23:25:42,373 MuTect - [MUTECT] Processed 11000688 reads in 723 ms
[2015-09-30T22:25Z] INFO  23:25:42,928 MuTect - [MUTECT] Processed 31001064 reads in 650 ms
[2015-09-30T22:25Z] INFO  23:25:42,960 MuTect - [MUTECT] Processed 19001401 reads in 662 ms
[2015-09-30T22:25Z] INFO  23:25:43,027 MuTect - [MUTECT] Processed 12000754 reads in 654 ms
[2015-09-30T22:25Z] INFO  23:25:43,362 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:43,535 MuTect - [MUTECT] Processed 32001077 reads in 607 ms
[2015-09-30T22:25Z] INFO  23:25:43,576 ProgressMeter -      9:71152115        4.61e+05   30.0 s       65.0 s     16.3%         3.1 m     2.6 m
[2015-09-30T22:25Z] INFO  23:25:43,649 MuTect - [MUTECT] Processed 20001412 reads in 689 ms
[2015-09-30T22:25Z] INFO  23:25:43,698 MuTect - [MUTECT] Processed 13000838 reads in 671 ms
[2015-09-30T22:25Z] INFO  23:25:44,175 MuTect - [MUTECT] Processed 33001083 reads in 640 ms
[2015-09-30T22:25Z] INFO  23:25:44,333 MuTect - [MUTECT] Processed 21001413 reads in 684 ms
[2015-09-30T22:25Z] INFO  23:25:44,396 MuTect - [MUTECT] Processed 14000848 reads in 698 ms
[2015-09-30T22:25Z] INFO  23:25:44,410 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:44,562 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:44,804 MuTect - [MUTECT] Processed 34001163 reads in 629 ms
[2015-09-30T22:25Z] INFO  23:25:45,009 MuTect - [MUTECT] Processed 22001454 reads in 676 ms
[2015-09-30T22:25Z] INFO  23:25:45,063 MuTect - [MUTECT] Processed 15000893 reads in 667 ms
[2015-09-30T22:25Z] INFO  23:25:45,412 MuTect - [MUTECT] Processed 35001233 reads in 608 ms
[2015-09-30T22:25Z] INFO  23:25:45,558 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:45,745 MuTect - [MUTECT] Processed 16000981 reads in 682 ms
[2015-09-30T22:25Z] INFO  23:25:45,917 MuTect - [MUTECT] Processed 23001506 reads in 908 ms
[2015-09-30T22:25Z] INFO  23:25:46,061 MuTect - [MUTECT] Processed 36001305 reads in 649 ms
[2015-09-30T22:25Z] INFO  23:25:46,413 MuTect - [MUTECT] Processed 17001043 reads in 668 ms
[2015-09-30T22:25Z] INFO  23:25:46,584 MuTect - [MUTECT] Processed 24001547 reads in 667 ms
[2015-09-30T22:25Z] INFO  23:25:46,717 MuTect - [MUTECT] Processed 37001331 reads in 656 ms
[2015-09-30T22:25Z] INFO  23:25:46,767 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:47,002 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:47,122 MuTect - [MUTECT] Processed 18001099 reads in 709 ms
[2015-09-30T22:25Z] INFO  23:25:47,221 MuTect - [MUTECT] Processed 25001593 reads in 637 ms
[2015-09-30T22:25Z] INFO  23:25:47,438 MuTect - [MUTECT] Processed 38001387 reads in 721 ms
[2015-09-30T22:25Z] INFO  23:25:47,761 MuTect - [MUTECT] Processed 19001185 reads in 639 ms
[2015-09-30T22:25Z] INFO  23:25:47,919 MuTect - [MUTECT] Processed 26001596 reads in 698 ms
[2015-09-30T22:25Z] INFO  23:25:48,119 MuTect - [MUTECT] Processed 39001402 reads in 681 ms
[2015-09-30T22:25Z] INFO  23:25:48,371 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:48,376 MuTect - [MUTECT] Processed 20001242 reads in 615 ms
[2015-09-30T22:25Z] INFO  23:25:48,612 MuTect - [MUTECT] Processed 27001619 reads in 693 ms
[2015-09-30T22:25Z] INFO  23:25:48,789 MuTect - [MUTECT] Processed 40001406 reads in 670 ms
[2015-09-30T22:25Z] INFO  23:25:49,008 MuTect - [MUTECT] Processed 21001254 reads in 632 ms
[2015-09-30T22:25Z] INFO  23:25:49,036 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:49,318 MuTect - [MUTECT] Processed 28001655 reads in 706 ms
[2015-09-30T22:25Z] INFO  23:25:49,444 MuTect - [MUTECT] Processed 41001410 reads in 655 ms
[2015-09-30T22:25Z] INFO  23:25:49,563 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:49,670 MuTect - [MUTECT] Processed 22001315 reads in 662 ms
[2015-09-30T22:25Z] INFO  23:25:49,982 ProgressMeter -     9:104432516        1.25e+06   30.0 s       23.0 s     29.1%       103.0 s    73.0 s
[2015-09-30T22:25Z] INFO  23:25:50,000 MuTect - [MUTECT] Processed 29001675 reads in 682 ms
[2015-09-30T22:25Z] INFO  23:25:50,128 MuTect - [MUTECT] Processed 42001504 reads in 684 ms
[2015-09-30T22:25Z] INFO  23:25:50,296 MuTect - [MUTECT] Processed 23001403 reads in 626 ms
[2015-09-30T22:25Z] INFO  23:25:50,699 MuTect - [MUTECT] Processed 30001738 reads in 699 ms
[2015-09-30T22:25Z] INFO  23:25:50,805 MuTect - [MUTECT] Processed 43001504 reads in 677 ms
[2015-09-30T22:25Z] INFO  23:25:50,914 MuTect - [MUTECT] Processed 24001485 reads in 618 ms
[2015-09-30T22:25Z] INFO  23:25:50,960 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:51,133 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:51,369 MuTect - [MUTECT] Processed 31001743 reads in 670 ms
[2015-09-30T22:25Z] INFO  23:25:51,478 MuTect - [MUTECT] Processed 44001575 reads in 673 ms
[2015-09-30T22:25Z] INFO  23:25:51,544 MuTect - [MUTECT] Processed 25001520 reads in 630 ms
[2015-09-30T22:25Z] INFO  23:25:51,993 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:52,045 MuTect - [MUTECT] Processed 32001798 reads in 676 ms
[2015-09-30T22:25Z] INFO  23:25:52,185 MuTect - [MUTECT] Processed 26001560 reads in 641 ms
[2015-09-30T22:25Z] INFO  23:25:52,194 MuTect - [MUTECT] Processed 45001612 reads in 716 ms
[2015-09-30T22:25Z] INFO  23:25:52,727 MuTect - [MUTECT] Processed 33001851 reads in 682 ms
[2015-09-30T22:25Z] INFO  23:25:52,829 MuTect - [MUTECT] Processed 27001650 reads in 644 ms
[2015-09-30T22:25Z] INFO  23:25:52,878 MuTect - [MUTECT] Processed 46001659 reads in 684 ms
[2015-09-30T22:25Z] INFO  23:25:53,200 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:53,392 MuTect - [MUTECT] Processed 34001864 reads in 665 ms
[2015-09-30T22:25Z] INFO  23:25:53,405 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:53,457 MuTect - [MUTECT] Processed 28001701 reads in 628 ms
[2015-09-30T22:25Z] INFO  23:25:53,532 MuTect - [MUTECT] Processed 47001699 reads in 654 ms
[2015-09-30T22:25Z] INFO  23:25:54,081 MuTect - [MUTECT] Processed 35001869 reads in 689 ms
[2015-09-30T22:25Z] INFO  23:25:54,098 MuTect - [MUTECT] Processed 29001711 reads in 641 ms
[2015-09-30T22:25Z] INFO  23:25:54,222 MuTect - [MUTECT] Processed 48001709 reads in 690 ms
[2015-09-30T22:25Z] INFO  23:25:54,373 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:54,736 MuTect - [MUTECT] Processed 36001942 reads in 655 ms
[2015-09-30T22:25Z] INFO  23:25:54,748 MuTect - [MUTECT] Processed 30001802 reads in 650 ms
[2015-09-30T22:25Z] INFO  23:25:54,889 MuTect - [MUTECT] Processed 49001749 reads in 667 ms
[2015-09-30T22:25Z] INFO  23:25:55,274 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:55,393 MuTect - [MUTECT] Processed 37001960 reads in 657 ms
[2015-09-30T22:25Z] INFO  23:25:55,541 MuTect - [MUTECT] Processed 31002014 reads in 793 ms
[2015-09-30T22:25Z] INFO  23:25:55,553 MuTect - [MUTECT] Processed 50001796 reads in 664 ms
[2015-09-30T22:25Z] INFO  23:25:55,858 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:56,039 MuTect - [MUTECT] Processed 38002019 reads in 646 ms
[2015-09-30T22:25Z] INFO  23:25:56,255 MuTect - [MUTECT] Processed 51001798 reads in 702 ms
[2015-09-30T22:25Z] INFO  23:25:56,466 MuTect - [MUTECT] Processed 32002033 reads in 925 ms
[2015-09-30T22:25Z] INFO  23:25:56,720 MuTect - [MUTECT] Processed 39002026 reads in 681 ms
[2015-09-30T22:25Z] INFO  23:25:56,775 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:56,952 MuTect - [MUTECT] Processed 52001874 reads in 697 ms
[2015-09-30T22:25Z] INFO  23:25:57,092 MuTect - [MUTECT] Processed 33002051 reads in 626 ms
[2015-09-30T22:25Z] INFO  23:25:57,405 MuTect - [MUTECT] Processed 40002034 reads in 685 ms
[2015-09-30T22:25Z] INFO  23:25:57,484 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:57,669 MuTect - [MUTECT] Processed 53001881 reads in 717 ms
[2015-09-30T22:25Z] INFO  23:25:57,728 MuTect - [MUTECT] Processed 34002144 reads in 636 ms
[2015-09-30T22:25Z] INFO  23:25:58,333 MuTect - [MUTECT] Processed 35002179 reads in 605 ms
[2015-09-30T22:25Z] INFO  23:25:58,353 MuTect - [MUTECT] Processed 54001919 reads in 684 ms
[2015-09-30T22:25Z] INFO  23:25:58,387 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:58,960 MuTect - [MUTECT] Processed 36002246 reads in 627 ms
[2015-09-30T22:25Z] INFO  23:25:59,052 MuTect - [MUTECT] Processed 55001934 reads in 699 ms
[2015-09-30T22:25Z] INFO  23:25:59,501 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:25Z] INFO  23:25:59,563 MuTect - [MUTECT] Processed 37002276 reads in 603 ms
[2015-09-30T22:25Z] INFO  23:25:59,728 MuTect - [MUTECT] Processed 56001981 reads in 676 ms
[2015-09-30T22:26Z] INFO  23:26:00,207 MuTect - [MUTECT] Processed 38002427 reads in 644 ms
[2015-09-30T22:26Z] INFO  23:26:00,405 MuTect - [MUTECT] Processed 57002050 reads in 677 ms
[2015-09-30T22:26Z] INFO  23:26:00,821 MuTect - [MUTECT] Processed 39002567 reads in 614 ms
[2015-09-30T22:26Z] INFO  23:26:00,896 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:01,115 MuTect - [MUTECT] Processed 58002088 reads in 710 ms
[2015-09-30T22:26Z] INFO  23:26:01,175 MuTect - [MUTECT] Processed 41002084 reads in 3770 ms
[2015-09-30T22:26Z] INFO  23:26:01,427 MuTect - [MUTECT] Processed 40002584 reads in 606 ms
[2015-09-30T22:26Z] INFO  23:26:01,762 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:01,814 MuTect - [MUTECT] Processed 59002152 reads in 699 ms
[2015-09-30T22:26Z] INFO  23:26:01,883 MuTect - [MUTECT] Processed 42002167 reads in 708 ms
[2015-09-30T22:26Z] INFO  23:26:02,051 MuTect - [MUTECT] Processed 41002640 reads in 624 ms
[2015-09-30T22:26Z] INFO  23:26:02,115 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:02,496 MuTect - [MUTECT] Processed 60002222 reads in 682 ms
[2015-09-30T22:26Z] INFO  23:26:02,541 MuTect - [MUTECT] Processed 43002183 reads in 658 ms
[2015-09-30T22:26Z] INFO  23:26:02,672 MuTect - [MUTECT] Processed 42002672 reads in 621 ms
[2015-09-30T22:26Z] INFO  23:26:02,882 ProgressMeter -     9:131289358        1.28e+06   30.0 s       23.0 s     22.1%         2.3 m   105.0 s
[2015-09-30T22:26Z] INFO  23:26:03,146 MuTect - [MUTECT] Processed 61002240 reads in 650 ms
[2015-09-30T22:26Z] INFO  23:26:03,192 MuTect - [MUTECT] Processed 44002264 reads in 651 ms
[2015-09-30T22:26Z] INFO  23:26:03,199 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:03,297 MuTect - [MUTECT] Processed 43002762 reads in 625 ms
[2015-09-30T22:26Z] INFO  23:26:03,795 MuTect - [MUTECT] Processed 62002293 reads in 649 ms
[2015-09-30T22:26Z] INFO  23:26:03,847 MuTect - [MUTECT] Processed 45002306 reads in 655 ms
[2015-09-30T22:26Z] INFO  23:26:03,940 MuTect - [MUTECT] Processed 44002828 reads in 643 ms
[2015-09-30T22:26Z] INFO  23:26:03,990 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:04,464 MuTect - [MUTECT] Processed 63002306 reads in 669 ms
[2015-09-30T22:26Z] INFO  23:26:04,534 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:04,548 MuTect - [MUTECT] Processed 46002320 reads in 701 ms
[2015-09-30T22:26Z] INFO  23:26:04,572 MuTect - [MUTECT] Processed 45002927 reads in 632 ms
[2015-09-30T22:26Z] INFO  23:26:05,137 MuTect - [MUTECT] Processed 64002324 reads in 673 ms
[2015-09-30T22:26Z] INFO  23:26:05,193 MuTect - [MUTECT] Processed 46002986 reads in 620 ms
[2015-09-30T22:26Z] INFO  23:26:05,195 MuTect - [MUTECT] Processed 47002394 reads in 647 ms
[2015-09-30T22:26Z] INFO  23:26:05,597 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:05,816 MuTect - [MUTECT] Processed 65002325 reads in 679 ms
[2015-09-30T22:26Z] INFO  23:26:05,819 MuTect - [MUTECT] Processed 47003071 reads in 627 ms
[2015-09-30T22:26Z] INFO  23:26:05,861 MuTect - [MUTECT] Processed 48002417 reads in 666 ms
[2015-09-30T22:26Z] INFO  23:26:06,217 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:06,443 MuTect - [MUTECT] Processed 48003177 reads in 624 ms
[2015-09-30T22:26Z] INFO  23:26:06,509 MuTect - [MUTECT] Processed 66002377 reads in 693 ms
[2015-09-30T22:26Z] INFO  23:26:06,533 MuTect - [MUTECT] Processed 49002512 reads in 672 ms
[2015-09-30T22:26Z] INFO  23:26:06,987 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:07,044 MuTect - [MUTECT] Processed 49003254 reads in 601 ms
[2015-09-30T22:26Z] INFO  23:26:07,175 MuTect - [MUTECT] Processed 67002410 reads in 666 ms
[2015-09-30T22:26Z] INFO  23:26:07,185 MuTect - [MUTECT] Processed 50002548 reads in 652 ms
[2015-09-30T22:26Z] INFO  23:26:07,657 MuTect - [MUTECT] Processed 50003337 reads in 613 ms
[2015-09-30T22:26Z] INFO  23:26:07,823 MuTect - [MUTECT] Processed 51002602 reads in 638 ms
[2015-09-30T22:26Z] INFO  23:26:07,859 MuTect - [MUTECT] Processed 68002480 reads in 684 ms
[2015-09-30T22:26Z] INFO  23:26:07,899 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:08,216 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:08,294 MuTect - [MUTECT] Processed 51003450 reads in 637 ms
[2015-09-30T22:26Z] INFO  23:26:08,441 MuTect - [MUTECT] Processed 52002670 reads in 618 ms
[2015-09-30T22:26Z] INFO  23:26:08,498 MuTect - [MUTECT] Processed 69002547 reads in 639 ms
[2015-09-30T22:26Z] INFO  23:26:08,968 MuTect - [MUTECT] Processed 52003531 reads in 674 ms
[2015-09-30T22:26Z] INFO  23:26:09,001 MuTect - [MUTECT] Processed 53002745 reads in 560 ms
[2015-09-30T22:26Z] INFO  23:26:09,152 MuTect - [MUTECT] Processed 70002560 reads in 654 ms
[2015-09-30T22:26Z] INFO  23:26:09,590 MuTect - [MUTECT] Processed 53003580 reads in 622 ms
[2015-09-30T22:26Z] INFO  23:26:09,621 MuTect - [MUTECT] Processed 54002750 reads in 620 ms
[2015-09-30T22:26Z] INFO  23:26:09,663 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:09,789 MuTect - [MUTECT] Processed 71002595 reads in 637 ms
[2015-09-30T22:26Z] INFO  23:26:10,212 MuTect - [MUTECT] Processed 54003651 reads in 622 ms
[2015-09-30T22:26Z] INFO  23:26:10,261 MuTect - [MUTECT] Processed 55002776 reads in 640 ms
[2015-09-30T22:26Z] INFO  23:26:10,289 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:10,361 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:10,451 MuTect - [MUTECT] Processed 72002684 reads in 662 ms
[2015-09-30T22:26Z] INFO  23:26:10,842 MuTect - [MUTECT] Processed 55003661 reads in 630 ms
[2015-09-30T22:26Z] INFO  23:26:10,925 MuTect - [MUTECT] Processed 56002793 reads in 664 ms
[2015-09-30T22:26Z] INFO  23:26:11,184 MuTect - [MUTECT] Processed 73002717 reads in 733 ms
[2015-09-30T22:26Z] INFO  23:26:11,466 MuTect - [MUTECT] Processed 56003718 reads in 623 ms
[2015-09-30T22:26Z] INFO  23:26:11,584 MuTect - [MUTECT] Processed 57002802 reads in 659 ms
[2015-09-30T22:26Z] INFO  23:26:11,870 MuTect - [MUTECT] Processed 74002727 reads in 686 ms
[2015-09-30T22:26Z] INFO  23:26:12,022 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:12,081 MuTect - [MUTECT] Processed 57003791 reads in 616 ms
[2015-09-30T22:26Z] INFO  23:26:12,266 MuTect - [MUTECT] Processed 58002803 reads in 682 ms
[2015-09-30T22:26Z] INFO  23:26:12,374 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:12,537 MuTect - [MUTECT] Processed 75002769 reads in 667 ms
[2015-09-30T22:26Z] INFO  23:26:12,686 MuTect - [MUTECT] Processed 58003807 reads in 605 ms
[2015-09-30T22:26Z] INFO  23:26:12,887 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:12,888 MuTect - [MUTECT] Processed 59002805 reads in 622 ms
[2015-09-30T22:26Z] INFO  23:26:13,228 MuTect - [MUTECT] Processed 76002788 reads in 691 ms
[2015-09-30T22:26Z] INFO  23:26:13,282 MuTect - [MUTECT] Processed 59003858 reads in 596 ms
[2015-09-30T22:26Z] INFO  23:26:13,550 MuTect - [MUTECT] Processed 60002901 reads in 661 ms
[2015-09-30T22:26Z] INFO  23:26:13,577 ProgressMeter -      9:86914397        1.66e+06   60.0 s       36.0 s     61.8%        97.0 s    37.0 s
[2015-09-30T22:26Z] INFO  23:26:13,876 MuTect - [MUTECT] Processed 77002902 reads in 648 ms
[2015-09-30T22:26Z] INFO  23:26:13,914 MuTect - [MUTECT] Processed 60003959 reads in 632 ms
[2015-09-30T22:26Z] INFO  23:26:14,219 MuTect - [MUTECT] Processed 61002950 reads in 670 ms
[2015-09-30T22:26Z] INFO  23:26:14,392 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:14,525 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:14,540 MuTect - [MUTECT] Processed 78002919 reads in 664 ms
[2015-09-30T22:26Z] INFO  23:26:14,590 MuTect - [MUTECT] Processed 61003988 reads in 676 ms
[2015-09-30T22:26Z] INFO  23:26:14,895 MuTect - [MUTECT] Processed 62002987 reads in 676 ms
[2015-09-30T22:26Z] INFO  23:26:15,197 MuTect - [MUTECT] Processed 79002983 reads in 656 ms
[2015-09-30T22:26Z] INFO  23:26:15,251 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:15,455 MuTect - [MUTECT] Processed 62004069 reads in 865 ms
[2015-09-30T22:26Z] INFO  23:26:15,548 MuTect - [MUTECT] Processed 63003027 reads in 653 ms
[2015-09-30T22:26Z] INFO  23:26:15,837 MuTect - [MUTECT] Processed 80002986 reads in 641 ms
[2015-09-30T22:26Z] INFO  23:26:16,147 MuTect - [MUTECT] Processed 63004103 reads in 692 ms
[2015-09-30T22:26Z] INFO  23:26:16,182 MuTect - [MUTECT] Processed 64003074 reads in 634 ms
[2015-09-30T22:26Z] INFO  23:26:16,507 MuTect - [MUTECT] Processed 81002995 reads in 669 ms
[2015-09-30T22:26Z] INFO  23:26:16,805 MuTect - [MUTECT] Processed 65003098 reads in 623 ms
[2015-09-30T22:26Z] INFO  23:26:16,841 MuTect - [MUTECT] Processed 64004212 reads in 693 ms
[2015-09-30T22:26Z] INFO  23:26:16,865 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:16,909 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:17,148 MuTect - [MUTECT] Processed 82002995 reads in 642 ms
[2015-09-30T22:26Z] INFO  23:26:17,471 MuTect - [MUTECT] Processed 66003109 reads in 666 ms
[2015-09-30T22:26Z] INFO  23:26:17,529 MuTect - [MUTECT] Processed 65004304 reads in 689 ms
[2015-09-30T22:26Z] INFO  23:26:17,661 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:17,791 MuTect - [MUTECT] Processed 83003027 reads in 643 ms
[2015-09-30T22:26Z] INFO  23:26:18,138 MuTect - [MUTECT] Processed 67003214 reads in 667 ms
[2015-09-30T22:26Z] INFO  23:26:18,258 MuTect - [MUTECT] Processed 66004448 reads in 729 ms
[2015-09-30T22:26Z] INFO  23:26:18,429 MuTect - [MUTECT] Processed 84003050 reads in 638 ms
[2015-09-30T22:26Z] INFO  23:26:18,811 MuTect - [MUTECT] Processed 68003229 reads in 673 ms
[2015-09-30T22:26Z] INFO  23:26:18,919 MuTect - [MUTECT] Processed 67004514 reads in 661 ms
[2015-09-30T22:26Z] INFO  23:26:19,050 MuTect - [MUTECT] Processed 85003081 reads in 621 ms
[2015-09-30T22:26Z] INFO  23:26:19,050 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:19,176 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:19,470 MuTect - [MUTECT] Processed 69003272 reads in 659 ms
[2015-09-30T22:26Z] INFO  23:26:19,613 MuTect - [MUTECT] Processed 68004547 reads in 694 ms
[2015-09-30T22:26Z] INFO  23:26:19,676 MuTect - [MUTECT] Processed 86003153 reads in 626 ms
[2015-09-30T22:26Z] INFO  23:26:19,888 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:19,983 ProgressMeter -     9:116269008        2.82e+06   60.0 s       21.0 s     62.9%        95.0 s    35.0 s
[2015-09-30T22:26Z] INFO  23:26:20,174 MuTect - [MUTECT] Processed 70003312 reads in 704 ms
[2015-09-30T22:26Z] INFO  23:26:20,330 MuTect - [MUTECT] Processed 69004577 reads in 717 ms
[2015-09-30T22:26Z] INFO  23:26:20,331 MuTect - [MUTECT] Processed 87003222 reads in 655 ms
[2015-09-30T22:26Z] INFO  23:26:20,830 MuTect - [MUTECT] Processed 71003331 reads in 656 ms
[2015-09-30T22:26Z] INFO  23:26:20,967 MuTect - [MUTECT] Processed 88003289 reads in 636 ms
[2015-09-30T22:26Z] INFO  23:26:21,048 MuTect - [MUTECT] Processed 70004613 reads in 718 ms
[2015-09-30T22:26Z] INFO  23:26:21,410 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:21,482 MuTect - [MUTECT] Processed 72003394 reads in 652 ms
[2015-09-30T22:26Z] INFO  23:26:21,547 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:21,602 MuTect - [MUTECT] Processed 89003413 reads in 635 ms
[2015-09-30T22:26Z] INFO  23:26:21,659 MuTect - [MUTECT] Processed 71004676 reads in 611 ms
[2015-09-30T22:26Z] INFO  23:26:22,036 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:22,145 MuTect - [MUTECT] Processed 73003426 reads in 663 ms
[2015-09-30T22:26Z] INFO  23:26:22,252 MuTect - [MUTECT] Processed 90003451 reads in 650 ms
[2015-09-30T22:26Z] INFO  23:26:22,293 MuTect - [MUTECT] Processed 72004745 reads in 634 ms
[2015-09-30T22:26Z] INFO  23:26:22,789 MuTect - [MUTECT] Processed 74003500 reads in 644 ms
[2015-09-30T22:26Z] INFO  23:26:22,882 MuTect - [MUTECT] Processed 91003488 reads in 630 ms
[2015-09-30T22:26Z] INFO  23:26:22,993 MuTect - [MUTECT] Processed 73004836 reads in 700 ms
[2015-09-30T22:26Z] INFO  23:26:23,474 MuTect - [MUTECT] Processed 75003504 reads in 685 ms
[2015-09-30T22:26Z] INFO  23:26:23,506 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:23,545 MuTect - [MUTECT] Processed 92003562 reads in 663 ms
[2015-09-30T22:26Z] INFO  23:26:23,633 MuTect - [MUTECT] Processed 74004875 reads in 640 ms
[2015-09-30T22:26Z] INFO  23:26:24,016 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:24,131 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:24,150 MuTect - [MUTECT] Processed 76003505 reads in 676 ms
[2015-09-30T22:26Z] INFO  23:26:24,179 MuTect - [MUTECT] Processed 93003565 reads in 634 ms
[2015-09-30T22:26Z] INFO  23:26:24,286 MuTect - [MUTECT] Processed 75004995 reads in 653 ms
[2015-09-30T22:26Z] INFO  23:26:24,798 MuTect - [MUTECT] Processed 94003587 reads in 619 ms
[2015-09-30T22:26Z] INFO  23:26:24,809 MuTect - [MUTECT] Processed 77003529 reads in 659 ms
[2015-09-30T22:26Z] INFO  23:26:24,924 MuTect - [MUTECT] Processed 76005089 reads in 638 ms
[2015-09-30T22:26Z] INFO  23:26:25,452 MuTect - [MUTECT] Processed 95003604 reads in 654 ms
[2015-09-30T22:26Z] INFO  23:26:25,494 MuTect - [MUTECT] Processed 78003549 reads in 685 ms
[2015-09-30T22:26Z] INFO  23:26:25,549 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:25,580 MuTect - [MUTECT] Processed 77005203 reads in 656 ms
[2015-09-30T22:26Z] INFO  23:26:26,104 MuTect - [MUTECT] Processed 96003656 reads in 652 ms
[2015-09-30T22:26Z] INFO  23:26:26,168 MuTect - [MUTECT] Processed 79003591 reads in 674 ms
[2015-09-30T22:26Z] INFO  23:26:26,222 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:26,228 MuTect - [MUTECT] Processed 78005258 reads in 648 ms
[2015-09-30T22:26Z] INFO  23:26:26,278 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:26,743 MuTect - [MUTECT] Processed 97003692 reads in 639 ms
[2015-09-30T22:26Z] INFO  23:26:26,848 MuTect - [MUTECT] Processed 80003598 reads in 680 ms
[2015-09-30T22:26Z] INFO  23:26:26,867 MuTect - [MUTECT] Processed 79005363 reads in 639 ms
[2015-09-30T22:26Z] INFO  23:26:27,378 MuTect - [MUTECT] Processed 98003739 reads in 635 ms
[2015-09-30T22:26Z] INFO  23:26:27,512 MuTect - [MUTECT] Processed 80005477 reads in 645 ms
[2015-09-30T22:26Z] INFO  23:26:27,704 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:28,046 MuTect - [MUTECT] Processed 99003777 reads in 668 ms
[2015-09-30T22:26Z] INFO  23:26:28,204 MuTect - [MUTECT] Processed 81005580 reads in 692 ms
[2015-09-30T22:26Z] INFO  23:26:28,276 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:28,558 MuTect - [MUTECT] Processed 81003621 reads in 1709 ms
[2015-09-30T22:26Z] INFO  23:26:28,664 MuTect - [MUTECT] Processed 100003779 reads in 618 ms
[2015-09-30T22:26Z] INFO  23:26:28,850 MuTect - [MUTECT] Processed 82005699 reads in 646 ms
[2015-09-30T22:26Z] INFO  23:26:29,294 MuTect - [MUTECT] Processed 101003864 reads in 630 ms
[2015-09-30T22:26Z] INFO  23:26:29,298 MuTect - [MUTECT] Processed 82003716 reads in 741 ms
[2015-09-30T22:26Z] INFO  23:26:29,520 MuTect - [MUTECT] Processed 83005782 reads in 670 ms
[2015-09-30T22:26Z] INFO  23:26:29,789 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:29,911 MuTect - [MUTECT] Processed 102003928 reads in 617 ms
[2015-09-30T22:26Z] INFO  23:26:29,916 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:30,019 MuTect - [MUTECT] Processed 83003747 reads in 721 ms
[2015-09-30T22:26Z] INFO  23:26:30,164 MuTect - [MUTECT] Processed 84005793 reads in 644 ms
[2015-09-30T22:26Z] INFO  23:26:30,416 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:30,568 MuTect - [MUTECT] Processed 103003939 reads in 657 ms
[2015-09-30T22:26Z] INFO  23:26:30,680 MuTect - [MUTECT] Processed 84003769 reads in 661 ms
[2015-09-30T22:26Z] INFO  23:26:30,818 MuTect - [MUTECT] Processed 85005841 reads in 654 ms
[2015-09-30T22:26Z] INFO  23:26:31,194 MuTect - [MUTECT] Processed 104003960 reads in 626 ms
[2015-09-30T22:26Z] INFO  23:26:31,326 MuTect - [MUTECT] Processed 85003841 reads in 646 ms
[2015-09-30T22:26Z] INFO  23:26:31,472 MuTect - [MUTECT] Processed 86005912 reads in 654 ms
[2015-09-30T22:26Z] INFO  23:26:31,824 MuTect - [MUTECT] Processed 105004011 reads in 630 ms
[2015-09-30T22:26Z] INFO  23:26:32,008 MuTect - [MUTECT] Processed 86003900 reads in 682 ms
[2015-09-30T22:26Z] INFO  23:26:32,101 MuTect - [MUTECT] Processed 87005996 reads in 629 ms
[2015-09-30T22:26Z] INFO  23:26:32,125 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:32,169 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:32,453 MuTect - [MUTECT] Processed 106004065 reads in 629 ms
[2015-09-30T22:26Z] INFO  23:26:32,593 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:32,661 MuTect - [MUTECT] Processed 87003932 reads in 653 ms
[2015-09-30T22:26Z] INFO  23:26:32,766 MuTect - [MUTECT] Processed 88006052 reads in 665 ms
[2015-09-30T22:26Z] INFO  23:26:32,883 ProgressMeter -     9:134330301        2.74e+06   60.0 s       21.0 s     45.6%         2.2 m    71.0 s
[2015-09-30T22:26Z] INFO  23:26:33,099 MuTect - [MUTECT] Processed 107004120 reads in 646 ms
[2015-09-30T22:26Z] INFO  23:26:33,327 MuTect - [MUTECT] Processed 88003994 reads in 666 ms
[2015-09-30T22:26Z] INFO  23:26:33,460 MuTect - [MUTECT] Processed 89006079 reads in 694 ms
[2015-09-30T22:26Z] INFO  23:26:33,747 MuTect - [MUTECT] Processed 108004175 reads in 648 ms
[2015-09-30T22:26Z] INFO  23:26:33,994 MuTect - [MUTECT] Processed 89004057 reads in 667 ms
[2015-09-30T22:26Z] INFO  23:26:34,119 MuTect - [MUTECT] Processed 90006184 reads in 659 ms
[2015-09-30T22:26Z] INFO  23:26:34,185 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:34,400 MuTect - [MUTECT] Processed 109004183 reads in 653 ms
[2015-09-30T22:26Z] INFO  23:26:34,491 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:34,653 MuTect - [MUTECT] Processed 90004074 reads in 659 ms
[2015-09-30T22:26Z] INFO  23:26:34,797 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:34,827 MuTect - [MUTECT] Processed 91006290 reads in 708 ms
[2015-09-30T22:26Z] INFO  23:26:35,027 MuTect - [MUTECT] Processed 110004251 reads in 627 ms
[2015-09-30T22:26Z] INFO  23:26:35,302 MuTect - [MUTECT] Processed 91004110 reads in 649 ms
[2015-09-30T22:26Z] INFO  23:26:35,498 MuTect - [MUTECT] Processed 92006385 reads in 671 ms
[2015-09-30T22:26Z] INFO  23:26:35,697 MuTect - [MUTECT] Processed 111004266 reads in 670 ms
[2015-09-30T22:26Z] INFO  23:26:35,995 MuTect - [MUTECT] Processed 92004214 reads in 693 ms
[2015-09-30T22:26Z] INFO  23:26:36,162 MuTect - [MUTECT] Processed 93006441 reads in 664 ms
[2015-09-30T22:26Z] INFO  23:26:36,339 MuTect - [MUTECT] Processed 112004334 reads in 642 ms
[2015-09-30T22:26Z] INFO  23:26:36,407 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:36,650 MuTect - [MUTECT] Processed 93004226 reads in 655 ms
[2015-09-30T22:26Z] INFO  23:26:36,811 MuTect - [MUTECT] Processed 94006531 reads in 649 ms
[2015-09-30T22:26Z] INFO  23:26:36,855 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:36,963 MuTect - [MUTECT] Processed 113004423 reads in 624 ms
[2015-09-30T22:26Z] INFO  23:26:37,119 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:37,330 MuTect - [MUTECT] Processed 94004290 reads in 680 ms
[2015-09-30T22:26Z] INFO  23:26:37,516 MuTect - [MUTECT] Processed 95006593 reads in 705 ms
[2015-09-30T22:26Z] INFO  23:26:37,585 MuTect - [MUTECT] Processed 114004467 reads in 622 ms
[2015-09-30T22:26Z] INFO  23:26:38,026 MuTect - [MUTECT] Processed 95004298 reads in 696 ms
[2015-09-30T22:26Z] INFO  23:26:38,174 MuTect - [MUTECT] Processed 96006627 reads in 658 ms
[2015-09-30T22:26Z] INFO  23:26:38,243 MuTect - [MUTECT] Processed 115004525 reads in 658 ms
[2015-09-30T22:26Z] INFO  23:26:38,678 MuTect - [MUTECT] Processed 96004314 reads in 652 ms
[2015-09-30T22:26Z] INFO  23:26:38,773 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:38,815 MuTect - [MUTECT] Processed 97006629 reads in 641 ms
[2015-09-30T22:26Z] INFO  23:26:38,880 MuTect - [MUTECT] Processed 116004585 reads in 637 ms
[2015-09-30T22:26Z] INFO  23:26:39,121 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:39,257 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:39,328 MuTect - [MUTECT] Processed 97004356 reads in 650 ms
[2015-09-30T22:26Z] INFO  23:26:39,496 MuTect - [MUTECT] Processed 98006688 reads in 681 ms
[2015-09-30T22:26Z] INFO  23:26:39,569 MuTect - [MUTECT] Processed 117004589 reads in 689 ms
[2015-09-30T22:26Z] INFO  23:26:39,955 MuTect - [MUTECT] Processed 98004410 reads in 627 ms
[2015-09-30T22:26Z] INFO  23:26:40,158 MuTect - [MUTECT] Processed 99006724 reads in 662 ms
[2015-09-30T22:26Z] INFO  23:26:40,222 MuTect - [MUTECT] Processed 118004624 reads in 653 ms
[2015-09-30T22:26Z] INFO  23:26:40,736 MuTect - [MUTECT] Processed 99004449 reads in 781 ms
[2015-09-30T22:26Z] INFO  23:26:40,831 MuTect - [MUTECT] Processed 100006772 reads in 673 ms
[2015-09-30T22:26Z] INFO  23:26:40,911 MuTect - [MUTECT] Processed 119004645 reads in 689 ms
[2015-09-30T22:26Z] INFO  23:26:41,105 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:41,473 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:41,480 MuTect - [MUTECT] Processed 100004456 reads in 744 ms
[2015-09-30T22:26Z] INFO  23:26:41,496 MuTect - [MUTECT] Processed 101006774 reads in 665 ms
[2015-09-30T22:26Z] INFO  23:26:41,579 MuTect - [MUTECT] Processed 120004752 reads in 668 ms
[2015-09-30T22:26Z] INFO  23:26:41,608 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:42,152 MuTect - [MUTECT] Processed 101004527 reads in 672 ms
[2015-09-30T22:26Z] INFO  23:26:42,190 MuTect - [MUTECT] Processed 102006842 reads in 694 ms
[2015-09-30T22:26Z] INFO  23:26:42,239 MuTect - [MUTECT] Processed 121004808 reads in 660 ms
[2015-09-30T22:26Z] INFO  23:26:42,271 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:26Z] INFO  23:26:42,477 ProgressMeter -            done        2.89e+06   88.0 s       30.0 s    100.0%        88.0 s     0.0 s
[2015-09-30T22:26Z] INFO  23:26:42,478 ProgressMeter - Total runtime 88.90 secs, 1.48 min, 0.02 hours
[2015-09-30T22:26Z] INFO  23:26:42,543 MicroScheduler - 73679 reads were filtered out during the traversal out of approximately 1208677 total reads (6.10%)
[2015-09-30T22:26Z] INFO  23:26:42,543 MicroScheduler -   -> 54256 reads (4.49% of total) failing DuplicateReadFilter
[2015-09-30T22:26Z] INFO  23:26:42,543 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:26Z] INFO  23:26:42,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:26Z] INFO  23:26:42,543 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:26Z] INFO  23:26:42,543 MicroScheduler -   -> 19423 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:26Z] INFO  23:26:42,853 MuTect - [MUTECT] Processed 103006859 reads in 663 ms
[2015-09-30T22:26Z] INFO  23:26:42,875 MuTect - [MUTECT] Processed 122004865 reads in 636 ms
[2015-09-30T22:26Z] INFO  23:26:43,398 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:43,479 MuTect - [MUTECT] Processed 123004871 reads in 604 ms
[2015-09-30T22:26Z] INFO  23:26:43,522 MuTect - [MUTECT] Processed 104006924 reads in 669 ms
[2015-09-30T22:26Z] INFO  23:26:43,543 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:26Z] bgzip syn3-9_65505265_96581951-raw-mutect.vcf
[2015-09-30T22:26Z] tabix index syn3-9_65505265_96581951-raw-mutect.vcf.gz
[2015-09-30T22:26Z] INFO  23:26:43,992 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:44,121 MuTect - [MUTECT] Processed 124004962 reads in 642 ms
[2015-09-30T22:26Z] INFO  23:26:44,196 MuTect - [MUTECT] Processed 105007030 reads in 674 ms
[2015-09-30T22:26Z] INFO  23:26:44,756 MuTect - [MUTECT] Processed 125004962 reads in 635 ms
[2015-09-30T22:26Z] INFO  23:26:44,827 MuTect - [MUTECT] Processed 106007067 reads in 631 ms
[2015-09-30T22:26Z] INFO  23:26:45,401 MuTect - [MUTECT] Processed 126005001 reads in 645 ms
[2015-09-30T22:26Z] INFO  23:26:45,516 MuTect - [MUTECT] Processed 107007136 reads in 689 ms
[2015-09-30T22:26Z] INFO  23:26:45,877 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:46,084 MuTect - [MUTECT] Processed 127005057 reads in 683 ms
[2015-09-30T22:26Z] INFO  23:26:46,146 MuTect - [MUTECT] Processed 108007245 reads in 630 ms
[2015-09-30T22:26Z] MuTect: MuTect
[2015-09-30T22:26Z] INFO  23:26:46,242 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:46,727 MuTect - [MUTECT] Processed 128005075 reads in 643 ms
[2015-09-30T22:26Z] INFO  23:26:46,822 MuTect - [MUTECT] Processed 109007353 reads in 676 ms
[2015-09-30T22:26Z] INFO  23:26:47,397 MuTect - [MUTECT] Processed 129005112 reads in 670 ms
[2015-09-30T22:26Z] INFO  23:26:47,570 MuTect - [MUTECT] Processed 110007394 reads in 748 ms
[2015-09-30T22:26Z] INFO  23:26:47,996 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:48,039 MuTect - [MUTECT] Processed 130005126 reads in 642 ms
[2015-09-30T22:26Z] INFO  23:26:48,159 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/10/syn3-10_0_31134673-raw-mutect-regions.bed to be BED
[2015-09-30T22:26Z] INFO  23:26:48,213 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:26Z] INFO  23:26:48,213 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:26Z] INFO  23:26:48,213 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:26Z] INFO  23:26:48,213 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:26Z] INFO  23:26:48,217 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/10/syn3-10_0_31134673-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/10/tx/tmpHbDLmi/syn3-10_0_31134673-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:26Z] INFO  23:26:48,217 HelpFormatter - Date/Time: 2015/09/30 23:26:48
[2015-09-30T22:26Z] INFO  23:26:48,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:26Z] INFO  23:26:48,217 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:26Z] INFO  23:26:48,244 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:26Z] INFO  23:26:48,247 MuTect - [MUTECT] Processed 111007394 reads in 677 ms
[2015-09-30T22:26Z] INFO  23:26:48,249 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:26Z] INFO  23:26:48,301 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:26Z] INFO  23:26:48,348 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:26Z] INFO  23:26:48,355 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:26Z] INFO  23:26:48,421 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:48,442 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2015-09-30T22:26Z] INFO  23:26:48,470 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:26Z] INFO  23:26:48,639 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:26Z] INFO  23:26:48,692 MuTect - [MUTECT] Processed 131005143 reads in 653 ms
[2015-09-30T22:26Z] INFO  23:26:48,740 IntervalUtils - Processing 1286154 bp from intervals
[2015-09-30T22:26Z] INFO  23:26:48,744 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:26Z] INFO  23:26:48,744 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:26Z] INFO  23:26:48,897 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:26Z] INFO  23:26:48,904 MuTect - [MUTECT] Processed 112007403 reads in 657 ms
[2015-09-30T22:26Z] INFO  23:26:49,053 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:26Z] INFO  23:26:49,053 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:26Z] INFO  23:26:49,053 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:26Z] INFO  23:26:49,054 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:26Z] INFO  23:26:49,349 MuTect - [MUTECT] Processed 132005227 reads in 657 ms
[2015-09-30T22:26Z] INFO  23:26:49,648 MuTect - [MUTECT] Processed 113007536 reads in 744 ms
[2015-09-30T22:26Z] INFO  23:26:49,978 MuTect - [MUTECT] Processed 133005280 reads in 629 ms
[2015-09-30T22:26Z] INFO  23:26:49,984 ProgressMeter -     9:125877457        4.12e+06   90.0 s       21.0 s     92.3%        97.0 s     7.0 s
[2015-09-30T22:26Z] INFO  23:26:50,316 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:50,364 MuTect - [MUTECT] Processed 114007582 reads in 716 ms
[2015-09-30T22:26Z] INFO  23:26:50,633 MuTect - [MUTECT] Processed 134005291 reads in 655 ms
[2015-09-30T22:26Z] INFO  23:26:50,781 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:51,112 MuTect - [MUTECT] Processed 115007600 reads in 748 ms
[2015-09-30T22:26Z] INFO  23:26:51,309 MuTect - [MUTECT] Processed 135005324 reads in 676 ms
[2015-09-30T22:26Z] INFO  23:26:51,530 MuTect - [MUTECT] Processed 1000048 reads in 2427 ms
[2015-09-30T22:26Z] INFO  23:26:51,880 MuTect - [MUTECT] Processed 116007619 reads in 768 ms
[2015-09-30T22:26Z] INFO  23:26:51,967 MuTect - [MUTECT] Processed 136005341 reads in 658 ms
[2015-09-30T22:26Z] INFO  23:26:52,245 MuTect - [MUTECT] Processed 2000141 reads in 716 ms
[2015-09-30T22:26Z] INFO  23:26:52,562 MuTect - [MUTECT] Processed 117007655 reads in 682 ms
[2015-09-30T22:26Z] INFO  23:26:52,623 MuTect - [MUTECT] Processed 137005379 reads in 656 ms
[2015-09-30T22:26Z] INFO  23:26:52,744 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:52,963 MuTect - [MUTECT] Processed 3000176 reads in 718 ms
[2015-09-30T22:26Z] INFO  23:26:53,010 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:53,198 MuTect - [MUTECT] Processed 118007692 reads in 636 ms
[2015-09-30T22:26Z] INFO  23:26:53,250 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:53,282 MuTect - [MUTECT] Processed 138005402 reads in 659 ms
[2015-09-30T22:26Z] INFO  23:26:53,715 MuTect - [MUTECT] Processed 4000244 reads in 752 ms
[2015-09-30T22:26Z] INFO  23:26:53,854 MuTect - [MUTECT] Processed 119007724 reads in 656 ms
[2015-09-30T22:26Z] INFO  23:26:53,942 MuTect - [MUTECT] Processed 139005530 reads in 660 ms
[2015-09-30T22:26Z] INFO  23:26:54,456 MuTect - [MUTECT] Processed 5000259 reads in 741 ms
[2015-09-30T22:26Z] INFO  23:26:54,552 MuTect - [MUTECT] Processed 120007793 reads in 698 ms
[2015-09-30T22:26Z] INFO  23:26:54,589 MuTect - [MUTECT] Processed 140005538 reads in 647 ms
[2015-09-30T22:26Z] INFO  23:26:55,008 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:55,183 MuTect - [MUTECT] Processed 6000300 reads in 727 ms
[2015-09-30T22:26Z] INFO  23:26:55,211 MuTect - [MUTECT] Processed 141005647 reads in 622 ms
[2015-09-30T22:26Z] INFO  23:26:55,224 MuTect - [MUTECT] Processed 121007896 reads in 672 ms
[2015-09-30T22:26Z] INFO  23:26:55,226 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:55,780 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:55,845 MuTect - [MUTECT] Processed 142005682 reads in 634 ms
[2015-09-30T22:26Z] INFO  23:26:55,917 MuTect - [MUTECT] Processed 122007988 reads in 693 ms
[2015-09-30T22:26Z] INFO  23:26:55,956 MuTect - [MUTECT] Processed 7000362 reads in 773 ms
[2015-09-30T22:26Z] INFO  23:26:56,476 MuTect - [MUTECT] Processed 143005741 reads in 631 ms
[2015-09-30T22:26Z] INFO  23:26:56,619 MuTect - [MUTECT] Processed 123008019 reads in 702 ms
[2015-09-30T22:26Z] INFO  23:26:56,654 MuTect - [MUTECT] Processed 8000383 reads in 698 ms
[2015-09-30T22:26Z] INFO  23:26:57,109 MuTect - [MUTECT] Processed 144005782 reads in 633 ms
[2015-09-30T22:26Z] INFO  23:26:57,257 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:57,300 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:57,326 MuTect - [MUTECT] Processed 124008021 reads in 707 ms
[2015-09-30T22:26Z] INFO  23:26:57,435 MuTect - [MUTECT] Processed 9000404 reads in 781 ms
[2015-09-30T22:26Z] INFO  23:26:57,724 MuTect - [MUTECT] Processed 145005783 reads in 615 ms
[2015-09-30T22:26Z] INFO  23:26:58,020 MuTect - [MUTECT] Processed 125008147 reads in 694 ms
[2015-09-30T22:26Z] INFO  23:26:58,159 MuTect - [MUTECT] Processed 10000494 reads in 724 ms
[2015-09-30T22:26Z] INFO  23:26:58,235 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:58,400 MuTect - [MUTECT] Processed 146005789 reads in 676 ms
[2015-09-30T22:26Z] INFO  23:26:58,674 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:26Z] INFO  23:26:58,678 ProgressMeter -            done        4.45e+06   98.0 s       22.0 s    100.0%        98.0 s     0.0 s
[2015-09-30T22:26Z] INFO  23:26:58,678 ProgressMeter - Total runtime 98.70 secs, 1.64 min, 0.03 hours
[2015-09-30T22:26Z] INFO  23:26:58,717 MuTect - [MUTECT] Processed 126008213 reads in 697 ms
[2015-09-30T22:26Z] INFO  23:26:58,741 MicroScheduler - 109368 reads were filtered out during the traversal out of approximately 1750783 total reads (6.25%)
[2015-09-30T22:26Z] INFO  23:26:58,741 MicroScheduler -   -> 81655 reads (4.66% of total) failing DuplicateReadFilter
[2015-09-30T22:26Z] INFO  23:26:58,741 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:26Z] INFO  23:26:58,741 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:26Z] INFO  23:26:58,741 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:26Z] INFO  23:26:58,741 MicroScheduler -   -> 27713 reads (1.58% of total) failing UnmappedReadFilter
[2015-09-30T22:26Z] INFO  23:26:58,918 MuTect - [MUTECT] Processed 11000543 reads in 759 ms
[2015-09-30T22:26Z] INFO  23:26:59,403 MuTect - [MUTECT] Processed 127008271 reads in 685 ms
[2015-09-30T22:26Z] INFO  23:26:59,528 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:26Z] INFO  23:26:59,715 MuTect - [MUTECT] Processed 12000619 reads in 797 ms
[2015-09-30T22:26Z] INFO  23:26:59,807 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:26Z] bgzip syn3-9_96714155_127734373-raw-mutect.vcf
[2015-09-30T22:26Z] tabix index syn3-9_96714155_127734373-raw-mutect.vcf.gz
[2015-09-30T22:27Z] INFO  23:27:00,100 MuTect - [MUTECT] Processed 128008376 reads in 698 ms
[2015-09-30T22:27Z] INFO  23:27:00,468 MuTect - [MUTECT] Processed 13000666 reads in 753 ms
[2015-09-30T22:27Z] INFO  23:27:00,783 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:00,792 MuTect - [MUTECT] Processed 129008497 reads in 692 ms
[2015-09-30T22:27Z] INFO  23:27:01,224 MuTect - [MUTECT] Processed 14000771 reads in 756 ms
[2015-09-30T22:27Z] INFO  23:27:01,527 MuTect - [MUTECT] Processed 130008563 reads in 735 ms
[2015-09-30T22:27Z] INFO  23:27:01,918 MuTect - [MUTECT] Processed 15000898 reads in 694 ms
[2015-09-30T22:27Z] INFO  23:27:01,954 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:02,211 MuTect - [MUTECT] Processed 131008626 reads in 684 ms
[2015-09-30T22:27Z] MuTect: MuTect
[2015-09-30T22:27Z] INFO  23:27:02,674 MuTect - [MUTECT] Processed 16000958 reads in 756 ms
[2015-09-30T22:27Z] INFO  23:27:02,885 ProgressMeter -     9:137688705        4.22e+06   90.0 s       21.0 s     67.8%         2.2 m    42.0 s
[2015-09-30T22:27Z] INFO  23:27:02,903 MuTect - [MUTECT] Processed 132008678 reads in 692 ms
[2015-09-30T22:27Z] INFO  23:27:03,341 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:03,431 MuTect - [MUTECT] Processed 17001004 reads in 757 ms
[2015-09-30T22:27Z] INFO  23:27:03,594 MuTect - [MUTECT] Processed 133008743 reads in 691 ms
[2015-09-30T22:27Z] INFO  23:27:04,130 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:04,136 MuTect - [MUTECT] Processed 18001037 reads in 704 ms
[2015-09-30T22:27Z] INFO  23:27:04,263 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/10/syn3-10_31137165_62208748-raw-mutect-regions.bed to be BED
[2015-09-30T22:27Z] INFO  23:27:04,286 MuTect - [MUTECT] Processed 134008782 reads in 692 ms
[2015-09-30T22:27Z] INFO  23:27:04,317 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:27Z] INFO  23:27:04,317 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:27Z] INFO  23:27:04,318 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:27Z] INFO  23:27:04,318 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:27Z] INFO  23:27:04,321 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/10/syn3-10_31137165_62208748-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/10/tx/tmpgNcBn5/syn3-10_31137165_62208748-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:27Z] INFO  23:27:04,321 HelpFormatter - Date/Time: 2015/09/30 23:27:04
[2015-09-30T22:27Z] INFO  23:27:04,321 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:27Z] INFO  23:27:04,322 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:27Z] INFO  23:27:04,348 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:27Z] INFO  23:27:04,352 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:27Z] INFO  23:27:04,409 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:27Z] INFO  23:27:04,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:27Z] INFO  23:27:04,463 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:27Z] INFO  23:27:04,486 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:27Z] INFO  23:27:04,497 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:27Z] INFO  23:27:04,671 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:27Z] INFO  23:27:04,765 IntervalUtils - Processing 1121601 bp from intervals
[2015-09-30T22:27Z] INFO  23:27:04,769 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:27Z] INFO  23:27:04,769 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:27Z] INFO  23:27:04,863 MuTect - [MUTECT] Processed 19001128 reads in 728 ms
[2015-09-30T22:27Z] INFO  23:27:04,922 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:27Z] INFO  23:27:05,008 MuTect - [MUTECT] Processed 135008862 reads in 722 ms
[2015-09-30T22:27Z] INFO  23:27:05,080 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:27Z] INFO  23:27:05,080 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:27Z] INFO  23:27:05,081 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:27Z] INFO  23:27:05,082 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:27Z] INFO  23:27:05,572 MuTect - [MUTECT] Processed 20001202 reads in 709 ms
[2015-09-30T22:27Z] INFO  23:27:05,644 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:05,735 MuTect - [MUTECT] Processed 136008955 reads in 727 ms
[2015-09-30T22:27Z] INFO  23:27:06,231 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:06,278 MuTect - [MUTECT] Processed 21001253 reads in 706 ms
[2015-09-30T22:27Z] INFO  23:27:06,410 MuTect - [MUTECT] Processed 137009017 reads in 675 ms
[2015-09-30T22:27Z] INFO  23:27:06,965 MuTect - [MUTECT] Processed 22001270 reads in 687 ms
[2015-09-30T22:27Z] INFO  23:27:07,091 MuTect - [MUTECT] Processed 138009087 reads in 681 ms
[2015-09-30T22:27Z] INFO  23:27:07,491 MuTect - [MUTECT] Processed 1000047 reads in 2363 ms
[2015-09-30T22:27Z] INFO  23:27:07,692 MuTect - [MUTECT] Processed 23001383 reads in 727 ms
[2015-09-30T22:27Z] INFO  23:27:07,802 MuTect - [MUTECT] Processed 139009137 reads in 711 ms
[2015-09-30T22:27Z] INFO  23:27:08,188 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:08,262 MuTect - [MUTECT] Processed 2000106 reads in 771 ms
[2015-09-30T22:27Z] INFO  23:27:08,386 MuTect - [MUTECT] Processed 24001438 reads in 694 ms
[2015-09-30T22:27Z] INFO  23:27:08,486 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:08,496 MuTect - [MUTECT] Processed 140009211 reads in 694 ms
[2015-09-30T22:27Z] INFO  23:27:09,046 MuTect - [MUTECT] Processed 3000122 reads in 784 ms
[2015-09-30T22:27Z] INFO  23:27:09,065 MuTect - [MUTECT] Processed 25001449 reads in 679 ms
[2015-09-30T22:27Z] INFO  23:27:09,226 MuTect - [MUTECT] Processed 141009224 reads in 730 ms
[2015-09-30T22:27Z] INFO  23:27:09,554 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:09,745 MuTect - [MUTECT] Processed 26001530 reads in 680 ms
[2015-09-30T22:27Z] INFO  23:27:09,888 MuTect - [MUTECT] Processed 4000122 reads in 842 ms
[2015-09-30T22:27Z] INFO  23:27:09,960 MuTect - [MUTECT] Processed 142009242 reads in 734 ms
[2015-09-30T22:27Z] INFO  23:27:10,408 MuTect - [MUTECT] Processed 27001635 reads in 663 ms
[2015-09-30T22:27Z] INFO  23:27:10,586 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:10,612 MuTect - [MUTECT] Processed 5000182 reads in 724 ms
[2015-09-30T22:27Z] INFO  23:27:10,653 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:10,677 MuTect - [MUTECT] Processed 143009284 reads in 717 ms
[2015-09-30T22:27Z] INFO  23:27:11,323 MuTect - [MUTECT] Processed 6000216 reads in 711 ms
[2015-09-30T22:27Z] INFO  23:27:11,331 MuTect - [MUTECT] Processed 144009326 reads in 654 ms
[2015-09-30T22:27Z] INFO  23:27:11,470 MuTect - [MUTECT] Processed 28001727 reads in 1062 ms
[2015-09-30T22:27Z] INFO  23:27:12,364 MuTect - [MUTECT] Processed 145009336 reads in 1033 ms
[2015-09-30T22:27Z] INFO  23:27:12,568 MuTect - [MUTECT] Processed 7000261 reads in 1245 ms
[2015-09-30T22:27Z] INFO  23:27:12,686 MuTect - [MUTECT] Processed 29001755 reads in 1216 ms
[2015-09-30T22:27Z] INFO  23:27:12,746 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:13,040 MuTect - [MUTECT] Processed 146009356 reads in 676 ms
[2015-09-30T22:27Z] INFO  23:27:13,260 MuTect - [MUTECT] Processed 8000294 reads in 692 ms
[2015-09-30T22:27Z] INFO  23:27:13,359 MuTect - [MUTECT] Processed 30001821 reads in 673 ms
[2015-09-30T22:27Z] INFO  23:27:13,803 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:13,853 MuTect - [MUTECT] Processed 147009367 reads in 813 ms
[2015-09-30T22:27Z] INFO  23:27:13,937 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:13,974 MuTect - [MUTECT] Processed 9000339 reads in 714 ms
[2015-09-30T22:27Z] INFO  23:27:14,099 MuTect - [MUTECT] Processed 31001842 reads in 740 ms
[2015-09-30T22:27Z] INFO  23:27:14,530 MuTect - [MUTECT] Processed 148009448 reads in 677 ms
[2015-09-30T22:27Z] INFO  23:27:14,633 MuTect - [MUTECT] Processed 10000356 reads in 659 ms
[2015-09-30T22:27Z] INFO  23:27:14,851 MuTect - [MUTECT] Processed 32001850 reads in 751 ms
[2015-09-30T22:27Z] INFO  23:27:15,188 MuTect - [MUTECT] Processed 149009506 reads in 658 ms
[2015-09-30T22:27Z] INFO  23:27:15,263 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:15,301 MuTect - [MUTECT] Processed 11000409 reads in 668 ms
[2015-09-30T22:27Z] INFO  23:27:15,505 MuTect - [MUTECT] Processed 33001906 reads in 655 ms
[2015-09-30T22:27Z] INFO  23:27:15,804 MuTect - [MUTECT] Processed 150009526 reads in 616 ms
[2015-09-30T22:27Z] INFO  23:27:15,994 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:16,040 MuTect - [MUTECT] Processed 12000535 reads in 738 ms
[2015-09-30T22:27Z] INFO  23:27:16,176 MuTect - [MUTECT] Processed 34001939 reads in 671 ms
[2015-09-30T22:27Z] INFO  23:27:16,351 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:16,425 MuTect - [MUTECT] Processed 151009526 reads in 621 ms
[2015-09-30T22:27Z] INFO  23:27:16,702 MuTect - [MUTECT] Processed 13000581 reads in 663 ms
[2015-09-30T22:27Z] INFO  23:27:16,873 MuTect - [MUTECT] Processed 35002040 reads in 697 ms
[2015-09-30T22:27Z] INFO  23:27:17,070 MuTect - [MUTECT] Processed 152009563 reads in 645 ms
[2015-09-30T22:27Z] INFO  23:27:17,382 MuTect - [MUTECT] Processed 14000624 reads in 680 ms
[2015-09-30T22:27Z] INFO  23:27:17,519 MuTect - [MUTECT] Processed 36002060 reads in 646 ms
[2015-09-30T22:27Z] INFO  23:27:17,726 MuTect - [MUTECT] Processed 153009569 reads in 656 ms
[2015-09-30T22:27Z] INFO  23:27:18,135 MuTect - [MUTECT] Processed 37002076 reads in 616 ms
[2015-09-30T22:27Z] INFO  23:27:18,229 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:18,229 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:18,244 MuTect - [MUTECT] Processed 15000658 reads in 862 ms
[2015-09-30T22:27Z] INFO  23:27:18,386 MuTect - [MUTECT] Processed 154009624 reads in 660 ms
[2015-09-30T22:27Z] INFO  23:27:18,761 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:18,821 MuTect - [MUTECT] Processed 38002112 reads in 686 ms
[2015-09-30T22:27Z] INFO  23:27:18,995 MuTect - [MUTECT] Processed 16000726 reads in 751 ms
[2015-09-30T22:27Z] INFO  23:27:19,045 MuTect - [MUTECT] Processed 155009721 reads in 659 ms
[2015-09-30T22:27Z] INFO  23:27:19,056 ProgressMeter -     10:11970713        1.16e+06   30.0 s       25.0 s     32.2%        93.0 s    63.0 s
[2015-09-30T22:27Z] INFO  23:27:19,475 MuTect - [MUTECT] Processed 39002172 reads in 654 ms
[2015-09-30T22:27Z] INFO  23:27:19,693 MuTect - [MUTECT] Processed 156009777 reads in 648 ms
[2015-09-30T22:27Z] INFO  23:27:20,076 MuTect - [MUTECT] Processed 17000727 reads in 1081 ms
[2015-09-30T22:27Z] INFO  23:27:20,144 MuTect - [MUTECT] Processed 40002295 reads in 669 ms
[2015-09-30T22:27Z] INFO  23:27:20,329 MuTect - [MUTECT] Processed 157009828 reads in 636 ms
[2015-09-30T22:27Z] INFO  23:27:20,556 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:20,795 MuTect - [MUTECT] Processed 41002330 reads in 651 ms
[2015-09-30T22:27Z] INFO  23:27:20,860 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:20,997 MuTect - [MUTECT] Processed 158009951 reads in 668 ms
[2015-09-30T22:27Z] INFO  23:27:21,049 MuTect - [MUTECT] Processed 18000779 reads in 973 ms
[2015-09-30T22:27Z] INFO  23:27:21,084 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:21,435 MuTect - [MUTECT] Processed 42002345 reads in 640 ms
[2015-09-30T22:27Z] INFO  23:27:21,671 MuTect - [MUTECT] Processed 159010036 reads in 674 ms
[2015-09-30T22:27Z] INFO  23:27:21,921 MuTect - [MUTECT] Processed 19000865 reads in 872 ms
[2015-09-30T22:27Z] INFO  23:27:22,104 MuTect - [MUTECT] Processed 43002377 reads in 669 ms
[2015-09-30T22:27Z] INFO  23:27:22,329 MuTect - [MUTECT] Processed 160010111 reads in 658 ms
[2015-09-30T22:27Z] INFO  23:27:22,618 MuTect - [MUTECT] Processed 20000944 reads in 697 ms
[2015-09-30T22:27Z] INFO  23:27:22,716 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:22,759 MuTect - [MUTECT] Processed 44002431 reads in 655 ms
[2015-09-30T22:27Z] INFO  23:27:23,004 MuTect - [MUTECT] Processed 161010199 reads in 675 ms
[2015-09-30T22:27Z] INFO  23:27:23,111 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:23,277 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:23,328 MuTect - [MUTECT] Processed 21001038 reads in 710 ms
[2015-09-30T22:27Z] INFO  23:27:23,407 MuTect - [MUTECT] Processed 45002500 reads in 648 ms
[2015-09-30T22:27Z] INFO  23:27:23,686 MuTect - [MUTECT] Processed 162010263 reads in 682 ms
[2015-09-30T22:27Z] INFO  23:27:24,013 MuTect - [MUTECT] Processed 22001053 reads in 685 ms
[2015-09-30T22:27Z] INFO  23:27:24,186 MuTect - [MUTECT] Processed 46002553 reads in 778 ms
[2015-09-30T22:27Z] INFO  23:27:24,326 MuTect - [MUTECT] Processed 163010375 reads in 640 ms
[2015-09-30T22:27Z] INFO  23:27:24,691 MuTect - [MUTECT] Processed 23001092 reads in 678 ms
[2015-09-30T22:27Z] INFO  23:27:24,821 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:24,844 MuTect - [MUTECT] Processed 47002638 reads in 659 ms
[2015-09-30T22:27Z] INFO  23:27:25,033 MuTect - [MUTECT] Processed 164010531 reads in 707 ms
[2015-09-30T22:27Z] INFO  23:27:25,352 MuTect - [MUTECT] Processed 24001104 reads in 661 ms
[2015-09-30T22:27Z] INFO  23:27:25,479 MuTect - [MUTECT] Processed 48002657 reads in 635 ms
[2015-09-30T22:27Z] INFO  23:27:25,485 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:25,563 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:25,740 MuTect - [MUTECT] Processed 165010534 reads in 707 ms
[2015-09-30T22:27Z] INFO  23:27:26,006 MuTect - [MUTECT] Processed 25001147 reads in 654 ms
[2015-09-30T22:27Z] INFO  23:27:26,151 MuTect - [MUTECT] Processed 49002750 reads in 672 ms
[2015-09-30T22:27Z] INFO  23:27:26,394 MuTect - [MUTECT] Processed 166010631 reads in 654 ms
[2015-09-30T22:27Z] INFO  23:27:26,685 MuTect - [MUTECT] Processed 26001199 reads in 679 ms
[2015-09-30T22:27Z] INFO  23:27:26,824 MuTect - [MUTECT] Processed 50002820 reads in 673 ms
[2015-09-30T22:27Z] INFO  23:27:27,030 MuTect - [MUTECT] Processed 167010670 reads in 636 ms
[2015-09-30T22:27Z] INFO  23:27:27,063 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:27,368 MuTect - [MUTECT] Processed 27001295 reads in 683 ms
[2015-09-30T22:27Z] INFO  23:27:27,450 MuTect - [MUTECT] Processed 51002863 reads in 626 ms
[2015-09-30T22:27Z] INFO  23:27:27,670 MuTect - [MUTECT] Processed 168010803 reads in 640 ms
[2015-09-30T22:27Z] INFO  23:27:27,868 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:27,885 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:28,058 MuTect - [MUTECT] Processed 28001375 reads in 690 ms
[2015-09-30T22:27Z] INFO  23:27:28,132 MuTect - [MUTECT] Processed 52002877 reads in 682 ms
[2015-09-30T22:27Z] INFO  23:27:28,359 MuTect - [MUTECT] Processed 169010849 reads in 689 ms
[2015-09-30T22:27Z] INFO  23:27:28,746 MuTect - [MUTECT] Processed 29001457 reads in 687 ms
[2015-09-30T22:27Z] INFO  23:27:28,822 MuTect - [MUTECT] Processed 53002951 reads in 690 ms
[2015-09-30T22:27Z] INFO  23:27:29,012 MuTect - [MUTECT] Processed 170010923 reads in 653 ms
[2015-09-30T22:27Z] INFO  23:27:29,273 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:29,398 MuTect - [MUTECT] Processed 30001516 reads in 653 ms
[2015-09-30T22:27Z] INFO  23:27:29,482 MuTect - [MUTECT] Processed 54002996 reads in 660 ms
[2015-09-30T22:27Z] INFO  23:27:29,659 MuTect - [MUTECT] Processed 171010935 reads in 647 ms
[2015-09-30T22:27Z] INFO  23:27:30,025 MuTect - [MUTECT] Processed 31001551 reads in 627 ms
[2015-09-30T22:27Z] INFO  23:27:30,138 MuTect - [MUTECT] Processed 55003023 reads in 656 ms
[2015-09-30T22:27Z] INFO  23:27:30,229 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:30,291 MuTect - [MUTECT] Processed 172011071 reads in 632 ms
[2015-09-30T22:27Z] INFO  23:27:30,444 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:30,778 MuTect - [MUTECT] Processed 32001610 reads in 753 ms
[2015-09-30T22:27Z] INFO  23:27:30,811 MuTect - [MUTECT] Processed 56003131 reads in 673 ms
[2015-09-30T22:27Z] INFO  23:27:30,906 MuTect - [MUTECT] Processed 173011123 reads in 615 ms
[2015-09-30T22:27Z] INFO  23:27:31,352 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:31,469 MuTect - [MUTECT] Processed 33001610 reads in 691 ms
[2015-09-30T22:27Z] INFO  23:27:31,489 MuTect - [MUTECT] Processed 57003139 reads in 678 ms
[2015-09-30T22:27Z] INFO  23:27:31,512 MuTect - [MUTECT] Processed 174011326 reads in 606 ms
[2015-09-30T22:27Z] INFO  23:27:32,123 MuTect - [MUTECT] Processed 175011412 reads in 611 ms
[2015-09-30T22:27Z] INFO  23:27:32,123 MuTect - [MUTECT] Processed 34001622 reads in 654 ms
[2015-09-30T22:27Z] INFO  23:27:32,150 MuTect - [MUTECT] Processed 58003141 reads in 661 ms
[2015-09-30T22:27Z] INFO  23:27:32,591 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:32,768 MuTect - [MUTECT] Processed 35001653 reads in 645 ms
[2015-09-30T22:27Z] INFO  23:27:32,825 MuTect - [MUTECT] Processed 59003250 reads in 674 ms
[2015-09-30T22:27Z] INFO  23:27:32,886 ProgressMeter -     9:139964605        5.46e+06  120.0 s       21.0 s     87.9%         2.3 m    16.0 s
[2015-09-30T22:27Z] INFO  23:27:32,895 MuTect - [MUTECT] Processed 176011427 reads in 772 ms
[2015-09-30T22:27Z] INFO  23:27:33,491 MuTect - [MUTECT] Processed 36001787 reads in 723 ms
[2015-09-30T22:27Z] INFO  23:27:33,506 MuTect - [MUTECT] Processed 60003256 reads in 682 ms
[2015-09-30T22:27Z] INFO  23:27:33,545 MuTect - [MUTECT] Processed 177011455 reads in 650 ms
[2015-09-30T22:27Z] INFO  23:27:33,605 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:34,185 MuTect - [MUTECT] Processed 61003308 reads in 679 ms
[2015-09-30T22:27Z] INFO  23:27:34,241 MuTect - [MUTECT] Processed 37001818 reads in 750 ms
[2015-09-30T22:27Z] INFO  23:27:34,458 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:34,860 MuTect - [MUTECT] Processed 62003323 reads in 675 ms
[2015-09-30T22:27Z] INFO  23:27:35,004 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:35,083 ProgressMeter -     10:47151281        1.16e+06   30.0 s       25.0 s     43.0%        69.0 s    39.0 s
[2015-09-30T22:27Z] INFO  23:27:35,112 MuTect - [MUTECT] Processed 38001925 reads in 871 ms
[2015-09-30T22:27Z] INFO  23:27:35,400 MuTect - [MUTECT] Processed 178011510 reads in 1855 ms
[2015-09-30T22:27Z] INFO  23:27:35,560 MuTect - [MUTECT] Processed 63003351 reads in 700 ms
[2015-09-30T22:27Z] INFO  23:27:35,721 MuTect - [MUTECT] Processed 39001940 reads in 609 ms
[2015-09-30T22:27Z] INFO  23:27:36,069 MuTect - [MUTECT] Processed 179011535 reads in 669 ms
[2015-09-30T22:27Z] INFO  23:27:36,262 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:36,265 MuTect - [MUTECT] Processed 64003371 reads in 705 ms
[2015-09-30T22:27Z] INFO  23:27:36,412 MuTect - [MUTECT] Processed 40002027 reads in 691 ms
[2015-09-30T22:27Z] INFO  23:27:36,677 MuTect - [MUTECT] Processed 180011624 reads in 608 ms
[2015-09-30T22:27Z] INFO  23:27:36,982 MuTect - [MUTECT] Processed 65003412 reads in 717 ms
[2015-09-30T22:27Z] INFO  23:27:37,132 MuTect - [MUTECT] Processed 41002095 reads in 720 ms
[2015-09-30T22:27Z] INFO  23:27:37,285 MuTect - [MUTECT] Processed 181011678 reads in 608 ms
[2015-09-30T22:27Z] INFO  23:27:37,695 MuTect - [MUTECT] Processed 66003472 reads in 713 ms
[2015-09-30T22:27Z] INFO  23:27:37,833 MuTect - [MUTECT] Processed 42002124 reads in 701 ms
[2015-09-30T22:27Z] INFO  23:27:37,898 MuTect - [MUTECT] Processed 182011782 reads in 613 ms
[2015-09-30T22:27Z] INFO  23:27:38,152 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:38,200 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:38,367 MuTect - [MUTECT] Processed 67003496 reads in 672 ms
[2015-09-30T22:27Z] INFO  23:27:38,433 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:38,497 MuTect - [MUTECT] Processed 43002147 reads in 664 ms
[2015-09-30T22:27Z] INFO  23:27:38,552 MuTect - [MUTECT] Processed 183011877 reads in 654 ms
[2015-09-30T22:27Z] INFO  23:27:39,057 MuTect - [MUTECT] Processed 68003514 reads in 690 ms
[2015-09-30T22:27Z] INFO  23:27:39,134 MuTect - [MUTECT] Processed 44002194 reads in 637 ms
[2015-09-30T22:27Z] INFO  23:27:39,159 MuTect - [MUTECT] Processed 184011928 reads in 607 ms
[2015-09-30T22:27Z] INFO  23:27:39,712 MuTect - [MUTECT] Processed 45002294 reads in 578 ms
[2015-09-30T22:27Z] INFO  23:27:39,743 MuTect - [MUTECT] Processed 69003520 reads in 686 ms
[2015-09-30T22:27Z] INFO  23:27:39,789 MuTect - [MUTECT] Processed 185011992 reads in 630 ms
[2015-09-30T22:27Z] INFO  23:27:40,342 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:40,346 MuTect - [MUTECT] Processed 46002337 reads in 634 ms
[2015-09-30T22:27Z] INFO  23:27:40,442 MuTect - [MUTECT] Processed 70003575 reads in 699 ms
[2015-09-30T22:27Z] INFO  23:27:40,447 MuTect - [MUTECT] Processed 186012018 reads in 658 ms
[2015-09-30T22:27Z] INFO  23:27:40,952 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:41,000 MuTect - [MUTECT] Processed 47002380 reads in 654 ms
[2015-09-30T22:27Z] INFO  23:27:41,072 MuTect - [MUTECT] Processed 187012065 reads in 625 ms
[2015-09-30T22:27Z] INFO  23:27:41,152 MuTect - [MUTECT] Processed 71003584 reads in 710 ms
[2015-09-30T22:27Z] INFO  23:27:41,655 MuTect - [MUTECT] Processed 48002424 reads in 655 ms
[2015-09-30T22:27Z] INFO  23:27:41,762 MuTect - [MUTECT] Processed 188012154 reads in 690 ms
[2015-09-30T22:27Z] INFO  23:27:41,778 MuTect - [MUTECT] Processed 72003668 reads in 626 ms
[2015-09-30T22:27Z] INFO  23:27:42,358 MuTect - [MUTECT] Processed 49002459 reads in 703 ms
[2015-09-30T22:27Z] INFO  23:27:42,468 MuTect - [MUTECT] Processed 189012216 reads in 706 ms
[2015-09-30T22:27Z] INFO  23:27:42,480 MuTect - [MUTECT] Processed 73003712 reads in 702 ms
[2015-09-30T22:27Z] INFO  23:27:42,528 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:42,614 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:43,079 MuTect - [MUTECT] Processed 50002540 reads in 721 ms
[2015-09-30T22:27Z] INFO  23:27:43,126 MuTect - [MUTECT] Processed 74003729 reads in 646 ms
[2015-09-30T22:27Z] INFO  23:27:43,135 MuTect - [MUTECT] Processed 190012285 reads in 666 ms
[2015-09-30T22:27Z] INFO  23:27:43,399 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:43,766 MuTect - [MUTECT] Processed 75003774 reads in 640 ms
[2015-09-30T22:27Z] INFO  23:27:43,768 MuTect - [MUTECT] Processed 51002559 reads in 689 ms
[2015-09-30T22:27Z] INFO  23:27:43,784 MuTect - [MUTECT] Processed 191012338 reads in 650 ms
[2015-09-30T22:27Z] INFO  23:27:44,423 MuTect - [MUTECT] Processed 52002614 reads in 655 ms
[2015-09-30T22:27Z] INFO  23:27:44,425 MuTect - [MUTECT] Processed 76003774 reads in 659 ms
[2015-09-30T22:27Z] INFO  23:27:44,440 MuTect - [MUTECT] Processed 192012396 reads in 656 ms
[2015-09-30T22:27Z] INFO  23:27:44,688 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:45,093 MuTect - [MUTECT] Processed 53002708 reads in 670 ms
[2015-09-30T22:27Z] INFO  23:27:45,105 MuTect - [MUTECT] Processed 77003809 reads in 680 ms
[2015-09-30T22:27Z] INFO  23:27:45,105 MuTect - [MUTECT] Processed 193012399 reads in 665 ms
[2015-09-30T22:27Z] INFO  23:27:45,576 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:45,735 MuTect - [MUTECT] Processed 78003809 reads in 630 ms
[2015-09-30T22:27Z] INFO  23:27:45,751 MuTect - [MUTECT] Processed 194012451 reads in 646 ms
[2015-09-30T22:27Z] INFO  23:27:45,783 MuTect - [MUTECT] Processed 54002710 reads in 690 ms
[2015-09-30T22:27Z] INFO  23:27:45,785 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:46,373 MuTect - [MUTECT] Processed 79003824 reads in 638 ms
[2015-09-30T22:27Z] INFO  23:27:46,416 MuTect - [MUTECT] Processed 195012476 reads in 665 ms
[2015-09-30T22:27Z] INFO  23:27:46,439 MuTect - [MUTECT] Processed 55002750 reads in 656 ms
[2015-09-30T22:27Z] INFO  23:27:46,992 MuTect - [MUTECT] Processed 80003889 reads in 619 ms
[2015-09-30T22:27Z] INFO  23:27:47,125 MuTect - [MUTECT] Processed 56002858 reads in 686 ms
[2015-09-30T22:27Z] INFO  23:27:47,159 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:47,258 MuTect - [MUTECT] Processed 196012595 reads in 842 ms
[2015-09-30T22:27Z] INFO  23:27:47,628 MuTect - [MUTECT] Processed 81003917 reads in 636 ms
[2015-09-30T22:27Z] INFO  23:27:47,789 MuTect - [MUTECT] Processed 57002901 reads in 664 ms
[2015-09-30T22:27Z] INFO  23:27:47,868 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:47,955 MuTect - [MUTECT] Processed 197012615 reads in 697 ms
[2015-09-30T22:27Z] INFO  23:27:48,089 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:48,264 MuTect - [MUTECT] Processed 82004017 reads in 636 ms
[2015-09-30T22:27Z] INFO  23:27:48,487 MuTect - [MUTECT] Processed 58002923 reads in 698 ms
[2015-09-30T22:27Z] INFO  23:27:48,623 MuTect - [MUTECT] Processed 198012677 reads in 668 ms
[2015-09-30T22:27Z] INFO  23:27:48,927 MuTect - [MUTECT] Processed 83004044 reads in 663 ms
[2015-09-30T22:27Z] INFO  23:27:49,057 ProgressMeter -     10:26355747        2.65e+06   60.0 s       22.0 s     80.8%        74.0 s    14.0 s
[2015-09-30T22:27Z] INFO  23:27:49,152 MuTect - [MUTECT] Processed 59002933 reads in 665 ms
[2015-09-30T22:27Z] INFO  23:27:49,315 MuTect - [MUTECT] Processed 199012708 reads in 692 ms
[2015-09-30T22:27Z] INFO  23:27:49,425 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:49,636 MuTect - [MUTECT] Processed 84004104 reads in 709 ms
[2015-09-30T22:27Z] INFO  23:27:49,826 MuTect - [MUTECT] Processed 60002936 reads in 674 ms
[2015-09-30T22:27Z] INFO  23:27:50,009 MuTect - [MUTECT] Processed 200012735 reads in 694 ms
[2015-09-30T22:27Z] INFO  23:27:50,144 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:50,295 MuTect - [MUTECT] Processed 85004104 reads in 659 ms
[2015-09-30T22:27Z] INFO  23:27:50,508 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:50,512 MuTect - [MUTECT] Processed 61002974 reads in 685 ms
[2015-09-30T22:27Z] INFO  23:27:50,674 MuTect - [MUTECT] Processed 201012808 reads in 665 ms
[2015-09-30T22:27Z] INFO  23:27:50,964 MuTect - [MUTECT] Processed 86004207 reads in 669 ms
[2015-09-30T22:27Z] INFO  23:27:51,180 MuTect - [MUTECT] Processed 62003036 reads in 669 ms
[2015-09-30T22:27Z] INFO  23:27:51,349 MuTect - [MUTECT] Processed 202012871 reads in 675 ms
[2015-09-30T22:27Z] INFO  23:27:51,643 MuTect - [MUTECT] Processed 87004207 reads in 679 ms
[2015-09-30T22:27Z] INFO  23:27:51,828 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:51,847 MuTect - [MUTECT] Processed 63003085 reads in 667 ms
[2015-09-30T22:27Z] INFO  23:27:52,013 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:27Z] INFO  23:27:52,017 ProgressMeter -            done        6.09e+06    2.3 m       22.0 s    100.0%         2.3 m     0.0 s
[2015-09-30T22:27Z] INFO  23:27:52,018 ProgressMeter - Total runtime 139.14 secs, 2.32 min, 0.04 hours
[2015-09-30T22:27Z] INFO  23:27:52,083 MicroScheduler - 174214 reads were filtered out during the traversal out of approximately 2434104 total reads (7.16%)
[2015-09-30T22:27Z] INFO  23:27:52,083 MicroScheduler -   -> 133213 reads (5.47% of total) failing DuplicateReadFilter
[2015-09-30T22:27Z] INFO  23:27:52,083 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:27Z] INFO  23:27:52,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:27Z] INFO  23:27:52,083 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:27Z] INFO  23:27:52,083 MicroScheduler -   -> 41001 reads (1.68% of total) failing UnmappedReadFilter
[2015-09-30T22:27Z] INFO  23:27:52,354 MuTect - [MUTECT] Processed 88004273 reads in 711 ms
[2015-09-30T22:27Z] INFO  23:27:52,504 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:52,549 MuTect - [MUTECT] Processed 64003123 reads in 702 ms
[2015-09-30T22:27Z] INFO  23:27:52,834 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:53,057 MuTect - [MUTECT] Processed 89004296 reads in 703 ms
[2015-09-30T22:27Z] INFO  23:27:53,075 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:27Z] bgzip syn3-9_127737328_141213431-raw-mutect.vcf
[2015-09-30T22:27Z] INFO  23:27:53,241 MuTect - [MUTECT] Processed 65003123 reads in 692 ms
[2015-09-30T22:27Z] tabix index syn3-9_127737328_141213431-raw-mutect.vcf.gz
[2015-09-30T22:27Z] INFO  23:27:53,784 MuTect - [MUTECT] Processed 90004355 reads in 726 ms
[2015-09-30T22:27Z] INFO  23:27:53,899 MuTect - [MUTECT] Processed 66003183 reads in 658 ms
[2015-09-30T22:27Z] INFO  23:27:54,507 MuTect - [MUTECT] Processed 91004374 reads in 724 ms
[2015-09-30T22:27Z] INFO  23:27:54,531 MuTect - [MUTECT] Processed 67003185 reads in 632 ms
[2015-09-30T22:27Z] INFO  23:27:55,186 MuTect - [MUTECT] Processed 68003223 reads in 655 ms
[2015-09-30T22:27Z] INFO  23:27:55,197 MuTect - [MUTECT] Processed 92004374 reads in 690 ms
[2015-09-30T22:27Z] INFO  23:27:55,286 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:55,523 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:27Z] MuTect: MuTect
[2015-09-30T22:27Z] INFO  23:27:55,822 MuTect - [MUTECT] Processed 69003282 reads in 636 ms
[2015-09-30T22:27Z] INFO  23:27:55,931 MuTect - [MUTECT] Processed 93004380 reads in 734 ms
[2015-09-30T22:27Z] INFO  23:27:56,528 MuTect - [MUTECT] Processed 70003322 reads in 706 ms
[2015-09-30T22:27Z] INFO  23:27:56,657 MuTect - [MUTECT] Processed 94004455 reads in 726 ms
[2015-09-30T22:27Z] INFO  23:27:57,207 MuTect - [MUTECT] Processed 71003322 reads in 679 ms
[2015-09-30T22:27Z] INFO  23:27:57,360 MuTect - [MUTECT] Processed 95004474 reads in 703 ms
[2015-09-30T22:27Z] INFO  23:27:57,748 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/10/syn3-10_62267938_93388847-raw-mutect-regions.bed to be BED
[2015-09-30T22:27Z] INFO  23:27:57,806 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:27Z] INFO  23:27:57,806 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:27Z] INFO  23:27:57,806 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:27Z] INFO  23:27:57,806 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:27Z] INFO  23:27:57,810 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/10/syn3-10_62267938_93388847-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/10/tx/tmpJ3i1N5/syn3-10_62267938_93388847-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:27Z] INFO  23:27:57,810 HelpFormatter - Date/Time: 2015/09/30 23:27:57
[2015-09-30T22:27Z] INFO  23:27:57,810 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:27Z] INFO  23:27:57,810 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:27Z] INFO  23:27:57,839 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:27Z] INFO  23:27:57,843 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:27Z] INFO  23:27:57,852 MuTect - [MUTECT] Processed 72003335 reads in 645 ms
[2015-09-30T22:27Z] INFO  23:27:57,871 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:57,897 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:27Z] INFO  23:27:57,950 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:27Z] INFO  23:27:57,958 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:27Z] INFO  23:27:57,981 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:27Z] INFO  23:27:57,992 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:27Z] INFO  23:27:58,102 MuTect - [MUTECT] Processed 96004474 reads in 742 ms
[2015-09-30T22:27Z] INFO  23:27:58,175 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:27Z] INFO  23:27:58,281 IntervalUtils - Processing 1412566 bp from intervals
[2015-09-30T22:27Z] INFO  23:27:58,285 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:27Z] INFO  23:27:58,285 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:27Z] INFO  23:27:58,518 MuTect - [MUTECT] Processed 73003404 reads in 666 ms
[2015-09-30T22:27Z] INFO  23:27:58,738 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:27Z] INFO  23:27:58,792 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:27Z] INFO  23:27:58,904 MuTect - [MUTECT] Processed 97004512 reads in 802 ms
[2015-09-30T22:27Z] INFO  23:27:58,912 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:27Z] INFO  23:27:58,912 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:27Z] INFO  23:27:58,913 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:27Z] INFO  23:27:58,914 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:27Z] INFO  23:27:59,250 MuTect - [MUTECT] Processed 74003448 reads in 732 ms
[2015-09-30T22:27Z] INFO  23:27:59,638 MuTect - [MUTECT] Processed 98004584 reads in 734 ms
[2015-09-30T22:27Z] INFO  23:27:59,914 MuTect - [MUTECT] Processed 75003512 reads in 664 ms
[2015-09-30T22:28Z] INFO  23:28:00,348 MuTect - [MUTECT] Processed 99004680 reads in 710 ms
[2015-09-30T22:28Z] INFO  23:28:00,492 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:00,599 MuTect - [MUTECT] Processed 76003542 reads in 685 ms
[2015-09-30T22:28Z] INFO  23:28:01,065 MuTect - [MUTECT] Processed 100004746 reads in 717 ms
[2015-09-30T22:28Z] INFO  23:28:01,267 MuTect - [MUTECT] Processed 77003575 reads in 668 ms
[2015-09-30T22:28Z] INFO  23:28:01,276 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:01,358 MuTect - [MUTECT] Processed 1000021 reads in 2398 ms
[2015-09-30T22:28Z] INFO  23:28:01,860 MuTect - [MUTECT] Processed 101004867 reads in 795 ms
[2015-09-30T22:28Z] INFO  23:28:01,996 MuTect - [MUTECT] Processed 78003582 reads in 729 ms
[2015-09-30T22:28Z] INFO  23:28:02,117 MuTect - [MUTECT] Processed 2000061 reads in 759 ms
[2015-09-30T22:28Z] INFO  23:28:02,131 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:28Z] INFO  23:28:02,135 ProgressMeter -            done        3.26e+06   73.0 s       22.0 s    100.0%        73.0 s     0.0 s
[2015-09-30T22:28Z] INFO  23:28:02,135 ProgressMeter - Total runtime 73.08 secs, 1.22 min, 0.02 hours
[2015-09-30T22:28Z] INFO  23:28:02,198 MicroScheduler - 72729 reads were filtered out during the traversal out of approximately 1219424 total reads (5.96%)
[2015-09-30T22:28Z] INFO  23:28:02,198 MicroScheduler -   -> 53666 reads (4.40% of total) failing DuplicateReadFilter
[2015-09-30T22:28Z] INFO  23:28:02,199 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:28Z] INFO  23:28:02,199 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:28Z] INFO  23:28:02,199 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:28Z] INFO  23:28:02,199 MicroScheduler -   -> 19063 reads (1.56% of total) failing UnmappedReadFilter
[2015-09-30T22:28Z] INFO  23:28:02,705 MuTect - [MUTECT] Processed 79003639 reads in 709 ms
[2015-09-30T22:28Z] INFO  23:28:02,818 MuTect - [MUTECT] Processed 3000165 reads in 701 ms
[2015-09-30T22:28Z] INFO  23:28:03,087 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:03,207 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:28Z] bgzip syn3-10_0_31134673-raw-mutect.vcf
[2015-09-30T22:28Z] tabix index syn3-10_0_31134673-raw-mutect.vcf.gz
[2015-09-30T22:28Z] INFO  23:28:03,392 MuTect - [MUTECT] Processed 80003699 reads in 687 ms
[2015-09-30T22:28Z] INFO  23:28:03,575 MuTect - [MUTECT] Processed 4000198 reads in 757 ms
[2015-09-30T22:28Z] INFO  23:28:03,644 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:04,053 MuTect - [MUTECT] Processed 81003699 reads in 661 ms
[2015-09-30T22:28Z] INFO  23:28:04,313 MuTect - [MUTECT] Processed 5000293 reads in 738 ms
[2015-09-30T22:28Z] INFO  23:28:04,730 MuTect - [MUTECT] Processed 82003739 reads in 677 ms
[2015-09-30T22:28Z] INFO  23:28:05,054 MuTect - [MUTECT] Processed 6000319 reads in 741 ms
[2015-09-30T22:28Z] INFO  23:28:05,084 ProgressMeter -     10:61572531        2.72e+06   60.0 s       22.0 s     95.8%        62.0 s     2.0 s
[2015-09-30T22:28Z] INFO  23:28:05,393 MuTect - [MUTECT] Processed 83003798 reads in 663 ms
[2015-09-30T22:28Z] MuTect: MuTect
[2015-09-30T22:28Z] INFO  23:28:05,771 MuTect - [MUTECT] Processed 7000377 reads in 716 ms
[2015-09-30T22:28Z] INFO  23:28:05,845 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:06,038 MuTect - [MUTECT] Processed 84003808 reads in 645 ms
[2015-09-30T22:28Z] INFO  23:28:06,096 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:06,488 MuTect - [MUTECT] Processed 8000467 reads in 718 ms
[2015-09-30T22:28Z] INFO  23:28:06,683 MuTect - [MUTECT] Processed 85003820 reads in 645 ms
[2015-09-30T22:28Z] INFO  23:28:07,195 MuTect - [MUTECT] Processed 9000510 reads in 707 ms
[2015-09-30T22:28Z] INFO  23:28:07,333 MuTect - [MUTECT] Processed 86003827 reads in 650 ms
[2015-09-30T22:28Z] INFO  23:28:07,374 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:28Z] INFO  23:28:07,377 ProgressMeter -            done        2.83e+06   62.0 s       21.0 s    100.0%        62.0 s     0.0 s
[2015-09-30T22:28Z] INFO  23:28:07,378 ProgressMeter - Total runtime 62.30 secs, 1.04 min, 0.02 hours
[2015-09-30T22:28Z] INFO  23:28:07,441 MicroScheduler - 60104 reads were filtered out during the traversal out of approximately 1025918 total reads (5.86%)
[2015-09-30T22:28Z] INFO  23:28:07,441 MicroScheduler -   -> 43693 reads (4.26% of total) failing DuplicateReadFilter
[2015-09-30T22:28Z] INFO  23:28:07,441 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:28Z] INFO  23:28:07,442 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:28Z] INFO  23:28:07,442 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:28Z] INFO  23:28:07,442 MicroScheduler -   -> 16411 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:28Z] INFO  23:28:07,735 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/10/syn3-10_93389481_124436664-raw-mutect-regions.bed to be BED
[2015-09-30T22:28Z] INFO  23:28:07,792 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:28Z] INFO  23:28:07,792 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:28Z] INFO  23:28:07,792 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:28Z] INFO  23:28:07,792 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:28Z] INFO  23:28:07,796 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/10/syn3-10_93389481_124436664-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/10/tx/tmpJf3JHk/syn3-10_93389481_124436664-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:28Z] INFO  23:28:07,796 HelpFormatter - Date/Time: 2015/09/30 23:28:07
[2015-09-30T22:28Z] INFO  23:28:07,796 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:28Z] INFO  23:28:07,796 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:28Z] INFO  23:28:07,824 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:28Z] INFO  23:28:07,829 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:28Z] INFO  23:28:07,881 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:28Z] INFO  23:28:07,930 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:28Z] INFO  23:28:07,937 MuTect - [MUTECT] Processed 10000559 reads in 742 ms
[2015-09-30T22:28Z] INFO  23:28:07,938 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:28Z] INFO  23:28:07,961 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:28Z] INFO  23:28:07,973 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:28Z] INFO  23:28:08,149 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:28Z] INFO  23:28:08,277 IntervalUtils - Processing 2054965 bp from intervals
[2015-09-30T22:28Z] INFO  23:28:08,281 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:28Z] INFO  23:28:08,282 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:28Z] INFO  23:28:08,459 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:28Z] INFO  23:28:08,486 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:08,643 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:28Z] INFO  23:28:08,643 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:28Z] INFO  23:28:08,644 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:28Z] INFO  23:28:08,645 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:28Z] INFO  23:28:08,656 MuTect - [MUTECT] Processed 11000584 reads in 719 ms
[2015-09-30T22:28Z] INFO  23:28:08,694 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:28Z] bgzip syn3-10_31137165_62208748-raw-mutect.vcf
[2015-09-30T22:28Z] tabix index syn3-10_31137165_62208748-raw-mutect.vcf.gz
[2015-09-30T22:28Z] INFO  23:28:09,422 MuTect - [MUTECT] Processed 12000612 reads in 766 ms
[2015-09-30T22:28Z] INFO  23:28:10,137 MuTect - [MUTECT] Processed 13000652 reads in 715 ms
[2015-09-30T22:28Z] INFO  23:28:10,841 MuTect - [MUTECT] Processed 14000731 reads in 704 ms
[2015-09-30T22:28Z] INFO  23:28:10,860 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:11,416 MuTect - [MUTECT] Processed 1000007 reads in 2725 ms
[2015-09-30T22:28Z] INFO  23:28:11,579 MuTect - [MUTECT] Processed 15000738 reads in 738 ms
[2015-09-30T22:28Z] MuTect: MuTect
[2015-09-30T22:28Z] INFO  23:28:12,265 MuTect - [MUTECT] Processed 16000811 reads in 686 ms
[2015-09-30T22:28Z] INFO  23:28:12,547 MuTect - [MUTECT] Processed 2000019 reads in 1130 ms
[2015-09-30T22:28Z] INFO  23:28:13,022 MuTect - [MUTECT] Processed 17000835 reads in 757 ms
[2015-09-30T22:28Z] INFO  23:28:13,488 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:13,500 MuTect - [MUTECT] Processed 3000040 reads in 954 ms
[2015-09-30T22:28Z] INFO  23:28:13,748 MuTect - [MUTECT] Processed 18000835 reads in 726 ms
[2015-09-30T22:28Z] INFO  23:28:14,034 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:14,185 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/10/syn3-10_124438084_135534747-raw-mutect-regions.bed to be BED
[2015-09-30T22:28Z] INFO  23:28:14,221 MuTect - [MUTECT] Processed 4000070 reads in 721 ms
[2015-09-30T22:28Z] INFO  23:28:14,240 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:28Z] INFO  23:28:14,240 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:28Z] INFO  23:28:14,240 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:28Z] INFO  23:28:14,240 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:28Z] INFO  23:28:14,244 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/10/syn3-10_124438084_135534747-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/10/tx/tmpszJmVn/syn3-10_124438084_135534747-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:28Z] INFO  23:28:14,244 HelpFormatter - Date/Time: 2015/09/30 23:28:14
[2015-09-30T22:28Z] INFO  23:28:14,244 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:28Z] INFO  23:28:14,244 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:28Z] INFO  23:28:14,272 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:28Z] INFO  23:28:14,276 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:28Z] INFO  23:28:14,329 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:28Z] INFO  23:28:14,377 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:28Z] INFO  23:28:14,385 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:28Z] INFO  23:28:14,420 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2015-09-30T22:28Z] INFO  23:28:14,451 MuTect - [MUTECT] Processed 19000879 reads in 703 ms
[2015-09-30T22:28Z] INFO  23:28:14,453 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:28Z] INFO  23:28:14,630 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:28Z] INFO  23:28:14,706 IntervalUtils - Processing 577156 bp from intervals
[2015-09-30T22:28Z] INFO  23:28:14,710 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:28Z] INFO  23:28:14,710 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:28Z] INFO  23:28:14,764 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:28Z] INFO  23:28:14,966 MuTect - [MUTECT] Processed 5000111 reads in 745 ms
[2015-09-30T22:28Z] INFO  23:28:14,992 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:28Z] INFO  23:28:14,992 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:28Z] INFO  23:28:14,993 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:28Z] INFO  23:28:14,993 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:28Z] INFO  23:28:15,159 MuTect - [MUTECT] Processed 20000901 reads in 708 ms
[2015-09-30T22:28Z] INFO  23:28:15,671 MuTect - [MUTECT] Processed 6000142 reads in 705 ms
[2015-09-30T22:28Z] INFO  23:28:15,896 MuTect - [MUTECT] Processed 21000974 reads in 737 ms
[2015-09-30T22:28Z] INFO  23:28:16,021 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:16,394 MuTect - [MUTECT] Processed 7000151 reads in 723 ms
[2015-09-30T22:28Z] INFO  23:28:16,604 MuTect - [MUTECT] Processed 22001032 reads in 708 ms
[2015-09-30T22:28Z] INFO  23:28:16,753 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:17,075 MuTect - [MUTECT] Processed 8000196 reads in 681 ms
[2015-09-30T22:28Z] INFO  23:28:17,289 MuTect - [MUTECT] Processed 23001134 reads in 684 ms
[2015-09-30T22:28Z] INFO  23:28:17,812 MuTect - [MUTECT] Processed 9000201 reads in 737 ms
[2015-09-30T22:28Z] INFO  23:28:17,911 MuTect - [MUTECT] Processed 1000012 reads in 2842 ms
[2015-09-30T22:28Z] INFO  23:28:18,228 MuTect - [MUTECT] Processed 24001232 reads in 940 ms
[2015-09-30T22:28Z] INFO  23:28:18,491 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:18,599 MuTect - [MUTECT] Processed 10000289 reads in 787 ms
[2015-09-30T22:28Z] INFO  23:28:18,698 MuTect - [MUTECT] Processed 2000113 reads in 787 ms
[2015-09-30T22:28Z] INFO  23:28:18,946 MuTect - [MUTECT] Processed 25001268 reads in 718 ms
[2015-09-30T22:28Z] INFO  23:28:19,322 MuTect - [MUTECT] Processed 11000289 reads in 723 ms
[2015-09-30T22:28Z] INFO  23:28:19,338 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:19,552 MuTect - [MUTECT] Processed 3000145 reads in 854 ms
[2015-09-30T22:28Z] INFO  23:28:19,685 MuTect - [MUTECT] Processed 26001314 reads in 739 ms
[2015-09-30T22:28Z] INFO  23:28:19,976 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:20,031 MuTect - [MUTECT] Processed 12000324 reads in 708 ms
[2015-09-30T22:28Z] INFO  23:28:20,236 MuTect - [MUTECT] Processed 4000164 reads in 684 ms
[2015-09-30T22:28Z] INFO  23:28:20,428 MuTect - [MUTECT] Processed 27001347 reads in 743 ms
[2015-09-30T22:28Z] INFO  23:28:20,714 MuTect - [MUTECT] Processed 13000380 reads in 684 ms
[2015-09-30T22:28Z] INFO  23:28:20,869 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:20,911 MuTect - [MUTECT] Processed 5000176 reads in 674 ms
[2015-09-30T22:28Z] INFO  23:28:21,126 MuTect - [MUTECT] Processed 28001409 reads in 698 ms
[2015-09-30T22:28Z] INFO  23:28:21,439 MuTect - [MUTECT] Processed 14000382 reads in 725 ms
[2015-09-30T22:28Z] INFO  23:28:21,564 MuTect - [MUTECT] Processed 6000273 reads in 654 ms
[2015-09-30T22:28Z] INFO  23:28:21,767 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:21,794 MuTect - [MUTECT] Processed 29001528 reads in 668 ms
[2015-09-30T22:28Z] INFO  23:28:22,097 MuTect - [MUTECT] Processed 15000429 reads in 658 ms
[2015-09-30T22:28Z] INFO  23:28:22,277 MuTect - [MUTECT] Processed 7000337 reads in 713 ms
[2015-09-30T22:28Z] INFO  23:28:22,440 MuTect - [MUTECT] Processed 30001534 reads in 646 ms
[2015-09-30T22:28Z] INFO  23:28:22,502 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:22,832 MuTect - [MUTECT] Processed 16000495 reads in 734 ms
[2015-09-30T22:28Z] INFO  23:28:22,980 MuTect - [MUTECT] Processed 8000432 reads in 702 ms
[2015-09-30T22:28Z] INFO  23:28:23,098 MuTect - [MUTECT] Processed 31001579 reads in 658 ms
[2015-09-30T22:28Z] INFO  23:28:23,210 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:23,543 MuTect - [MUTECT] Processed 17000555 reads in 712 ms
[2015-09-30T22:28Z] INFO  23:28:23,648 MuTect - [MUTECT] Processed 9000453 reads in 669 ms
[2015-09-30T22:28Z] INFO  23:28:23,759 MuTect - [MUTECT] Processed 32001626 reads in 661 ms
[2015-09-30T22:28Z] INFO  23:28:24,285 MuTect - [MUTECT] Processed 18000570 reads in 742 ms
[2015-09-30T22:28Z] INFO  23:28:24,344 MuTect - [MUTECT] Processed 10000503 reads in 696 ms
[2015-09-30T22:28Z] INFO  23:28:24,361 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:24,405 MuTect - [MUTECT] Processed 33001693 reads in 646 ms
[2015-09-30T22:28Z] INFO  23:28:24,807 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:25,012 MuTect - [MUTECT] Processed 19000588 reads in 727 ms
[2015-09-30T22:28Z] INFO  23:28:25,017 MuTect - [MUTECT] Processed 11000539 reads in 673 ms
[2015-09-30T22:28Z] INFO  23:28:25,082 MuTect - [MUTECT] Processed 34001751 reads in 676 ms
[2015-09-30T22:28Z] INFO  23:28:25,413 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:25,678 MuTect - [MUTECT] Processed 12000567 reads in 661 ms
[2015-09-30T22:28Z] INFO  23:28:25,733 MuTect - [MUTECT] Processed 20000653 reads in 721 ms
[2015-09-30T22:28Z] INFO  23:28:25,748 MuTect - [MUTECT] Processed 35001810 reads in 667 ms
[2015-09-30T22:28Z] INFO  23:28:26,425 MuTect - [MUTECT] Processed 36001894 reads in 677 ms
[2015-09-30T22:28Z] INFO  23:28:26,431 MuTect - [MUTECT] Processed 21000698 reads in 698 ms
[2015-09-30T22:28Z] INFO  23:28:26,709 MuTect - [MUTECT] Processed 13000662 reads in 1030 ms
[2015-09-30T22:28Z] INFO  23:28:26,907 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:27,109 MuTect - [MUTECT] Processed 37001907 reads in 684 ms
[2015-09-30T22:28Z] INFO  23:28:27,109 MuTect - [MUTECT] Processed 22000757 reads in 678 ms
[2015-09-30T22:28Z] INFO  23:28:27,146 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:27,393 MuTect - [MUTECT] Processed 14000689 reads in 685 ms
[2015-09-30T22:28Z] INFO  23:28:27,722 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:27,778 MuTect - [MUTECT] Processed 23000812 reads in 669 ms
[2015-09-30T22:28Z] INFO  23:28:27,793 MuTect - [MUTECT] Processed 38001992 reads in 684 ms
[2015-09-30T22:28Z] INFO  23:28:28,053 MuTect - [MUTECT] Processed 15000739 reads in 660 ms
[2015-09-30T22:28Z] INFO  23:28:28,456 MuTect - [MUTECT] Processed 24000826 reads in 678 ms
[2015-09-30T22:28Z] INFO  23:28:28,479 MuTect - [MUTECT] Processed 39002101 reads in 686 ms
[2015-09-30T22:28Z] INFO  23:28:28,713 MuTect - [MUTECT] Processed 16000758 reads in 660 ms
[2015-09-30T22:28Z] INFO  23:28:28,915 ProgressMeter -     10:73057800        1.21e+06   30.0 s       24.0 s     32.7%        91.0 s    61.0 s
[2015-09-30T22:28Z] INFO  23:28:29,120 MuTect - [MUTECT] Processed 25000871 reads in 664 ms
[2015-09-30T22:28Z] INFO  23:28:29,168 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:29,178 MuTect - [MUTECT] Processed 40002151 reads in 699 ms
[2015-09-30T22:28Z] INFO  23:28:29,382 MuTect - [MUTECT] Processed 17000766 reads in 669 ms
[2015-09-30T22:28Z] INFO  23:28:29,566 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:29,786 MuTect - [MUTECT] Processed 26000948 reads in 666 ms
[2015-09-30T22:28Z] INFO  23:28:29,846 MuTect - [MUTECT] Processed 41002280 reads in 668 ms
[2015-09-30T22:28Z] INFO  23:28:30,016 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:30,486 MuTect - [MUTECT] Processed 27000964 reads in 700 ms
[2015-09-30T22:28Z] INFO  23:28:30,535 MuTect - [MUTECT] Processed 42002355 reads in 689 ms
[2015-09-30T22:28Z] INFO  23:28:30,544 MuTect - [MUTECT] Processed 18000824 reads in 1161 ms
[2015-09-30T22:28Z] INFO  23:28:31,147 MuTect - [MUTECT] Processed 28001017 reads in 661 ms
[2015-09-30T22:28Z] INFO  23:28:31,191 MuTect - [MUTECT] Processed 43002442 reads in 656 ms
[2015-09-30T22:28Z] INFO  23:28:31,276 MuTect - [MUTECT] Processed 19000922 reads in 733 ms
[2015-09-30T22:28Z] INFO  23:28:31,537 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:31,789 MuTect - [MUTECT] Processed 29001150 reads in 642 ms
[2015-09-30T22:28Z] INFO  23:28:31,837 MuTect - [MUTECT] Processed 44002495 reads in 645 ms
[2015-09-30T22:28Z] INFO  23:28:31,951 MuTect - [MUTECT] Processed 20000945 reads in 675 ms
[2015-09-30T22:28Z] INFO  23:28:32,245 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:32,341 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:32,475 MuTect - [MUTECT] Processed 45002607 reads in 639 ms
[2015-09-30T22:28Z] INFO  23:28:32,500 MuTect - [MUTECT] Processed 30001180 reads in 711 ms
[2015-09-30T22:28Z] INFO  23:28:32,606 MuTect - [MUTECT] Processed 21001009 reads in 655 ms
[2015-09-30T22:28Z] INFO  23:28:33,093 MuTect - [MUTECT] Processed 46002647 reads in 618 ms
[2015-09-30T22:28Z] INFO  23:28:33,201 MuTect - [MUTECT] Processed 31001197 reads in 701 ms
[2015-09-30T22:28Z] INFO  23:28:33,285 MuTect - [MUTECT] Processed 22001073 reads in 679 ms
[2015-09-30T22:28Z] INFO  23:28:33,701 MuTect - [MUTECT] Processed 47002718 reads in 608 ms
[2015-09-30T22:28Z] INFO  23:28:33,876 MuTect - [MUTECT] Processed 32001287 reads in 675 ms
[2015-09-30T22:28Z] INFO  23:28:33,981 MuTect - [MUTECT] Processed 23001129 reads in 696 ms
[2015-09-30T22:28Z] INFO  23:28:34,061 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:34,325 MuTect - [MUTECT] Processed 48002750 reads in 624 ms
[2015-09-30T22:28Z] INFO  23:28:34,334 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:34,571 MuTect - [MUTECT] Processed 33001364 reads in 695 ms
[2015-09-30T22:28Z] INFO  23:28:34,658 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:34,662 MuTect - [MUTECT] Processed 24001172 reads in 681 ms
[2015-09-30T22:28Z] INFO  23:28:34,983 MuTect - [MUTECT] Processed 49002814 reads in 658 ms
[2015-09-30T22:28Z] INFO  23:28:35,253 MuTect - [MUTECT] Processed 34001369 reads in 682 ms
[2015-09-30T22:28Z] INFO  23:28:35,370 MuTect - [MUTECT] Processed 25001232 reads in 708 ms
[2015-09-30T22:28Z] INFO  23:28:35,622 MuTect - [MUTECT] Processed 50002878 reads in 639 ms
[2015-09-30T22:28Z] INFO  23:28:35,911 MuTect - [MUTECT] Processed 35001402 reads in 658 ms
[2015-09-30T22:28Z] INFO  23:28:36,047 MuTect - [MUTECT] Processed 26001308 reads in 677 ms
[2015-09-30T22:28Z] INFO  23:28:36,261 MuTect - [MUTECT] Processed 51002923 reads in 639 ms
[2015-09-30T22:28Z] INFO  23:28:36,329 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:36,534 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:36,559 MuTect - [MUTECT] Processed 36001514 reads in 648 ms
[2015-09-30T22:28Z] INFO  23:28:36,717 MuTect - [MUTECT] Processed 27001310 reads in 670 ms
[2015-09-30T22:28Z] INFO  23:28:36,905 MuTect - [MUTECT] Processed 52002995 reads in 643 ms
[2015-09-30T22:28Z] INFO  23:28:37,114 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:37,259 MuTect - [MUTECT] Processed 37001595 reads in 700 ms
[2015-09-30T22:28Z] INFO  23:28:37,355 MuTect - [MUTECT] Processed 28001374 reads in 638 ms
[2015-09-30T22:28Z] INFO  23:28:37,571 MuTect - [MUTECT] Processed 53003042 reads in 667 ms
[2015-09-30T22:28Z] INFO  23:28:37,936 MuTect - [MUTECT] Processed 38001619 reads in 677 ms
[2015-09-30T22:28Z] INFO  23:28:38,013 MuTect - [MUTECT] Processed 29001412 reads in 658 ms
[2015-09-30T22:28Z] INFO  23:28:38,204 MuTect - [MUTECT] Processed 54003115 reads in 633 ms
[2015-09-30T22:28Z] INFO  23:28:38,641 MuTect - [MUTECT] Processed 39001722 reads in 705 ms
[2015-09-30T22:28Z] INFO  23:28:38,644 MuTect - [MUTECT] Processed 30001466 reads in 631 ms
[2015-09-30T22:28Z] INFO  23:28:38,646 ProgressMeter -     10:99081462        1.30e+06   30.0 s       23.0 s     24.1%         2.1 m    94.0 s
[2015-09-30T22:28Z] INFO  23:28:38,708 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:38,884 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:38,884 MuTect - [MUTECT] Processed 55003151 reads in 680 ms
[2015-09-30T22:28Z] INFO  23:28:39,335 MuTect - [MUTECT] Processed 40001761 reads in 694 ms
[2015-09-30T22:28Z] INFO  23:28:39,396 MuTect - [MUTECT] Processed 31001508 reads in 752 ms
[2015-09-30T22:28Z] INFO  23:28:39,575 MuTect - [MUTECT] Processed 56003166 reads in 691 ms
[2015-09-30T22:28Z] INFO  23:28:39,601 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:40,059 MuTect - [MUTECT] Processed 41001770 reads in 724 ms
[2015-09-30T22:28Z] INFO  23:28:40,083 MuTect - [MUTECT] Processed 32001513 reads in 686 ms
[2015-09-30T22:28Z] INFO  23:28:40,232 MuTect - [MUTECT] Processed 57003203 reads in 657 ms
[2015-09-30T22:28Z] INFO  23:28:40,727 MuTect - [MUTECT] Processed 42001869 reads in 668 ms
[2015-09-30T22:28Z] INFO  23:28:40,746 MuTect - [MUTECT] Processed 33001671 reads in 664 ms
[2015-09-30T22:28Z] INFO  23:28:40,904 MuTect - [MUTECT] Processed 58003222 reads in 672 ms
[2015-09-30T22:28Z] INFO  23:28:40,913 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:41,278 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:41,384 MuTect - [MUTECT] Processed 43001964 reads in 657 ms
[2015-09-30T22:28Z] INFO  23:28:41,427 MuTect - [MUTECT] Processed 34001679 reads in 681 ms
[2015-09-30T22:28Z] INFO  23:28:41,644 MuTect - [MUTECT] Processed 59003259 reads in 740 ms
[2015-09-30T22:28Z] INFO  23:28:41,795 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:42,054 MuTect - [MUTECT] Processed 44002027 reads in 670 ms
[2015-09-30T22:28Z] INFO  23:28:42,091 MuTect - [MUTECT] Processed 35001685 reads in 664 ms
[2015-09-30T22:28Z] INFO  23:28:42,312 MuTect - [MUTECT] Processed 60003283 reads in 668 ms
[2015-09-30T22:28Z] INFO  23:28:42,723 MuTect - [MUTECT] Processed 45002054 reads in 669 ms
[2015-09-30T22:28Z] INFO  23:28:42,782 MuTect - [MUTECT] Processed 36001766 reads in 691 ms
[2015-09-30T22:28Z] INFO  23:28:42,957 MuTect - [MUTECT] Processed 61003396 reads in 645 ms
[2015-09-30T22:28Z] INFO  23:28:43,202 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:43,402 MuTect - [MUTECT] Processed 46002122 reads in 679 ms
[2015-09-30T22:28Z] INFO  23:28:43,477 MuTect - [MUTECT] Processed 37001821 reads in 695 ms
[2015-09-30T22:28Z] INFO  23:28:43,607 MuTect - [MUTECT] Processed 62003481 reads in 650 ms
[2015-09-30T22:28Z] INFO  23:28:43,680 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:44,091 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:44,134 MuTect - [MUTECT] Processed 47002211 reads in 732 ms
[2015-09-30T22:28Z] INFO  23:28:44,167 MuTect - [MUTECT] Processed 38001861 reads in 690 ms
[2015-09-30T22:28Z] INFO  23:28:44,340 MuTect - [MUTECT] Processed 63003485 reads in 733 ms
[2015-09-30T22:28Z] INFO  23:28:44,799 MuTect - [MUTECT] Processed 39001925 reads in 632 ms
[2015-09-30T22:28Z] INFO  23:28:44,839 MuTect - [MUTECT] Processed 48002235 reads in 705 ms
[2015-09-30T22:28Z] INFO  23:28:44,995 ProgressMeter -    10:134563252        1.09e+06   30.0 s       27.0 s     71.4%        42.0 s    12.0 s
[2015-09-30T22:28Z] INFO  23:28:45,068 MuTect - [MUTECT] Processed 64003568 reads in 728 ms
[2015-09-30T22:28Z] INFO  23:28:45,388 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:45,436 MuTect - [MUTECT] Processed 40002042 reads in 637 ms
[2015-09-30T22:28Z] INFO  23:28:45,495 MuTect - [MUTECT] Processed 49002305 reads in 656 ms
[2015-09-30T22:28Z] INFO  23:28:45,671 MuTect - [MUTECT] Processed 65003705 reads in 603 ms
[2015-09-30T22:28Z] INFO  23:28:46,055 MuTect - [MUTECT] Processed 41002193 reads in 619 ms
[2015-09-30T22:28Z] INFO  23:28:46,107 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:46,154 MuTect - [MUTECT] Processed 50002327 reads in 659 ms
[2015-09-30T22:28Z] INFO  23:28:46,269 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:46,269 MuTect - [MUTECT] Processed 66003843 reads in 598 ms
[2015-09-30T22:28Z] INFO  23:28:46,664 MuTect - [MUTECT] Processed 42002335 reads in 609 ms
[2015-09-30T22:28Z] INFO  23:28:46,824 MuTect - [MUTECT] Processed 51002395 reads in 670 ms
[2015-09-30T22:28Z] INFO  23:28:46,872 MuTect - [MUTECT] Processed 67003859 reads in 603 ms
[2015-09-30T22:28Z] INFO  23:28:47,269 MuTect - [MUTECT] Processed 43002340 reads in 604 ms
[2015-09-30T22:28Z] INFO  23:28:47,488 MuTect - [MUTECT] Processed 68003924 reads in 616 ms
[2015-09-30T22:28Z] INFO  23:28:47,542 MuTect - [MUTECT] Processed 52002465 reads in 718 ms
[2015-09-30T22:28Z] INFO  23:28:47,676 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:47,887 MuTect - [MUTECT] Processed 44002479 reads in 619 ms
[2015-09-30T22:28Z] INFO  23:28:48,141 MuTect - [MUTECT] Processed 69003930 reads in 653 ms
[2015-09-30T22:28Z] INFO  23:28:48,176 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:48,274 MuTect - [MUTECT] Processed 53002485 reads in 732 ms
[2015-09-30T22:28Z] INFO  23:28:48,403 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:48,500 MuTect - [MUTECT] Processed 45002505 reads in 613 ms
[2015-09-30T22:28Z] INFO  23:28:48,793 MuTect - [MUTECT] Processed 70003973 reads in 652 ms
[2015-09-30T22:28Z] INFO  23:28:48,966 MuTect - [MUTECT] Processed 54002502 reads in 692 ms
[2015-09-30T22:28Z] INFO  23:28:49,208 MuTect - [MUTECT] Processed 46002627 reads in 708 ms
[2015-09-30T22:28Z] INFO  23:28:49,459 MuTect - [MUTECT] Processed 71004005 reads in 666 ms
[2015-09-30T22:28Z] INFO  23:28:49,606 MuTect - [MUTECT] Processed 55002514 reads in 640 ms
[2015-09-30T22:28Z] INFO  23:28:49,894 MuTect - [MUTECT] Processed 47002700 reads in 686 ms
[2015-09-30T22:28Z] INFO  23:28:49,982 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:50,131 MuTect - [MUTECT] Processed 72004018 reads in 672 ms
[2015-09-30T22:28Z] INFO  23:28:50,239 MuTect - [MUTECT] Processed 56002631 reads in 633 ms
[2015-09-30T22:28Z] INFO  23:28:50,467 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:50,608 MuTect - [MUTECT] Processed 48002773 reads in 714 ms
[2015-09-30T22:28Z] INFO  23:28:50,637 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:50,816 MuTect - [MUTECT] Processed 73004029 reads in 685 ms
[2015-09-30T22:28Z] INFO  23:28:50,875 MuTect - [MUTECT] Processed 57002663 reads in 636 ms
[2015-09-30T22:28Z] INFO  23:28:51,253 MuTect - [MUTECT] Processed 49002871 reads in 645 ms
[2015-09-30T22:28Z] INFO  23:28:51,447 MuTect - [MUTECT] Processed 74004122 reads in 631 ms
[2015-09-30T22:28Z] INFO  23:28:51,553 MuTect - [MUTECT] Processed 58002705 reads in 678 ms
[2015-09-30T22:28Z] INFO  23:28:51,892 MuTect - [MUTECT] Processed 50002884 reads in 639 ms
[2015-09-30T22:28Z] INFO  23:28:52,067 MuTect - [MUTECT] Processed 75004191 reads in 620 ms
[2015-09-30T22:28Z] INFO  23:28:52,224 MuTect - [MUTECT] Processed 59002757 reads in 671 ms
[2015-09-30T22:28Z] INFO  23:28:52,256 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:52,555 MuTect - [MUTECT] Processed 51002919 reads in 663 ms
[2015-09-30T22:28Z] INFO  23:28:52,689 MuTect - [MUTECT] Processed 76004279 reads in 622 ms
[2015-09-30T22:28Z] INFO  23:28:52,814 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:52,852 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:52,903 MuTect - [MUTECT] Processed 60002799 reads in 679 ms
[2015-09-30T22:28Z] INFO  23:28:53,227 MuTect - [MUTECT] Processed 52002974 reads in 672 ms
[2015-09-30T22:28Z] INFO  23:28:53,296 MuTect - [MUTECT] Processed 77004310 reads in 607 ms
[2015-09-30T22:28Z] INFO  23:28:53,603 MuTect - [MUTECT] Processed 61002832 reads in 700 ms
[2015-09-30T22:28Z] INFO  23:28:53,868 MuTect - [MUTECT] Processed 53003038 reads in 641 ms
[2015-09-30T22:28Z] INFO  23:28:53,961 MuTect - [MUTECT] Processed 78004331 reads in 665 ms
[2015-09-30T22:28Z] INFO  23:28:54,280 MuTect - [MUTECT] Processed 62002934 reads in 677 ms
[2015-09-30T22:28Z] INFO  23:28:54,498 MuTect - [MUTECT] Processed 54003067 reads in 630 ms
[2015-09-30T22:28Z] INFO  23:28:54,604 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:54,623 MuTect - [MUTECT] Processed 79004346 reads in 662 ms
[2015-09-30T22:28Z] INFO  23:28:54,962 MuTect - [MUTECT] Processed 63003022 reads in 682 ms
[2015-09-30T22:28Z] INFO  23:28:54,976 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:55,105 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:55,154 MuTect - [MUTECT] Processed 55003125 reads in 656 ms
[2015-09-30T22:28Z] INFO  23:28:55,280 MuTect - [MUTECT] Processed 80004346 reads in 657 ms
[2015-09-30T22:28Z] INFO  23:28:55,646 MuTect - [MUTECT] Processed 64003130 reads in 684 ms
[2015-09-30T22:28Z] INFO  23:28:55,816 MuTect - [MUTECT] Processed 56003224 reads in 662 ms
[2015-09-30T22:28Z] INFO  23:28:55,925 MuTect - [MUTECT] Processed 81004479 reads in 645 ms
[2015-09-30T22:28Z] INFO  23:28:56,329 MuTect - [MUTECT] Processed 65003170 reads in 683 ms
[2015-09-30T22:28Z] INFO  23:28:56,471 MuTect - [MUTECT] Processed 57003258 reads in 655 ms
[2015-09-30T22:28Z] INFO  23:28:56,575 MuTect - [MUTECT] Processed 82004580 reads in 650 ms
[2015-09-30T22:28Z] INFO  23:28:57,013 MuTect - [MUTECT] Processed 66003186 reads in 684 ms
[2015-09-30T22:28Z] INFO  23:28:57,014 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:57,143 MuTect - [MUTECT] Processed 58003352 reads in 672 ms
[2015-09-30T22:28Z] INFO  23:28:57,185 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:57,203 MuTect - [MUTECT] Processed 83004645 reads in 628 ms
[2015-09-30T22:28Z] INFO  23:28:57,294 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:57,649 MuTect - [MUTECT] Processed 67003309 reads in 636 ms
[2015-09-30T22:28Z] INFO  23:28:57,849 MuTect - [MUTECT] Processed 84004743 reads in 646 ms
[2015-09-30T22:28Z] INFO  23:28:57,980 MuTect - [MUTECT] Processed 59003393 reads in 837 ms
[2015-09-30T22:28Z] INFO  23:28:58,249 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:28Z] INFO  23:28:58,253 ProgressMeter -            done        1.66e+06   43.0 s       26.0 s    100.0%        43.0 s     0.0 s
[2015-09-30T22:28Z] INFO  23:28:58,253 ProgressMeter - Total runtime 43.26 secs, 0.72 min, 0.01 hours
[2015-09-30T22:28Z] INFO  23:28:58,309 MuTect - [MUTECT] Processed 68003385 reads in 660 ms
[2015-09-30T22:28Z] INFO  23:28:58,317 MicroScheduler - 48313 reads were filtered out during the traversal out of approximately 714188 total reads (6.76%)
[2015-09-30T22:28Z] INFO  23:28:58,317 MicroScheduler -   -> 36860 reads (5.16% of total) failing DuplicateReadFilter
[2015-09-30T22:28Z] INFO  23:28:58,317 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:28Z] INFO  23:28:58,317 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:28Z] INFO  23:28:58,317 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:28Z] INFO  23:28:58,318 MicroScheduler -   -> 11453 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:28Z] INFO  23:28:58,492 MuTect - [MUTECT] Processed 85004745 reads in 643 ms
[2015-09-30T22:28Z] INFO  23:28:58,918 ProgressMeter -     10:79795236        2.57e+06   60.0 s       23.0 s     66.3%        90.0 s    30.0 s
[2015-09-30T22:28Z] INFO  23:28:58,971 MuTect - [MUTECT] Processed 69003449 reads in 662 ms
[2015-09-30T22:28Z] INFO  23:28:59,130 MuTect - [MUTECT] Processed 86004765 reads in 638 ms
[2015-09-30T22:28Z] INFO  23:28:59,211 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:59,282 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:28Z] bgzip syn3-10_124438084_135534747-raw-mutect.vcf
[2015-09-30T22:28Z] tabix index syn3-10_124438084_135534747-raw-mutect.vcf.gz
[2015-09-30T22:28Z] INFO  23:28:59,461 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:28Z] INFO  23:28:59,618 MuTect - [MUTECT] Processed 70003479 reads in 647 ms
[2015-09-30T22:28Z] INFO  23:28:59,821 MuTect - [MUTECT] Processed 87004841 reads in 691 ms
[2015-09-30T22:29Z] INFO  23:29:00,259 MuTect - [MUTECT] Processed 71003511 reads in 641 ms
[2015-09-30T22:29Z] INFO  23:29:00,499 MuTect - [MUTECT] Processed 88004929 reads in 677 ms
[2015-09-30T22:29Z] INFO  23:29:00,861 MuTect - [MUTECT] Processed 72003548 reads in 602 ms
[2015-09-30T22:29Z] INFO  23:29:01,156 MuTect - [MUTECT] Processed 89005011 reads in 658 ms
[2015-09-30T22:29Z] INFO  23:29:01,460 MuTect - [MUTECT] Processed 73003597 reads in 599 ms
[2015-09-30T22:29Z] INFO  23:29:01,469 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:01,673 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:01,834 MuTect - [MUTECT] Processed 90005062 reads in 678 ms
[2015-09-30T22:29Z] MuTect: MuTect
[2015-09-30T22:29Z] INFO  23:29:02,081 MuTect - [MUTECT] Processed 74003686 reads in 621 ms
[2015-09-30T22:29Z] INFO  23:29:02,583 MuTect - [MUTECT] Processed 91005085 reads in 749 ms
[2015-09-30T22:29Z] INFO  23:29:02,703 MuTect - [MUTECT] Processed 75003789 reads in 622 ms
[2015-09-30T22:29Z] INFO  23:29:03,294 MuTect - [MUTECT] Processed 92005129 reads in 711 ms
[2015-09-30T22:29Z] INFO  23:29:03,316 MuTect - [MUTECT] Processed 76003807 reads in 613 ms
[2015-09-30T22:29Z] INFO  23:29:03,633 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:03,949 MuTect - [MUTECT] Processed 77003875 reads in 633 ms
[2015-09-30T22:29Z] INFO  23:29:03,963 MuTect - [MUTECT] Processed 93005149 reads in 669 ms
[2015-09-30T22:29Z] INFO  23:29:03,996 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/11/syn3-11_0_31082819-raw-mutect-regions.bed to be BED
[2015-09-30T22:29Z] INFO  23:29:04,052 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:29Z] INFO  23:29:04,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:29Z] INFO  23:29:04,052 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:29Z] INFO  23:29:04,052 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:29Z] INFO  23:29:04,056 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/11/syn3-11_0_31082819-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/11/tx/tmprJRx28/syn3-11_0_31082819-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:29Z] INFO  23:29:04,056 HelpFormatter - Date/Time: 2015/09/30 23:29:04
[2015-09-30T22:29Z] INFO  23:29:04,056 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:29Z] INFO  23:29:04,056 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:29Z] INFO  23:29:04,084 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:29Z] INFO  23:29:04,088 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:29Z] INFO  23:29:04,143 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:29Z] INFO  23:29:04,191 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:29Z] INFO  23:29:04,199 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:29Z] INFO  23:29:04,278 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2015-09-30T22:29Z] INFO  23:29:04,302 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:29Z] INFO  23:29:04,481 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:29Z] INFO  23:29:04,585 MuTect - [MUTECT] Processed 78003994 reads in 635 ms
[2015-09-30T22:29Z] INFO  23:29:04,600 IntervalUtils - Processing 1954600 bp from intervals
[2015-09-30T22:29Z] INFO  23:29:04,604 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:29Z] INFO  23:29:04,604 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:29Z] INFO  23:29:04,648 MuTect - [MUTECT] Processed 94005172 reads in 685 ms
[2015-09-30T22:29Z] INFO  23:29:04,660 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:04,773 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:29Z] INFO  23:29:04,940 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:29Z] INFO  23:29:04,941 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:29Z] INFO  23:29:04,941 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:29Z] INFO  23:29:04,942 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:29Z] INFO  23:29:05,202 MuTect - [MUTECT] Processed 79004025 reads in 618 ms
[2015-09-30T22:29Z] INFO  23:29:05,324 MuTect - [MUTECT] Processed 95005184 reads in 676 ms
[2015-09-30T22:29Z] INFO  23:29:05,835 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:05,866 MuTect - [MUTECT] Processed 80004048 reads in 664 ms
[2015-09-30T22:29Z] INFO  23:29:06,011 MuTect - [MUTECT] Processed 96005184 reads in 687 ms
[2015-09-30T22:29Z] INFO  23:29:06,531 MuTect - [MUTECT] Processed 81004140 reads in 665 ms
[2015-09-30T22:29Z] INFO  23:29:06,738 MuTect - [MUTECT] Processed 97005222 reads in 727 ms
[2015-09-30T22:29Z] INFO  23:29:07,092 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:07,178 MuTect - [MUTECT] Processed 82004205 reads in 647 ms
[2015-09-30T22:29Z] INFO  23:29:07,416 MuTect - [MUTECT] Processed 98005269 reads in 678 ms
[2015-09-30T22:29Z] INFO  23:29:07,492 MuTect - [MUTECT] Processed 1000021 reads in 2504 ms
[2015-09-30T22:29Z] INFO  23:29:07,810 MuTect - [MUTECT] Processed 83004255 reads in 632 ms
[2015-09-30T22:29Z] INFO  23:29:08,060 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:08,100 MuTect - [MUTECT] Processed 99005277 reads in 684 ms
[2015-09-30T22:29Z] INFO  23:29:08,225 MuTect - [MUTECT] Processed 2000044 reads in 733 ms
[2015-09-30T22:29Z] INFO  23:29:08,404 MuTect - [MUTECT] Processed 84004320 reads in 594 ms
[2015-09-30T22:29Z] INFO  23:29:08,647 ProgressMeter -    10:103903796        2.71e+06   60.0 s       22.0 s     46.4%         2.2 m    69.0 s
[2015-09-30T22:29Z] INFO  23:29:08,800 MuTect - [MUTECT] Processed 100005281 reads in 700 ms
[2015-09-30T22:29Z] INFO  23:29:09,005 MuTect - [MUTECT] Processed 85004349 reads in 601 ms
[2015-09-30T22:29Z] INFO  23:29:09,063 MuTect - [MUTECT] Processed 3000110 reads in 838 ms
[2015-09-30T22:29Z] INFO  23:29:09,401 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:09,470 MuTect - [MUTECT] Processed 101005288 reads in 670 ms
[2015-09-30T22:29Z] INFO  23:29:09,553 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:09,601 MuTect - [MUTECT] Processed 86004381 reads in 596 ms
[2015-09-30T22:29Z] INFO  23:29:09,824 MuTect - [MUTECT] Processed 4000167 reads in 761 ms
[2015-09-30T22:29Z] INFO  23:29:10,107 MuTect - [MUTECT] Processed 102005294 reads in 637 ms
[2015-09-30T22:29Z] INFO  23:29:10,139 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:10,216 MuTect - [MUTECT] Processed 87004419 reads in 615 ms
[2015-09-30T22:29Z] INFO  23:29:10,577 MuTect - [MUTECT] Processed 5000268 reads in 753 ms
[2015-09-30T22:29Z] INFO  23:29:10,779 MuTect - [MUTECT] Processed 103005390 reads in 672 ms
[2015-09-30T22:29Z] INFO  23:29:10,819 MuTect - [MUTECT] Processed 88004473 reads in 603 ms
[2015-09-30T22:29Z] INFO  23:29:11,422 MuTect - [MUTECT] Processed 89004558 reads in 603 ms
[2015-09-30T22:29Z] INFO  23:29:11,475 MuTect - [MUTECT] Processed 104005419 reads in 695 ms
[2015-09-30T22:29Z] INFO  23:29:11,584 MuTect - [MUTECT] Processed 6000342 reads in 1006 ms
[2015-09-30T22:29Z] INFO  23:29:12,003 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:12,013 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:12,088 MuTect - [MUTECT] Processed 90004632 reads in 666 ms
[2015-09-30T22:29Z] INFO  23:29:12,161 MuTect - [MUTECT] Processed 105005506 reads in 687 ms
[2015-09-30T22:29Z] INFO  23:29:12,273 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:12,290 MuTect - [MUTECT] Processed 7000459 reads in 707 ms
[2015-09-30T22:29Z] INFO  23:29:12,725 MuTect - [MUTECT] Processed 91004737 reads in 637 ms
[2015-09-30T22:29Z] INFO  23:29:12,864 MuTect - [MUTECT] Processed 106005538 reads in 703 ms
[2015-09-30T22:29Z] INFO  23:29:13,008 MuTect - [MUTECT] Processed 8000573 reads in 718 ms
[2015-09-30T22:29Z] INFO  23:29:13,398 MuTect - [MUTECT] Processed 92004862 reads in 673 ms
[2015-09-30T22:29Z] INFO  23:29:13,516 MuTect - [MUTECT] Processed 107005551 reads in 652 ms
[2015-09-30T22:29Z] INFO  23:29:13,787 MuTect - [MUTECT] Processed 9000616 reads in 779 ms
[2015-09-30T22:29Z] INFO  23:29:14,132 MuTect - [MUTECT] Processed 93004911 reads in 734 ms
[2015-09-30T22:29Z] INFO  23:29:14,174 MuTect - [MUTECT] Processed 108005556 reads in 658 ms
[2015-09-30T22:29Z] INFO  23:29:14,177 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:14,244 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:14,520 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:14,568 MuTect - [MUTECT] Processed 10000704 reads in 781 ms
[2015-09-30T22:29Z] INFO  23:29:14,812 MuTect - [MUTECT] Processed 109005577 reads in 638 ms
[2015-09-30T22:29Z] INFO  23:29:14,824 MuTect - [MUTECT] Processed 94004976 reads in 692 ms
[2015-09-30T22:29Z] INFO  23:29:15,433 MuTect - [MUTECT] Processed 110005578 reads in 621 ms
[2015-09-30T22:29Z] INFO  23:29:15,468 MuTect - [MUTECT] Processed 95005031 reads in 644 ms
[2015-09-30T22:29Z] INFO  23:29:15,787 MuTect - [MUTECT] Processed 11000870 reads in 1219 ms
[2015-09-30T22:29Z] INFO  23:29:16,117 MuTect - [MUTECT] Processed 96005120 reads in 649 ms
[2015-09-30T22:29Z] INFO  23:29:16,199 MuTect - [MUTECT] Processed 111005678 reads in 766 ms
[2015-09-30T22:29Z] INFO  23:29:16,426 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:16,490 MuTect - [MUTECT] Processed 12000986 reads in 703 ms
[2015-09-30T22:29Z] INFO  23:29:16,728 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:16,791 MuTect - [MUTECT] Processed 97005179 reads in 674 ms
[2015-09-30T22:29Z] INFO  23:29:16,850 MuTect - [MUTECT] Processed 112005703 reads in 651 ms
[2015-09-30T22:29Z] INFO  23:29:16,957 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:17,135 MuTect - [MUTECT] Processed 13001108 reads in 645 ms
[2015-09-30T22:29Z] INFO  23:29:17,437 MuTect - [MUTECT] Processed 98005211 reads in 646 ms
[2015-09-30T22:29Z] INFO  23:29:17,499 MuTect - [MUTECT] Processed 113005738 reads in 649 ms
[2015-09-30T22:29Z] INFO  23:29:17,859 MuTect - [MUTECT] Processed 14001248 reads in 724 ms
[2015-09-30T22:29Z] INFO  23:29:18,088 MuTect - [MUTECT] Processed 99005271 reads in 651 ms
[2015-09-30T22:29Z] INFO  23:29:18,127 MuTect - [MUTECT] Processed 114005751 reads in 628 ms
[2015-09-30T22:29Z] INFO  23:29:18,488 MuTect - [MUTECT] Processed 15001327 reads in 629 ms
[2015-09-30T22:29Z] INFO  23:29:18,760 MuTect - [MUTECT] Processed 100005344 reads in 672 ms
[2015-09-30T22:29Z] INFO  23:29:18,810 MuTect - [MUTECT] Processed 115005768 reads in 683 ms
[2015-09-30T22:29Z] INFO  23:29:19,293 MuTect - [MUTECT] Processed 16001354 reads in 805 ms
[2015-09-30T22:29Z] INFO  23:29:19,295 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:19,415 MuTect - [MUTECT] Processed 101005423 reads in 655 ms
[2015-09-30T22:29Z] INFO  23:29:19,418 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:19,504 MuTect - [MUTECT] Processed 116005777 reads in 694 ms
[2015-09-30T22:29Z] INFO  23:29:19,591 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:20,013 MuTect - [MUTECT] Processed 17001433 reads in 720 ms
[2015-09-30T22:29Z] INFO  23:29:20,077 MuTect - [MUTECT] Processed 102005464 reads in 662 ms
[2015-09-30T22:29Z] INFO  23:29:20,240 MuTect - [MUTECT] Processed 117005840 reads in 736 ms
[2015-09-30T22:29Z] INFO  23:29:20,703 MuTect - [MUTECT] Processed 18001493 reads in 690 ms
[2015-09-30T22:29Z] INFO  23:29:20,725 MuTect - [MUTECT] Processed 103005567 reads in 648 ms
[2015-09-30T22:29Z] INFO  23:29:20,951 MuTect - [MUTECT] Processed 118005871 reads in 711 ms
[2015-09-30T22:29Z] INFO  23:29:21,356 MuTect - [MUTECT] Processed 19001513 reads in 653 ms
[2015-09-30T22:29Z] INFO  23:29:21,363 MuTect - [MUTECT] Processed 104005603 reads in 638 ms
[2015-09-30T22:29Z] INFO  23:29:21,497 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:21,537 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:21,618 MuTect - [MUTECT] Processed 119005936 reads in 667 ms
[2015-09-30T22:29Z] INFO  23:29:22,025 MuTect - [MUTECT] Processed 20001610 reads in 669 ms
[2015-09-30T22:29Z] INFO  23:29:22,040 MuTect - [MUTECT] Processed 105005629 reads in 677 ms
[2015-09-30T22:29Z] INFO  23:29:22,041 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:22,273 MuTect - [MUTECT] Processed 120005947 reads in 655 ms
[2015-09-30T22:29Z] INFO  23:29:22,700 MuTect - [MUTECT] Processed 106005724 reads in 660 ms
[2015-09-30T22:29Z] INFO  23:29:22,708 MuTect - [MUTECT] Processed 21001623 reads in 683 ms
[2015-09-30T22:29Z] INFO  23:29:22,913 MuTect - [MUTECT] Processed 121005959 reads in 640 ms
[2015-09-30T22:29Z] INFO  23:29:23,376 MuTect - [MUTECT] Processed 22001649 reads in 668 ms
[2015-09-30T22:29Z] INFO  23:29:23,403 MuTect - [MUTECT] Processed 107005818 reads in 703 ms
[2015-09-30T22:29Z] INFO  23:29:23,563 MuTect - [MUTECT] Processed 122006042 reads in 650 ms
[2015-09-30T22:29Z] INFO  23:29:23,726 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:24,034 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:24,074 MuTect - [MUTECT] Processed 23001689 reads in 698 ms
[2015-09-30T22:29Z] INFO  23:29:24,123 MuTect - [MUTECT] Processed 108005824 reads in 720 ms
[2015-09-30T22:29Z] INFO  23:29:24,202 MuTect - [MUTECT] Processed 123006107 reads in 639 ms
[2015-09-30T22:29Z] INFO  23:29:24,411 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:24,771 MuTect - [MUTECT] Processed 24001710 reads in 697 ms
[2015-09-30T22:29Z] INFO  23:29:24,796 MuTect - [MUTECT] Processed 109005926 reads in 673 ms
[2015-09-30T22:29Z] INFO  23:29:24,891 MuTect - [MUTECT] Processed 124006110 reads in 689 ms
[2015-09-30T22:29Z] INFO  23:29:25,448 MuTect - [MUTECT] Processed 25001839 reads in 677 ms
[2015-09-30T22:29Z] INFO  23:29:25,536 MuTect - [MUTECT] Processed 110005939 reads in 740 ms
[2015-09-30T22:29Z] INFO  23:29:25,631 MuTect - [MUTECT] Processed 125006113 reads in 740 ms
[2015-09-30T22:29Z] INFO  23:29:25,898 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:26,094 MuTect - [MUTECT] Processed 26001866 reads in 646 ms
[2015-09-30T22:29Z] INFO  23:29:26,208 MuTect - [MUTECT] Processed 111005998 reads in 672 ms
[2015-09-30T22:29Z] INFO  23:29:26,281 MuTect - [MUTECT] Processed 126006156 reads in 650 ms
[2015-09-30T22:29Z] INFO  23:29:26,366 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:26,885 MuTect - [MUTECT] Processed 112006004 reads in 677 ms
[2015-09-30T22:29Z] INFO  23:29:26,958 MuTect - [MUTECT] Processed 127006159 reads in 677 ms
[2015-09-30T22:29Z] INFO  23:29:26,990 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:27,266 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:29Z] INFO  23:29:27,270 ProgressMeter -            done        3.82e+06   88.0 s       23.0 s    100.0%        88.0 s     0.0 s
[2015-09-30T22:29Z] INFO  23:29:27,270 ProgressMeter - Total runtime 88.36 secs, 1.47 min, 0.02 hours
[2015-09-30T22:29Z] INFO  23:29:27,334 MicroScheduler - 96325 reads were filtered out during the traversal out of approximately 1522862 total reads (6.33%)
[2015-09-30T22:29Z] INFO  23:29:27,334 MicroScheduler -   -> 72157 reads (4.74% of total) failing DuplicateReadFilter
[2015-09-30T22:29Z] INFO  23:29:27,335 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:29Z] INFO  23:29:27,335 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:29Z] INFO  23:29:27,335 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:29Z] INFO  23:29:27,335 MicroScheduler -   -> 24168 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:29Z] INFO  23:29:27,546 MuTect - [MUTECT] Processed 113006033 reads in 661 ms
[2015-09-30T22:29Z] INFO  23:29:28,241 MuTect - [MUTECT] Processed 114006038 reads in 695 ms
[2015-09-30T22:29Z] INFO  23:29:28,450 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:29Z] bgzip syn3-10_62267938_93388847-raw-mutect.vcf
[2015-09-30T22:29Z] tabix index syn3-10_62267938_93388847-raw-mutect.vcf.gz
[2015-09-30T22:29Z] INFO  23:29:28,895 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:28,915 MuTect - [MUTECT] Processed 115006105 reads in 674 ms
[2015-09-30T22:29Z] INFO  23:29:29,269 MuTect - [MUTECT] Processed 27002538 reads in 3175 ms
[2015-09-30T22:29Z] INFO  23:29:29,581 MuTect - [MUTECT] Processed 116006190 reads in 666 ms
[2015-09-30T22:29Z] INFO  23:29:30,256 MuTect - [MUTECT] Processed 117006226 reads in 675 ms
[2015-09-30T22:29Z] MuTect: MuTect
[2015-09-30T22:29Z] INFO  23:29:30,923 MuTect - [MUTECT] Processed 118006239 reads in 667 ms
[2015-09-30T22:29Z] INFO  23:29:31,410 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:31,600 MuTect - [MUTECT] Processed 119006324 reads in 677 ms
[2015-09-30T22:29Z] INFO  23:29:32,285 MuTect - [MUTECT] Processed 120006372 reads in 685 ms
[2015-09-30T22:29Z] INFO  23:29:32,958 MuTect - [MUTECT] Processed 121006413 reads in 673 ms
[2015-09-30T22:29Z] INFO  23:29:33,033 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/11/syn3-11_31085657_62105890-raw-mutect-regions.bed to be BED
[2015-09-30T22:29Z] INFO  23:29:33,088 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:29Z] INFO  23:29:33,088 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:29Z] INFO  23:29:33,088 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:29Z] INFO  23:29:33,088 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:29Z] INFO  23:29:33,092 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/11/syn3-11_31085657_62105890-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/11/tx/tmpd9bN9E/syn3-11_31085657_62105890-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:29Z] INFO  23:29:33,092 HelpFormatter - Date/Time: 2015/09/30 23:29:33
[2015-09-30T22:29Z] INFO  23:29:33,092 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:29Z] INFO  23:29:33,092 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:29Z] INFO  23:29:33,120 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:29Z] INFO  23:29:33,124 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:29Z] INFO  23:29:33,173 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:29Z] INFO  23:29:33,221 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:29Z] INFO  23:29:33,228 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:29Z] INFO  23:29:33,269 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:29Z] INFO  23:29:33,280 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:29Z] INFO  23:29:33,454 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:29Z] INFO  23:29:33,561 IntervalUtils - Processing 1559957 bp from intervals
[2015-09-30T22:29Z] INFO  23:29:33,565 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:29Z] INFO  23:29:33,565 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:29Z] INFO  23:29:33,639 MuTect - [MUTECT] Processed 122006432 reads in 681 ms
[2015-09-30T22:29Z] INFO  23:29:33,740 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:29Z] INFO  23:29:33,755 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:33,919 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:29Z] INFO  23:29:33,920 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:29Z] INFO  23:29:33,920 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:29Z] INFO  23:29:33,921 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:29Z] INFO  23:29:34,345 MuTect - [MUTECT] Processed 123006457 reads in 706 ms
[2015-09-30T22:29Z] INFO  23:29:34,943 ProgressMeter -      11:1017809        6.57e+05   30.0 s       45.0 s     10.9%         4.6 m     4.1 m
[2015-09-30T22:29Z] INFO  23:29:35,031 MuTect - [MUTECT] Processed 124006514 reads in 686 ms
[2015-09-30T22:29Z] INFO  23:29:35,740 MuTect - [MUTECT] Processed 125006544 reads in 709 ms
[2015-09-30T22:29Z] INFO  23:29:36,138 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:36,174 MuTect - [MUTECT] Processed 28002829 reads in 6904 ms
[2015-09-30T22:29Z] INFO  23:29:36,398 MuTect - [MUTECT] Processed 1000012 reads in 2416 ms
[2015-09-30T22:29Z] INFO  23:29:36,439 MuTect - [MUTECT] Processed 126006616 reads in 699 ms
[2015-09-30T22:29Z] INFO  23:29:36,566 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:37,115 MuTect - [MUTECT] Processed 2000029 reads in 717 ms
[2015-09-30T22:29Z] INFO  23:29:37,119 MuTect - [MUTECT] Processed 127006670 reads in 680 ms
[2015-09-30T22:29Z] INFO  23:29:37,444 MuTect - [MUTECT] Processed 29002923 reads in 1271 ms
[2015-09-30T22:29Z] INFO  23:29:37,795 MuTect - [MUTECT] Processed 3000100 reads in 680 ms
[2015-09-30T22:29Z] INFO  23:29:37,846 MuTect - [MUTECT] Processed 128006710 reads in 727 ms
[2015-09-30T22:29Z] INFO  23:29:38,062 MuTect - [MUTECT] Processed 30003017 reads in 618 ms
[2015-09-30T22:29Z] INFO  23:29:38,104 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:38,523 MuTect - [MUTECT] Processed 4000110 reads in 728 ms
[2015-09-30T22:29Z] INFO  23:29:38,524 MuTect - [MUTECT] Processed 129006768 reads in 678 ms
[2015-09-30T22:29Z] INFO  23:29:38,564 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:38,648 ProgressMeter -    10:114181775        4.33e+06   90.0 s       20.0 s     70.1%         2.1 m    38.0 s
[2015-09-30T22:29Z] INFO  23:29:38,762 MuTect - [MUTECT] Processed 31003115 reads in 700 ms
[2015-09-30T22:29Z] INFO  23:29:38,891 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:39,203 MuTect - [MUTECT] Processed 130006810 reads in 679 ms
[2015-09-30T22:29Z] INFO  23:29:39,314 MuTect - [MUTECT] Processed 5000112 reads in 791 ms
[2015-09-30T22:29Z] INFO  23:29:39,700 MuTect - [MUTECT] Processed 32003309 reads in 938 ms
[2015-09-30T22:29Z] INFO  23:29:39,889 MuTect - [MUTECT] Processed 131006856 reads in 686 ms
[2015-09-30T22:29Z] INFO  23:29:40,026 MuTect - [MUTECT] Processed 6000114 reads in 712 ms
[2015-09-30T22:29Z] INFO  23:29:40,569 MuTect - [MUTECT] Processed 132006885 reads in 680 ms
[2015-09-30T22:29Z] INFO  23:29:40,665 MuTect - [MUTECT] Processed 7000142 reads in 638 ms
[2015-09-30T22:29Z] INFO  23:29:40,721 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:40,900 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:41,207 MuTect - [MUTECT] Processed 133006976 reads in 638 ms
[2015-09-30T22:29Z] INFO  23:29:41,314 MuTect - [MUTECT] Processed 8000191 reads in 649 ms
[2015-09-30T22:29Z] INFO  23:29:41,846 MuTect - [MUTECT] Processed 134007042 reads in 639 ms
[2015-09-30T22:29Z] INFO  23:29:41,982 MuTect - [MUTECT] Processed 9000279 reads in 669 ms
[2015-09-30T22:29Z] INFO  23:29:42,539 MuTect - [MUTECT] Processed 135007054 reads in 692 ms
[2015-09-30T22:29Z] INFO  23:29:42,656 MuTect - [MUTECT] Processed 10000332 reads in 674 ms
[2015-09-30T22:29Z] INFO  23:29:43,137 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:43,209 MuTect - [MUTECT] Processed 136007070 reads in 671 ms
[2015-09-30T22:29Z] INFO  23:29:43,216 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:43,360 MuTect - [MUTECT] Processed 11000445 reads in 703 ms
[2015-09-30T22:29Z] INFO  23:29:43,575 MuTect - [MUTECT] Processed 33003378 reads in 3875 ms
[2015-09-30T22:29Z] INFO  23:29:43,742 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:43,924 MuTect - [MUTECT] Processed 137007113 reads in 715 ms
[2015-09-30T22:29Z] INFO  23:29:44,014 MuTect - [MUTECT] Processed 12000552 reads in 655 ms
[2015-09-30T22:29Z] INFO  23:29:44,241 MuTect - [MUTECT] Processed 34003378 reads in 666 ms
[2015-09-30T22:29Z] INFO  23:29:44,586 MuTect - [MUTECT] Processed 138007144 reads in 662 ms
[2015-09-30T22:29Z] INFO  23:29:44,652 MuTect - [MUTECT] Processed 13000566 reads in 638 ms
[2015-09-30T22:29Z] INFO  23:29:44,918 MuTect - [MUTECT] Processed 35003414 reads in 677 ms
[2015-09-30T22:29Z] INFO  23:29:45,220 MuTect - [MUTECT] Processed 139007189 reads in 634 ms
[2015-09-30T22:29Z] INFO  23:29:45,297 MuTect - [MUTECT] Processed 14000649 reads in 645 ms
[2015-09-30T22:29Z] INFO  23:29:45,529 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:45,697 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:45,850 MuTect - [MUTECT] Processed 140007269 reads in 630 ms
[2015-09-30T22:29Z] INFO  23:29:45,939 MuTect - [MUTECT] Processed 15000650 reads in 642 ms
[2015-09-30T22:29Z] INFO  23:29:46,488 MuTect - [MUTECT] Processed 141007324 reads in 638 ms
[2015-09-30T22:29Z] INFO  23:29:46,589 MuTect - [MUTECT] Processed 16000737 reads in 650 ms
[2015-09-30T22:29Z] INFO  23:29:47,134 MuTect - [MUTECT] Processed 142007376 reads in 645 ms
[2015-09-30T22:29Z] INFO  23:29:47,228 MuTect - [MUTECT] Processed 17000862 reads in 639 ms
[2015-09-30T22:29Z] INFO  23:29:47,630 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:47,797 MuTect - [MUTECT] Processed 143007445 reads in 664 ms
[2015-09-30T22:29Z] INFO  23:29:47,894 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:47,909 MuTect - [MUTECT] Processed 18000898 reads in 681 ms
[2015-09-30T22:29Z] INFO  23:29:48,454 MuTect - [MUTECT] Processed 144007446 reads in 657 ms
[2015-09-30T22:29Z] INFO  23:29:48,628 MuTect - [MUTECT] Processed 19000957 reads in 719 ms
[2015-09-30T22:29Z] INFO  23:29:49,172 MuTect - [MUTECT] Processed 145007447 reads in 718 ms
[2015-09-30T22:29Z] INFO  23:29:49,340 MuTect - [MUTECT] Processed 20000969 reads in 712 ms
[2015-09-30T22:29Z] INFO  23:29:49,884 MuTect - [MUTECT] Processed 146007521 reads in 712 ms
[2015-09-30T22:29Z] INFO  23:29:49,991 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:49,993 MuTect - [MUTECT] Processed 21001046 reads in 653 ms
[2015-09-30T22:29Z] INFO  23:29:50,353 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:50,562 MuTect - [MUTECT] Processed 147007535 reads in 678 ms
[2015-09-30T22:29Z] INFO  23:29:50,635 MuTect - [MUTECT] Processed 22001089 reads in 642 ms
[2015-09-30T22:29Z] INFO  23:29:51,199 MuTect - [MUTECT] Processed 148007607 reads in 637 ms
[2015-09-30T22:29Z] INFO  23:29:51,269 MuTect - [MUTECT] Processed 23001118 reads in 634 ms
[2015-09-30T22:29Z] INFO  23:29:51,816 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:51,839 MuTect - [MUTECT] Processed 36003458 reads in 6921 ms
[2015-09-30T22:29Z] INFO  23:29:51,855 MuTect - [MUTECT] Processed 149007651 reads in 656 ms
[2015-09-30T22:29Z] INFO  23:29:51,958 MuTect - [MUTECT] Processed 24001199 reads in 689 ms
[2015-09-30T22:29Z] INFO  23:29:52,290 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:52,480 MuTect - [MUTECT] Processed 150007763 reads in 625 ms
[2015-09-30T22:29Z] INFO  23:29:52,567 MuTect - [MUTECT] Processed 37003480 reads in 728 ms
[2015-09-30T22:29Z] INFO  23:29:52,599 MuTect - [MUTECT] Processed 25001261 reads in 641 ms
[2015-09-30T22:29Z] INFO  23:29:52,660 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:53,121 MuTect - [MUTECT] Processed 151007805 reads in 641 ms
[2015-09-30T22:29Z] INFO  23:29:53,248 MuTect - [MUTECT] Processed 38003665 reads in 681 ms
[2015-09-30T22:29Z] INFO  23:29:53,285 MuTect - [MUTECT] Processed 26001265 reads in 686 ms
[2015-09-30T22:29Z] INFO  23:29:53,771 MuTect - [MUTECT] Processed 152007862 reads in 650 ms
[2015-09-30T22:29Z] INFO  23:29:53,922 MuTect - [MUTECT] Processed 27001285 reads in 637 ms
[2015-09-30T22:29Z] INFO  23:29:54,056 MuTect - [MUTECT] Processed 39003767 reads in 808 ms
[2015-09-30T22:29Z] INFO  23:29:54,098 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:54,434 MuTect - [MUTECT] Processed 153007938 reads in 663 ms
[2015-09-30T22:29Z] INFO  23:29:54,546 MuTect - [MUTECT] Processed 28001348 reads in 624 ms
[2015-09-30T22:29Z] INFO  23:29:54,775 MuTect - [MUTECT] Processed 40003770 reads in 719 ms
[2015-09-30T22:29Z] INFO  23:29:54,900 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:55,021 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:55,103 MuTect - [MUTECT] Processed 154008017 reads in 669 ms
[2015-09-30T22:29Z] INFO  23:29:55,201 MuTect - [MUTECT] Processed 29001373 reads in 655 ms
[2015-09-30T22:29Z] INFO  23:29:55,474 MuTect - [MUTECT] Processed 41003777 reads in 699 ms
[2015-09-30T22:29Z] INFO  23:29:55,721 MuTect - [MUTECT] Processed 155008039 reads in 618 ms
[2015-09-30T22:29Z] INFO  23:29:55,851 MuTect - [MUTECT] Processed 30001443 reads in 650 ms
[2015-09-30T22:29Z] INFO  23:29:56,140 MuTect - [MUTECT] Processed 42003912 reads in 666 ms
[2015-09-30T22:29Z] INFO  23:29:56,249 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:56,361 MuTect - [MUTECT] Processed 156008076 reads in 640 ms
[2015-09-30T22:29Z] INFO  23:29:56,526 MuTect - [MUTECT] Processed 31001483 reads in 675 ms
[2015-09-30T22:29Z] INFO  23:29:56,831 MuTect - [MUTECT] Processed 43003976 reads in 691 ms
[2015-09-30T22:29Z] INFO  23:29:56,977 MuTect - [MUTECT] Processed 157008165 reads in 616 ms
[2015-09-30T22:29Z] INFO  23:29:57,184 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:57,224 MuTect - [MUTECT] Processed 32001515 reads in 698 ms
[2015-09-30T22:29Z] INFO  23:29:57,254 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:57,465 MuTect - [MUTECT] Processed 44004007 reads in 634 ms
[2015-09-30T22:29Z] INFO  23:29:57,605 MuTect - [MUTECT] Processed 158008188 reads in 628 ms
[2015-09-30T22:29Z] INFO  23:29:57,918 MuTect - [MUTECT] Processed 33001603 reads in 694 ms
[2015-09-30T22:29Z] INFO  23:29:58,118 MuTect - [MUTECT] Processed 45004044 reads in 653 ms
[2015-09-30T22:29Z] INFO  23:29:58,248 MuTect - [MUTECT] Processed 159008267 reads in 643 ms
[2015-09-30T22:29Z] INFO  23:29:58,443 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:58,647 MuTect - [MUTECT] Processed 34001676 reads in 729 ms
[2015-09-30T22:29Z] INFO  23:29:58,814 MuTect - [MUTECT] Processed 46004086 reads in 696 ms
[2015-09-30T22:29Z] INFO  23:29:58,906 MuTect - [MUTECT] Processed 160008358 reads in 658 ms
[2015-09-30T22:29Z] INFO  23:29:59,322 MuTect - [MUTECT] Processed 35001789 reads in 675 ms
[2015-09-30T22:29Z] INFO  23:29:59,451 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:59,528 MuTect - [MUTECT] Processed 47004151 reads in 714 ms
[2015-09-30T22:29Z] INFO  23:29:59,575 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:29Z] INFO  23:29:59,626 MuTect - [MUTECT] Processed 161008399 reads in 720 ms
[2015-09-30T22:29Z] INFO  23:29:59,978 MuTect - [MUTECT] Processed 36001801 reads in 656 ms
[2015-09-30T22:30Z] INFO  23:30:00,164 MuTect - [MUTECT] Processed 48004162 reads in 636 ms
[2015-09-30T22:30Z] INFO  23:30:00,270 MuTect - [MUTECT] Processed 162008444 reads in 644 ms
[2015-09-30T22:30Z] INFO  23:30:00,334 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:00,656 MuTect - [MUTECT] Processed 37001812 reads in 678 ms
[2015-09-30T22:30Z] INFO  23:30:00,847 MuTect - [MUTECT] Processed 49004252 reads in 683 ms
[2015-09-30T22:30Z] INFO  23:30:00,999 MuTect - [MUTECT] Processed 163008483 reads in 729 ms
[2015-09-30T22:30Z] INFO  23:30:01,347 MuTect - [MUTECT] Processed 38001898 reads in 691 ms
[2015-09-30T22:30Z] INFO  23:30:01,510 MuTect - [MUTECT] Processed 50004299 reads in 663 ms
[2015-09-30T22:30Z] INFO  23:30:01,642 MuTect - [MUTECT] Processed 164008519 reads in 643 ms
[2015-09-30T22:30Z] INFO  23:30:01,763 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:01,996 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:01,997 MuTect - [MUTECT] Processed 39001980 reads in 650 ms
[2015-09-30T22:30Z] INFO  23:30:02,181 MuTect - [MUTECT] Processed 51004316 reads in 671 ms
[2015-09-30T22:30Z] INFO  23:30:02,309 MuTect - [MUTECT] Processed 165008556 reads in 667 ms
[2015-09-30T22:30Z] INFO  23:30:02,379 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:02,666 MuTect - [MUTECT] Processed 40001988 reads in 669 ms
[2015-09-30T22:30Z] INFO  23:30:02,857 MuTect - [MUTECT] Processed 52004416 reads in 676 ms
[2015-09-30T22:30Z] INFO  23:30:02,984 MuTect - [MUTECT] Processed 166008665 reads in 675 ms
[2015-09-30T22:30Z] INFO  23:30:03,341 MuTect - [MUTECT] Processed 41002021 reads in 675 ms
[2015-09-30T22:30Z] INFO  23:30:03,501 MuTect - [MUTECT] Processed 53004528 reads in 644 ms
[2015-09-30T22:30Z] INFO  23:30:03,636 MuTect - [MUTECT] Processed 167008714 reads in 652 ms
[2015-09-30T22:30Z] INFO  23:30:03,922 ProgressMeter -     11:46337909        1.21e+06   30.0 s       24.0 s     30.7%        97.0 s    67.0 s
[2015-09-30T22:30Z] INFO  23:30:04,024 MuTect - [MUTECT] Processed 42002065 reads in 683 ms
[2015-09-30T22:30Z] INFO  23:30:04,063 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:04,169 MuTect - [MUTECT] Processed 54004626 reads in 668 ms
[2015-09-30T22:30Z] INFO  23:30:04,251 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:04,294 MuTect - [MUTECT] Processed 168008799 reads in 658 ms
[2015-09-30T22:30Z] INFO  23:30:04,435 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:04,687 MuTect - [MUTECT] Processed 43002136 reads in 662 ms
[2015-09-30T22:30Z] INFO  23:30:04,849 MuTect - [MUTECT] Processed 55004699 reads in 680 ms
[2015-09-30T22:30Z] INFO  23:30:04,944 ProgressMeter -      11:2337148        1.28e+06   60.0 s       46.0 s     21.1%         4.7 m     3.7 m
[2015-09-30T22:30Z] INFO  23:30:04,951 MuTect - [MUTECT] Processed 169008802 reads in 657 ms
[2015-09-30T22:30Z] INFO  23:30:05,309 MuTect - [MUTECT] Processed 44002199 reads in 623 ms
[2015-09-30T22:30Z] INFO  23:30:05,529 MuTect - [MUTECT] Processed 56004718 reads in 680 ms
[2015-09-30T22:30Z] INFO  23:30:05,608 MuTect - [MUTECT] Processed 170008886 reads in 657 ms
[2015-09-30T22:30Z] INFO  23:30:05,914 MuTect - [MUTECT] Processed 45002290 reads in 605 ms
[2015-09-30T22:30Z] INFO  23:30:06,200 MuTect - [MUTECT] Processed 57004812 reads in 671 ms
[2015-09-30T22:30Z] INFO  23:30:06,244 MuTect - [MUTECT] Processed 171008970 reads in 636 ms
[2015-09-30T22:30Z] INFO  23:30:06,259 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:06,546 MuTect - [MUTECT] Processed 46002341 reads in 632 ms
[2015-09-30T22:30Z] INFO  23:30:06,586 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:06,801 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:06,879 MuTect - [MUTECT] Processed 172009043 reads in 635 ms
[2015-09-30T22:30Z] INFO  23:30:06,916 MuTect - [MUTECT] Processed 58004910 reads in 716 ms
[2015-09-30T22:30Z] INFO  23:30:07,172 MuTect - [MUTECT] Processed 47002381 reads in 626 ms
[2015-09-30T22:30Z] INFO  23:30:07,544 MuTect - [MUTECT] Processed 173009140 reads in 665 ms
[2015-09-30T22:30Z] INFO  23:30:07,616 MuTect - [MUTECT] Processed 59004967 reads in 700 ms
[2015-09-30T22:30Z] INFO  23:30:07,787 MuTect - [MUTECT] Processed 48002434 reads in 615 ms
[2015-09-30T22:30Z] INFO  23:30:08,233 MuTect - [MUTECT] Processed 174009181 reads in 689 ms
[2015-09-30T22:30Z] INFO  23:30:08,324 MuTect - [MUTECT] Processed 60005097 reads in 708 ms
[2015-09-30T22:30Z] INFO  23:30:08,399 MuTect - [MUTECT] Processed 49002489 reads in 612 ms
[2015-09-30T22:30Z] INFO  23:30:08,490 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:08,649 ProgressMeter -    10:124266072        6.03e+06  120.0 s       19.0 s     97.8%         2.0 m     2.0 s
[2015-09-30T22:30Z] INFO  23:30:08,826 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:08,883 MuTect - [MUTECT] Processed 175009239 reads in 650 ms
[2015-09-30T22:30Z] INFO  23:30:09,021 MuTect - [MUTECT] Processed 50002498 reads in 622 ms
[2015-09-30T22:30Z] INFO  23:30:09,022 MuTect - [MUTECT] Processed 61005099 reads in 698 ms
[2015-09-30T22:30Z] INFO  23:30:09,117 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:09,545 MuTect - [MUTECT] Processed 176009309 reads in 662 ms
[2015-09-30T22:30Z] INFO  23:30:09,645 MuTect - [MUTECT] Processed 51002524 reads in 624 ms
[2015-09-30T22:30Z] INFO  23:30:09,720 MuTect - [MUTECT] Processed 62005122 reads in 698 ms
[2015-09-30T22:30Z] INFO  23:30:10,160 MuTect - [MUTECT] Processed 177009366 reads in 614 ms
[2015-09-30T22:30Z] INFO  23:30:10,324 MuTect - [MUTECT] Processed 52002539 reads in 679 ms
[2015-09-30T22:30Z] INFO  23:30:10,381 MuTect - [MUTECT] Processed 63005215 reads in 660 ms
[2015-09-30T22:30Z] INFO  23:30:10,722 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:10,746 MuTect - [MUTECT] Processed 178009379 reads in 587 ms
[2015-09-30T22:30Z] INFO  23:30:10,998 MuTect - [MUTECT] Processed 53002571 reads in 674 ms
[2015-09-30T22:30Z] INFO  23:30:11,060 MuTect - [MUTECT] Processed 64005238 reads in 680 ms
[2015-09-30T22:30Z] INFO  23:30:11,375 MuTect - [MUTECT] Processed 179009417 reads in 629 ms
[2015-09-30T22:30Z] INFO  23:30:11,382 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:11,518 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:30Z] INFO  23:30:11,521 ProgressMeter -            done        6.31e+06    2.0 m       19.0 s    100.0%         2.0 m     0.0 s
[2015-09-30T22:30Z] INFO  23:30:11,522 ProgressMeter - Total runtime 122.88 secs, 2.05 min, 0.03 hours
[2015-09-30T22:30Z] INFO  23:30:11,589 MicroScheduler - 133952 reads were filtered out during the traversal out of approximately 2142049 total reads (6.25%)
[2015-09-30T22:30Z] INFO  23:30:11,589 MicroScheduler -   -> 99953 reads (4.67% of total) failing DuplicateReadFilter
[2015-09-30T22:30Z] INFO  23:30:11,589 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:30Z] INFO  23:30:11,589 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:30Z] INFO  23:30:11,590 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:30Z] INFO  23:30:11,590 MicroScheduler -   -> 33999 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:30Z] INFO  23:30:11,651 MuTect - [MUTECT] Processed 54002605 reads in 653 ms
[2015-09-30T22:30Z] INFO  23:30:11,783 MuTect - [MUTECT] Processed 65005276 reads in 723 ms
[2015-09-30T22:30Z] INFO  23:30:12,329 MuTect - [MUTECT] Processed 55002700 reads in 678 ms
[2015-09-30T22:30Z] INFO  23:30:12,523 MuTect - [MUTECT] Processed 66005364 reads in 740 ms
[2015-09-30T22:30Z] INFO  23:30:13,003 MuTect - [MUTECT] Processed 56002776 reads in 674 ms
[2015-09-30T22:30Z] INFO  23:30:13,017 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:30Z] INFO  23:30:13,032 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:13,221 MuTect - [MUTECT] Processed 67005425 reads in 698 ms
[2015-09-30T22:30Z] bgzip syn3-10_93389481_124436664-raw-mutect.vcf
[2015-09-30T22:30Z] tabix index syn3-10_93389481_124436664-raw-mutect.vcf.gz
[2015-09-30T22:30Z] INFO  23:30:13,626 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:13,695 MuTect - [MUTECT] Processed 57002880 reads in 692 ms
[2015-09-30T22:30Z] INFO  23:30:13,951 MuTect - [MUTECT] Processed 68005518 reads in 729 ms
[2015-09-30T22:30Z] INFO  23:30:14,341 MuTect - [MUTECT] Processed 58002926 reads in 646 ms
[2015-09-30T22:30Z] INFO  23:30:14,611 MuTect - [MUTECT] Processed 69005572 reads in 661 ms
[2015-09-30T22:30Z] INFO  23:30:15,266 MuTect - [MUTECT] Processed 70005585 reads in 655 ms
[2015-09-30T22:30Z] INFO  23:30:15,836 MuTect - [MUTECT] Processed 59003014 reads in 1495 ms
[2015-09-30T22:30Z] INFO  23:30:15,885 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:15,932 MuTect - [MUTECT] Processed 71005632 reads in 666 ms
[2015-09-30T22:30Z] INFO  23:30:16,452 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:16,577 MuTect - [MUTECT] Processed 72005732 reads in 645 ms
[2015-09-30T22:30Z] INFO  23:30:16,713 MuTect - [MUTECT] Processed 60003031 reads in 877 ms
[2015-09-30T22:30Z] INFO  23:30:17,222 MuTect - [MUTECT] Processed 73005797 reads in 645 ms
[2015-09-30T22:30Z] INFO  23:30:17,342 MuTect - [MUTECT] Processed 61003109 reads in 629 ms
[2015-09-30T22:30Z] INFO  23:30:17,918 MuTect - [MUTECT] Processed 74005797 reads in 696 ms
[2015-09-30T22:30Z] INFO  23:30:17,973 MuTect - [MUTECT] Processed 62003170 reads in 631 ms
[2015-09-30T22:30Z] MuTect: MuTect
[2015-09-30T22:30Z] INFO  23:30:18,142 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:18,550 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:18,627 MuTect - [MUTECT] Processed 63003255 reads in 654 ms
[2015-09-30T22:30Z] INFO  23:30:18,668 MuTect - [MUTECT] Processed 75005850 reads in 750 ms
[2015-09-30T22:30Z] INFO  23:30:19,295 MuTect - [MUTECT] Processed 64003277 reads in 668 ms
[2015-09-30T22:30Z] INFO  23:30:19,393 MuTect - [MUTECT] Processed 76005951 reads in 725 ms
[2015-09-30T22:30Z] INFO  23:30:19,939 MuTect - [MUTECT] Processed 65003297 reads in 644 ms
[2015-09-30T22:30Z] INFO  23:30:20,099 MuTect - [MUTECT] Processed 77006015 reads in 706 ms
[2015-09-30T22:30Z] INFO  23:30:20,370 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/11/syn3-11_62123540_93141822-raw-mutect-regions.bed to be BED
[2015-09-30T22:30Z] INFO  23:30:20,425 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:30Z] INFO  23:30:20,426 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:30Z] INFO  23:30:20,426 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:30Z] INFO  23:30:20,426 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:30Z] INFO  23:30:20,429 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/11/syn3-11_62123540_93141822-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/11/tx/tmpUv3INx/syn3-11_62123540_93141822-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:30Z] INFO  23:30:20,429 HelpFormatter - Date/Time: 2015/09/30 23:30:20
[2015-09-30T22:30Z] INFO  23:30:20,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:30Z] INFO  23:30:20,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:30Z] INFO  23:30:20,457 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:30Z] INFO  23:30:20,461 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:30Z] INFO  23:30:20,515 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:30Z] INFO  23:30:20,563 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:30Z] INFO  23:30:20,571 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:30Z] INFO  23:30:20,580 MuTect - [MUTECT] Processed 66003376 reads in 641 ms
[2015-09-30T22:30Z] INFO  23:30:20,594 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:30Z] INFO  23:30:20,667 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:30Z] INFO  23:30:20,711 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:20,785 MuTect - [MUTECT] Processed 78006069 reads in 686 ms
[2015-09-30T22:30Z] INFO  23:30:20,792 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:20,844 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:30Z] INFO  23:30:20,967 IntervalUtils - Processing 2336441 bp from intervals
[2015-09-30T22:30Z] INFO  23:30:20,971 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:30Z] INFO  23:30:20,971 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:30Z] INFO  23:30:21,129 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:30Z] INFO  23:30:21,292 MuTect - [MUTECT] Processed 67003401 reads in 712 ms
[2015-09-30T22:30Z] INFO  23:30:21,296 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:30Z] INFO  23:30:21,296 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:30Z] INFO  23:30:21,297 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:30Z] INFO  23:30:21,298 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:30Z] INFO  23:30:21,485 MuTect - [MUTECT] Processed 79006098 reads in 700 ms
[2015-09-30T22:30Z] INFO  23:30:21,971 MuTect - [MUTECT] Processed 68003444 reads in 679 ms
[2015-09-30T22:30Z] INFO  23:30:22,195 MuTect - [MUTECT] Processed 80006123 reads in 710 ms
[2015-09-30T22:30Z] INFO  23:30:22,653 MuTect - [MUTECT] Processed 69003531 reads in 682 ms
[2015-09-30T22:30Z] INFO  23:30:22,920 MuTect - [MUTECT] Processed 81006201 reads in 725 ms
[2015-09-30T22:30Z] INFO  23:30:23,123 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:23,333 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:23,349 MuTect - [MUTECT] Processed 70003531 reads in 696 ms
[2015-09-30T22:30Z] INFO  23:30:23,619 MuTect - [MUTECT] Processed 82006228 reads in 699 ms
[2015-09-30T22:30Z] INFO  23:30:23,681 MuTect - [MUTECT] Processed 1000101 reads in 2321 ms
[2015-09-30T22:30Z] INFO  23:30:24,046 MuTect - [MUTECT] Processed 71003638 reads in 697 ms
[2015-09-30T22:30Z] INFO  23:30:24,397 MuTect - [MUTECT] Processed 83006247 reads in 778 ms
[2015-09-30T22:30Z] INFO  23:30:24,444 MuTect - [MUTECT] Processed 2000143 reads in 762 ms
[2015-09-30T22:30Z] INFO  23:30:24,746 MuTect - [MUTECT] Processed 72003728 reads in 700 ms
[2015-09-30T22:30Z] INFO  23:30:25,148 MuTect - [MUTECT] Processed 3000156 reads in 705 ms
[2015-09-30T22:30Z] INFO  23:30:25,157 MuTect - [MUTECT] Processed 84006293 reads in 760 ms
[2015-09-30T22:30Z] INFO  23:30:25,382 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:25,641 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:25,726 MuTect - [MUTECT] Processed 73003747 reads in 980 ms
[2015-09-30T22:30Z] INFO  23:30:25,809 MuTect - [MUTECT] Processed 4000168 reads in 660 ms
[2015-09-30T22:30Z] INFO  23:30:26,241 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:26,434 MuTect - [MUTECT] Processed 85006363 reads in 1277 ms
[2015-09-30T22:30Z] INFO  23:30:26,456 MuTect - [MUTECT] Processed 5000195 reads in 648 ms
[2015-09-30T22:30Z] INFO  23:30:26,709 MuTect - [MUTECT] Processed 74003769 reads in 983 ms
[2015-09-30T22:30Z] INFO  23:30:27,090 MuTect - [MUTECT] Processed 6000210 reads in 634 ms
[2015-09-30T22:30Z] INFO  23:30:27,129 MuTect - [MUTECT] Processed 86006365 reads in 695 ms
[2015-09-30T22:30Z] INFO  23:30:27,423 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:27,455 MuTect - [MUTECT] Processed 75003817 reads in 746 ms
[2015-09-30T22:30Z] INFO  23:30:27,742 MuTect - [MUTECT] Processed 7000231 reads in 652 ms
[2015-09-30T22:30Z] INFO  23:30:27,825 MuTect - [MUTECT] Processed 87006377 reads in 696 ms
[2015-09-30T22:30Z] INFO  23:30:28,009 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:28,133 MuTect - [MUTECT] Processed 76003819 reads in 678 ms
[2015-09-30T22:30Z] INFO  23:30:28,391 MuTect - [MUTECT] Processed 8000309 reads in 649 ms
[2015-09-30T22:30Z] INFO  23:30:28,497 MuTect - [MUTECT] Processed 88006412 reads in 672 ms
[2015-09-30T22:30Z] INFO  23:30:28,593 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:28,848 MuTect - [MUTECT] Processed 77003875 reads in 715 ms
[2015-09-30T22:30Z] INFO  23:30:29,006 MuTect - [MUTECT] Processed 9000367 reads in 615 ms
[2015-09-30T22:30Z] INFO  23:30:29,179 MuTect - [MUTECT] Processed 89006460 reads in 682 ms
[2015-09-30T22:30Z] INFO  23:30:29,542 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:29,557 MuTect - [MUTECT] Processed 78003951 reads in 709 ms
[2015-09-30T22:30Z] INFO  23:30:29,644 MuTect - [MUTECT] Processed 10000425 reads in 638 ms
[2015-09-30T22:30Z] INFO  23:30:29,850 MuTect - [MUTECT] Processed 90006528 reads in 671 ms
[2015-09-30T22:30Z] INFO  23:30:30,285 MuTect - [MUTECT] Processed 79003953 reads in 728 ms
[2015-09-30T22:30Z] INFO  23:30:30,295 MuTect - [MUTECT] Processed 11000515 reads in 651 ms
[2015-09-30T22:30Z] INFO  23:30:30,505 MuTect - [MUTECT] Processed 91006587 reads in 655 ms
[2015-09-30T22:30Z] INFO  23:30:30,541 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:30,625 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:30,961 MuTect - [MUTECT] Processed 12000543 reads in 666 ms
[2015-09-30T22:30Z] INFO  23:30:31,020 MuTect - [MUTECT] Processed 80004036 reads in 735 ms
[2015-09-30T22:30Z] INFO  23:30:31,143 MuTect - [MUTECT] Processed 92006590 reads in 638 ms
[2015-09-30T22:30Z] INFO  23:30:31,607 MuTect - [MUTECT] Processed 13000596 reads in 646 ms
[2015-09-30T22:30Z] INFO  23:30:31,731 MuTect - [MUTECT] Processed 81004101 reads in 711 ms
[2015-09-30T22:30Z] INFO  23:30:31,753 MuTect - [MUTECT] Processed 93006628 reads in 610 ms
[2015-09-30T22:30Z] INFO  23:30:31,890 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:32,263 MuTect - [MUTECT] Processed 14000714 reads in 656 ms
[2015-09-30T22:30Z] INFO  23:30:32,364 MuTect - [MUTECT] Processed 94006697 reads in 611 ms
[2015-09-30T22:30Z] INFO  23:30:32,426 MuTect - [MUTECT] Processed 82004139 reads in 695 ms
[2015-09-30T22:30Z] INFO  23:30:32,667 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:32,910 MuTect - [MUTECT] Processed 15000801 reads in 647 ms
[2015-09-30T22:30Z] INFO  23:30:32,983 MuTect - [MUTECT] Processed 95006793 reads in 619 ms
[2015-09-30T22:30Z] INFO  23:30:33,064 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:33,140 MuTect - [MUTECT] Processed 83004169 reads in 714 ms
[2015-09-30T22:30Z] INFO  23:30:33,533 MuTect - [MUTECT] Processed 16000878 reads in 623 ms
[2015-09-30T22:30Z] INFO  23:30:33,634 MuTect - [MUTECT] Processed 96006872 reads in 651 ms
[2015-09-30T22:30Z] INFO  23:30:33,837 MuTect - [MUTECT] Processed 84004210 reads in 697 ms
[2015-09-30T22:30Z] INFO  23:30:33,923 ProgressMeter -     11:55904509        2.54e+06   60.0 s       23.0 s     60.6%        99.0 s    39.0 s
[2015-09-30T22:30Z] INFO  23:30:34,139 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:34,152 MuTect - [MUTECT] Processed 17000947 reads in 619 ms
[2015-09-30T22:30Z] INFO  23:30:34,257 MuTect - [MUTECT] Processed 97006881 reads in 623 ms
[2015-09-30T22:30Z] INFO  23:30:34,505 MuTect - [MUTECT] Processed 85004261 reads in 668 ms
[2015-09-30T22:30Z] INFO  23:30:34,804 MuTect - [MUTECT] Processed 18001028 reads in 652 ms
[2015-09-30T22:30Z] INFO  23:30:34,886 MuTect - [MUTECT] Processed 98006954 reads in 629 ms
[2015-09-30T22:30Z] INFO  23:30:34,905 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:34,945 ProgressMeter -      11:6622496        2.24e+06   90.0 s       40.0 s     42.6%         3.5 m     2.0 m
[2015-09-30T22:30Z] INFO  23:30:35,356 MuTect - [MUTECT] Processed 86004339 reads in 850 ms
[2015-09-30T22:30Z] INFO  23:30:35,473 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:35,490 MuTect - [MUTECT] Processed 19001077 reads in 686 ms
[2015-09-30T22:30Z] INFO  23:30:35,532 MuTect - [MUTECT] Processed 99006987 reads in 646 ms
[2015-09-30T22:30Z] INFO  23:30:36,120 MuTect - [MUTECT] Processed 87004341 reads in 765 ms
[2015-09-30T22:30Z] INFO  23:30:36,177 MuTect - [MUTECT] Processed 100006987 reads in 645 ms
[2015-09-30T22:30Z] INFO  23:30:36,187 MuTect - [MUTECT] Processed 20001119 reads in 697 ms
[2015-09-30T22:30Z] INFO  23:30:36,527 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:36,816 MuTect - [MUTECT] Processed 101007107 reads in 639 ms
[2015-09-30T22:30Z] INFO  23:30:36,869 MuTect - [MUTECT] Processed 21001175 reads in 682 ms
[2015-09-30T22:30Z] INFO  23:30:36,909 MuTect - [MUTECT] Processed 88004366 reads in 789 ms
[2015-09-30T22:30Z] INFO  23:30:36,913 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:37,470 MuTect - [MUTECT] Processed 102007200 reads in 654 ms
[2015-09-30T22:30Z] INFO  23:30:37,522 MuTect - [MUTECT] Processed 22001196 reads in 653 ms
[2015-09-30T22:30Z] INFO  23:30:37,529 MuTect - [MUTECT] Processed 89004472 reads in 620 ms
[2015-09-30T22:30Z] INFO  23:30:37,706 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:38,146 MuTect - [MUTECT] Processed 90004599 reads in 617 ms
[2015-09-30T22:30Z] INFO  23:30:38,167 MuTect - [MUTECT] Processed 103007224 reads in 697 ms
[2015-09-30T22:30Z] INFO  23:30:38,179 MuTect - [MUTECT] Processed 23001264 reads in 657 ms
[2015-09-30T22:30Z] INFO  23:30:38,760 MuTect - [MUTECT] Processed 91004646 reads in 614 ms
[2015-09-30T22:30Z] INFO  23:30:38,833 MuTect - [MUTECT] Processed 24001293 reads in 654 ms
[2015-09-30T22:30Z] INFO  23:30:38,907 MuTect - [MUTECT] Processed 104007253 reads in 740 ms
[2015-09-30T22:30Z] INFO  23:30:38,917 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:39,308 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:39,385 MuTect - [MUTECT] Processed 92004732 reads in 625 ms
[2015-09-30T22:30Z] INFO  23:30:39,462 MuTect - [MUTECT] Processed 25001387 reads in 629 ms
[2015-09-30T22:30Z] INFO  23:30:39,598 MuTect - [MUTECT] Processed 105007318 reads in 691 ms
[2015-09-30T22:30Z] INFO  23:30:39,827 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:40,056 MuTect - [MUTECT] Processed 93004747 reads in 671 ms
[2015-09-30T22:30Z] INFO  23:30:40,101 MuTect - [MUTECT] Processed 26001459 reads in 639 ms
[2015-09-30T22:30Z] INFO  23:30:40,292 MuTect - [MUTECT] Processed 106007406 reads in 694 ms
[2015-09-30T22:30Z] INFO  23:30:40,717 MuTect - [MUTECT] Processed 94004833 reads in 661 ms
[2015-09-30T22:30Z] INFO  23:30:40,765 MuTect - [MUTECT] Processed 27001552 reads in 664 ms
[2015-09-30T22:30Z] INFO  23:30:40,998 MuTect - [MUTECT] Processed 107007464 reads in 706 ms
[2015-09-30T22:30Z] INFO  23:30:41,069 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:41,380 MuTect - [MUTECT] Processed 28001622 reads in 615 ms
[2015-09-30T22:30Z] INFO  23:30:41,564 MuTect - [MUTECT] Processed 95004900 reads in 847 ms
[2015-09-30T22:30Z] INFO  23:30:41,703 MuTect - [MUTECT] Processed 108007534 reads in 705 ms
[2015-09-30T22:30Z] INFO  23:30:41,897 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:42,040 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:42,079 MuTect - [MUTECT] Processed 29001651 reads in 699 ms
[2015-09-30T22:30Z] INFO  23:30:42,251 MuTect - [MUTECT] Processed 96004946 reads in 687 ms
[2015-09-30T22:30Z] INFO  23:30:42,451 MuTect - [MUTECT] Processed 109007555 reads in 748 ms
[2015-09-30T22:30Z] INFO  23:30:42,701 MuTect - [MUTECT] Processed 30001656 reads in 622 ms
[2015-09-30T22:30Z] INFO  23:30:42,922 MuTect - [MUTECT] Processed 97004996 reads in 671 ms
[2015-09-30T22:30Z] INFO  23:30:43,140 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:43,179 MuTect - [MUTECT] Processed 110007625 reads in 728 ms
[2015-09-30T22:30Z] INFO  23:30:43,333 MuTect - [MUTECT] Processed 31001732 reads in 632 ms
[2015-09-30T22:30Z] INFO  23:30:43,599 MuTect - [MUTECT] Processed 98005021 reads in 677 ms
[2015-09-30T22:30Z] INFO  23:30:43,889 MuTect - [MUTECT] Processed 111007645 reads in 710 ms
[2015-09-30T22:30Z] INFO  23:30:43,944 MuTect - [MUTECT] Processed 32001769 reads in 611 ms
[2015-09-30T22:30Z] INFO  23:30:44,228 MuTect - [MUTECT] Processed 99005074 reads in 629 ms
[2015-09-30T22:30Z] INFO  23:30:44,295 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:44,314 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:44,550 MuTect - [MUTECT] Processed 33001850 reads in 606 ms
[2015-09-30T22:30Z] INFO  23:30:44,607 MuTect - [MUTECT] Processed 112007656 reads in 718 ms
[2015-09-30T22:30Z] INFO  23:30:44,841 MuTect - [MUTECT] Processed 100005160 reads in 613 ms
[2015-09-30T22:30Z] INFO  23:30:45,048 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:45,148 MuTect - [MUTECT] Processed 34001965 reads in 598 ms
[2015-09-30T22:30Z] INFO  23:30:45,327 MuTect - [MUTECT] Processed 113007684 reads in 720 ms
[2015-09-30T22:30Z] INFO  23:30:45,487 MuTect - [MUTECT] Processed 101005162 reads in 646 ms
[2015-09-30T22:30Z] INFO  23:30:45,745 MuTect - [MUTECT] Processed 35002076 reads in 597 ms
[2015-09-30T22:30Z] INFO  23:30:46,025 MuTect - [MUTECT] Processed 114007762 reads in 698 ms
[2015-09-30T22:30Z] INFO  23:30:46,164 MuTect - [MUTECT] Processed 102005182 reads in 677 ms
[2015-09-30T22:30Z] INFO  23:30:46,400 MuTect - [MUTECT] Processed 36002169 reads in 655 ms
[2015-09-30T22:30Z] INFO  23:30:46,532 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:46,716 MuTect - [MUTECT] Processed 115007785 reads in 691 ms
[2015-09-30T22:30Z] INFO  23:30:46,781 MuTect - [MUTECT] Processed 103005238 reads in 617 ms
[2015-09-30T22:30Z] INFO  23:30:46,783 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:46,999 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:47,013 MuTect - [MUTECT] Processed 37002288 reads in 613 ms
[2015-09-30T22:30Z] INFO  23:30:47,407 MuTect - [MUTECT] Processed 104005278 reads in 626 ms
[2015-09-30T22:30Z] INFO  23:30:47,413 MuTect - [MUTECT] Processed 116007870 reads in 697 ms
[2015-09-30T22:30Z] INFO  23:30:47,686 MuTect - [MUTECT] Processed 38002294 reads in 673 ms
[2015-09-30T22:30Z] INFO  23:30:48,049 MuTect - [MUTECT] Processed 105005286 reads in 642 ms
[2015-09-30T22:30Z] INFO  23:30:48,105 MuTect - [MUTECT] Processed 117007912 reads in 692 ms
[2015-09-30T22:30Z] INFO  23:30:48,292 MuTect - [MUTECT] Processed 39002388 reads in 606 ms
[2015-09-30T22:30Z] INFO  23:30:48,660 MuTect - [MUTECT] Processed 106005338 reads in 611 ms
[2015-09-30T22:30Z] INFO  23:30:48,711 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:48,817 MuTect - [MUTECT] Processed 118007917 reads in 712 ms
[2015-09-30T22:30Z] INFO  23:30:48,924 MuTect - [MUTECT] Processed 40002438 reads in 632 ms
[2015-09-30T22:30Z] INFO  23:30:49,038 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:49,171 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:49,304 MuTect - [MUTECT] Processed 107005374 reads in 644 ms
[2015-09-30T22:30Z] INFO  23:30:49,492 MuTect - [MUTECT] Processed 119008006 reads in 675 ms
[2015-09-30T22:30Z] INFO  23:30:49,541 MuTect - [MUTECT] Processed 41002542 reads in 617 ms
[2015-09-30T22:30Z] INFO  23:30:49,951 MuTect - [MUTECT] Processed 108005421 reads in 647 ms
[2015-09-30T22:30Z] INFO  23:30:50,145 MuTect - [MUTECT] Processed 42002630 reads in 604 ms
[2015-09-30T22:30Z] INFO  23:30:50,169 MuTect - [MUTECT] Processed 120008123 reads in 677 ms
[2015-09-30T22:30Z] INFO  23:30:50,585 MuTect - [MUTECT] Processed 109005509 reads in 634 ms
[2015-09-30T22:30Z] INFO  23:30:50,792 MuTect - [MUTECT] Processed 43002694 reads in 647 ms
[2015-09-30T22:30Z] INFO  23:30:50,830 MuTect - [MUTECT] Processed 121008134 reads in 660 ms
[2015-09-30T22:30Z] INFO  23:30:50,966 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:51,225 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:51,235 MuTect - [MUTECT] Processed 110005512 reads in 650 ms
[2015-09-30T22:30Z] INFO  23:30:51,299 ProgressMeter -     11:64519426        1.22e+06   30.0 s       24.0 s     16.8%         3.0 m     2.5 m
[2015-09-30T22:30Z] INFO  23:30:51,411 MuTect - [MUTECT] Processed 44002756 reads in 619 ms
[2015-09-30T22:30Z] INFO  23:30:51,532 MuTect - [MUTECT] Processed 122008147 reads in 703 ms
[2015-09-30T22:30Z] INFO  23:30:51,553 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:51,867 MuTect - [MUTECT] Processed 111005567 reads in 632 ms
[2015-09-30T22:30Z] INFO  23:30:52,018 MuTect - [MUTECT] Processed 45002822 reads in 607 ms
[2015-09-30T22:30Z] INFO  23:30:52,192 MuTect - [MUTECT] Processed 123008185 reads in 659 ms
[2015-09-30T22:30Z] INFO  23:30:52,499 MuTect - [MUTECT] Processed 112005631 reads in 632 ms
[2015-09-30T22:30Z] INFO  23:30:52,634 MuTect - [MUTECT] Processed 46002902 reads in 616 ms
[2015-09-30T22:30Z] INFO  23:30:52,881 MuTect - [MUTECT] Processed 124008191 reads in 690 ms
[2015-09-30T22:30Z] INFO  23:30:53,179 MuTect - [MUTECT] Processed 113005672 reads in 680 ms
[2015-09-30T22:30Z] INFO  23:30:53,187 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:53,241 MuTect - [MUTECT] Processed 47002988 reads in 607 ms
[2015-09-30T22:30Z] INFO  23:30:53,378 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:53,566 MuTect - [MUTECT] Processed 125008242 reads in 685 ms
[2015-09-30T22:30Z] INFO  23:30:53,868 MuTect - [MUTECT] Processed 48003085 reads in 627 ms
[2015-09-30T22:30Z] INFO  23:30:53,873 MuTect - [MUTECT] Processed 114005694 reads in 694 ms
[2015-09-30T22:30Z] INFO  23:30:53,947 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:54,253 MuTect - [MUTECT] Processed 126008331 reads in 687 ms
[2015-09-30T22:30Z] INFO  23:30:54,498 MuTect - [MUTECT] Processed 49003236 reads in 630 ms
[2015-09-30T22:30Z] INFO  23:30:54,545 MuTect - [MUTECT] Processed 115005742 reads in 672 ms
[2015-09-30T22:30Z] INFO  23:30:54,925 MuTect - [MUTECT] Processed 127008359 reads in 672 ms
[2015-09-30T22:30Z] INFO  23:30:55,143 MuTect - [MUTECT] Processed 50003331 reads in 645 ms
[2015-09-30T22:30Z] INFO  23:30:55,231 MuTect - [MUTECT] Processed 116005788 reads in 686 ms
[2015-09-30T22:30Z] INFO  23:30:55,484 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:55,506 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:55,634 MuTect - [MUTECT] Processed 128008445 reads in 709 ms
[2015-09-30T22:30Z] INFO  23:30:55,758 MuTect - [MUTECT] Processed 51003349 reads in 614 ms
[2015-09-30T22:30Z] INFO  23:30:55,887 MuTect - [MUTECT] Processed 117005836 reads in 656 ms
[2015-09-30T22:30Z] INFO  23:30:56,300 MuTect - [MUTECT] Processed 129008445 reads in 666 ms
[2015-09-30T22:30Z] INFO  23:30:56,307 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:56,377 MuTect - [MUTECT] Processed 52003481 reads in 620 ms
[2015-09-30T22:30Z] INFO  23:30:56,578 MuTect - [MUTECT] Processed 118005852 reads in 691 ms
[2015-09-30T22:30Z] INFO  23:30:56,962 MuTect - [MUTECT] Processed 130008569 reads in 662 ms
[2015-09-30T22:30Z] INFO  23:30:57,018 MuTect - [MUTECT] Processed 53003537 reads in 641 ms
[2015-09-30T22:30Z] INFO  23:30:57,234 MuTect - [MUTECT] Processed 119005989 reads in 656 ms
[2015-09-30T22:30Z] INFO  23:30:57,537 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:57,642 MuTect - [MUTECT] Processed 131008612 reads in 680 ms
[2015-09-30T22:30Z] INFO  23:30:57,653 MuTect - [MUTECT] Processed 54003562 reads in 635 ms
[2015-09-30T22:30Z] INFO  23:30:57,696 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:57,874 MuTect - [MUTECT] Processed 120006001 reads in 640 ms
[2015-09-30T22:30Z] INFO  23:30:58,314 MuTect - [MUTECT] Processed 132008662 reads in 672 ms
[2015-09-30T22:30Z] INFO  23:30:58,326 MuTect - [MUTECT] Processed 55003641 reads in 673 ms
[2015-09-30T22:30Z] INFO  23:30:58,539 MuTect - [MUTECT] Processed 121006008 reads in 665 ms
[2015-09-30T22:30Z] INFO  23:30:58,659 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:58,946 MuTect - [MUTECT] Processed 56003734 reads in 620 ms
[2015-09-30T22:30Z] INFO  23:30:59,008 MuTect - [MUTECT] Processed 133008709 reads in 694 ms
[2015-09-30T22:30Z] INFO  23:30:59,208 MuTect - [MUTECT] Processed 122006091 reads in 669 ms
[2015-09-30T22:30Z] INFO  23:30:59,567 MuTect - [MUTECT] Processed 57003820 reads in 621 ms
[2015-09-30T22:30Z] INFO  23:30:59,652 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:59,723 MuTect - [MUTECT] Processed 134008716 reads in 715 ms
[2015-09-30T22:30Z] INFO  23:30:59,815 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:30Z] INFO  23:30:59,857 MuTect - [MUTECT] Processed 123006210 reads in 649 ms
[2015-09-30T22:31Z] INFO  23:31:00,165 MuTect - [MUTECT] Processed 58003886 reads in 598 ms
[2015-09-30T22:31Z] INFO  23:31:00,408 MuTect - [MUTECT] Processed 135008815 reads in 685 ms
[2015-09-30T22:31Z] INFO  23:31:00,495 MuTect - [MUTECT] Processed 124006220 reads in 638 ms
[2015-09-30T22:31Z] INFO  23:31:00,780 MuTect - [MUTECT] Processed 59003907 reads in 615 ms
[2015-09-30T22:31Z] INFO  23:31:01,121 MuTect - [MUTECT] Processed 125006259 reads in 625 ms
[2015-09-30T22:31Z] INFO  23:31:01,121 MuTect - [MUTECT] Processed 136008917 reads in 713 ms
[2015-09-30T22:31Z] INFO  23:31:01,152 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:01,383 MuTect - [MUTECT] Processed 60003920 reads in 603 ms
[2015-09-30T22:31Z] INFO  23:31:01,723 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:01,737 MuTect - [MUTECT] Processed 126006261 reads in 617 ms
[2015-09-30T22:31Z] INFO  23:31:01,832 MuTect - [MUTECT] Processed 137008950 reads in 711 ms
[2015-09-30T22:31Z] INFO  23:31:01,989 MuTect - [MUTECT] Processed 61004008 reads in 606 ms
[2015-09-30T22:31Z] INFO  23:31:02,378 MuTect - [MUTECT] Processed 127006265 reads in 641 ms
[2015-09-30T22:31Z] INFO  23:31:02,398 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:02,540 MuTect - [MUTECT] Processed 138009000 reads in 708 ms
[2015-09-30T22:31Z] INFO  23:31:02,623 MuTect - [MUTECT] Processed 62004022 reads in 634 ms
[2015-09-30T22:31Z] INFO  23:31:03,208 MuTect - [MUTECT] Processed 63004160 reads in 585 ms
[2015-09-30T22:31Z] INFO  23:31:03,680 MuTect - [MUTECT] Processed 139009084 reads in 1140 ms
[2015-09-30T22:31Z] INFO  23:31:03,796 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:03,802 MuTect - [MUTECT] Processed 64004230 reads in 594 ms
[2015-09-30T22:31Z] INFO  23:31:03,874 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:03,883 MuTect - [MUTECT] Processed 128006267 reads in 1505 ms
[2015-09-30T22:31Z] INFO  23:31:03,925 ProgressMeter -     11:61093024        3.78e+06   90.0 s       23.0 s     90.6%        99.0 s     9.0 s
[2015-09-30T22:31Z] INFO  23:31:04,389 MuTect - [MUTECT] Processed 140009124 reads in 709 ms
[2015-09-30T22:31Z] INFO  23:31:04,425 MuTect - [MUTECT] Processed 65004261 reads in 623 ms
[2015-09-30T22:31Z] INFO  23:31:04,509 MuTect - [MUTECT] Processed 129006272 reads in 626 ms
[2015-09-30T22:31Z] INFO  23:31:04,946 ProgressMeter -     11:13376101        3.55e+06  120.0 s       33.0 s     66.6%         3.0 m    60.0 s
[2015-09-30T22:31Z] INFO  23:31:05,045 MuTect - [MUTECT] Processed 66004299 reads in 620 ms
[2015-09-30T22:31Z] INFO  23:31:05,054 MuTect - [MUTECT] Processed 141009145 reads in 665 ms
[2015-09-30T22:31Z] INFO  23:31:05,120 MuTect - [MUTECT] Processed 130006326 reads in 611 ms
[2015-09-30T22:31Z] INFO  23:31:05,440 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:05,635 MuTect - [MUTECT] Processed 67004410 reads in 590 ms
[2015-09-30T22:31Z] INFO  23:31:05,732 MuTect - [MUTECT] Processed 142009174 reads in 678 ms
[2015-09-30T22:31Z] INFO  23:31:05,739 MuTect - [MUTECT] Processed 131006371 reads in 619 ms
[2015-09-30T22:31Z] INFO  23:31:05,827 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:06,217 MuTect - [MUTECT] Processed 68004415 reads in 582 ms
[2015-09-30T22:31Z] INFO  23:31:06,349 MuTect - [MUTECT] Processed 132006440 reads in 610 ms
[2015-09-30T22:31Z] INFO  23:31:06,468 MuTect - [MUTECT] Processed 143009262 reads in 736 ms
[2015-09-30T22:31Z] INFO  23:31:06,615 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:06,821 MuTect - [MUTECT] Processed 69004540 reads in 604 ms
[2015-09-30T22:31Z] INFO  23:31:06,971 MuTect - [MUTECT] Processed 133006445 reads in 622 ms
[2015-09-30T22:31Z] INFO  23:31:07,169 MuTect - [MUTECT] Processed 144009297 reads in 701 ms
[2015-09-30T22:31Z] INFO  23:31:07,452 MuTect - [MUTECT] Processed 70004585 reads in 631 ms
[2015-09-30T22:31Z] INFO  23:31:07,586 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:07,594 MuTect - [MUTECT] Processed 134006479 reads in 623 ms
[2015-09-30T22:31Z] INFO  23:31:07,865 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:07,869 MuTect - [MUTECT] Processed 145009315 reads in 700 ms
[2015-09-30T22:31Z] INFO  23:31:08,098 MuTect - [MUTECT] Processed 71004617 reads in 646 ms
[2015-09-30T22:31Z] INFO  23:31:08,200 MuTect - [MUTECT] Processed 135006522 reads in 606 ms
[2015-09-30T22:31Z] INFO  23:31:08,583 MuTect - [MUTECT] Processed 146009329 reads in 714 ms
[2015-09-30T22:31Z] INFO  23:31:08,718 MuTect - [MUTECT] Processed 72004686 reads in 620 ms
[2015-09-30T22:31Z] INFO  23:31:08,800 MuTect - [MUTECT] Processed 136006563 reads in 600 ms
[2015-09-30T22:31Z] INFO  23:31:09,290 MuTect - [MUTECT] Processed 147009376 reads in 706 ms
[2015-09-30T22:31Z] INFO  23:31:09,337 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:09,345 MuTect - [MUTECT] Processed 73004687 reads in 627 ms
[2015-09-30T22:31Z] INFO  23:31:09,397 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:09,400 MuTect - [MUTECT] Processed 137006672 reads in 600 ms
[2015-09-30T22:31Z] INFO  23:31:09,929 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:09,958 MuTect - [MUTECT] Processed 74004708 reads in 612 ms
[2015-09-30T22:31Z] INFO  23:31:09,982 MuTect - [MUTECT] Processed 148009432 reads in 692 ms
[2015-09-30T22:31Z] INFO  23:31:09,985 MuTect - [MUTECT] Processed 138006705 reads in 585 ms
[2015-09-30T22:31Z] INFO  23:31:10,582 MuTect - [MUTECT] Processed 139006799 reads in 597 ms
[2015-09-30T22:31Z] INFO  23:31:10,583 MuTect - [MUTECT] Processed 75004732 reads in 626 ms
[2015-09-30T22:31Z] INFO  23:31:10,692 MuTect - [MUTECT] Processed 149009490 reads in 711 ms
[2015-09-30T22:31Z] INFO  23:31:11,185 MuTect - [MUTECT] Processed 140006903 reads in 603 ms
[2015-09-30T22:31Z] INFO  23:31:11,220 MuTect - [MUTECT] Processed 76004786 reads in 637 ms
[2015-09-30T22:31Z] INFO  23:31:11,401 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:11,406 MuTect - [MUTECT] Processed 150009516 reads in 714 ms
[2015-09-30T22:31Z] INFO  23:31:11,794 MuTect - [MUTECT] Processed 141006962 reads in 609 ms
[2015-09-30T22:31Z] INFO  23:31:11,866 MuTect - [MUTECT] Processed 77004883 reads in 646 ms
[2015-09-30T22:31Z] INFO  23:31:12,046 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:12,098 MuTect - [MUTECT] Processed 151009537 reads in 692 ms
[2015-09-30T22:31Z] INFO  23:31:12,153 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:12,463 MuTect - [MUTECT] Processed 142006972 reads in 669 ms
[2015-09-30T22:31Z] INFO  23:31:12,523 MuTect - [MUTECT] Processed 78004994 reads in 657 ms
[2015-09-30T22:31Z] INFO  23:31:12,798 MuTect - [MUTECT] Processed 152009555 reads in 700 ms
[2015-09-30T22:31Z] INFO  23:31:13,122 MuTect - [MUTECT] Processed 143007040 reads in 659 ms
[2015-09-30T22:31Z] INFO  23:31:13,171 MuTect - [MUTECT] Processed 79005031 reads in 648 ms
[2015-09-30T22:31Z] INFO  23:31:13,513 MuTect - [MUTECT] Processed 153009601 reads in 715 ms
[2015-09-30T22:31Z] INFO  23:31:13,529 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:13,808 MuTect - [MUTECT] Processed 144007053 reads in 686 ms
[2015-09-30T22:31Z] INFO  23:31:14,044 MuTect - [MUTECT] Processed 80005109 reads in 873 ms
[2015-09-30T22:31Z] INFO  23:31:14,218 MuTect - [MUTECT] Processed 154009622 reads in 705 ms
[2015-09-30T22:31Z] INFO  23:31:14,486 MuTect - [MUTECT] Processed 145007138 reads in 678 ms
[2015-09-30T22:31Z] INFO  23:31:14,502 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:14,668 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:14,693 MuTect - [MUTECT] Processed 81005229 reads in 649 ms
[2015-09-30T22:31Z] INFO  23:31:14,801 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:31Z] INFO  23:31:14,804 ProgressMeter -            done        4.24e+06  100.0 s       23.0 s    100.0%       100.0 s     0.0 s
[2015-09-30T22:31Z] INFO  23:31:14,804 ProgressMeter - Total runtime 100.88 secs, 1.68 min, 0.03 hours
[2015-09-30T22:31Z] INFO  23:31:14,867 MicroScheduler - 111450 reads were filtered out during the traversal out of approximately 1718607 total reads (6.48%)
[2015-09-30T22:31Z] INFO  23:31:14,867 MicroScheduler -   -> 83082 reads (4.83% of total) failing DuplicateReadFilter
[2015-09-30T22:31Z] INFO  23:31:14,867 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:31Z] INFO  23:31:14,868 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:31Z] INFO  23:31:14,868 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:31Z] INFO  23:31:14,868 MicroScheduler -   -> 28368 reads (1.65% of total) failing UnmappedReadFilter
[2015-09-30T22:31Z] INFO  23:31:14,890 MuTect - [MUTECT] Processed 155009739 reads in 672 ms
[2015-09-30T22:31Z] INFO  23:31:15,339 MuTect - [MUTECT] Processed 82005302 reads in 646 ms
[2015-09-30T22:31Z] INFO  23:31:15,579 MuTect - [MUTECT] Processed 156009757 reads in 689 ms
[2015-09-30T22:31Z] INFO  23:31:15,939 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:31Z] INFO  23:31:15,969 MuTect - [MUTECT] Processed 83005334 reads in 630 ms
[2015-09-30T22:31Z] bgzip syn3-11_31085657_62105890-raw-mutect.vcf
[2015-09-30T22:31Z] tabix index syn3-11_31085657_62105890-raw-mutect.vcf.gz
[2015-09-30T22:31Z] INFO  23:31:16,228 MuTect - [MUTECT] Processed 157009812 reads in 648 ms
[2015-09-30T22:31Z] INFO  23:31:16,582 MuTect - [MUTECT] Processed 84005407 reads in 613 ms
[2015-09-30T22:31Z] INFO  23:31:16,655 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:16,912 MuTect - [MUTECT] Processed 158009816 reads in 685 ms
[2015-09-30T22:31Z] INFO  23:31:16,921 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:17,206 MuTect - [MUTECT] Processed 85005411 reads in 624 ms
[2015-09-30T22:31Z] INFO  23:31:17,593 MuTect - [MUTECT] Processed 159009904 reads in 681 ms
[2015-09-30T22:31Z] INFO  23:31:17,844 MuTect - [MUTECT] Processed 86005411 reads in 637 ms
[2015-09-30T22:31Z] MuTect: MuTect
[2015-09-30T22:31Z] INFO  23:31:18,301 MuTect - [MUTECT] Processed 160009959 reads in 708 ms
[2015-09-30T22:31Z] INFO  23:31:18,471 MuTect - [MUTECT] Processed 87005454 reads in 628 ms
[2015-09-30T22:31Z] INFO  23:31:18,805 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:18,964 MuTect - [MUTECT] Processed 161009965 reads in 663 ms
[2015-09-30T22:31Z] INFO  23:31:19,064 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:19,078 MuTect - [MUTECT] Processed 88005480 reads in 607 ms
[2015-09-30T22:31Z] INFO  23:31:19,612 MuTect - [MUTECT] Processed 162010023 reads in 648 ms
[2015-09-30T22:31Z] INFO  23:31:19,672 MuTect - [MUTECT] Processed 89005571 reads in 594 ms
[2015-09-30T22:31Z] INFO  23:31:20,245 MuTect - [MUTECT] Processed 163010086 reads in 633 ms
[2015-09-30T22:31Z] INFO  23:31:20,264 MuTect - [MUTECT] Processed 90005587 reads in 592 ms
[2015-09-30T22:31Z] INFO  23:31:20,316 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/11/syn3-11_93147865_124180877-raw-mutect-regions.bed to be BED
[2015-09-30T22:31Z] INFO  23:31:20,372 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:31Z] INFO  23:31:20,373 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:31Z] INFO  23:31:20,373 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:31Z] INFO  23:31:20,373 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:31Z] INFO  23:31:20,376 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/11/syn3-11_93147865_124180877-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/11/tx/tmpZGXPLF/syn3-11_93147865_124180877-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:31Z] INFO  23:31:20,377 HelpFormatter - Date/Time: 2015/09/30 23:31:20
[2015-09-30T22:31Z] INFO  23:31:20,377 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:31Z] INFO  23:31:20,377 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:31Z] INFO  23:31:20,404 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:31Z] INFO  23:31:20,409 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:31Z] INFO  23:31:20,459 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:31Z] INFO  23:31:20,507 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:31Z] INFO  23:31:20,514 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:31Z] INFO  23:31:20,537 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:31Z] INFO  23:31:20,548 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:31Z] INFO  23:31:20,727 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:31Z] INFO  23:31:20,760 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:20,836 IntervalUtils - Processing 1648208 bp from intervals
[2015-09-30T22:31Z] INFO  23:31:20,841 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:31Z] INFO  23:31:20,841 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:31Z] INFO  23:31:20,895 MuTect - [MUTECT] Processed 91005663 reads in 631 ms
[2015-09-30T22:31Z] INFO  23:31:20,933 MuTect - [MUTECT] Processed 164010143 reads in 688 ms
[2015-09-30T22:31Z] INFO  23:31:20,998 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:31Z] INFO  23:31:21,300 ProgressMeter -     11:66136696        2.50e+06   60.0 s       24.0 s     33.8%         3.0 m   117.0 s
[2015-09-30T22:31Z] INFO  23:31:21,368 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:21,505 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:31Z] INFO  23:31:21,505 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:31Z] INFO  23:31:21,505 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:31Z] INFO  23:31:21,506 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:31Z] INFO  23:31:21,514 MuTect - [MUTECT] Processed 92005756 reads in 619 ms
[2015-09-30T22:31Z] INFO  23:31:21,579 MuTect - [MUTECT] Processed 165010149 reads in 646 ms
[2015-09-30T22:31Z] INFO  23:31:22,099 MuTect - [MUTECT] Processed 93005823 reads in 585 ms
[2015-09-30T22:31Z] INFO  23:31:22,293 MuTect - [MUTECT] Processed 166010205 reads in 714 ms
[2015-09-30T22:31Z] INFO  23:31:22,707 MuTect - [MUTECT] Processed 94005851 reads in 608 ms
[2015-09-30T22:31Z] INFO  23:31:22,820 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:23,060 MuTect - [MUTECT] Processed 167010290 reads in 767 ms
[2015-09-30T22:31Z] INFO  23:31:23,346 MuTect - [MUTECT] Processed 95005870 reads in 639 ms
[2015-09-30T22:31Z] INFO  23:31:23,721 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:23,757 MuTect - [MUTECT] Processed 168010370 reads in 697 ms
[2015-09-30T22:31Z] INFO  23:31:23,965 MuTect - [MUTECT] Processed 96005911 reads in 619 ms
[2015-09-30T22:31Z] INFO  23:31:24,003 MuTect - [MUTECT] Processed 1000081 reads in 2449 ms
[2015-09-30T22:31Z] INFO  23:31:24,452 MuTect - [MUTECT] Processed 169010469 reads in 695 ms
[2015-09-30T22:31Z] INFO  23:31:24,601 MuTect - [MUTECT] Processed 97005985 reads in 636 ms
[2015-09-30T22:31Z] INFO  23:31:24,800 MuTect - [MUTECT] Processed 2000149 reads in 797 ms
[2015-09-30T22:31Z] INFO  23:31:24,951 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:25,124 MuTect - [MUTECT] Processed 170010500 reads in 672 ms
[2015-09-30T22:31Z] INFO  23:31:25,185 MuTect - [MUTECT] Processed 98006122 reads in 584 ms
[2015-09-30T22:31Z] INFO  23:31:25,550 MuTect - [MUTECT] Processed 3000230 reads in 750 ms
[2015-09-30T22:31Z] INFO  23:31:25,764 MuTect - [MUTECT] Processed 171010571 reads in 640 ms
[2015-09-30T22:31Z] INFO  23:31:25,767 MuTect - [MUTECT] Processed 99006135 reads in 582 ms
[2015-09-30T22:31Z] INFO  23:31:26,009 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:26,260 MuTect - [MUTECT] Processed 4000273 reads in 710 ms
[2015-09-30T22:31Z] INFO  23:31:26,333 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:26,356 MuTect - [MUTECT] Processed 100006263 reads in 588 ms
[2015-09-30T22:31Z] INFO  23:31:26,420 MuTect - [MUTECT] Processed 172010687 reads in 656 ms
[2015-09-30T22:31Z] INFO  23:31:26,945 MuTect - [MUTECT] Processed 101006294 reads in 590 ms
[2015-09-30T22:31Z] INFO  23:31:26,972 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:26,975 MuTect - [MUTECT] Processed 5000387 reads in 715 ms
[2015-09-30T22:31Z] INFO  23:31:27,070 MuTect - [MUTECT] Processed 173010785 reads in 650 ms
[2015-09-30T22:31Z] INFO  23:31:27,542 MuTect - [MUTECT] Processed 102006404 reads in 597 ms
[2015-09-30T22:31Z] INFO  23:31:27,713 MuTect - [MUTECT] Processed 6000420 reads in 738 ms
[2015-09-30T22:31Z] INFO  23:31:27,735 MuTect - [MUTECT] Processed 174010922 reads in 665 ms
[2015-09-30T22:31Z] INFO  23:31:28,148 MuTect - [MUTECT] Processed 103006467 reads in 606 ms
[2015-09-30T22:31Z] INFO  23:31:28,166 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:28,372 MuTect - [MUTECT] Processed 7000473 reads in 659 ms
[2015-09-30T22:31Z] INFO  23:31:28,400 MuTect - [MUTECT] Processed 175010946 reads in 665 ms
[2015-09-30T22:31Z] INFO  23:31:28,746 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:28,746 MuTect - [MUTECT] Processed 104006584 reads in 598 ms
[2015-09-30T22:31Z] INFO  23:31:29,060 MuTect - [MUTECT] Processed 176011073 reads in 660 ms
[2015-09-30T22:31Z] INFO  23:31:29,085 MuTect - [MUTECT] Processed 8000519 reads in 713 ms
[2015-09-30T22:31Z] INFO  23:31:29,106 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:29,339 MuTect - [MUTECT] Processed 105006645 reads in 593 ms
[2015-09-30T22:31Z] INFO  23:31:29,726 MuTect - [MUTECT] Processed 177011172 reads in 666 ms
[2015-09-30T22:31Z] INFO  23:31:29,766 MuTect - [MUTECT] Processed 9000532 reads in 680 ms
[2015-09-30T22:31Z] INFO  23:31:29,938 MuTect - [MUTECT] Processed 106006659 reads in 599 ms
[2015-09-30T22:31Z] INFO  23:31:30,394 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:30,412 MuTect - [MUTECT] Processed 178011186 reads in 686 ms
[2015-09-30T22:31Z] INFO  23:31:30,446 MuTect - [MUTECT] Processed 10000535 reads in 681 ms
[2015-09-30T22:31Z] INFO  23:31:30,543 MuTect - [MUTECT] Processed 107006765 reads in 605 ms
[2015-09-30T22:31Z] INFO  23:31:31,084 MuTect - [MUTECT] Processed 179011211 reads in 672 ms
[2015-09-30T22:31Z] INFO  23:31:31,146 MuTect - [MUTECT] Processed 11000543 reads in 700 ms
[2015-09-30T22:31Z] INFO  23:31:31,152 MuTect - [MUTECT] Processed 108006899 reads in 609 ms
[2015-09-30T22:31Z] INFO  23:31:31,262 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:31,313 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:31,768 MuTect - [MUTECT] Processed 109007040 reads in 616 ms
[2015-09-30T22:31Z] INFO  23:31:31,787 MuTect - [MUTECT] Processed 180011249 reads in 703 ms
[2015-09-30T22:31Z] INFO  23:31:31,813 MuTect - [MUTECT] Processed 12000547 reads in 666 ms
[2015-09-30T22:31Z] INFO  23:31:32,400 MuTect - [MUTECT] Processed 110007042 reads in 632 ms
[2015-09-30T22:31Z] INFO  23:31:32,480 MuTect - [MUTECT] Processed 13000625 reads in 668 ms
[2015-09-30T22:31Z] INFO  23:31:32,536 MuTect - [MUTECT] Processed 181011357 reads in 749 ms
[2015-09-30T22:31Z] INFO  23:31:32,898 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:33,028 MuTect - [MUTECT] Processed 111007052 reads in 628 ms
[2015-09-30T22:31Z] INFO  23:31:33,187 MuTect - [MUTECT] Processed 14000666 reads in 707 ms
[2015-09-30T22:31Z] INFO  23:31:33,264 MuTect - [MUTECT] Processed 182011397 reads in 728 ms
[2015-09-30T22:31Z] INFO  23:31:33,377 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:33,661 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:33,687 MuTect - [MUTECT] Processed 112007152 reads in 659 ms
[2015-09-30T22:31Z] INFO  23:31:33,903 MuTect - [MUTECT] Processed 15000716 reads in 716 ms
[2015-09-30T22:31Z] INFO  23:31:33,982 MuTect - [MUTECT] Processed 183011400 reads in 718 ms
[2015-09-30T22:31Z] INFO  23:31:34,313 MuTect - [MUTECT] Processed 113007219 reads in 626 ms
[2015-09-30T22:31Z] INFO  23:31:34,617 MuTect - [MUTECT] Processed 16000790 reads in 714 ms
[2015-09-30T22:31Z] INFO  23:31:34,670 MuTect - [MUTECT] Processed 184011411 reads in 688 ms
[2015-09-30T22:31Z] INFO  23:31:34,931 MuTect - [MUTECT] Processed 114007219 reads in 618 ms
[2015-09-30T22:31Z] INFO  23:31:34,947 ProgressMeter -     11:22696390        4.99e+06    2.5 m       30.0 s     92.4%         2.7 m    12.0 s
[2015-09-30T22:31Z] INFO  23:31:35,324 MuTect - [MUTECT] Processed 17000820 reads in 707 ms
[2015-09-30T22:31Z] INFO  23:31:35,370 MuTect - [MUTECT] Processed 185011475 reads in 700 ms
[2015-09-30T22:31Z] INFO  23:31:35,531 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:35,531 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:35,554 MuTect - [MUTECT] Processed 115007239 reads in 623 ms
[2015-09-30T22:31Z] INFO  23:31:36,018 MuTect - [MUTECT] Processed 18000903 reads in 694 ms
[2015-09-30T22:31Z] INFO  23:31:36,130 MuTect - [MUTECT] Processed 186011487 reads in 760 ms
[2015-09-30T22:31Z] INFO  23:31:36,183 MuTect - [MUTECT] Processed 116007336 reads in 629 ms
[2015-09-30T22:31Z] INFO  23:31:36,373 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:36,679 MuTect - [MUTECT] Processed 19000913 reads in 661 ms
[2015-09-30T22:31Z] INFO  23:31:36,810 MuTect - [MUTECT] Processed 117007439 reads in 627 ms
[2015-09-30T22:31Z] INFO  23:31:36,892 MuTect - [MUTECT] Processed 187011514 reads in 762 ms
[2015-09-30T22:31Z] INFO  23:31:37,372 MuTect - [MUTECT] Processed 20000961 reads in 693 ms
[2015-09-30T22:31Z] INFO  23:31:37,437 MuTect - [MUTECT] Processed 118007485 reads in 627 ms
[2015-09-30T22:31Z] INFO  23:31:37,581 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:37,596 MuTect - [MUTECT] Processed 188011547 reads in 704 ms
[2015-09-30T22:31Z] INFO  23:31:38,063 MuTect - [MUTECT] Processed 119007512 reads in 626 ms
[2015-09-30T22:31Z] INFO  23:31:38,099 MuTect - [MUTECT] Processed 21001028 reads in 727 ms
[2015-09-30T22:31Z] INFO  23:31:38,176 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:38,269 MuTect - [MUTECT] Processed 189011628 reads in 673 ms
[2015-09-30T22:31Z] INFO  23:31:38,676 MuTect - [MUTECT] Processed 120007640 reads in 613 ms
[2015-09-30T22:31Z] INFO  23:31:38,793 MuTect - [MUTECT] Processed 22001032 reads in 694 ms
[2015-09-30T22:31Z] INFO  23:31:38,968 MuTect - [MUTECT] Processed 190011659 reads in 699 ms
[2015-09-30T22:31Z] INFO  23:31:38,968 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:39,288 MuTect - [MUTECT] Processed 121007766 reads in 612 ms
[2015-09-30T22:31Z] INFO  23:31:39,479 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:39,497 MuTect - [MUTECT] Processed 23001142 reads in 703 ms
[2015-09-30T22:31Z] INFO  23:31:39,714 MuTect - [MUTECT] Processed 191011681 reads in 746 ms
[2015-09-30T22:31Z] INFO  23:31:39,964 MuTect - [MUTECT] Processed 122007845 reads in 676 ms
[2015-09-30T22:31Z] INFO  23:31:40,255 MuTect - [MUTECT] Processed 24001146 reads in 759 ms
[2015-09-30T22:31Z] INFO  23:31:40,426 MuTect - [MUTECT] Processed 192011706 reads in 712 ms
[2015-09-30T22:31Z] INFO  23:31:40,729 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:40,787 MuTect - [MUTECT] Processed 123007856 reads in 823 ms
[2015-09-30T22:31Z] INFO  23:31:41,014 MuTect - [MUTECT] Processed 25001166 reads in 759 ms
[2015-09-30T22:31Z] INFO  23:31:41,125 MuTect - [MUTECT] Processed 193011752 reads in 699 ms
[2015-09-30T22:31Z] INFO  23:31:41,517 MuTect - [MUTECT] Processed 124007859 reads in 730 ms
[2015-09-30T22:31Z] INFO  23:31:41,522 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:31Z] INFO  23:31:41,526 ProgressMeter -            done        5.34e+06    2.6 m       29.0 s    100.0%         2.6 m     0.0 s
[2015-09-30T22:31Z] INFO  23:31:41,526 ProgressMeter - Total runtime 156.59 secs, 2.61 min, 0.04 hours
[2015-09-30T22:31Z] INFO  23:31:41,590 MicroScheduler - 159416 reads were filtered out during the traversal out of approximately 2299924 total reads (6.93%)
[2015-09-30T22:31Z] INFO  23:31:41,591 MicroScheduler -   -> 118463 reads (5.15% of total) failing DuplicateReadFilter
[2015-09-30T22:31Z] INFO  23:31:41,591 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:31Z] INFO  23:31:41,591 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:31Z] INFO  23:31:41,591 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:31Z] INFO  23:31:41,591 MicroScheduler -   -> 40953 reads (1.78% of total) failing UnmappedReadFilter
[2015-09-30T22:31Z] INFO  23:31:41,769 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:41,770 MuTect - [MUTECT] Processed 26001193 reads in 756 ms
[2015-09-30T22:31Z] INFO  23:31:41,778 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:42,169 MuTect - [MUTECT] Processed 125007946 reads in 652 ms
[2015-09-30T22:31Z] INFO  23:31:42,471 MuTect - [MUTECT] Processed 27001214 reads in 701 ms
[2015-09-30T22:31Z] INFO  23:31:42,605 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:31Z] INFO  23:31:42,787 MuTect - [MUTECT] Processed 126008009 reads in 618 ms
[2015-09-30T22:31Z] INFO  23:31:43,209 MuTect - [MUTECT] Processed 28001223 reads in 738 ms
[2015-09-30T22:31Z] INFO  23:31:43,404 MuTect - [MUTECT] Processed 127008019 reads in 617 ms
[2015-09-30T22:31Z] bgzip syn3-11_0_31082819-raw-mutect.vcf
[2015-09-30T22:31Z] tabix index syn3-11_0_31082819-raw-mutect.vcf.gz
[2015-09-30T22:31Z] INFO  23:31:43,801 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:43,885 MuTect - [MUTECT] Processed 29001276 reads in 676 ms
[2015-09-30T22:31Z] INFO  23:31:44,037 MuTect - [MUTECT] Processed 128008064 reads in 632 ms
[2015-09-30T22:31Z] INFO  23:31:44,304 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:44,557 MuTect - [MUTECT] Processed 30001297 reads in 672 ms
[2015-09-30T22:31Z] INFO  23:31:44,743 MuTect - [MUTECT] Processed 129008078 reads in 707 ms
[2015-09-30T22:31Z] INFO  23:31:45,227 MuTect - [MUTECT] Processed 31001320 reads in 670 ms
[2015-09-30T22:31Z] INFO  23:31:45,360 MuTect - [MUTECT] Processed 130008150 reads in 617 ms
[2015-09-30T22:31Z] INFO  23:31:45,944 MuTect - [MUTECT] Processed 32001329 reads in 717 ms
[2015-09-30T22:31Z] INFO  23:31:45,997 MuTect - [MUTECT] Processed 131008244 reads in 637 ms
[2015-09-30T22:31Z] INFO  23:31:46,160 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:31Z] MuTect: MuTect
[2015-09-30T22:31Z] INFO  23:31:46,626 MuTect - [MUTECT] Processed 132008290 reads in 629 ms
[2015-09-30T22:31Z] INFO  23:31:46,628 MuTect - [MUTECT] Processed 33001366 reads in 684 ms
[2015-09-30T22:31Z] INFO  23:31:46,853 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:47,281 MuTect - [MUTECT] Processed 133008312 reads in 655 ms
[2015-09-30T22:31Z] INFO  23:31:47,331 MuTect - [MUTECT] Processed 34001386 reads in 703 ms
[2015-09-30T22:31Z] INFO  23:31:47,933 MuTect - [MUTECT] Processed 134008443 reads in 652 ms
[2015-09-30T22:31Z] INFO  23:31:48,043 MuTect - [MUTECT] Processed 35001429 reads in 712 ms
[2015-09-30T22:31Z] INFO  23:31:48,225 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/11/syn3-11_124188917_135006516-raw-mutect-regions.bed to be BED
[2015-09-30T22:31Z] INFO  23:31:48,255 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:48,280 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:31Z] INFO  23:31:48,280 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:31Z] INFO  23:31:48,280 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:31Z] INFO  23:31:48,281 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:31Z] INFO  23:31:48,284 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/11/syn3-11_124188917_135006516-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/11/tx/tmpNBUSae/syn3-11_124188917_135006516-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:31Z] INFO  23:31:48,284 HelpFormatter - Date/Time: 2015/09/30 23:31:48
[2015-09-30T22:31Z] INFO  23:31:48,284 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:31Z] INFO  23:31:48,284 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:31Z] INFO  23:31:48,312 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:31Z] INFO  23:31:48,316 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:31Z] INFO  23:31:48,370 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:31Z] INFO  23:31:48,417 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:31Z] INFO  23:31:48,424 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:31Z] INFO  23:31:48,448 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:31Z] INFO  23:31:48,459 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:31Z] INFO  23:31:48,584 MuTect - [MUTECT] Processed 135008542 reads in 651 ms
[2015-09-30T22:31Z] INFO  23:31:48,636 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:31Z] INFO  23:31:48,704 IntervalUtils - Processing 489980 bp from intervals
[2015-09-30T22:31Z] INFO  23:31:48,708 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:31Z] INFO  23:31:48,708 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:31Z] INFO  23:31:48,719 MuTect - [MUTECT] Processed 36001441 reads in 676 ms
[2015-09-30T22:31Z] INFO  23:31:48,761 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:31Z] INFO  23:31:48,989 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:31Z] INFO  23:31:48,989 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:31Z] INFO  23:31:48,989 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:31Z] INFO  23:31:48,990 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:31Z] INFO  23:31:49,238 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:49,241 MuTect - [MUTECT] Processed 136008612 reads in 657 ms
[2015-09-30T22:31Z] INFO  23:31:49,432 MuTect - [MUTECT] Processed 37001495 reads in 713 ms
[2015-09-30T22:31Z] INFO  23:31:49,926 MuTect - [MUTECT] Processed 137008668 reads in 685 ms
[2015-09-30T22:31Z] INFO  23:31:50,144 MuTect - [MUTECT] Processed 38001557 reads in 712 ms
[2015-09-30T22:31Z] INFO  23:31:50,454 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:50,604 MuTect - [MUTECT] Processed 138008673 reads in 678 ms
[2015-09-30T22:31Z] INFO  23:31:50,849 MuTect - [MUTECT] Processed 39001629 reads in 705 ms
[2015-09-30T22:31Z] INFO  23:31:51,221 MuTect - [MUTECT] Processed 139008780 reads in 617 ms
[2015-09-30T22:31Z] INFO  23:31:51,389 MuTect - [MUTECT] Processed 1000004 reads in 2353 ms
[2015-09-30T22:31Z] INFO  23:31:51,506 MuTect - [MUTECT] Processed 40001691 reads in 657 ms
[2015-09-30T22:31Z] INFO  23:31:51,508 ProgressMeter -    11:108536223        1.61e+06   30.0 s       18.0 s     36.6%        82.0 s    52.0 s
[2015-09-30T22:31Z] INFO  23:31:51,892 MuTect - [MUTECT] Processed 140008830 reads in 671 ms
[2015-09-30T22:31Z] INFO  23:31:51,986 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:52,199 MuTect - [MUTECT] Processed 41001745 reads in 693 ms
[2015-09-30T22:31Z] INFO  23:31:52,307 MuTect - [MUTECT] Processed 2000056 reads in 918 ms
[2015-09-30T22:31Z] INFO  23:31:52,514 MuTect - [MUTECT] Processed 141008839 reads in 622 ms
[2015-09-30T22:31Z] INFO  23:31:52,675 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:52,951 MuTect - [MUTECT] Processed 42001760 reads in 752 ms
[2015-09-30T22:31Z] INFO  23:31:52,989 MuTect - [MUTECT] Processed 3000059 reads in 682 ms
[2015-09-30T22:31Z] INFO  23:31:53,129 MuTect - [MUTECT] Processed 142008868 reads in 615 ms
[2015-09-30T22:31Z] INFO  23:31:53,244 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:53,615 MuTect - [MUTECT] Processed 4000091 reads in 626 ms
[2015-09-30T22:31Z] INFO  23:31:53,648 MuTect - [MUTECT] Processed 43001813 reads in 697 ms
[2015-09-30T22:31Z] INFO  23:31:53,749 MuTect - [MUTECT] Processed 143008979 reads in 620 ms
[2015-09-30T22:31Z] INFO  23:31:54,260 MuTect - [MUTECT] Processed 5000115 reads in 645 ms
[2015-09-30T22:31Z] INFO  23:31:54,349 MuTect - [MUTECT] Processed 44001827 reads in 701 ms
[2015-09-30T22:31Z] INFO  23:31:54,375 MuTect - [MUTECT] Processed 144009026 reads in 626 ms
[2015-09-30T22:31Z] INFO  23:31:54,514 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:54,907 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:54,932 MuTect - [MUTECT] Processed 6000188 reads in 672 ms
[2015-09-30T22:31Z] INFO  23:31:54,986 MuTect - [MUTECT] Processed 145009083 reads in 611 ms
[2015-09-30T22:31Z] INFO  23:31:55,058 MuTect - [MUTECT] Processed 45001889 reads in 709 ms
[2015-09-30T22:31Z] INFO  23:31:55,563 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:55,586 MuTect - [MUTECT] Processed 146009087 reads in 600 ms
[2015-09-30T22:31Z] INFO  23:31:55,593 MuTect - [MUTECT] Processed 7000214 reads in 661 ms
[2015-09-30T22:31Z] INFO  23:31:55,720 MuTect - [MUTECT] Processed 46001896 reads in 662 ms
[2015-09-30T22:31Z] INFO  23:31:56,213 MuTect - [MUTECT] Processed 147009185 reads in 627 ms
[2015-09-30T22:31Z] INFO  23:31:56,289 MuTect - [MUTECT] Processed 8000238 reads in 696 ms
[2015-09-30T22:31Z] INFO  23:31:56,396 MuTect - [MUTECT] Processed 47001946 reads in 676 ms
[2015-09-30T22:31Z] INFO  23:31:56,819 MuTect - [MUTECT] Processed 148009295 reads in 606 ms
[2015-09-30T22:31Z] INFO  23:31:56,873 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:56,997 MuTect - [MUTECT] Processed 9000272 reads in 708 ms
[2015-09-30T22:31Z] INFO  23:31:57,066 MuTect - [MUTECT] Processed 48002045 reads in 670 ms
[2015-09-30T22:31Z] INFO  23:31:57,308 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:57,486 MuTect - [MUTECT] Processed 149009379 reads in 667 ms
[2015-09-30T22:31Z] INFO  23:31:57,651 MuTect - [MUTECT] Processed 10000380 reads in 654 ms
[2015-09-30T22:31Z] INFO  23:31:57,729 MuTect - [MUTECT] Processed 49002118 reads in 663 ms
[2015-09-30T22:31Z] INFO  23:31:57,820 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:58,153 MuTect - [MUTECT] Processed 150009488 reads in 667 ms
[2015-09-30T22:31Z] INFO  23:31:58,312 MuTect - [MUTECT] Processed 11000457 reads in 661 ms
[2015-09-30T22:31Z] INFO  23:31:58,395 MuTect - [MUTECT] Processed 50002146 reads in 666 ms
[2015-09-30T22:31Z] INFO  23:31:58,784 MuTect - [MUTECT] Processed 151009566 reads in 631 ms
[2015-09-30T22:31Z] INFO  23:31:58,977 MuTect - [MUTECT] Processed 12000476 reads in 665 ms
[2015-09-30T22:31Z] INFO  23:31:59,065 MuTect - [MUTECT] Processed 51002226 reads in 670 ms
[2015-09-30T22:31Z] INFO  23:31:59,191 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:59,281 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:31Z] INFO  23:31:59,470 MuTect - [MUTECT] Processed 152009577 reads in 686 ms
[2015-09-30T22:31Z] INFO  23:31:59,674 MuTect - [MUTECT] Processed 13000478 reads in 697 ms
[2015-09-30T22:31Z] INFO  23:31:59,729 MuTect - [MUTECT] Processed 52002303 reads in 664 ms
[2015-09-30T22:32Z] INFO  23:32:00,162 MuTect - [MUTECT] Processed 153009602 reads in 692 ms
[2015-09-30T22:32Z] INFO  23:32:00,353 MuTect - [MUTECT] Processed 14000525 reads in 679 ms
[2015-09-30T22:32Z] INFO  23:32:00,378 MuTect - [MUTECT] Processed 53002396 reads in 648 ms
[2015-09-30T22:32Z] INFO  23:32:00,381 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:00,844 MuTect - [MUTECT] Processed 154009653 reads in 682 ms
[2015-09-30T22:32Z] INFO  23:32:01,021 MuTect - [MUTECT] Processed 15000600 reads in 668 ms
[2015-09-30T22:32Z] INFO  23:32:01,047 MuTect - [MUTECT] Processed 54002399 reads in 670 ms
[2015-09-30T22:32Z] INFO  23:32:01,301 ProgressMeter -     11:71640331        4.25e+06  100.0 s       23.0 s     57.8%         2.9 m    73.0 s
[2015-09-30T22:32Z] INFO  23:32:01,484 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:01,485 MuTect - [MUTECT] Processed 155009696 reads in 641 ms
[2015-09-30T22:32Z] INFO  23:32:01,661 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:01,682 MuTect - [MUTECT] Processed 16000618 reads in 661 ms
[2015-09-30T22:32Z] INFO  23:32:01,727 MuTect - [MUTECT] Processed 55002492 reads in 680 ms
[2015-09-30T22:32Z] INFO  23:32:02,148 MuTect - [MUTECT] Processed 156009770 reads in 663 ms
[2015-09-30T22:32Z] INFO  23:32:02,360 MuTect - [MUTECT] Processed 17000666 reads in 678 ms
[2015-09-30T22:32Z] INFO  23:32:02,438 MuTect - [MUTECT] Processed 56002546 reads in 711 ms
[2015-09-30T22:32Z] INFO  23:32:02,441 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:02,756 MuTect - [MUTECT] Processed 157009812 reads in 608 ms
[2015-09-30T22:32Z] INFO  23:32:02,990 MuTect - [MUTECT] Processed 18000749 reads in 630 ms
[2015-09-30T22:32Z] INFO  23:32:03,096 MuTect - [MUTECT] Processed 57002651 reads in 658 ms
[2015-09-30T22:32Z] INFO  23:32:03,370 MuTect - [MUTECT] Processed 158009826 reads in 614 ms
[2015-09-30T22:32Z] INFO  23:32:03,649 MuTect - [MUTECT] Processed 19000825 reads in 659 ms
[2015-09-30T22:32Z] INFO  23:32:03,765 MuTect - [MUTECT] Processed 58002698 reads in 669 ms
[2015-09-30T22:32Z] INFO  23:32:03,787 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:03,885 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:04,268 MuTect - [MUTECT] Processed 159009937 reads in 898 ms
[2015-09-30T22:32Z] INFO  23:32:04,354 MuTect - [MUTECT] Processed 20000865 reads in 705 ms
[2015-09-30T22:32Z] INFO  23:32:04,392 MuTect - [MUTECT] Processed 59002703 reads in 627 ms
[2015-09-30T22:32Z] INFO  23:32:04,546 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:04,931 MuTect - [MUTECT] Processed 160010053 reads in 663 ms
[2015-09-30T22:32Z] INFO  23:32:05,018 MuTect - [MUTECT] Processed 60002751 reads in 626 ms
[2015-09-30T22:32Z] INFO  23:32:05,135 MuTect - [MUTECT] Processed 21000974 reads in 781 ms
[2015-09-30T22:32Z] INFO  23:32:05,546 MuTect - [MUTECT] Processed 161010108 reads in 615 ms
[2015-09-30T22:32Z] INFO  23:32:05,686 MuTect - [MUTECT] Processed 61002769 reads in 668 ms
[2015-09-30T22:32Z] INFO  23:32:05,849 MuTect - [MUTECT] Processed 22001086 reads in 714 ms
[2015-09-30T22:32Z] INFO  23:32:06,043 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:06,049 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:06,188 MuTect - [MUTECT] Processed 162010141 reads in 642 ms
[2015-09-30T22:32Z] INFO  23:32:06,374 MuTect - [MUTECT] Processed 62002810 reads in 688 ms
[2015-09-30T22:32Z] INFO  23:32:06,545 MuTect - [MUTECT] Processed 23001154 reads in 696 ms
[2015-09-30T22:32Z] INFO  23:32:06,834 MuTect - [MUTECT] Processed 163010276 reads in 646 ms
[2015-09-30T22:32Z] INFO  23:32:07,057 MuTect - [MUTECT] Processed 63002876 reads in 683 ms
[2015-09-30T22:32Z] INFO  23:32:07,060 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:07,249 MuTect - [MUTECT] Processed 24001220 reads in 704 ms
[2015-09-30T22:32Z] INFO  23:32:07,515 MuTect - [MUTECT] Processed 164010276 reads in 681 ms
[2015-09-30T22:32Z] INFO  23:32:07,710 MuTect - [MUTECT] Processed 64002884 reads in 653 ms
[2015-09-30T22:32Z] INFO  23:32:07,954 MuTect - [MUTECT] Processed 25001232 reads in 705 ms
[2015-09-30T22:32Z] INFO  23:32:08,099 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:08,197 MuTect - [MUTECT] Processed 165010278 reads in 682 ms
[2015-09-30T22:32Z] INFO  23:32:08,363 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:08,395 MuTect - [MUTECT] Processed 65002904 reads in 685 ms
[2015-09-30T22:32Z] INFO  23:32:08,676 MuTect - [MUTECT] Processed 26001295 reads in 722 ms
[2015-09-30T22:32Z] INFO  23:32:08,855 MuTect - [MUTECT] Processed 166010332 reads in 658 ms
[2015-09-30T22:32Z] INFO  23:32:09,032 MuTect - [MUTECT] Processed 66002916 reads in 637 ms
[2015-09-30T22:32Z] INFO  23:32:09,362 MuTect - [MUTECT] Processed 27001384 reads in 686 ms
[2015-09-30T22:32Z] INFO  23:32:09,515 MuTect - [MUTECT] Processed 167010443 reads in 660 ms
[2015-09-30T22:32Z] INFO  23:32:09,643 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:09,681 MuTect - [MUTECT] Processed 67003008 reads in 649 ms
[2015-09-30T22:32Z] INFO  23:32:10,048 MuTect - [MUTECT] Processed 28001506 reads in 686 ms
[2015-09-30T22:32Z] INFO  23:32:10,144 MuTect - [MUTECT] Processed 168010466 reads in 629 ms
[2015-09-30T22:32Z] INFO  23:32:10,248 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:10,498 MuTect - [MUTECT] Processed 68003030 reads in 817 ms
[2015-09-30T22:32Z] INFO  23:32:10,711 MuTect - [MUTECT] Processed 29001579 reads in 663 ms
[2015-09-30T22:32Z] INFO  23:32:10,726 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:10,778 MuTect - [MUTECT] Processed 169010549 reads in 634 ms
[2015-09-30T22:32Z] INFO  23:32:11,143 MuTect - [MUTECT] Processed 69003098 reads in 645 ms
[2015-09-30T22:32Z] INFO  23:32:11,398 MuTect - [MUTECT] Processed 30001642 reads in 687 ms
[2015-09-30T22:32Z] INFO  23:32:11,424 MuTect - [MUTECT] Processed 170010559 reads in 646 ms
[2015-09-30T22:32Z] INFO  23:32:11,785 MuTect - [MUTECT] Processed 70003106 reads in 642 ms
[2015-09-30T22:32Z] INFO  23:32:12,032 MuTect - [MUTECT] Processed 171010564 reads in 608 ms
[2015-09-30T22:32Z] INFO  23:32:12,071 MuTect - [MUTECT] Processed 31001748 reads in 672 ms
[2015-09-30T22:32Z] INFO  23:32:12,101 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:12,435 MuTect - [MUTECT] Processed 71003124 reads in 650 ms
[2015-09-30T22:32Z] INFO  23:32:12,439 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:12,608 MuTect - [MUTECT] Processed 172010661 reads in 576 ms
[2015-09-30T22:32Z] INFO  23:32:12,758 MuTect - [MUTECT] Processed 32001750 reads in 688 ms
[2015-09-30T22:32Z] INFO  23:32:12,876 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:13,144 MuTect - [MUTECT] Processed 72003131 reads in 709 ms
[2015-09-30T22:32Z] INFO  23:32:13,185 MuTect - [MUTECT] Processed 173010731 reads in 577 ms
[2015-09-30T22:32Z] INFO  23:32:13,407 MuTect - [MUTECT] Processed 33001780 reads in 649 ms
[2015-09-30T22:32Z] INFO  23:32:13,805 MuTect - [MUTECT] Processed 174010832 reads in 620 ms
[2015-09-30T22:32Z] INFO  23:32:13,815 MuTect - [MUTECT] Processed 73003225 reads in 671 ms
[2015-09-30T22:32Z] INFO  23:32:14,012 MuTect - [MUTECT] Processed 34001817 reads in 605 ms
[2015-09-30T22:32Z] INFO  23:32:14,164 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:14,478 MuTect - [MUTECT] Processed 175010839 reads in 673 ms
[2015-09-30T22:32Z] INFO  23:32:14,497 MuTect - [MUTECT] Processed 74003292 reads in 682 ms
[2015-09-30T22:32Z] INFO  23:32:14,520 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:14,715 MuTect - [MUTECT] Processed 35001818 reads in 703 ms
[2015-09-30T22:32Z] INFO  23:32:15,107 MuTect - [MUTECT] Processed 176010882 reads in 628 ms
[2015-09-30T22:32Z] INFO  23:32:15,182 MuTect - [MUTECT] Processed 75003353 reads in 685 ms
[2015-09-30T22:32Z] INFO  23:32:15,256 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:15,439 MuTect - [MUTECT] Processed 36001835 reads in 724 ms
[2015-09-30T22:32Z] INFO  23:32:15,725 MuTect - [MUTECT] Processed 177011011 reads in 619 ms
[2015-09-30T22:32Z] INFO  23:32:15,857 MuTect - [MUTECT] Processed 76003450 reads in 675 ms
[2015-09-30T22:32Z] INFO  23:32:16,122 MuTect - [MUTECT] Processed 37001922 reads in 683 ms
[2015-09-30T22:32Z] INFO  23:32:16,376 MuTect - [MUTECT] Processed 178011100 reads in 651 ms
[2015-09-30T22:32Z] INFO  23:32:16,529 MuTect - [MUTECT] Processed 77003500 reads in 672 ms
[2015-09-30T22:32Z] INFO  23:32:16,635 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:16,748 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:16,795 MuTect - [MUTECT] Processed 38001980 reads in 672 ms
[2015-09-30T22:32Z] INFO  23:32:17,033 MuTect - [MUTECT] Processed 179011180 reads in 657 ms
[2015-09-30T22:32Z] INFO  23:32:17,164 MuTect - [MUTECT] Processed 78003553 reads in 635 ms
[2015-09-30T22:32Z] INFO  23:32:17,443 MuTect - [MUTECT] Processed 39002101 reads in 649 ms
[2015-09-30T22:32Z] INFO  23:32:17,657 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:17,668 MuTect - [MUTECT] Processed 180011229 reads in 635 ms
[2015-09-30T22:32Z] INFO  23:32:17,781 MuTect - [MUTECT] Processed 79003572 reads in 617 ms
[2015-09-30T22:32Z] INFO  23:32:18,086 MuTect - [MUTECT] Processed 40002107 reads in 643 ms
[2015-09-30T22:32Z] INFO  23:32:18,306 MuTect - [MUTECT] Processed 181011314 reads in 638 ms
[2015-09-30T22:32Z] INFO  23:32:18,423 MuTect - [MUTECT] Processed 80003612 reads in 642 ms
[2015-09-30T22:32Z] INFO  23:32:18,796 MuTect - [MUTECT] Processed 41002117 reads in 710 ms
[2015-09-30T22:32Z] INFO  23:32:18,927 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:18,969 MuTect - [MUTECT] Processed 182011327 reads in 663 ms
[2015-09-30T22:32Z] INFO  23:32:18,992 ProgressMeter -    11:134039153        1.20e+06   30.0 s       25.0 s     88.2%        33.0 s     3.0 s
[2015-09-30T22:32Z] INFO  23:32:19,000 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:19,039 MuTect - [MUTECT] Processed 81003679 reads in 616 ms
[2015-09-30T22:32Z] INFO  23:32:19,538 MuTect - [MUTECT] Processed 42002160 reads in 742 ms
[2015-09-30T22:32Z] INFO  23:32:19,650 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:19,660 MuTect - [MUTECT] Processed 82003814 reads in 621 ms
[2015-09-30T22:32Z] INFO  23:32:19,696 MuTect - [MUTECT] Processed 183011400 reads in 727 ms
[2015-09-30T22:32Z] INFO  23:32:20,164 MuTect - [MUTECT] Processed 43002173 reads in 626 ms
[2015-09-30T22:32Z] INFO  23:32:20,292 MuTect - [MUTECT] Processed 83003864 reads in 632 ms
[2015-09-30T22:32Z] INFO  23:32:20,352 MuTect - [MUTECT] Processed 184011417 reads in 656 ms
[2015-09-30T22:32Z] INFO  23:32:20,776 MuTect - [MUTECT] Processed 44002222 reads in 612 ms
[2015-09-30T22:32Z] INFO  23:32:20,938 MuTect - [MUTECT] Processed 84003934 reads in 646 ms
[2015-09-30T22:32Z] INFO  23:32:20,999 MuTect - [MUTECT] Processed 185011430 reads in 647 ms
[2015-09-30T22:32Z] INFO  23:32:21,182 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:21,297 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:21,459 MuTect - [MUTECT] Processed 45002251 reads in 683 ms
[2015-09-30T22:32Z] INFO  23:32:21,508 ProgressMeter -    11:117711223        3.04e+06   60.0 s       19.0 s     65.8%        91.0 s    31.0 s
[2015-09-30T22:32Z] INFO  23:32:21,576 MuTect - [MUTECT] Processed 85004041 reads in 638 ms
[2015-09-30T22:32Z] INFO  23:32:21,652 MuTect - [MUTECT] Processed 186011464 reads in 653 ms
[2015-09-30T22:32Z] INFO  23:32:21,675 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:22,165 MuTect - [MUTECT] Processed 46002349 reads in 706 ms
[2015-09-30T22:32Z] INFO  23:32:22,230 MuTect - [MUTECT] Processed 86004053 reads in 654 ms
[2015-09-30T22:32Z] INFO  23:32:22,317 MuTect - [MUTECT] Processed 187011545 reads in 664 ms
[2015-09-30T22:32Z] INFO  23:32:22,876 MuTect - [MUTECT] Processed 87004091 reads in 646 ms
[2015-09-30T22:32Z] INFO  23:32:22,882 MuTect - [MUTECT] Processed 47002454 reads in 717 ms
[2015-09-30T22:32Z] INFO  23:32:22,937 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:32Z] INFO  23:32:22,940 ProgressMeter -            done        1.40e+06   33.0 s       24.0 s    100.0%        33.0 s     0.0 s
[2015-09-30T22:32Z] INFO  23:32:22,940 ProgressMeter - Total runtime 33.95 secs, 0.57 min, 0.01 hours
[2015-09-30T22:32Z] INFO  23:32:22,966 MuTect - [MUTECT] Processed 188011572 reads in 650 ms
[2015-09-30T22:32Z] INFO  23:32:23,007 MicroScheduler - 36329 reads were filtered out during the traversal out of approximately 559076 total reads (6.50%)
[2015-09-30T22:32Z] INFO  23:32:23,008 MicroScheduler -   -> 27097 reads (4.85% of total) failing DuplicateReadFilter
[2015-09-30T22:32Z] INFO  23:32:23,008 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:32Z] INFO  23:32:23,008 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:32Z] INFO  23:32:23,008 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:32Z] INFO  23:32:23,008 MicroScheduler -   -> 9232 reads (1.65% of total) failing UnmappedReadFilter
[2015-09-30T22:32Z] INFO  23:32:23,527 MuTect - [MUTECT] Processed 88004093 reads in 651 ms
[2015-09-30T22:32Z] INFO  23:32:23,533 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:23,593 MuTect - [MUTECT] Processed 189011575 reads in 627 ms
[2015-09-30T22:32Z] INFO  23:32:23,808 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:24,009 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:32Z] bgzip syn3-11_124188917_135006516-raw-mutect.vcf
[2015-09-30T22:32Z] tabix index syn3-11_124188917_135006516-raw-mutect.vcf.gz
[2015-09-30T22:32Z] INFO  23:32:24,191 MuTect - [MUTECT] Processed 89004121 reads in 664 ms
[2015-09-30T22:32Z] INFO  23:32:24,202 MuTect - [MUTECT] Processed 190011636 reads in 609 ms
[2015-09-30T22:32Z] INFO  23:32:24,803 MuTect - [MUTECT] Processed 191011724 reads in 601 ms
[2015-09-30T22:32Z] INFO  23:32:24,848 MuTect - [MUTECT] Processed 90004186 reads in 657 ms
[2015-09-30T22:32Z] INFO  23:32:25,402 MuTect - [MUTECT] Processed 192011779 reads in 599 ms
[2015-09-30T22:32Z] INFO  23:32:25,515 MuTect - [MUTECT] Processed 91004202 reads in 667 ms
[2015-09-30T22:32Z] INFO  23:32:25,945 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:25,996 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:26,018 MuTect - [MUTECT] Processed 193011793 reads in 616 ms
[2015-09-30T22:32Z] INFO  23:32:26,187 MuTect - [MUTECT] Processed 92004241 reads in 672 ms
[2015-09-30T22:32Z] MuTect: MuTect
[2015-09-30T22:32Z] INFO  23:32:26,614 MuTect - [MUTECT] Processed 194011889 reads in 596 ms
[2015-09-30T22:32Z] INFO  23:32:26,836 MuTect - [MUTECT] Processed 93004287 reads in 649 ms
[2015-09-30T22:32Z] INFO  23:32:27,231 MuTect - [MUTECT] Processed 195011952 reads in 617 ms
[2015-09-30T22:32Z] INFO  23:32:27,450 MuTect - [MUTECT] Processed 94004293 reads in 614 ms
[2015-09-30T22:32Z] INFO  23:32:27,829 MuTect - [MUTECT] Processed 196011954 reads in 598 ms
[2015-09-30T22:32Z] INFO  23:32:28,076 MuTect - [MUTECT] Processed 95004386 reads in 626 ms
[2015-09-30T22:32Z] INFO  23:32:28,180 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:28,295 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:28,458 MuTect - [MUTECT] Processed 197011998 reads in 629 ms
[2015-09-30T22:32Z] INFO  23:32:28,497 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/12/syn3-12_0_31107241-raw-mutect-regions.bed to be BED
[2015-09-30T22:32Z] INFO  23:32:28,552 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:32Z] INFO  23:32:28,552 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:32Z] INFO  23:32:28,553 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:32Z] INFO  23:32:28,553 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:32Z] INFO  23:32:28,556 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/12/syn3-12_0_31107241-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/12/tx/tmp5bGvcB/syn3-12_0_31107241-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:32Z] INFO  23:32:28,556 HelpFormatter - Date/Time: 2015/09/30 23:32:28
[2015-09-30T22:32Z] INFO  23:32:28,556 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:32Z] INFO  23:32:28,557 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:32Z] INFO  23:32:28,584 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:32Z] INFO  23:32:28,588 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:32Z] INFO  23:32:28,638 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:32Z] INFO  23:32:28,682 MuTect - [MUTECT] Processed 96004410 reads in 606 ms
[2015-09-30T22:32Z] INFO  23:32:28,686 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:32Z] INFO  23:32:28,693 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:32Z] INFO  23:32:28,717 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:32Z] INFO  23:32:28,728 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:32Z] INFO  23:32:28,905 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:32Z] INFO  23:32:29,025 IntervalUtils - Processing 1912448 bp from intervals
[2015-09-30T22:32Z] INFO  23:32:29,029 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:32Z] INFO  23:32:29,029 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:32Z] INFO  23:32:29,101 MuTect - [MUTECT] Processed 198012043 reads in 643 ms
[2015-09-30T22:32Z] INFO  23:32:29,183 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:32Z] INFO  23:32:29,297 MuTect - [MUTECT] Processed 97004506 reads in 615 ms
[2015-09-30T22:32Z] INFO  23:32:29,361 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:32Z] INFO  23:32:29,361 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:32Z] INFO  23:32:29,361 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:32Z] INFO  23:32:29,362 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:32Z] INFO  23:32:29,736 MuTect - [MUTECT] Processed 199012059 reads in 635 ms
[2015-09-30T22:32Z] INFO  23:32:29,932 MuTect - [MUTECT] Processed 98004578 reads in 635 ms
[2015-09-30T22:32Z] INFO  23:32:30,283 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:30,374 MuTect - [MUTECT] Processed 200012080 reads in 638 ms
[2015-09-30T22:32Z] INFO  23:32:30,460 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:30,602 MuTect - [MUTECT] Processed 99004686 reads in 670 ms
[2015-09-30T22:32Z] INFO  23:32:31,013 MuTect - [MUTECT] Processed 201012138 reads in 639 ms
[2015-09-30T22:32Z] INFO  23:32:31,291 MuTect - [MUTECT] Processed 100004787 reads in 689 ms
[2015-09-30T22:32Z] INFO  23:32:31,302 ProgressMeter -     11:76868409        5.47e+06    2.2 m       23.0 s     77.1%         2.8 m    38.0 s
[2015-09-30T22:32Z] INFO  23:32:31,678 MuTect - [MUTECT] Processed 202012223 reads in 665 ms
[2015-09-30T22:32Z] INFO  23:32:31,711 MuTect - [MUTECT] Processed 1000200 reads in 2302 ms
[2015-09-30T22:32Z] INFO  23:32:31,957 MuTect - [MUTECT] Processed 101004867 reads in 666 ms
[2015-09-30T22:32Z] INFO  23:32:32,291 MuTect - [MUTECT] Processed 203012314 reads in 613 ms
[2015-09-30T22:32Z] INFO  23:32:32,364 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:32,651 MuTect - [MUTECT] Processed 102004930 reads in 694 ms
[2015-09-30T22:32Z] INFO  23:32:32,723 MuTect - [MUTECT] Processed 2000247 reads in 1012 ms
[2015-09-30T22:32Z] INFO  23:32:32,734 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:32,899 MuTect - [MUTECT] Processed 204012382 reads in 608 ms
[2015-09-30T22:32Z] INFO  23:32:33,260 MuTect - [MUTECT] Processed 103005022 reads in 609 ms
[2015-09-30T22:32Z] INFO  23:32:33,545 MuTect - [MUTECT] Processed 205012466 reads in 646 ms
[2015-09-30T22:32Z] INFO  23:32:33,594 MuTect - [MUTECT] Processed 3000277 reads in 871 ms
[2015-09-30T22:32Z] INFO  23:32:33,866 MuTect - [MUTECT] Processed 104005136 reads in 606 ms
[2015-09-30T22:32Z] INFO  23:32:34,126 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:34,155 MuTect - [MUTECT] Processed 206012526 reads in 610 ms
[2015-09-30T22:32Z] INFO  23:32:34,358 MuTect - [MUTECT] Processed 4000295 reads in 764 ms
[2015-09-30T22:32Z] INFO  23:32:34,509 MuTect - [MUTECT] Processed 105005136 reads in 643 ms
[2015-09-30T22:32Z] INFO  23:32:34,570 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:34,769 MuTect - [MUTECT] Processed 207012567 reads in 614 ms
[2015-09-30T22:32Z] INFO  23:32:34,800 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:35,184 MuTect - [MUTECT] Processed 106005219 reads in 675 ms
[2015-09-30T22:32Z] INFO  23:32:35,277 MuTect - [MUTECT] Processed 5000406 reads in 919 ms
[2015-09-30T22:32Z] INFO  23:32:35,408 MuTect - [MUTECT] Processed 208012601 reads in 639 ms
[2015-09-30T22:32Z] INFO  23:32:35,804 MuTect - [MUTECT] Processed 107005234 reads in 620 ms
[2015-09-30T22:32Z] INFO  23:32:35,998 MuTect - [MUTECT] Processed 6000416 reads in 721 ms
[2015-09-30T22:32Z] INFO  23:32:36,060 MuTect - [MUTECT] Processed 209012661 reads in 652 ms
[2015-09-30T22:32Z] INFO  23:32:36,462 MuTect - [MUTECT] Processed 108005290 reads in 658 ms
[2015-09-30T22:32Z] INFO  23:32:36,640 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:36,712 MuTect - [MUTECT] Processed 210012734 reads in 652 ms
[2015-09-30T22:32Z] INFO  23:32:36,717 MuTect - [MUTECT] Processed 7000428 reads in 719 ms
[2015-09-30T22:32Z] INFO  23:32:36,990 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:37,054 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:37,120 MuTect - [MUTECT] Processed 109005422 reads in 658 ms
[2015-09-30T22:32Z] INFO  23:32:37,415 MuTect - [MUTECT] Processed 211012753 reads in 703 ms
[2015-09-30T22:32Z] INFO  23:32:37,446 MuTect - [MUTECT] Processed 8000431 reads in 729 ms
[2015-09-30T22:32Z] INFO  23:32:37,813 MuTect - [MUTECT] Processed 110005498 reads in 693 ms
[2015-09-30T22:32Z] INFO  23:32:38,023 MuTect - [MUTECT] Processed 212012760 reads in 608 ms
[2015-09-30T22:32Z] INFO  23:32:38,104 MuTect - [MUTECT] Processed 9000537 reads in 658 ms
[2015-09-30T22:32Z] INFO  23:32:38,509 MuTect - [MUTECT] Processed 111005558 reads in 696 ms
[2015-09-30T22:32Z] INFO  23:32:38,620 MuTect - [MUTECT] Processed 213012763 reads in 597 ms
[2015-09-30T22:32Z] INFO  23:32:38,755 MuTect - [MUTECT] Processed 10000643 reads in 651 ms
[2015-09-30T22:32Z] INFO  23:32:39,053 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:39,159 MuTect - [MUTECT] Processed 112005560 reads in 650 ms
[2015-09-30T22:32Z] INFO  23:32:39,220 MuTect - [MUTECT] Processed 214012765 reads in 600 ms
[2015-09-30T22:32Z] INFO  23:32:39,243 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:39,353 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:39,461 MuTect - [MUTECT] Processed 11000647 reads in 706 ms
[2015-09-30T22:32Z] INFO  23:32:39,793 MuTect - [MUTECT] Processed 113005605 reads in 634 ms
[2015-09-30T22:32Z] INFO  23:32:39,830 MuTect - [MUTECT] Processed 215012778 reads in 610 ms
[2015-09-30T22:32Z] INFO  23:32:40,177 MuTect - [MUTECT] Processed 12000671 reads in 716 ms
[2015-09-30T22:32Z] INFO  23:32:40,465 MuTect - [MUTECT] Processed 114005638 reads in 672 ms
[2015-09-30T22:32Z] INFO  23:32:40,468 MuTect - [MUTECT] Processed 216012848 reads in 638 ms
[2015-09-30T22:32Z] INFO  23:32:40,909 MuTect - [MUTECT] Processed 13000703 reads in 732 ms
[2015-09-30T22:32Z] INFO  23:32:41,111 MuTect - [MUTECT] Processed 217012912 reads in 643 ms
[2015-09-30T22:32Z] INFO  23:32:41,114 MuTect - [MUTECT] Processed 115005643 reads in 649 ms
[2015-09-30T22:32Z] INFO  23:32:41,427 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:41,483 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:41,642 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:41,646 MuTect - [MUTECT] Processed 14000828 reads in 736 ms
[2015-09-30T22:32Z] INFO  23:32:41,714 MuTect - [MUTECT] Processed 218012992 reads in 603 ms
[2015-09-30T22:32Z] INFO  23:32:41,751 MuTect - [MUTECT] Processed 116005710 reads in 637 ms
[2015-09-30T22:32Z] INFO  23:32:42,339 MuTect - [MUTECT] Processed 219013017 reads in 625 ms
[2015-09-30T22:32Z] INFO  23:32:42,340 MuTect - [MUTECT] Processed 15000901 reads in 695 ms
[2015-09-30T22:32Z] INFO  23:32:42,424 MuTect - [MUTECT] Processed 117005726 reads in 673 ms
[2015-09-30T22:32Z] INFO  23:32:43,008 MuTect - [MUTECT] Processed 220013111 reads in 669 ms
[2015-09-30T22:32Z] INFO  23:32:43,042 MuTect - [MUTECT] Processed 16001004 reads in 702 ms
[2015-09-30T22:32Z] INFO  23:32:43,095 MuTect - [MUTECT] Processed 118005726 reads in 671 ms
[2015-09-30T22:32Z] INFO  23:32:43,649 MuTect - [MUTECT] Processed 221013128 reads in 641 ms
[2015-09-30T22:32Z] INFO  23:32:43,669 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:43,700 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:43,807 MuTect - [MUTECT] Processed 119005758 reads in 712 ms
[2015-09-30T22:32Z] INFO  23:32:43,824 MuTect - [MUTECT] Processed 17001024 reads in 782 ms
[2015-09-30T22:32Z] INFO  23:32:44,205 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:44,315 MuTect - [MUTECT] Processed 222013153 reads in 666 ms
[2015-09-30T22:32Z] INFO  23:32:44,465 MuTect - [MUTECT] Processed 120005826 reads in 658 ms
[2015-09-30T22:32Z] INFO  23:32:44,582 MuTect - [MUTECT] Processed 18001121 reads in 758 ms
[2015-09-30T22:32Z] INFO  23:32:44,976 MuTect - [MUTECT] Processed 223013190 reads in 660 ms
[2015-09-30T22:32Z] INFO  23:32:45,161 MuTect - [MUTECT] Processed 121005833 reads in 696 ms
[2015-09-30T22:32Z] INFO  23:32:45,272 MuTect - [MUTECT] Processed 19001123 reads in 690 ms
[2015-09-30T22:32Z] INFO  23:32:45,593 MuTect - [MUTECT] Processed 224013239 reads in 618 ms
[2015-09-30T22:32Z] INFO  23:32:45,837 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:45,842 MuTect - [MUTECT] Processed 122005849 reads in 681 ms
[2015-09-30T22:32Z] INFO  23:32:45,951 MuTect - [MUTECT] Processed 20001128 reads in 679 ms
[2015-09-30T22:32Z] INFO  23:32:46,122 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:46,222 MuTect - [MUTECT] Processed 225013244 reads in 629 ms
[2015-09-30T22:32Z] INFO  23:32:46,485 MuTect - [MUTECT] Processed 123005905 reads in 643 ms
[2015-09-30T22:32Z] INFO  23:32:46,542 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:46,657 MuTect - [MUTECT] Processed 21001168 reads in 706 ms
[2015-09-30T22:32Z] INFO  23:32:46,847 MuTect - [MUTECT] Processed 226013279 reads in 625 ms
[2015-09-30T22:32Z] INFO  23:32:47,132 MuTect - [MUTECT] Processed 124005954 reads in 647 ms
[2015-09-30T22:32Z] INFO  23:32:47,363 MuTect - [MUTECT] Processed 22001198 reads in 706 ms
[2015-09-30T22:32Z] INFO  23:32:47,498 MuTect - [MUTECT] Processed 227013308 reads in 651 ms
[2015-09-30T22:32Z] INFO  23:32:47,786 MuTect - [MUTECT] Processed 125005966 reads in 654 ms
[2015-09-30T22:32Z] INFO  23:32:48,104 MuTect - [MUTECT] Processed 23001263 reads in 741 ms
[2015-09-30T22:32Z] INFO  23:32:48,141 MuTect - [MUTECT] Processed 228013343 reads in 643 ms
[2015-09-30T22:32Z] INFO  23:32:48,325 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:48,425 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:48,442 MuTect - [MUTECT] Processed 126005992 reads in 656 ms
[2015-09-30T22:32Z] INFO  23:32:48,762 MuTect - [MUTECT] Processed 229013409 reads in 621 ms
[2015-09-30T22:32Z] INFO  23:32:48,821 MuTect - [MUTECT] Processed 24001295 reads in 717 ms
[2015-09-30T22:32Z] INFO  23:32:48,954 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:49,079 MuTect - [MUTECT] Processed 127006100 reads in 637 ms
[2015-09-30T22:32Z] INFO  23:32:49,370 MuTect - [MUTECT] Processed 230013455 reads in 608 ms
[2015-09-30T22:32Z] INFO  23:32:49,503 MuTect - [MUTECT] Processed 25001383 reads in 682 ms
[2015-09-30T22:32Z] INFO  23:32:49,715 MuTect - [MUTECT] Processed 128006152 reads in 636 ms
[2015-09-30T22:32Z] INFO  23:32:50,049 MuTect - [MUTECT] Processed 231013471 reads in 679 ms
[2015-09-30T22:32Z] INFO  23:32:50,158 MuTect - [MUTECT] Processed 26001444 reads in 655 ms
[2015-09-30T22:32Z] INFO  23:32:50,382 MuTect - [MUTECT] Processed 129006188 reads in 667 ms
[2015-09-30T22:32Z] INFO  23:32:50,702 MuTect - [MUTECT] Processed 232013527 reads in 653 ms
[2015-09-30T22:32Z] INFO  23:32:50,770 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:50,812 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:50,832 MuTect - [MUTECT] Processed 27001566 reads in 674 ms
[2015-09-30T22:32Z] INFO  23:32:51,051 MuTect - [MUTECT] Processed 130006242 reads in 669 ms
[2015-09-30T22:32Z] INFO  23:32:51,321 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:51,448 MuTect - [MUTECT] Processed 233013534 reads in 746 ms
[2015-09-30T22:32Z] INFO  23:32:51,509 ProgressMeter -    11:121485810        4.48e+06   90.0 s       20.0 s     93.0%        96.0 s     6.0 s
[2015-09-30T22:32Z] INFO  23:32:51,533 MuTect - [MUTECT] Processed 28001667 reads in 701 ms
[2015-09-30T22:32Z] INFO  23:32:51,700 MuTect - [MUTECT] Processed 131006329 reads in 649 ms
[2015-09-30T22:32Z] INFO  23:32:52,144 MuTect - [MUTECT] Processed 234013681 reads in 696 ms
[2015-09-30T22:32Z] INFO  23:32:52,241 MuTect - [MUTECT] Processed 29001701 reads in 708 ms
[2015-09-30T22:32Z] INFO  23:32:52,398 MuTect - [MUTECT] Processed 132006363 reads in 698 ms
[2015-09-30T22:32Z] INFO  23:32:52,773 MuTect - [MUTECT] Processed 235013739 reads in 629 ms
[2015-09-30T22:32Z] INFO  23:32:52,917 MuTect - [MUTECT] Processed 30001713 reads in 676 ms
[2015-09-30T22:32Z] INFO  23:32:53,081 MuTect - [MUTECT] Processed 133006390 reads in 683 ms
[2015-09-30T22:32Z] INFO  23:32:53,203 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:53,363 MuTect - [MUTECT] Processed 236013739 reads in 590 ms
[2015-09-30T22:32Z] INFO  23:32:53,553 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:53,660 MuTect - [MUTECT] Processed 31001795 reads in 743 ms
[2015-09-30T22:32Z] INFO  23:32:53,769 MuTect - [MUTECT] Processed 134006417 reads in 688 ms
[2015-09-30T22:32Z] INFO  23:32:53,960 MuTect - [MUTECT] Processed 237013753 reads in 597 ms
[2015-09-30T22:32Z] INFO  23:32:54,359 MuTect - [MUTECT] Processed 32001821 reads in 698 ms
[2015-09-30T22:32Z] INFO  23:32:54,450 MuTect - [MUTECT] Processed 135006450 reads in 681 ms
[2015-09-30T22:32Z] INFO  23:32:54,565 MuTect - [MUTECT] Processed 238013777 reads in 605 ms
[2015-09-30T22:32Z] INFO  23:32:54,832 MuTect - [MUTECT] Inspected 69000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:55,028 MuTect - [MUTECT] Processed 33001828 reads in 670 ms
[2015-09-30T22:32Z] INFO  23:32:55,138 MuTect - [MUTECT] Processed 136006531 reads in 688 ms
[2015-09-30T22:32Z] INFO  23:32:55,232 MuTect - [MUTECT] Processed 239013797 reads in 667 ms
[2015-09-30T22:32Z] INFO  23:32:55,350 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:55,729 MuTect - [MUTECT] Processed 34001861 reads in 701 ms
[2015-09-30T22:32Z] INFO  23:32:55,802 MuTect - [MUTECT] Processed 137006578 reads in 664 ms
[2015-09-30T22:32Z] INFO  23:32:55,917 MuTect - [MUTECT] Processed 240013882 reads in 685 ms
[2015-09-30T22:32Z] INFO  23:32:56,029 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:56,411 MuTect - [MUTECT] Processed 35001891 reads in 682 ms
[2015-09-30T22:32Z] INFO  23:32:56,446 MuTect - [MUTECT] Processed 138006595 reads in 644 ms
[2015-09-30T22:32Z] INFO  23:32:56,558 MuTect - [MUTECT] Processed 241013935 reads in 641 ms
[2015-09-30T22:32Z] INFO  23:32:57,115 MuTect - [MUTECT] Processed 139006614 reads in 669 ms
[2015-09-30T22:32Z] INFO  23:32:57,126 MuTect - [MUTECT] Processed 36001974 reads in 715 ms
[2015-09-30T22:32Z] INFO  23:32:57,190 MuTect - [MUTECT] Processed 242013974 reads in 632 ms
[2015-09-30T22:32Z] INFO  23:32:57,290 MuTect - [MUTECT] Inspected 70000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:57,625 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:57,794 MuTect - [MUTECT] Processed 140006649 reads in 679 ms
[2015-09-30T22:32Z] INFO  23:32:57,805 MuTect - [MUTECT] Processed 37002050 reads in 679 ms
[2015-09-30T22:32Z] INFO  23:32:57,844 MuTect - [MUTECT] Processed 243014025 reads in 654 ms
[2015-09-30T22:32Z] INFO  23:32:58,192 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:32Z] INFO  23:32:58,196 ProgressMeter -            done        6.82e+06    2.6 m       22.0 s    100.0%         2.6 m     0.0 s
[2015-09-30T22:32Z] INFO  23:32:58,196 ProgressMeter - Total runtime 156.90 secs, 2.61 min, 0.04 hours
[2015-09-30T22:32Z] INFO  23:32:58,259 MicroScheduler - 196939 reads were filtered out during the traversal out of approximately 2881057 total reads (6.84%)
[2015-09-30T22:32Z] INFO  23:32:58,259 MicroScheduler -   -> 148730 reads (5.16% of total) failing DuplicateReadFilter
[2015-09-30T22:32Z] INFO  23:32:58,260 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:32Z] INFO  23:32:58,260 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:32Z] INFO  23:32:58,260 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:32Z] INFO  23:32:58,260 MicroScheduler -   -> 48209 reads (1.67% of total) failing UnmappedReadFilter
[2015-09-30T22:32Z] INFO  23:32:58,361 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:32Z] INFO  23:32:58,466 MuTect - [MUTECT] Processed 38002119 reads in 661 ms
[2015-09-30T22:32Z] INFO  23:32:58,508 MuTect - [MUTECT] Processed 141006689 reads in 714 ms
[2015-09-30T22:32Z] INFO  23:32:58,776 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:32Z] INFO  23:32:58,780 ProgressMeter -            done        4.74e+06   97.0 s       20.0 s    100.0%        97.0 s     0.0 s
[2015-09-30T22:32Z] INFO  23:32:58,780 ProgressMeter - Total runtime 97.28 secs, 1.62 min, 0.03 hours
[2015-09-30T22:32Z] INFO  23:32:58,843 MicroScheduler - 104344 reads were filtered out during the traversal out of approximately 1678830 total reads (6.22%)
[2015-09-30T22:32Z] INFO  23:32:58,844 MicroScheduler -   -> 77419 reads (4.61% of total) failing DuplicateReadFilter
[2015-09-30T22:32Z] INFO  23:32:58,844 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:32Z] INFO  23:32:58,844 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:32Z] INFO  23:32:58,844 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:32Z] INFO  23:32:58,844 MicroScheduler -   -> 26925 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:32Z] INFO  23:32:59,141 MuTect - [MUTECT] Processed 39002159 reads in 675 ms
[2015-09-30T22:32Z] INFO  23:32:59,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:32Z] INFO  23:32:59,363 ProgressMeter -      12:5724576        1.02e+06   30.0 s       29.0 s     20.1%         2.5 m   119.0 s
[2015-09-30T22:32Z] bgzip syn3-11_62123540_93141822-raw-mutect.vcf
[2015-09-30T22:32Z] tabix index syn3-11_62123540_93141822-raw-mutect.vcf.gz
[2015-09-30T22:32Z] INFO  23:32:59,835 MuTect - [MUTECT] Processed 40002205 reads in 694 ms
[2015-09-30T22:32Z] INFO  23:32:59,845 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:32Z] bgzip syn3-11_93147865_124180877-raw-mutect.vcf
[2015-09-30T22:32Z] tabix index syn3-11_93147865_124180877-raw-mutect.vcf.gz
[2015-09-30T22:33Z] INFO  23:33:00,548 MuTect - [MUTECT] Processed 41002271 reads in 713 ms
[2015-09-30T22:33Z] INFO  23:33:00,802 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:01,246 MuTect - [MUTECT] Processed 42002287 reads in 698 ms
[2015-09-30T22:33Z] INFO  23:33:01,956 MuTect - [MUTECT] Processed 43002363 reads in 710 ms
[2015-09-30T22:33Z] MuTect: MuTect
[2015-09-30T22:33Z] MuTect: MuTect
[2015-09-30T22:33Z] INFO  23:33:02,628 MuTect - [MUTECT] Processed 44002414 reads in 672 ms
[2015-09-30T22:33Z] INFO  23:33:03,148 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:03,296 MuTect - [MUTECT] Processed 45002447 reads in 668 ms
[2015-09-30T22:33Z] INFO  23:33:03,971 MuTect - [MUTECT] Processed 46002455 reads in 675 ms
[2015-09-30T22:33Z] INFO  23:33:04,643 MuTect - [MUTECT] Processed 47002499 reads in 672 ms
[2015-09-30T22:33Z] INFO  23:33:04,773 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/12/syn3-12_31116488_62142833-raw-mutect-regions.bed to be BED
[2015-09-30T22:33Z] INFO  23:33:04,828 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:33Z] INFO  23:33:04,829 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:33Z] INFO  23:33:04,829 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:33Z] INFO  23:33:04,829 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:33Z] INFO  23:33:04,832 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/12/syn3-12_31116488_62142833-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/12/tx/tmp9XiPjZ/syn3-12_31116488_62142833-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:33Z] INFO  23:33:04,833 HelpFormatter - Date/Time: 2015/09/30 23:33:04
[2015-09-30T22:33Z] INFO  23:33:04,833 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:33Z] INFO  23:33:04,833 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:33Z] INFO  23:33:04,859 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:33Z] INFO  23:33:04,863 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:33Z] INFO  23:33:04,912 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:33Z] INFO  23:33:04,932 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/12/syn3-12_62147092_93167456-raw-mutect-regions.bed to be BED
[2015-09-30T22:33Z] INFO  23:33:04,960 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:33Z] INFO  23:33:04,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:33Z] INFO  23:33:04,987 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:33Z] INFO  23:33:04,987 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:33Z] INFO  23:33:04,987 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:33Z] INFO  23:33:04,987 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:33Z] INFO  23:33:04,991 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/12/syn3-12_62147092_93167456-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/12/tx/tmpdG57CZ/syn3-12_62147092_93167456-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:33Z] INFO  23:33:04,991 HelpFormatter - Date/Time: 2015/09/30 23:33:04
[2015-09-30T22:33Z] INFO  23:33:04,991 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:33Z] INFO  23:33:04,991 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:33Z] INFO  23:33:05,005 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:33Z] INFO  23:33:05,018 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:33Z] INFO  23:33:05,022 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:33Z] INFO  23:33:05,027 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:33Z] INFO  23:33:05,076 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:33Z] INFO  23:33:05,123 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:33Z] INFO  23:33:05,130 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:33Z] INFO  23:33:05,230 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:33Z] INFO  23:33:05,247 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2015-09-30T22:33Z] INFO  23:33:05,281 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:33Z] INFO  23:33:05,338 MuTect - [MUTECT] Processed 48002559 reads in 694 ms
[2015-09-30T22:33Z] INFO  23:33:05,343 IntervalUtils - Processing 2217019 bp from intervals
[2015-09-30T22:33Z] INFO  23:33:05,347 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:33Z] INFO  23:33:05,347 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:33Z] INFO  23:33:05,455 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:33Z] INFO  23:33:05,462 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:05,521 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:33Z] INFO  23:33:05,543 IntervalUtils - Processing 991077 bp from intervals
[2015-09-30T22:33Z] INFO  23:33:05,547 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:33Z] INFO  23:33:05,547 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:33Z] INFO  23:33:05,677 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:33Z] INFO  23:33:05,678 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:33Z] INFO  23:33:05,678 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:33Z] INFO  23:33:05,679 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:33Z] INFO  23:33:05,695 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:33Z] INFO  23:33:05,812 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:33Z] INFO  23:33:05,812 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:33Z] INFO  23:33:05,812 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:33Z] INFO  23:33:05,813 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:33Z] INFO  23:33:06,066 MuTect - [MUTECT] Processed 49002618 reads in 729 ms
[2015-09-30T22:33Z] INFO  23:33:06,801 MuTect - [MUTECT] Processed 50002705 reads in 735 ms
[2015-09-30T22:33Z] INFO  23:33:07,541 MuTect - [MUTECT] Processed 51002724 reads in 740 ms
[2015-09-30T22:33Z] INFO  23:33:07,926 MuTect - [MUTECT] Processed 1000039 reads in 2194 ms
[2015-09-30T22:33Z] INFO  23:33:07,943 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:08,294 MuTect - [MUTECT] Processed 52002830 reads in 752 ms
[2015-09-30T22:33Z] INFO  23:33:08,415 MuTect - [MUTECT] Processed 1000007 reads in 2556 ms
[2015-09-30T22:33Z] INFO  23:33:08,917 MuTect - [MUTECT] Processed 2000084 reads in 990 ms
[2015-09-30T22:33Z] INFO  23:33:08,978 MuTect - [MUTECT] Processed 53002940 reads in 685 ms
[2015-09-30T22:33Z] INFO  23:33:09,176 MuTect - [MUTECT] Processed 2000012 reads in 761 ms
[2015-09-30T22:33Z] INFO  23:33:09,615 MuTect - [MUTECT] Processed 54003028 reads in 637 ms
[2015-09-30T22:33Z] INFO  23:33:09,687 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:09,815 MuTect - [MUTECT] Processed 3000087 reads in 899 ms
[2015-09-30T22:33Z] INFO  23:33:09,867 MuTect - [MUTECT] Processed 3000089 reads in 691 ms
[2015-09-30T22:33Z] INFO  23:33:10,254 MuTect - [MUTECT] Processed 55003086 reads in 639 ms
[2015-09-30T22:33Z] INFO  23:33:10,585 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:10,605 MuTect - [MUTECT] Processed 4000099 reads in 790 ms
[2015-09-30T22:33Z] INFO  23:33:10,722 MuTect - [MUTECT] Processed 4000139 reads in 855 ms
[2015-09-30T22:33Z] INFO  23:33:10,734 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:10,944 MuTect - [MUTECT] Processed 56003133 reads in 690 ms
[2015-09-30T22:33Z] INFO  23:33:11,445 MuTect - [MUTECT] Processed 5000137 reads in 840 ms
[2015-09-30T22:33Z] INFO  23:33:11,453 MuTect - [MUTECT] Processed 5000145 reads in 731 ms
[2015-09-30T22:33Z] INFO  23:33:11,616 MuTect - [MUTECT] Processed 57003182 reads in 672 ms
[2015-09-30T22:33Z] INFO  23:33:12,097 MuTect - [MUTECT] Processed 6000166 reads in 652 ms
[2015-09-30T22:33Z] INFO  23:33:12,204 MuTect - [MUTECT] Processed 6000190 reads in 750 ms
[2015-09-30T22:33Z] INFO  23:33:12,298 MuTect - [MUTECT] Processed 58003260 reads in 682 ms
[2015-09-30T22:33Z] INFO  23:33:12,448 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:12,779 MuTect - [MUTECT] Processed 7000258 reads in 682 ms
[2015-09-30T22:33Z] INFO  23:33:12,895 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:12,933 MuTect - [MUTECT] Processed 7000203 reads in 730 ms
[2015-09-30T22:33Z] INFO  23:33:12,965 MuTect - [MUTECT] Processed 59003284 reads in 667 ms
[2015-09-30T22:33Z] INFO  23:33:13,479 MuTect - [MUTECT] Processed 8000346 reads in 699 ms
[2015-09-30T22:33Z] INFO  23:33:13,480 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:13,679 MuTect - [MUTECT] Processed 60003386 reads in 714 ms
[2015-09-30T22:33Z] INFO  23:33:13,696 MuTect - [MUTECT] Processed 8000314 reads in 762 ms
[2015-09-30T22:33Z] INFO  23:33:14,180 MuTect - [MUTECT] Processed 9000367 reads in 702 ms
[2015-09-30T22:33Z] INFO  23:33:14,395 MuTect - [MUTECT] Processed 9000395 reads in 700 ms
[2015-09-30T22:33Z] INFO  23:33:14,805 MuTect - [MUTECT] Processed 10000410 reads in 625 ms
[2015-09-30T22:33Z] INFO  23:33:14,880 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:15,025 MuTect - [MUTECT] Processed 10000433 reads in 630 ms
[2015-09-30T22:33Z] INFO  23:33:15,427 MuTect - [MUTECT] Processed 61003438 reads in 1747 ms
[2015-09-30T22:33Z] INFO  23:33:15,437 MuTect - [MUTECT] Processed 11000457 reads in 632 ms
[2015-09-30T22:33Z] INFO  23:33:15,712 MuTect - [MUTECT] Processed 11000493 reads in 687 ms
[2015-09-30T22:33Z] INFO  23:33:16,014 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:16,109 MuTect - [MUTECT] Processed 62003571 reads in 683 ms
[2015-09-30T22:33Z] INFO  23:33:16,112 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:16,158 MuTect - [MUTECT] Processed 12000520 reads in 721 ms
[2015-09-30T22:33Z] INFO  23:33:16,357 MuTect - [MUTECT] Processed 12000577 reads in 645 ms
[2015-09-30T22:33Z] INFO  23:33:16,765 MuTect - [MUTECT] Processed 63003572 reads in 656 ms
[2015-09-30T22:33Z] INFO  23:33:16,837 MuTect - [MUTECT] Processed 13000540 reads in 679 ms
[2015-09-30T22:33Z] INFO  23:33:17,008 MuTect - [MUTECT] Processed 13000585 reads in 651 ms
[2015-09-30T22:33Z] INFO  23:33:17,327 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:17,464 MuTect - [MUTECT] Processed 14000561 reads in 627 ms
[2015-09-30T22:33Z] INFO  23:33:17,691 MuTect - [MUTECT] Processed 14000598 reads in 683 ms
[2015-09-30T22:33Z] INFO  23:33:17,900 MuTect - [MUTECT] Processed 64003655 reads in 1135 ms
[2015-09-30T22:33Z] INFO  23:33:18,140 MuTect - [MUTECT] Processed 15000612 reads in 676 ms
[2015-09-30T22:33Z] INFO  23:33:18,374 MuTect - [MUTECT] Processed 15000643 reads in 682 ms
[2015-09-30T22:33Z] INFO  23:33:18,453 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:18,578 MuTect - [MUTECT] Processed 65003702 reads in 678 ms
[2015-09-30T22:33Z] INFO  23:33:18,852 MuTect - [MUTECT] Processed 16000688 reads in 712 ms
[2015-09-30T22:33Z] INFO  23:33:18,877 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:19,035 MuTect - [MUTECT] Processed 16000679 reads in 662 ms
[2015-09-30T22:33Z] INFO  23:33:19,251 MuTect - [MUTECT] Processed 66003839 reads in 673 ms
[2015-09-30T22:33Z] INFO  23:33:19,562 MuTect - [MUTECT] Processed 17000701 reads in 710 ms
[2015-09-30T22:33Z] INFO  23:33:19,665 MuTect - [MUTECT] Processed 17000692 reads in 630 ms
[2015-09-30T22:33Z] INFO  23:33:19,773 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:19,938 MuTect - [MUTECT] Processed 67003904 reads in 686 ms
[2015-09-30T22:33Z] INFO  23:33:20,250 MuTect - [MUTECT] Processed 18000745 reads in 688 ms
[2015-09-30T22:33Z] INFO  23:33:20,333 MuTect - [MUTECT] Processed 18000692 reads in 668 ms
[2015-09-30T22:33Z] INFO  23:33:20,594 MuTect - [MUTECT] Processed 68003996 reads in 657 ms
[2015-09-30T22:33Z] INFO  23:33:20,973 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:20,998 MuTect - [MUTECT] Processed 19000698 reads in 665 ms
[2015-09-30T22:33Z] INFO  23:33:21,122 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:21,160 MuTect - [MUTECT] Processed 19000763 reads in 910 ms
[2015-09-30T22:33Z] INFO  23:33:21,250 MuTect - [MUTECT] Processed 69004049 reads in 656 ms
[2015-09-30T22:33Z] INFO  23:33:21,654 MuTect - [MUTECT] Processed 20000752 reads in 655 ms
[2015-09-30T22:33Z] INFO  23:33:21,892 MuTect - [MUTECT] Processed 70004093 reads in 642 ms
[2015-09-30T22:33Z] INFO  23:33:21,951 MuTect - [MUTECT] Processed 20000775 reads in 791 ms
[2015-09-30T22:33Z] INFO  23:33:22,124 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:22,370 MuTect - [MUTECT] Processed 21000796 reads in 717 ms
[2015-09-30T22:33Z] INFO  23:33:22,544 MuTect - [MUTECT] Processed 71004141 reads in 652 ms
[2015-09-30T22:33Z] INFO  23:33:22,557 MuTect - [MUTECT] Processed 21000827 reads in 606 ms
[2015-09-30T22:33Z] INFO  23:33:23,086 MuTect - [MUTECT] Processed 22000843 reads in 716 ms
[2015-09-30T22:33Z] INFO  23:33:23,186 MuTect - [MUTECT] Processed 22000836 reads in 629 ms
[2015-09-30T22:33Z] INFO  23:33:23,197 MuTect - [MUTECT] Processed 72004205 reads in 652 ms
[2015-09-30T22:33Z] INFO  23:33:23,298 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:23,773 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:23,775 MuTect - [MUTECT] Processed 23000908 reads in 689 ms
[2015-09-30T22:33Z] INFO  23:33:23,831 MuTect - [MUTECT] Processed 23000845 reads in 645 ms
[2015-09-30T22:33Z] INFO  23:33:23,880 MuTect - [MUTECT] Processed 73004234 reads in 684 ms
[2015-09-30T22:33Z] INFO  23:33:24,343 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:24,427 MuTect - [MUTECT] Processed 24000958 reads in 652 ms
[2015-09-30T22:33Z] INFO  23:33:24,547 MuTect - [MUTECT] Processed 24000876 reads in 716 ms
[2015-09-30T22:33Z] INFO  23:33:24,552 MuTect - [MUTECT] Processed 74004335 reads in 672 ms
[2015-09-30T22:33Z] INFO  23:33:25,126 MuTect - [MUTECT] Processed 25001034 reads in 699 ms
[2015-09-30T22:33Z] INFO  23:33:25,225 MuTect - [MUTECT] Processed 25000946 reads in 678 ms
[2015-09-30T22:33Z] INFO  23:33:25,257 MuTect - [MUTECT] Processed 75004338 reads in 705 ms
[2015-09-30T22:33Z] INFO  23:33:25,748 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:25,831 MuTect - [MUTECT] Processed 26001049 reads in 705 ms
[2015-09-30T22:33Z] INFO  23:33:25,888 MuTect - [MUTECT] Processed 26000963 reads in 663 ms
[2015-09-30T22:33Z] INFO  23:33:25,971 MuTect - [MUTECT] Processed 76004394 reads in 714 ms
[2015-09-30T22:33Z] INFO  23:33:26,278 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:26,521 MuTect - [MUTECT] Processed 27001080 reads in 690 ms
[2015-09-30T22:33Z] INFO  23:33:26,576 MuTect - [MUTECT] Processed 27000999 reads in 688 ms
[2015-09-30T22:33Z] INFO  23:33:26,736 MuTect - [MUTECT] Processed 77004424 reads in 765 ms
[2015-09-30T22:33Z] INFO  23:33:26,754 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:27,157 MuTect - [MUTECT] Processed 28001087 reads in 636 ms
[2015-09-30T22:33Z] INFO  23:33:27,252 MuTect - [MUTECT] Processed 28001070 reads in 676 ms
[2015-09-30T22:33Z] INFO  23:33:27,493 MuTect - [MUTECT] Processed 78004505 reads in 757 ms
[2015-09-30T22:33Z] INFO  23:33:27,807 MuTect - [MUTECT] Processed 29001094 reads in 649 ms
[2015-09-30T22:33Z] INFO  23:33:27,905 MuTect - [MUTECT] Processed 29001094 reads in 653 ms
[2015-09-30T22:33Z] INFO  23:33:28,123 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:28,163 MuTect - [MUTECT] Processed 79004553 reads in 670 ms
[2015-09-30T22:33Z] INFO  23:33:28,485 MuTect - [MUTECT] Processed 30001123 reads in 679 ms
[2015-09-30T22:33Z] INFO  23:33:28,590 MuTect - [MUTECT] Processed 30001109 reads in 685 ms
[2015-09-30T22:33Z] INFO  23:33:28,679 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:28,799 MuTect - [MUTECT] Processed 80004553 reads in 635 ms
[2015-09-30T22:33Z] INFO  23:33:29,124 MuTect - [MUTECT] Processed 31001182 reads in 639 ms
[2015-09-30T22:33Z] INFO  23:33:29,243 MuTect - [MUTECT] Processed 31001149 reads in 653 ms
[2015-09-30T22:33Z] INFO  23:33:29,364 ProgressMeter -      12:8328502        2.33e+06   60.0 s       25.0 s     40.7%         2.5 m    87.0 s
[2015-09-30T22:33Z] INFO  23:33:29,380 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:29,478 MuTect - [MUTECT] Processed 81004600 reads in 680 ms
[2015-09-30T22:33Z] INFO  23:33:29,780 MuTect - [MUTECT] Processed 32001222 reads in 656 ms
[2015-09-30T22:33Z] INFO  23:33:29,914 MuTect - [MUTECT] Processed 32001192 reads in 671 ms
[2015-09-30T22:33Z] INFO  23:33:30,267 MuTect - [MUTECT] Processed 82004657 reads in 789 ms
[2015-09-30T22:33Z] INFO  23:33:30,484 MuTect - [MUTECT] Processed 33001226 reads in 704 ms
[2015-09-30T22:33Z] INFO  23:33:30,517 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:30,571 MuTect - [MUTECT] Processed 33001257 reads in 657 ms
[2015-09-30T22:33Z] INFO  23:33:31,015 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:31,079 MuTect - [MUTECT] Processed 83004718 reads in 812 ms
[2015-09-30T22:33Z] INFO  23:33:31,127 MuTect - [MUTECT] Processed 34001262 reads in 643 ms
[2015-09-30T22:33Z] INFO  23:33:31,213 MuTect - [MUTECT] Processed 34001303 reads in 642 ms
[2015-09-30T22:33Z] INFO  23:33:31,755 MuTect - [MUTECT] Processed 84004762 reads in 676 ms
[2015-09-30T22:33Z] INFO  23:33:31,800 MuTect - [MUTECT] Processed 35001328 reads in 673 ms
[2015-09-30T22:33Z] INFO  23:33:31,890 MuTect - [MUTECT] Processed 35001409 reads in 677 ms
[2015-09-30T22:33Z] INFO  23:33:31,899 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:32,417 MuTect - [MUTECT] Processed 85004859 reads in 662 ms
[2015-09-30T22:33Z] INFO  23:33:32,464 MuTect - [MUTECT] Processed 36001405 reads in 664 ms
[2015-09-30T22:33Z] INFO  23:33:32,547 MuTect - [MUTECT] Processed 36001503 reads in 657 ms
[2015-09-30T22:33Z] INFO  23:33:32,871 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:33,089 MuTect - [MUTECT] Processed 86004901 reads in 672 ms
[2015-09-30T22:33Z] INFO  23:33:33,137 MuTect - [MUTECT] Processed 37001419 reads in 673 ms
[2015-09-30T22:33Z] INFO  23:33:33,183 MuTect - [MUTECT] Processed 37001580 reads in 636 ms
[2015-09-30T22:33Z] INFO  23:33:33,499 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:33,755 MuTect - [MUTECT] Processed 87004938 reads in 666 ms
[2015-09-30T22:33Z] INFO  23:33:33,798 MuTect - [MUTECT] Processed 38001473 reads in 661 ms
[2015-09-30T22:33Z] INFO  23:33:33,813 MuTect - [MUTECT] Processed 38001589 reads in 630 ms
[2015-09-30T22:33Z] INFO  23:33:34,032 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:34,449 MuTect - [MUTECT] Processed 88005011 reads in 694 ms
[2015-09-30T22:33Z] INFO  23:33:34,456 MuTect - [MUTECT] Processed 39001526 reads in 658 ms
[2015-09-30T22:33Z] INFO  23:33:34,485 MuTect - [MUTECT] Processed 39001709 reads in 671 ms
[2015-09-30T22:33Z] INFO  23:33:35,113 MuTect - [MUTECT] Processed 89005054 reads in 664 ms
[2015-09-30T22:33Z] INFO  23:33:35,118 MuTect - [MUTECT] Processed 40001815 reads in 634 ms
[2015-09-30T22:33Z] INFO  23:33:35,118 MuTect - [MUTECT] Processed 40001546 reads in 662 ms
[2015-09-30T22:33Z] INFO  23:33:35,288 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:35,770 MuTect - [MUTECT] Processed 41001622 reads in 652 ms
[2015-09-30T22:33Z] INFO  23:33:35,773 MuTect - [MUTECT] Processed 41001858 reads in 655 ms
[2015-09-30T22:33Z] INFO  23:33:35,801 MuTect - [MUTECT] Processed 90005079 reads in 688 ms
[2015-09-30T22:33Z] INFO  23:33:35,815 ProgressMeter -     12:78334186        1.57e+06   30.0 s       19.0 s     62.8%        47.0 s    17.0 s
[2015-09-30T22:33Z] INFO  23:33:35,909 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:36,129 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:36,411 MuTect - [MUTECT] Processed 42001690 reads in 641 ms
[2015-09-30T22:33Z] INFO  23:33:36,430 MuTect - [MUTECT] Processed 42001874 reads in 657 ms
[2015-09-30T22:33Z] INFO  23:33:36,478 MuTect - [MUTECT] Processed 91005168 reads in 677 ms
[2015-09-30T22:33Z] INFO  23:33:37,078 MuTect - [MUTECT] Processed 43001708 reads in 667 ms
[2015-09-30T22:33Z] INFO  23:33:37,088 MuTect - [MUTECT] Processed 43001904 reads in 658 ms
[2015-09-30T22:33Z] INFO  23:33:37,128 MuTect - [MUTECT] Processed 92005225 reads in 650 ms
[2015-09-30T22:33Z] INFO  23:33:37,738 MuTect - [MUTECT] Processed 44001774 reads in 660 ms
[2015-09-30T22:33Z] INFO  23:33:37,743 MuTect - [MUTECT] Processed 44002004 reads in 655 ms
[2015-09-30T22:33Z] INFO  23:33:37,849 MuTect - [MUTECT] Processed 93005261 reads in 721 ms
[2015-09-30T22:33Z] INFO  23:33:37,918 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:38,362 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:38,380 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:38,416 MuTect - [MUTECT] Processed 45001835 reads in 678 ms
[2015-09-30T22:33Z] INFO  23:33:38,424 MuTect - [MUTECT] Processed 45002012 reads in 681 ms
[2015-09-30T22:33Z] INFO  23:33:38,650 MuTect - [MUTECT] Processed 94005330 reads in 801 ms
[2015-09-30T22:33Z] INFO  23:33:39,068 MuTect - [MUTECT] Processed 46002104 reads in 644 ms
[2015-09-30T22:33Z] INFO  23:33:39,104 MuTect - [MUTECT] Processed 46001862 reads in 688 ms
[2015-09-30T22:33Z] INFO  23:33:39,436 MuTect - [MUTECT] Processed 95005414 reads in 786 ms
[2015-09-30T22:33Z] INFO  23:33:39,707 MuTect - [MUTECT] Processed 47002121 reads in 639 ms
[2015-09-30T22:33Z] INFO  23:33:39,789 MuTect - [MUTECT] Processed 47001897 reads in 685 ms
[2015-09-30T22:33Z] INFO  23:33:40,278 MuTect - [MUTECT] Processed 96005426 reads in 842 ms
[2015-09-30T22:33Z] INFO  23:33:40,367 MuTect - [MUTECT] Processed 48002235 reads in 660 ms
[2015-09-30T22:33Z] INFO  23:33:40,390 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:40,476 MuTect - [MUTECT] Processed 48001973 reads in 687 ms
[2015-09-30T22:33Z] INFO  23:33:40,608 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:40,984 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:41,053 MuTect - [MUTECT] Processed 97005484 reads in 775 ms
[2015-09-30T22:33Z] INFO  23:33:41,054 MuTect - [MUTECT] Processed 49002249 reads in 687 ms
[2015-09-30T22:33Z] INFO  23:33:41,140 MuTect - [MUTECT] Processed 49002022 reads in 664 ms
[2015-09-30T22:33Z] INFO  23:33:41,701 MuTect - [MUTECT] Processed 50002259 reads in 647 ms
[2015-09-30T22:33Z] INFO  23:33:41,745 MuTect - [MUTECT] Processed 98005491 reads in 692 ms
[2015-09-30T22:33Z] INFO  23:33:41,840 MuTect - [MUTECT] Processed 50002059 reads in 700 ms
[2015-09-30T22:33Z] INFO  23:33:42,333 MuTect - [MUTECT] Processed 51002331 reads in 632 ms
[2015-09-30T22:33Z] INFO  23:33:42,469 MuTect - [MUTECT] Processed 99005532 reads in 724 ms
[2015-09-30T22:33Z] INFO  23:33:42,529 MuTect - [MUTECT] Processed 51002087 reads in 689 ms
[2015-09-30T22:33Z] INFO  23:33:42,730 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:42,930 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:42,955 MuTect - [MUTECT] Processed 52002405 reads in 622 ms
[2015-09-30T22:33Z] INFO  23:33:43,197 MuTect - [MUTECT] Processed 100005612 reads in 728 ms
[2015-09-30T22:33Z] INFO  23:33:43,338 MuTect - [MUTECT] Processed 52002108 reads in 809 ms
[2015-09-30T22:33Z] INFO  23:33:43,607 MuTect - [MUTECT] Processed 53002450 reads in 652 ms
[2015-09-30T22:33Z] INFO  23:33:43,900 MuTect - [MUTECT] Processed 101005630 reads in 703 ms
[2015-09-30T22:33Z] INFO  23:33:43,919 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:44,058 MuTect - [MUTECT] Processed 53002147 reads in 720 ms
[2015-09-30T22:33Z] INFO  23:33:44,257 MuTect - [MUTECT] Processed 54002495 reads in 650 ms
[2015-09-30T22:33Z] INFO  23:33:44,664 MuTect - [MUTECT] Processed 102005640 reads in 764 ms
[2015-09-30T22:33Z] INFO  23:33:44,871 MuTect - [MUTECT] Processed 54002179 reads in 812 ms
[2015-09-30T22:33Z] INFO  23:33:44,927 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:44,944 MuTect - [MUTECT] Processed 55002569 reads in 687 ms
[2015-09-30T22:33Z] INFO  23:33:45,433 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:45,458 MuTect - [MUTECT] Processed 103005671 reads in 794 ms
[2015-09-30T22:33Z] INFO  23:33:45,594 MuTect - [MUTECT] Processed 55002228 reads in 724 ms
[2015-09-30T22:33Z] INFO  23:33:45,599 MuTect - [MUTECT] Processed 56002628 reads in 655 ms
[2015-09-30T22:33Z] INFO  23:33:45,680 ProgressMeter -     12:49375822        2.11e+06   40.0 s       18.0 s     32.8%         2.0 m    82.0 s
[2015-09-30T22:33Z] INFO  23:33:46,137 MuTect - [MUTECT] Processed 104005749 reads in 679 ms
[2015-09-30T22:33Z] INFO  23:33:46,228 MuTect - [MUTECT] Processed 57002646 reads in 629 ms
[2015-09-30T22:33Z] INFO  23:33:46,339 MuTect - [MUTECT] Processed 56002309 reads in 745 ms
[2015-09-30T22:33Z] INFO  23:33:46,788 MuTect - [MUTECT] Processed 105005840 reads in 651 ms
[2015-09-30T22:33Z] INFO  23:33:46,859 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:46,864 MuTect - [MUTECT] Processed 58002749 reads in 636 ms
[2015-09-30T22:33Z] INFO  23:33:46,945 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:47,043 MuTect - [MUTECT] Processed 57002379 reads in 704 ms
[2015-09-30T22:33Z] INFO  23:33:47,490 MuTect - [MUTECT] Processed 59002764 reads in 626 ms
[2015-09-30T22:33Z] INFO  23:33:47,643 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:47,722 MuTect - [MUTECT] Processed 58002437 reads in 679 ms
[2015-09-30T22:33Z] INFO  23:33:47,861 MuTect - [MUTECT] Processed 106005898 reads in 1073 ms
[2015-09-30T22:33Z] INFO  23:33:48,093 MuTect - [MUTECT] Processed 60002847 reads in 603 ms
[2015-09-30T22:33Z] INFO  23:33:48,398 MuTect - [MUTECT] Processed 59002530 reads in 676 ms
[2015-09-30T22:33Z] INFO  23:33:48,677 MuTect - [MUTECT] Processed 61002941 reads in 584 ms
[2015-09-30T22:33Z] INFO  23:33:48,739 MuTect - [MUTECT] Processed 107005898 reads in 878 ms
[2015-09-30T22:33Z] INFO  23:33:49,056 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:49,077 MuTect - [MUTECT] Processed 60002534 reads in 679 ms
[2015-09-30T22:33Z] INFO  23:33:49,319 MuTect - [MUTECT] Processed 62002972 reads in 642 ms
[2015-09-30T22:33Z] INFO  23:33:49,370 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:49,529 MuTect - [MUTECT] Processed 108005913 reads in 790 ms
[2015-09-30T22:33Z] INFO  23:33:49,739 MuTect - [MUTECT] Processed 61002550 reads in 662 ms
[2015-09-30T22:33Z] INFO  23:33:49,786 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:49,813 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:33Z] INFO  23:33:49,817 ProgressMeter -            done        2.52e+06   44.0 s       17.0 s    100.0%        44.0 s     0.0 s
[2015-09-30T22:33Z] INFO  23:33:49,817 ProgressMeter - Total runtime 44.00 secs, 0.73 min, 0.01 hours
[2015-09-30T22:33Z] INFO  23:33:49,882 MicroScheduler - 40107 reads were filtered out during the traversal out of approximately 727461 total reads (5.51%)
[2015-09-30T22:33Z] INFO  23:33:49,882 MicroScheduler -   -> 28556 reads (3.93% of total) failing DuplicateReadFilter
[2015-09-30T22:33Z] INFO  23:33:49,882 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:33Z] INFO  23:33:49,882 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:33Z] INFO  23:33:49,882 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:33Z] INFO  23:33:49,882 MicroScheduler -   -> 11551 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:33Z] INFO  23:33:49,956 MuTect - [MUTECT] Processed 63003066 reads in 637 ms
[2015-09-30T22:33Z] INFO  23:33:50,235 MuTect - [MUTECT] Processed 109005944 reads in 706 ms
[2015-09-30T22:33Z] INFO  23:33:50,606 MuTect - [MUTECT] Processed 64003087 reads in 650 ms
[2015-09-30T22:33Z] INFO  23:33:50,960 MuTect - [MUTECT] Processed 110005950 reads in 725 ms
[2015-09-30T22:33Z] INFO  23:33:51,009 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:33Z] bgzip syn3-12_62147092_93167456-raw-mutect.vcf
[2015-09-30T22:33Z] tabix index syn3-12_62147092_93167456-raw-mutect.vcf.gz
[2015-09-30T22:33Z] INFO  23:33:51,265 MuTect - [MUTECT] Processed 65003135 reads in 659 ms
[2015-09-30T22:33Z] INFO  23:33:51,282 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:51,679 MuTect - [MUTECT] Processed 111005999 reads in 719 ms
[2015-09-30T22:33Z] INFO  23:33:51,926 MuTect - [MUTECT] Processed 66003153 reads in 661 ms
[2015-09-30T22:33Z] INFO  23:33:52,239 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:52,333 MuTect - [MUTECT] Processed 112006039 reads in 654 ms
[2015-09-30T22:33Z] INFO  23:33:52,504 MuTect - [MUTECT] Processed 67003265 reads in 578 ms
[2015-09-30T22:33Z] INFO  23:33:52,983 MuTect - [MUTECT] Processed 113006077 reads in 650 ms
[2015-09-30T22:33Z] INFO  23:33:53,091 MuTect - [MUTECT] Processed 68003350 reads in 587 ms
[2015-09-30T22:33Z] INFO  23:33:53,335 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:33Z] MuTect: MuTect
[2015-09-30T22:33Z] INFO  23:33:53,655 MuTect - [MUTECT] Processed 114006104 reads in 672 ms
[2015-09-30T22:33Z] INFO  23:33:53,693 MuTect - [MUTECT] Processed 69003413 reads in 602 ms
[2015-09-30T22:33Z] INFO  23:33:54,302 MuTect - [MUTECT] Processed 70003482 reads in 609 ms
[2015-09-30T22:33Z] INFO  23:33:54,350 MuTect - [MUTECT] Processed 115006117 reads in 695 ms
[2015-09-30T22:33Z] INFO  23:33:54,523 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:54,912 MuTect - [MUTECT] Processed 71003608 reads in 610 ms
[2015-09-30T22:33Z] INFO  23:33:55,013 MuTect - [MUTECT] Processed 116006166 reads in 663 ms
[2015-09-30T22:33Z] INFO  23:33:55,448 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:55,562 MuTect - [MUTECT] Processed 72003716 reads in 650 ms
[2015-09-30T22:33Z] INFO  23:33:55,595 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/12/syn3-12_93169109_124189486-raw-mutect-regions.bed to be BED
[2015-09-30T22:33Z] INFO  23:33:55,645 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:33Z] INFO  23:33:55,646 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:33Z] INFO  23:33:55,646 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:33Z] INFO  23:33:55,646 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:33Z] INFO  23:33:55,649 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/12/syn3-12_93169109_124189486-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/12/tx/tmpuItBZJ/syn3-12_93169109_124189486-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:33Z] INFO  23:33:55,649 HelpFormatter - Date/Time: 2015/09/30 23:33:55
[2015-09-30T22:33Z] INFO  23:33:55,649 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:33Z] INFO  23:33:55,649 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:33Z] INFO  23:33:55,675 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:33Z] INFO  23:33:55,679 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:33Z] INFO  23:33:55,701 MuTect - [MUTECT] Processed 117006225 reads in 688 ms
[2015-09-30T22:33Z] INFO  23:33:55,730 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:33Z] INFO  23:33:55,773 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:33Z] INFO  23:33:55,780 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:33Z] INFO  23:33:55,839 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:33Z] INFO  23:33:55,881 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:33Z] INFO  23:33:56,044 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:33Z] INFO  23:33:56,173 IntervalUtils - Processing 2264179 bp from intervals
[2015-09-30T22:33Z] INFO  23:33:56,177 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:33Z] INFO  23:33:56,177 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:33Z] INFO  23:33:56,198 MuTect - [MUTECT] Processed 73003778 reads in 636 ms
[2015-09-30T22:33Z] INFO  23:33:56,324 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:33Z] INFO  23:33:56,421 MuTect - [MUTECT] Processed 118006295 reads in 720 ms
[2015-09-30T22:33Z] INFO  23:33:56,494 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:33Z] INFO  23:33:56,494 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:33Z] INFO  23:33:56,494 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:33Z] INFO  23:33:56,495 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:33Z] INFO  23:33:56,823 MuTect - [MUTECT] Processed 74003884 reads in 625 ms
[2015-09-30T22:33Z] INFO  23:33:57,056 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:57,129 MuTect - [MUTECT] Processed 119006346 reads in 708 ms
[2015-09-30T22:33Z] INFO  23:33:57,496 MuTect - [MUTECT] Processed 75003948 reads in 673 ms
[2015-09-30T22:33Z] INFO  23:33:57,520 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:57,829 MuTect - [MUTECT] Processed 120006435 reads in 700 ms
[2015-09-30T22:33Z] INFO  23:33:58,161 MuTect - [MUTECT] Processed 76003984 reads in 664 ms
[2015-09-30T22:33Z] INFO  23:33:58,482 MuTect - [MUTECT] Processed 121006445 reads in 653 ms
[2015-09-30T22:33Z] INFO  23:33:58,804 MuTect - [MUTECT] Processed 77004055 reads in 644 ms
[2015-09-30T22:33Z] INFO  23:33:59,130 MuTect - [MUTECT] Processed 122006474 reads in 647 ms
[2015-09-30T22:33Z] INFO  23:33:59,147 MuTect - [MUTECT] Processed 1000016 reads in 2608 ms
[2015-09-30T22:33Z] INFO  23:33:59,365 ProgressMeter -     12:15073667        3.82e+06   90.0 s       23.0 s     68.2%         2.2 m    41.0 s
[2015-09-30T22:33Z] INFO  23:33:59,411 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:59,437 MuTect - [MUTECT] Processed 78004067 reads in 633 ms
[2015-09-30T22:33Z] INFO  23:33:59,662 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:33Z] INFO  23:33:59,827 MuTect - [MUTECT] Processed 123006501 reads in 698 ms
[2015-09-30T22:33Z] INFO  23:33:59,924 MuTect - [MUTECT] Processed 2000054 reads in 777 ms
[2015-09-30T22:34Z] INFO  23:34:00,082 MuTect - [MUTECT] Processed 79004085 reads in 645 ms
[2015-09-30T22:34Z] INFO  23:34:00,507 MuTect - [MUTECT] Processed 124006535 reads in 680 ms
[2015-09-30T22:34Z] INFO  23:34:00,657 MuTect - [MUTECT] Processed 3000081 reads in 733 ms
[2015-09-30T22:34Z] INFO  23:34:00,726 MuTect - [MUTECT] Processed 80004115 reads in 644 ms
[2015-09-30T22:34Z] INFO  23:34:01,049 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:01,182 MuTect - [MUTECT] Processed 125006546 reads in 675 ms
[2015-09-30T22:34Z] INFO  23:34:01,359 MuTect - [MUTECT] Processed 4000129 reads in 702 ms
[2015-09-30T22:34Z] INFO  23:34:01,465 MuTect - [MUTECT] Processed 81004123 reads in 739 ms
[2015-09-30T22:34Z] INFO  23:34:01,847 MuTect - [MUTECT] Processed 126006554 reads in 665 ms
[2015-09-30T22:34Z] INFO  23:34:01,897 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:01,956 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:02,087 MuTect - [MUTECT] Processed 5000156 reads in 728 ms
[2015-09-30T22:34Z] INFO  23:34:02,131 MuTect - [MUTECT] Processed 82004170 reads in 665 ms
[2015-09-30T22:34Z] INFO  23:34:02,526 MuTect - [MUTECT] Processed 127006614 reads in 679 ms
[2015-09-30T22:34Z] INFO  23:34:02,807 MuTect - [MUTECT] Processed 83004197 reads in 677 ms
[2015-09-30T22:34Z] INFO  23:34:02,843 MuTect - [MUTECT] Processed 6000176 reads in 756 ms
[2015-09-30T22:34Z] INFO  23:34:03,222 MuTect - [MUTECT] Processed 128006654 reads in 696 ms
[2015-09-30T22:34Z] INFO  23:34:03,460 MuTect - [MUTECT] Processed 84004200 reads in 653 ms
[2015-09-30T22:34Z] INFO  23:34:03,523 MuTect - [MUTECT] Processed 7000208 reads in 680 ms
[2015-09-30T22:34Z] INFO  23:34:03,658 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:03,896 MuTect - [MUTECT] Processed 129006700 reads in 674 ms
[2015-09-30T22:34Z] INFO  23:34:04,122 MuTect - [MUTECT] Processed 85004209 reads in 662 ms
[2015-09-30T22:34Z] INFO  23:34:04,175 MuTect - [MUTECT] Processed 8000236 reads in 652 ms
[2015-09-30T22:34Z] INFO  23:34:04,360 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:04,655 MuTect - [MUTECT] Processed 130006736 reads in 759 ms
[2015-09-30T22:34Z] INFO  23:34:04,680 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:04,803 MuTect - [MUTECT] Processed 86004250 reads in 681 ms
[2015-09-30T22:34Z] INFO  23:34:04,841 MuTect - [MUTECT] Processed 9000313 reads in 666 ms
[2015-09-30T22:34Z] INFO  23:34:05,347 MuTect - [MUTECT] Processed 131006766 reads in 692 ms
[2015-09-30T22:34Z] INFO  23:34:05,451 MuTect - [MUTECT] Processed 87004263 reads in 648 ms
[2015-09-30T22:34Z] INFO  23:34:05,527 MuTect - [MUTECT] Processed 10000324 reads in 686 ms
[2015-09-30T22:34Z] INFO  23:34:06,034 MuTect - [MUTECT] Processed 132006782 reads in 687 ms
[2015-09-30T22:34Z] INFO  23:34:06,100 MuTect - [MUTECT] Processed 88004349 reads in 649 ms
[2015-09-30T22:34Z] INFO  23:34:06,218 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:06,256 MuTect - [MUTECT] Processed 11000412 reads in 729 ms
[2015-09-30T22:34Z] INFO  23:34:06,635 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:06,730 MuTect - [MUTECT] Processed 89004391 reads in 630 ms
[2015-09-30T22:34Z] INFO  23:34:06,794 MuTect - [MUTECT] Processed 133006794 reads in 760 ms
[2015-09-30T22:34Z] INFO  23:34:07,037 MuTect - [MUTECT] Processed 12000419 reads in 781 ms
[2015-09-30T22:34Z] INFO  23:34:07,210 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:07,355 MuTect - [MUTECT] Processed 90004489 reads in 625 ms
[2015-09-30T22:34Z] INFO  23:34:07,598 MuTect - [MUTECT] Processed 134006846 reads in 804 ms
[2015-09-30T22:34Z] INFO  23:34:07,744 MuTect - [MUTECT] Processed 13000461 reads in 707 ms
[2015-09-30T22:34Z] INFO  23:34:07,985 MuTect - [MUTECT] Processed 91004603 reads in 630 ms
[2015-09-30T22:34Z] INFO  23:34:08,384 MuTect - [MUTECT] Processed 135006866 reads in 786 ms
[2015-09-30T22:34Z] INFO  23:34:08,470 MuTect - [MUTECT] Processed 14000469 reads in 726 ms
[2015-09-30T22:34Z] INFO  23:34:08,593 MuTect - [MUTECT] Processed 92004648 reads in 608 ms
[2015-09-30T22:34Z] INFO  23:34:08,803 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:09,036 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:09,112 MuTect - [MUTECT] Processed 136006878 reads in 728 ms
[2015-09-30T22:34Z] INFO  23:34:09,225 MuTect - [MUTECT] Processed 93004733 reads in 632 ms
[2015-09-30T22:34Z] INFO  23:34:09,229 MuTect - [MUTECT] Processed 15000517 reads in 759 ms
[2015-09-30T22:34Z] INFO  23:34:09,825 MuTect - [MUTECT] Processed 137006902 reads in 713 ms
[2015-09-30T22:34Z] INFO  23:34:09,846 MuTect - [MUTECT] Processed 94004744 reads in 621 ms
[2015-09-30T22:34Z] INFO  23:34:09,957 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:09,995 MuTect - [MUTECT] Processed 16000573 reads in 766 ms
[2015-09-30T22:34Z] INFO  23:34:10,460 MuTect - [MUTECT] Processed 95004763 reads in 614 ms
[2015-09-30T22:34Z] INFO  23:34:10,561 MuTect - [MUTECT] Processed 138006916 reads in 736 ms
[2015-09-30T22:34Z] INFO  23:34:10,717 MuTect - [MUTECT] Processed 17000577 reads in 722 ms
[2015-09-30T22:34Z] INFO  23:34:10,928 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:11,064 MuTect - [MUTECT] Processed 96004821 reads in 604 ms
[2015-09-30T22:34Z] INFO  23:34:11,280 MuTect - [MUTECT] Processed 139006986 reads in 719 ms
[2015-09-30T22:34Z] INFO  23:34:11,420 MuTect - [MUTECT] Processed 18000608 reads in 703 ms
[2015-09-30T22:34Z] INFO  23:34:11,666 MuTect - [MUTECT] Processed 97004877 reads in 602 ms
[2015-09-30T22:34Z] INFO  23:34:11,678 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:11,986 MuTect - [MUTECT] Processed 140007004 reads in 706 ms
[2015-09-30T22:34Z] INFO  23:34:12,117 MuTect - [MUTECT] Processed 19000653 reads in 697 ms
[2015-09-30T22:34Z] INFO  23:34:12,282 MuTect - [MUTECT] Processed 98004926 reads in 616 ms
[2015-09-30T22:34Z] INFO  23:34:12,654 MuTect - [MUTECT] Processed 141007004 reads in 668 ms
[2015-09-30T22:34Z] INFO  23:34:12,703 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:12,803 MuTect - [MUTECT] Processed 20000663 reads in 686 ms
[2015-09-30T22:34Z] INFO  23:34:12,921 MuTect - [MUTECT] Processed 99004965 reads in 639 ms
[2015-09-30T22:34Z] INFO  23:34:13,069 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:13,350 MuTect - [MUTECT] Processed 142007096 reads in 696 ms
[2015-09-30T22:34Z] INFO  23:34:13,483 MuTect - [MUTECT] Processed 21000686 reads in 680 ms
[2015-09-30T22:34Z] INFO  23:34:13,588 MuTect - [MUTECT] Processed 100005018 reads in 667 ms
[2015-09-30T22:34Z] INFO  23:34:14,028 MuTect - [MUTECT] Processed 143007110 reads in 678 ms
[2015-09-30T22:34Z] INFO  23:34:14,136 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:14,159 MuTect - [MUTECT] Processed 22000745 reads in 676 ms
[2015-09-30T22:34Z] INFO  23:34:14,242 MuTect - [MUTECT] Processed 101005029 reads in 654 ms
[2015-09-30T22:34Z] INFO  23:34:14,756 MuTect - [MUTECT] Processed 144007135 reads in 728 ms
[2015-09-30T22:34Z] INFO  23:34:14,795 MuTect - [MUTECT] Processed 23000768 reads in 636 ms
[2015-09-30T22:34Z] INFO  23:34:14,931 MuTect - [MUTECT] Processed 102005052 reads in 689 ms
[2015-09-30T22:34Z] INFO  23:34:15,311 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:15,449 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:15,451 MuTect - [MUTECT] Processed 24000827 reads in 656 ms
[2015-09-30T22:34Z] INFO  23:34:15,455 MuTect - [MUTECT] Processed 145007216 reads in 699 ms
[2015-09-30T22:34Z] INFO  23:34:15,636 MuTect - [MUTECT] Processed 103005145 reads in 705 ms
[2015-09-30T22:34Z] INFO  23:34:15,681 ProgressMeter -     12:52710607        3.46e+06   70.0 s       20.0 s     53.5%         2.2 m    60.0 s
[2015-09-30T22:34Z] INFO  23:34:16,131 MuTect - [MUTECT] Processed 146007230 reads in 676 ms
[2015-09-30T22:34Z] INFO  23:34:16,140 MuTect - [MUTECT] Processed 25000880 reads in 689 ms
[2015-09-30T22:34Z] INFO  23:34:16,328 MuTect - [MUTECT] Processed 104005224 reads in 692 ms
[2015-09-30T22:34Z] INFO  23:34:16,579 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:16,792 MuTect - [MUTECT] Processed 26000916 reads in 652 ms
[2015-09-30T22:34Z] INFO  23:34:16,794 MuTect - [MUTECT] Processed 147007256 reads in 663 ms
[2015-09-30T22:34Z] INFO  23:34:16,998 MuTect - [MUTECT] Processed 105005313 reads in 670 ms
[2015-09-30T22:34Z] INFO  23:34:17,446 MuTect - [MUTECT] Processed 27000948 reads in 654 ms
[2015-09-30T22:34Z] INFO  23:34:17,447 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:17,480 MuTect - [MUTECT] Processed 148007285 reads in 686 ms
[2015-09-30T22:34Z] INFO  23:34:17,636 MuTect - [MUTECT] Processed 106005360 reads in 638 ms
[2015-09-30T22:34Z] INFO  23:34:17,926 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:18,112 MuTect - [MUTECT] Processed 28001029 reads in 666 ms
[2015-09-30T22:34Z] INFO  23:34:18,184 MuTect - [MUTECT] Processed 149007337 reads in 704 ms
[2015-09-30T22:34Z] INFO  23:34:18,254 MuTect - [MUTECT] Processed 107005372 reads in 618 ms
[2015-09-30T22:34Z] INFO  23:34:18,780 MuTect - [MUTECT] Processed 29001065 reads in 668 ms
[2015-09-30T22:34Z] INFO  23:34:18,851 MuTect - [MUTECT] Processed 150007377 reads in 667 ms
[2015-09-30T22:34Z] INFO  23:34:18,883 MuTect - [MUTECT] Processed 108005456 reads in 629 ms
[2015-09-30T22:34Z] INFO  23:34:19,144 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:19,453 MuTect - [MUTECT] Processed 30001070 reads in 672 ms
[2015-09-30T22:34Z] INFO  23:34:19,521 MuTect - [MUTECT] Processed 109005543 reads in 638 ms
[2015-09-30T22:34Z] INFO  23:34:19,554 MuTect - [MUTECT] Processed 151007445 reads in 703 ms
[2015-09-30T22:34Z] INFO  23:34:19,621 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:20,127 MuTect - [MUTECT] Processed 31001139 reads in 675 ms
[2015-09-30T22:34Z] INFO  23:34:20,180 MuTect - [MUTECT] Processed 110005587 reads in 659 ms
[2015-09-30T22:34Z] INFO  23:34:20,264 MuTect - [MUTECT] Processed 152007470 reads in 710 ms
[2015-09-30T22:34Z] INFO  23:34:20,418 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:20,819 MuTect - [MUTECT] Processed 111005650 reads in 639 ms
[2015-09-30T22:34Z] INFO  23:34:20,832 MuTect - [MUTECT] Processed 32001227 reads in 705 ms
[2015-09-30T22:34Z] INFO  23:34:21,467 MuTect - [MUTECT] Processed 112005657 reads in 648 ms
[2015-09-30T22:34Z] INFO  23:34:21,497 MuTect - [MUTECT] Processed 153007552 reads in 1233 ms
[2015-09-30T22:34Z] INFO  23:34:21,555 MuTect - [MUTECT] Processed 33001321 reads in 723 ms
[2015-09-30T22:34Z] INFO  23:34:21,618 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:21,790 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:22,120 MuTect - [MUTECT] Processed 113005741 reads in 653 ms
[2015-09-30T22:34Z] INFO  23:34:22,182 MuTect - [MUTECT] Processed 154007588 reads in 685 ms
[2015-09-30T22:34Z] INFO  23:34:22,227 MuTect - [MUTECT] Processed 34001338 reads in 672 ms
[2015-09-30T22:34Z] INFO  23:34:22,793 MuTect - [MUTECT] Processed 114005768 reads in 673 ms
[2015-09-30T22:34Z] INFO  23:34:22,893 MuTect - [MUTECT] Processed 155007684 reads in 711 ms
[2015-09-30T22:34Z] INFO  23:34:22,903 MuTect - [MUTECT] Processed 35001385 reads in 676 ms
[2015-09-30T22:34Z] INFO  23:34:23,394 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:23,412 MuTect - [MUTECT] Processed 115005830 reads in 619 ms
[2015-09-30T22:34Z] INFO  23:34:23,558 MuTect - [MUTECT] Processed 36001442 reads in 655 ms
[2015-09-30T22:34Z] INFO  23:34:23,587 MuTect - [MUTECT] Processed 156007685 reads in 694 ms
[2015-09-30T22:34Z] INFO  23:34:23,895 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:23,948 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:24,047 MuTect - [MUTECT] Processed 116005861 reads in 635 ms
[2015-09-30T22:34Z] INFO  23:34:24,235 MuTect - [MUTECT] Processed 37001521 reads in 677 ms
[2015-09-30T22:34Z] INFO  23:34:24,295 MuTect - [MUTECT] Processed 157007710 reads in 708 ms
[2015-09-30T22:34Z] INFO  23:34:24,669 MuTect - [MUTECT] Processed 117005927 reads in 622 ms
[2015-09-30T22:34Z] INFO  23:34:24,910 MuTect - [MUTECT] Processed 38001522 reads in 675 ms
[2015-09-30T22:34Z] INFO  23:34:24,987 MuTect - [MUTECT] Processed 158007749 reads in 692 ms
[2015-09-30T22:34Z] INFO  23:34:25,413 MuTect - [MUTECT] Processed 118006001 reads in 744 ms
[2015-09-30T22:34Z] INFO  23:34:25,571 MuTect - [MUTECT] Processed 39001604 reads in 661 ms
[2015-09-30T22:34Z] INFO  23:34:25,699 MuTect - [MUTECT] Processed 159007759 reads in 712 ms
[2015-09-30T22:34Z] INFO  23:34:25,968 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:26,002 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:26,078 MuTect - [MUTECT] Processed 119006126 reads in 665 ms
[2015-09-30T22:34Z] INFO  23:34:26,247 MuTect - [MUTECT] Processed 40001626 reads in 676 ms
[2015-09-30T22:34Z] INFO  23:34:26,344 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:26,407 MuTect - [MUTECT] Processed 160007833 reads in 708 ms
[2015-09-30T22:34Z] INFO  23:34:26,497 ProgressMeter -    12:104118625        1.50e+06   30.0 s       20.0 s     25.6%       117.0 s    87.0 s
[2015-09-30T22:34Z] INFO  23:34:26,586 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:34Z] INFO  23:34:26,591 ProgressMeter -            done        5.37e+06  117.0 s       21.0 s    100.0%       117.0 s     0.0 s
[2015-09-30T22:34Z] INFO  23:34:26,591 ProgressMeter - Total runtime 117.23 secs, 1.95 min, 0.03 hours
[2015-09-30T22:34Z] INFO  23:34:26,658 MicroScheduler - 118069 reads were filtered out during the traversal out of approximately 1906307 total reads (6.19%)
[2015-09-30T22:34Z] INFO  23:34:26,658 MicroScheduler -   -> 86879 reads (4.56% of total) failing DuplicateReadFilter
[2015-09-30T22:34Z] INFO  23:34:26,659 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:34Z] INFO  23:34:26,659 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:34Z] INFO  23:34:26,659 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:34Z] INFO  23:34:26,659 MicroScheduler -   -> 31190 reads (1.64% of total) failing UnmappedReadFilter
[2015-09-30T22:34Z] INFO  23:34:26,674 MuTect - [MUTECT] Processed 120006231 reads in 596 ms
[2015-09-30T22:34Z] INFO  23:34:26,920 MuTect - [MUTECT] Processed 41001646 reads in 672 ms
[2015-09-30T22:34Z] INFO  23:34:27,290 MuTect - [MUTECT] Processed 121006248 reads in 616 ms
[2015-09-30T22:34Z] INFO  23:34:27,613 MuTect - [MUTECT] Processed 42001711 reads in 694 ms
[2015-09-30T22:34Z] INFO  23:34:27,674 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:34Z] bgzip syn3-12_0_31107241-raw-mutect.vcf
[2015-09-30T22:34Z] tabix index syn3-12_0_31107241-raw-mutect.vcf.gz
[2015-09-30T22:34Z] INFO  23:34:27,933 MuTect - [MUTECT] Processed 122006331 reads in 643 ms
[2015-09-30T22:34Z] INFO  23:34:28,073 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:28,323 MuTect - [MUTECT] Processed 43001765 reads in 710 ms
[2015-09-30T22:34Z] INFO  23:34:28,551 MuTect - [MUTECT] Processed 123006405 reads in 618 ms
[2015-09-30T22:34Z] INFO  23:34:28,613 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:29,037 MuTect - [MUTECT] Processed 44001835 reads in 714 ms
[2015-09-30T22:34Z] INFO  23:34:29,178 MuTect - [MUTECT] Processed 124006425 reads in 627 ms
[2015-09-30T22:34Z] INFO  23:34:29,735 MuTect - [MUTECT] Processed 45001853 reads in 698 ms
[2015-09-30T22:34Z] INFO  23:34:29,790 MuTect - [MUTECT] Processed 125006494 reads in 612 ms
[2015-09-30T22:34Z] MuTect: MuTect
[2015-09-30T22:34Z] INFO  23:34:30,247 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:30,434 MuTect - [MUTECT] Processed 126006567 reads in 644 ms
[2015-09-30T22:34Z] INFO  23:34:30,437 MuTect - [MUTECT] Processed 46001875 reads in 702 ms
[2015-09-30T22:34Z] INFO  23:34:31,075 MuTect - [MUTECT] Processed 127006571 reads in 641 ms
[2015-09-30T22:34Z] INFO  23:34:31,137 MuTect - [MUTECT] Processed 47001930 reads in 700 ms
[2015-09-30T22:34Z] INFO  23:34:31,251 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:31,706 MuTect - [MUTECT] Processed 128006611 reads in 631 ms
[2015-09-30T22:34Z] INFO  23:34:31,828 MuTect - [MUTECT] Processed 48001983 reads in 691 ms
[2015-09-30T22:34Z] INFO  23:34:31,946 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/12/syn3-12_124191013_133851895-raw-mutect-regions.bed to be BED
[2015-09-30T22:34Z] INFO  23:34:32,001 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:34Z] INFO  23:34:32,001 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:34Z] INFO  23:34:32,001 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:34Z] INFO  23:34:32,002 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:34Z] INFO  23:34:32,005 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/12/syn3-12_124191013_133851895-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/12/tx/tmpaUt9Do/syn3-12_124191013_133851895-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:34Z] INFO  23:34:32,005 HelpFormatter - Date/Time: 2015/09/30 23:34:32
[2015-09-30T22:34Z] INFO  23:34:32,005 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:34Z] INFO  23:34:32,005 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:34Z] INFO  23:34:32,033 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:34Z] INFO  23:34:32,038 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:34Z] INFO  23:34:32,088 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:34Z] INFO  23:34:32,136 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:34Z] INFO  23:34:32,144 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:34Z] INFO  23:34:32,266 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:32,268 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2015-09-30T22:34Z] INFO  23:34:32,280 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:34Z] INFO  23:34:32,353 MuTect - [MUTECT] Processed 129006625 reads in 647 ms
[2015-09-30T22:34Z] INFO  23:34:32,457 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:34Z] INFO  23:34:32,527 IntervalUtils - Processing 487679 bp from intervals
[2015-09-30T22:34Z] INFO  23:34:32,531 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:34Z] INFO  23:34:32,531 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:34Z] INFO  23:34:32,545 MuTect - [MUTECT] Processed 49002049 reads in 717 ms
[2015-09-30T22:34Z] INFO  23:34:32,584 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:34Z] INFO  23:34:32,810 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:34Z] INFO  23:34:32,810 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:34Z] INFO  23:34:32,811 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:34Z] INFO  23:34:32,812 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:34Z] INFO  23:34:33,003 MuTect - [MUTECT] Processed 130006711 reads in 650 ms
[2015-09-30T22:34Z] INFO  23:34:33,296 MuTect - [MUTECT] Processed 50002148 reads in 751 ms
[2015-09-30T22:34Z] INFO  23:34:33,629 MuTect - [MUTECT] Processed 131006773 reads in 626 ms
[2015-09-30T22:34Z] INFO  23:34:33,748 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:34,019 MuTect - [MUTECT] Processed 51002174 reads in 723 ms
[2015-09-30T22:34Z] INFO  23:34:34,288 MuTect - [MUTECT] Processed 132006850 reads in 659 ms
[2015-09-30T22:34Z] INFO  23:34:34,433 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:34,749 MuTect - [MUTECT] Processed 52002253 reads in 730 ms
[2015-09-30T22:34Z] INFO  23:34:34,926 MuTect - [MUTECT] Processed 133006918 reads in 638 ms
[2015-09-30T22:34Z] INFO  23:34:35,204 MuTect - [MUTECT] Processed 1000049 reads in 2344 ms
[2015-09-30T22:34Z] INFO  23:34:35,430 MuTect - [MUTECT] Processed 53002294 reads in 681 ms
[2015-09-30T22:34Z] INFO  23:34:35,524 MuTect - [MUTECT] Processed 134006993 reads in 598 ms
[2015-09-30T22:34Z] INFO  23:34:36,075 MuTect - [MUTECT] Processed 54002384 reads in 645 ms
[2015-09-30T22:34Z] INFO  23:34:36,149 MuTect - [MUTECT] Processed 135007023 reads in 625 ms
[2015-09-30T22:34Z] INFO  23:34:36,220 MuTect - [MUTECT] Processed 2000064 reads in 1016 ms
[2015-09-30T22:34Z] INFO  23:34:36,228 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:36,452 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:36,748 MuTect - [MUTECT] Processed 136007023 reads in 599 ms
[2015-09-30T22:34Z] INFO  23:34:36,751 MuTect - [MUTECT] Processed 55002422 reads in 676 ms
[2015-09-30T22:34Z] INFO  23:34:36,914 MuTect - [MUTECT] Processed 3000092 reads in 694 ms
[2015-09-30T22:34Z] INFO  23:34:37,310 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:37,358 MuTect - [MUTECT] Processed 137007105 reads in 610 ms
[2015-09-30T22:34Z] INFO  23:34:37,396 MuTect - [MUTECT] Processed 56002464 reads in 645 ms
[2015-09-30T22:34Z] INFO  23:34:37,637 MuTect - [MUTECT] Processed 4000120 reads in 723 ms
[2015-09-30T22:34Z] INFO  23:34:37,968 MuTect - [MUTECT] Processed 138007119 reads in 610 ms
[2015-09-30T22:34Z] INFO  23:34:38,044 MuTect - [MUTECT] Processed 57002546 reads in 648 ms
[2015-09-30T22:34Z] INFO  23:34:38,397 MuTect - [MUTECT] Processed 5000167 reads in 760 ms
[2015-09-30T22:34Z] INFO  23:34:38,466 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:38,515 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:38,581 MuTect - [MUTECT] Processed 139007200 reads in 613 ms
[2015-09-30T22:34Z] INFO  23:34:38,686 MuTect - [MUTECT] Processed 58002550 reads in 642 ms
[2015-09-30T22:34Z] INFO  23:34:39,071 MuTect - [MUTECT] Processed 6000173 reads in 674 ms
[2015-09-30T22:34Z] INFO  23:34:39,190 MuTect - [MUTECT] Processed 140007212 reads in 609 ms
[2015-09-30T22:34Z] INFO  23:34:39,337 MuTect - [MUTECT] Processed 59002613 reads in 651 ms
[2015-09-30T22:34Z] INFO  23:34:39,731 MuTect - [MUTECT] Processed 7000217 reads in 660 ms
[2015-09-30T22:34Z] INFO  23:34:39,801 MuTect - [MUTECT] Processed 141007250 reads in 611 ms
[2015-09-30T22:34Z] INFO  23:34:39,882 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:39,987 MuTect - [MUTECT] Processed 60002629 reads in 650 ms
[2015-09-30T22:34Z] INFO  23:34:40,415 MuTect - [MUTECT] Processed 142007355 reads in 614 ms
[2015-09-30T22:34Z] INFO  23:34:40,441 MuTect - [MUTECT] Processed 8000322 reads in 710 ms
[2015-09-30T22:34Z] INFO  23:34:40,461 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:40,647 MuTect - [MUTECT] Processed 61002686 reads in 660 ms
[2015-09-30T22:34Z] INFO  23:34:40,807 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:41,050 MuTect - [MUTECT] Processed 143007365 reads in 635 ms
[2015-09-30T22:34Z] INFO  23:34:41,121 MuTect - [MUTECT] Processed 9000427 reads in 680 ms
[2015-09-30T22:34Z] INFO  23:34:41,322 MuTect - [MUTECT] Processed 62002691 reads in 675 ms
[2015-09-30T22:34Z] INFO  23:34:41,705 MuTect - [MUTECT] Processed 144007434 reads in 655 ms
[2015-09-30T22:34Z] INFO  23:34:41,802 MuTect - [MUTECT] Processed 10000469 reads in 681 ms
[2015-09-30T22:34Z] INFO  23:34:42,021 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:42,034 MuTect - [MUTECT] Processed 63002754 reads in 712 ms
[2015-09-30T22:34Z] INFO  23:34:42,377 MuTect - [MUTECT] Processed 145007555 reads in 672 ms
[2015-09-30T22:34Z] INFO  23:34:42,482 MuTect - [MUTECT] Processed 11000529 reads in 680 ms
[2015-09-30T22:34Z] INFO  23:34:42,685 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:42,707 MuTect - [MUTECT] Processed 64002831 reads in 673 ms
[2015-09-30T22:34Z] INFO  23:34:43,042 MuTect - [MUTECT] Processed 146007671 reads in 665 ms
[2015-09-30T22:34Z] INFO  23:34:43,176 MuTect - [MUTECT] Processed 12000531 reads in 694 ms
[2015-09-30T22:34Z] INFO  23:34:43,312 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:43,405 MuTect - [MUTECT] Processed 65002875 reads in 698 ms
[2015-09-30T22:34Z] INFO  23:34:43,742 MuTect - [MUTECT] Processed 147007728 reads in 700 ms
[2015-09-30T22:34Z] INFO  23:34:43,897 MuTect - [MUTECT] Processed 13000631 reads in 721 ms
[2015-09-30T22:34Z] INFO  23:34:44,133 MuTect - [MUTECT] Processed 66002928 reads in 728 ms
[2015-09-30T22:34Z] INFO  23:34:44,420 MuTect - [MUTECT] Processed 148007740 reads in 678 ms
[2015-09-30T22:34Z] INFO  23:34:44,434 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:44,619 MuTect - [MUTECT] Processed 14000724 reads in 722 ms
[2015-09-30T22:34Z] INFO  23:34:44,802 MuTect - [MUTECT] Processed 67002960 reads in 669 ms
[2015-09-30T22:34Z] INFO  23:34:45,002 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:45,108 MuTect - [MUTECT] Processed 149007826 reads in 688 ms
[2015-09-30T22:34Z] INFO  23:34:45,288 MuTect - [MUTECT] Processed 15000733 reads in 669 ms
[2015-09-30T22:34Z] INFO  23:34:45,485 MuTect - [MUTECT] Processed 68002966 reads in 683 ms
[2015-09-30T22:34Z] INFO  23:34:45,682 ProgressMeter -     12:55945702        4.71e+06  100.0 s       21.0 s     73.5%         2.3 m    36.0 s
[2015-09-30T22:34Z] INFO  23:34:45,748 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:45,785 MuTect - [MUTECT] Processed 150007918 reads in 677 ms
[2015-09-30T22:34Z] INFO  23:34:45,927 MuTect - [MUTECT] Processed 16000822 reads in 639 ms
[2015-09-30T22:34Z] INFO  23:34:46,151 MuTect - [MUTECT] Processed 69002980 reads in 666 ms
[2015-09-30T22:34Z] INFO  23:34:46,432 MuTect - [MUTECT] Processed 151007993 reads in 647 ms
[2015-09-30T22:34Z] INFO  23:34:46,644 MuTect - [MUTECT] Processed 17000855 reads in 717 ms
[2015-09-30T22:34Z] INFO  23:34:46,730 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:46,809 MuTect - [MUTECT] Processed 70002995 reads in 658 ms
[2015-09-30T22:34Z] INFO  23:34:47,070 MuTect - [MUTECT] Processed 152008108 reads in 637 ms
[2015-09-30T22:34Z] INFO  23:34:47,187 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:47,480 MuTect - [MUTECT] Processed 71003013 reads in 671 ms
[2015-09-30T22:34Z] INFO  23:34:47,569 MuTect - [MUTECT] Processed 18000890 reads in 925 ms
[2015-09-30T22:34Z] INFO  23:34:47,694 MuTect - [MUTECT] Processed 153008166 reads in 625 ms
[2015-09-30T22:34Z] INFO  23:34:48,040 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:48,162 MuTect - [MUTECT] Processed 72003039 reads in 682 ms
[2015-09-30T22:34Z] INFO  23:34:48,331 MuTect - [MUTECT] Processed 19000898 reads in 762 ms
[2015-09-30T22:34Z] INFO  23:34:48,347 MuTect - [MUTECT] Processed 154008227 reads in 653 ms
[2015-09-30T22:34Z] INFO  23:34:48,815 MuTect - [MUTECT] Processed 73003062 reads in 653 ms
[2015-09-30T22:34Z] INFO  23:34:48,963 MuTect - [MUTECT] Processed 155008253 reads in 616 ms
[2015-09-30T22:34Z] INFO  23:34:49,068 MuTect - [MUTECT] Processed 20000941 reads in 737 ms
[2015-09-30T22:34Z] INFO  23:34:49,367 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:49,402 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:49,461 MuTect - [MUTECT] Processed 74003157 reads in 646 ms
[2015-09-30T22:34Z] INFO  23:34:49,574 MuTect - [MUTECT] Processed 156008379 reads in 611 ms
[2015-09-30T22:34Z] INFO  23:34:49,798 MuTect - [MUTECT] Processed 21000965 reads in 730 ms
[2015-09-30T22:34Z] INFO  23:34:50,123 MuTect - [MUTECT] Processed 75003196 reads in 662 ms
[2015-09-30T22:34Z] INFO  23:34:50,168 MuTect - [MUTECT] Processed 157008479 reads in 594 ms
[2015-09-30T22:34Z] INFO  23:34:50,249 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:50,479 MuTect - [MUTECT] Processed 22001020 reads in 681 ms
[2015-09-30T22:34Z] INFO  23:34:50,773 MuTect - [MUTECT] Processed 76003244 reads in 650 ms
[2015-09-30T22:34Z] INFO  23:34:50,785 MuTect - [MUTECT] Processed 158008487 reads in 617 ms
[2015-09-30T22:34Z] INFO  23:34:51,187 MuTect - [MUTECT] Processed 23001075 reads in 708 ms
[2015-09-30T22:34Z] INFO  23:34:51,415 MuTect - [MUTECT] Processed 159008504 reads in 630 ms
[2015-09-30T22:34Z] INFO  23:34:51,428 MuTect - [MUTECT] Processed 77003353 reads in 655 ms
[2015-09-30T22:34Z] INFO  23:34:51,448 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:51,892 MuTect - [MUTECT] Processed 24001116 reads in 705 ms
[2015-09-30T22:34Z] INFO  23:34:51,938 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:52,036 MuTect - [MUTECT] Processed 160008582 reads in 621 ms
[2015-09-30T22:34Z] INFO  23:34:52,061 MuTect - [MUTECT] Processed 78003438 reads in 633 ms
[2015-09-30T22:34Z] INFO  23:34:52,452 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:52,623 MuTect - [MUTECT] Processed 25001142 reads in 731 ms
[2015-09-30T22:34Z] INFO  23:34:52,631 MuTect - [MUTECT] Processed 161008601 reads in 595 ms
[2015-09-30T22:34Z] INFO  23:34:52,680 MuTect - [MUTECT] Processed 79003513 reads in 619 ms
[2015-09-30T22:34Z] INFO  23:34:53,225 MuTect - [MUTECT] Processed 162008619 reads in 594 ms
[2015-09-30T22:34Z] INFO  23:34:53,335 MuTect - [MUTECT] Processed 26001241 reads in 712 ms
[2015-09-30T22:34Z] INFO  23:34:53,390 MuTect - [MUTECT] Processed 80003556 reads in 710 ms
[2015-09-30T22:34Z] INFO  23:34:53,619 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:53,815 MuTect - [MUTECT] Processed 163008683 reads in 590 ms
[2015-09-30T22:34Z] INFO  23:34:54,008 MuTect - [MUTECT] Processed 81003636 reads in 618 ms
[2015-09-30T22:34Z] INFO  23:34:54,045 MuTect - [MUTECT] Processed 27001305 reads in 710 ms
[2015-09-30T22:34Z] INFO  23:34:54,238 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:54,392 MuTect - [MUTECT] Processed 164008741 reads in 577 ms
[2015-09-30T22:34Z] INFO  23:34:54,628 MuTect - [MUTECT] Processed 82003753 reads in 620 ms
[2015-09-30T22:34Z] INFO  23:34:54,691 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:54,766 MuTect - [MUTECT] Processed 28001355 reads in 721 ms
[2015-09-30T22:34Z] INFO  23:34:54,991 MuTect - [MUTECT] Processed 165008794 reads in 599 ms
[2015-09-30T22:34Z] INFO  23:34:55,265 MuTect - [MUTECT] Processed 83003815 reads in 637 ms
[2015-09-30T22:34Z] INFO  23:34:55,435 MuTect - [MUTECT] Processed 29001365 reads in 668 ms
[2015-09-30T22:34Z] INFO  23:34:55,586 MuTect - [MUTECT] Processed 166008862 reads in 595 ms
[2015-09-30T22:34Z] INFO  23:34:55,604 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:55,886 MuTect - [MUTECT] Processed 84003888 reads in 620 ms
[2015-09-30T22:34Z] INFO  23:34:56,115 MuTect - [MUTECT] Processed 30001479 reads in 681 ms
[2015-09-30T22:34Z] INFO  23:34:56,191 MuTect - [MUTECT] Processed 167008931 reads in 605 ms
[2015-09-30T22:34Z] INFO  23:34:56,405 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:56,498 ProgressMeter -    12:110426818        2.98e+06   60.0 s       20.0 s     47.5%         2.1 m    66.0 s
[2015-09-30T22:34Z] INFO  23:34:56,512 MuTect - [MUTECT] Processed 85003938 reads in 627 ms
[2015-09-30T22:34Z] INFO  23:34:56,769 MuTect - [MUTECT] Processed 168009014 reads in 578 ms
[2015-09-30T22:34Z] INFO  23:34:56,830 MuTect - [MUTECT] Processed 31001537 reads in 715 ms
[2015-09-30T22:34Z] INFO  23:34:56,974 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:57,140 MuTect - [MUTECT] Processed 86003986 reads in 628 ms
[2015-09-30T22:34Z] INFO  23:34:57,365 MuTect - [MUTECT] Processed 169009037 reads in 596 ms
[2015-09-30T22:34Z] INFO  23:34:57,521 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:57,575 MuTect - [MUTECT] Processed 32001623 reads in 745 ms
[2015-09-30T22:34Z] INFO  23:34:57,797 MuTect - [MUTECT] Processed 87004017 reads in 657 ms
[2015-09-30T22:34Z] INFO  23:34:57,996 MuTect - [MUTECT] Processed 170009126 reads in 631 ms
[2015-09-30T22:34Z] INFO  23:34:58,216 MuTect - [MUTECT] Processed 33001692 reads in 641 ms
[2015-09-30T22:34Z] INFO  23:34:58,474 MuTect - [MUTECT] Processed 88004028 reads in 677 ms
[2015-09-30T22:34Z] INFO  23:34:58,548 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:58,621 MuTect - [MUTECT] Processed 171009207 reads in 625 ms
[2015-09-30T22:34Z] INFO  23:34:58,870 MuTect - [MUTECT] Processed 34001700 reads in 654 ms
[2015-09-30T22:34Z] INFO  23:34:59,132 MuTect - [MUTECT] Processed 89004068 reads in 658 ms
[2015-09-30T22:34Z] INFO  23:34:59,237 MuTect - [MUTECT] Processed 172009234 reads in 616 ms
[2015-09-30T22:34Z] INFO  23:34:59,424 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:59,511 MuTect - [MUTECT] Processed 35001701 reads in 641 ms
[2015-09-30T22:34Z] INFO  23:34:59,632 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:34Z] INFO  23:34:59,799 MuTect - [MUTECT] Processed 90004110 reads in 667 ms
[2015-09-30T22:34Z] INFO  23:34:59,878 MuTect - [MUTECT] Processed 173009265 reads in 641 ms
[2015-09-30T22:35Z] INFO  23:35:00,137 MuTect - [MUTECT] Processed 36001823 reads in 626 ms
[2015-09-30T22:35Z] INFO  23:35:00,479 MuTect - [MUTECT] Processed 91004130 reads in 680 ms
[2015-09-30T22:35Z] INFO  23:35:00,530 MuTect - [MUTECT] Processed 174009354 reads in 652 ms
[2015-09-30T22:35Z] INFO  23:35:00,779 MuTect - [MUTECT] Processed 37001832 reads in 642 ms
[2015-09-30T22:35Z] INFO  23:35:00,828 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:01,143 MuTect - [MUTECT] Processed 92004136 reads in 664 ms
[2015-09-30T22:35Z] INFO  23:35:01,164 MuTect - [MUTECT] Processed 175009377 reads in 634 ms
[2015-09-30T22:35Z] INFO  23:35:01,467 MuTect - [MUTECT] Processed 38001939 reads in 687 ms
[2015-09-30T22:35Z] INFO  23:35:01,796 MuTect - [MUTECT] Processed 93004244 reads in 653 ms
[2015-09-30T22:35Z] INFO  23:35:01,810 MuTect - [MUTECT] Processed 176009459 reads in 646 ms
[2015-09-30T22:35Z] INFO  23:35:01,849 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:02,019 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:02,186 MuTect - [MUTECT] Processed 39001955 reads in 720 ms
[2015-09-30T22:35Z] INFO  23:35:02,422 MuTect - [MUTECT] Processed 177009478 reads in 612 ms
[2015-09-30T22:35Z] INFO  23:35:02,460 MuTect - [MUTECT] Processed 94004261 reads in 664 ms
[2015-09-30T22:35Z] INFO  23:35:02,783 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:02,813 ProgressMeter -    12:133129500        1.03e+06   30.0 s       29.0 s     76.6%        39.0 s     9.0 s
[2015-09-30T22:35Z] INFO  23:35:02,833 MuTect - [MUTECT] Processed 40001963 reads in 646 ms
[2015-09-30T22:35Z] INFO  23:35:03,067 MuTect - [MUTECT] Processed 178009547 reads in 645 ms
[2015-09-30T22:35Z] INFO  23:35:03,149 MuTect - [MUTECT] Processed 95004353 reads in 689 ms
[2015-09-30T22:35Z] INFO  23:35:03,511 MuTect - [MUTECT] Processed 41001975 reads in 678 ms
[2015-09-30T22:35Z] INFO  23:35:03,755 MuTect - [MUTECT] Processed 179009555 reads in 688 ms
[2015-09-30T22:35Z] INFO  23:35:03,832 MuTect - [MUTECT] Processed 96004394 reads in 683 ms
[2015-09-30T22:35Z] INFO  23:35:04,069 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:04,174 MuTect - [MUTECT] Processed 42001986 reads in 664 ms
[2015-09-30T22:35Z] INFO  23:35:04,266 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:04,380 MuTect - [MUTECT] Processed 180009639 reads in 625 ms
[2015-09-30T22:35Z] INFO  23:35:04,474 MuTect - [MUTECT] Processed 97004482 reads in 642 ms
[2015-09-30T22:35Z] INFO  23:35:04,870 MuTect - [MUTECT] Processed 43002050 reads in 696 ms
[2015-09-30T22:35Z] INFO  23:35:05,005 MuTect - [MUTECT] Processed 181009767 reads in 625 ms
[2015-09-30T22:35Z] INFO  23:35:05,066 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:05,112 MuTect - [MUTECT] Processed 98004486 reads in 638 ms
[2015-09-30T22:35Z] INFO  23:35:05,549 MuTect - [MUTECT] Processed 44002089 reads in 679 ms
[2015-09-30T22:35Z] INFO  23:35:05,617 MuTect - [MUTECT] Processed 182009810 reads in 612 ms
[2015-09-30T22:35Z] INFO  23:35:05,747 MuTect - [MUTECT] Processed 99004557 reads in 635 ms
[2015-09-30T22:35Z] INFO  23:35:06,011 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:06,219 MuTect - [MUTECT] Processed 45002191 reads in 670 ms
[2015-09-30T22:35Z] INFO  23:35:06,226 MuTect - [MUTECT] Processed 183009920 reads in 609 ms
[2015-09-30T22:35Z] INFO  23:35:06,394 MuTect - [MUTECT] Processed 100004619 reads in 647 ms
[2015-09-30T22:35Z] INFO  23:35:06,547 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:06,830 MuTect - [MUTECT] Processed 184010032 reads in 604 ms
[2015-09-30T22:35Z] INFO  23:35:06,986 MuTect - [MUTECT] Processed 46002278 reads in 767 ms
[2015-09-30T22:35Z] INFO  23:35:07,021 MuTect - [MUTECT] Processed 101004702 reads in 627 ms
[2015-09-30T22:35Z] INFO  23:35:07,428 MuTect - [MUTECT] Processed 185010044 reads in 598 ms
[2015-09-30T22:35Z] INFO  23:35:07,446 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:07,640 MuTect - [MUTECT] Processed 102004742 reads in 619 ms
[2015-09-30T22:35Z] INFO  23:35:07,727 MuTect - [MUTECT] Processed 47002364 reads in 741 ms
[2015-09-30T22:35Z] INFO  23:35:08,019 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:08,034 MuTect - [MUTECT] Processed 186010125 reads in 606 ms
[2015-09-30T22:35Z] INFO  23:35:08,283 MuTect - [MUTECT] Processed 103004794 reads in 643 ms
[2015-09-30T22:35Z] INFO  23:35:08,444 MuTect - [MUTECT] Processed 48002448 reads in 717 ms
[2015-09-30T22:35Z] INFO  23:35:08,644 MuTect - [MUTECT] Processed 187010191 reads in 610 ms
[2015-09-30T22:35Z] INFO  23:35:08,705 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:08,927 MuTect - [MUTECT] Processed 104004836 reads in 644 ms
[2015-09-30T22:35Z] INFO  23:35:09,123 MuTect - [MUTECT] Processed 49002541 reads in 679 ms
[2015-09-30T22:35Z] INFO  23:35:09,241 MuTect - [MUTECT] Processed 188010311 reads in 597 ms
[2015-09-30T22:35Z] INFO  23:35:09,547 MuTect - [MUTECT] Processed 105004861 reads in 620 ms
[2015-09-30T22:35Z] INFO  23:35:09,818 MuTect - [MUTECT] Processed 50002543 reads in 695 ms
[2015-09-30T22:35Z] INFO  23:35:09,857 MuTect - [MUTECT] Processed 189010425 reads in 616 ms
[2015-09-30T22:35Z] INFO  23:35:09,960 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:09,968 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:10,174 MuTect - [MUTECT] Processed 106004953 reads in 627 ms
[2015-09-30T22:35Z] INFO  23:35:10,467 MuTect - [MUTECT] Processed 190010444 reads in 610 ms
[2015-09-30T22:35Z] INFO  23:35:10,498 MuTect - [MUTECT] Processed 51002619 reads in 680 ms
[2015-09-30T22:35Z] INFO  23:35:10,650 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:35Z] INFO  23:35:10,653 ProgressMeter -            done        1.37e+06   37.0 s       27.0 s    100.0%        37.0 s     0.0 s
[2015-09-30T22:35Z] INFO  23:35:10,653 ProgressMeter - Total runtime 37.84 secs, 0.63 min, 0.01 hours
[2015-09-30T22:35Z] INFO  23:35:10,719 MicroScheduler - 43026 reads were filtered out during the traversal out of approximately 616474 total reads (6.98%)
[2015-09-30T22:35Z] INFO  23:35:10,720 MicroScheduler -   -> 32771 reads (5.32% of total) failing DuplicateReadFilter
[2015-09-30T22:35Z] INFO  23:35:10,720 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:35Z] INFO  23:35:10,720 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:35Z] INFO  23:35:10,720 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:35Z] INFO  23:35:10,720 MicroScheduler -   -> 10255 reads (1.66% of total) failing UnmappedReadFilter
[2015-09-30T22:35Z] INFO  23:35:10,792 MuTect - [MUTECT] Processed 107004984 reads in 618 ms
[2015-09-30T22:35Z] INFO  23:35:10,883 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:11,077 MuTect - [MUTECT] Processed 191010580 reads in 610 ms
[2015-09-30T22:35Z] INFO  23:35:11,409 MuTect - [MUTECT] Processed 108005043 reads in 617 ms
[2015-09-30T22:35Z] INFO  23:35:11,672 MuTect - [MUTECT] Processed 192010595 reads in 595 ms
[2015-09-30T22:35Z] INFO  23:35:11,698 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:35Z] bgzip syn3-12_124191013_133851895-raw-mutect.vcf
[2015-09-30T22:35Z] tabix index syn3-12_124191013_133851895-raw-mutect.vcf.gz
[2015-09-30T22:35Z] INFO  23:35:11,939 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:12,060 MuTect - [MUTECT] Processed 109005094 reads in 651 ms
[2015-09-30T22:35Z] INFO  23:35:12,275 MuTect - [MUTECT] Processed 193010660 reads in 603 ms
[2015-09-30T22:35Z] INFO  23:35:12,702 MuTect - [MUTECT] Processed 110005206 reads in 642 ms
[2015-09-30T22:35Z] INFO  23:35:12,892 MuTect - [MUTECT] Processed 194010666 reads in 617 ms
[2015-09-30T22:35Z] INFO  23:35:13,188 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:13,372 MuTect - [MUTECT] Processed 111005305 reads in 670 ms
[2015-09-30T22:35Z] INFO  23:35:13,528 MuTect - [MUTECT] Processed 195010666 reads in 636 ms
[2015-09-30T22:35Z] INFO  23:35:13,877 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:14,010 MuTect - [MUTECT] Processed 112005364 reads in 638 ms
[2015-09-30T22:35Z] INFO  23:35:14,159 MuTect - [MUTECT] Processed 196010740 reads in 630 ms
[2015-09-30T22:35Z] INFO  23:35:14,669 MuTect - [MUTECT] Processed 113005471 reads in 659 ms
[2015-09-30T22:35Z] INFO  23:35:14,876 MuTect - [MUTECT] Processed 197010769 reads in 718 ms
[2015-09-30T22:35Z] INFO  23:35:15,352 MuTect - [MUTECT] Processed 114005486 reads in 683 ms
[2015-09-30T22:35Z] INFO  23:35:15,396 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:15,461 MuTect - [MUTECT] Processed 198010784 reads in 585 ms
[2015-09-30T22:35Z] INFO  23:35:15,684 ProgressMeter -     12:57926332        6.13e+06    2.2 m       21.0 s     94.0%         2.3 m     8.0 s
[2015-09-30T22:35Z] INFO  23:35:15,962 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:16,002 MuTect - [MUTECT] Processed 115005522 reads in 650 ms
[2015-09-30T22:35Z] INFO  23:35:16,056 MuTect - [MUTECT] Processed 199010804 reads in 595 ms
[2015-09-30T22:35Z] INFO  23:35:16,647 MuTect - [MUTECT] Processed 200010813 reads in 591 ms
[2015-09-30T22:35Z] INFO  23:35:16,674 MuTect - [MUTECT] Processed 116005537 reads in 672 ms
[2015-09-30T22:35Z] INFO  23:35:17,240 MuTect - [MUTECT] Processed 201010814 reads in 593 ms
[2015-09-30T22:35Z] MuTect: MuTect
[2015-09-30T22:35Z] INFO  23:35:17,308 MuTect - [MUTECT] Processed 117005627 reads in 634 ms
[2015-09-30T22:35Z] INFO  23:35:17,605 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:17,854 MuTect - [MUTECT] Processed 202010841 reads in 614 ms
[2015-09-30T22:35Z] INFO  23:35:17,942 MuTect - [MUTECT] Processed 118005649 reads in 634 ms
[2015-09-30T22:35Z] INFO  23:35:17,962 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:18,445 MuTect - [MUTECT] Processed 203010953 reads in 591 ms
[2015-09-30T22:35Z] INFO  23:35:18,587 MuTect - [MUTECT] Processed 119005654 reads in 645 ms
[2015-09-30T22:35Z] INFO  23:35:19,063 MuTect - [MUTECT] Processed 204011028 reads in 618 ms
[2015-09-30T22:35Z] INFO  23:35:19,239 MuTect - [MUTECT] Processed 120005666 reads in 652 ms
[2015-09-30T22:35Z] INFO  23:35:19,348 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/13/syn3-13_0_31036104-raw-mutect-regions.bed to be BED
[2015-09-30T22:35Z] INFO  23:35:19,404 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:35Z] INFO  23:35:19,404 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:35Z] INFO  23:35:19,404 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:35Z] INFO  23:35:19,404 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:35Z] INFO  23:35:19,408 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/13/syn3-13_0_31036104-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/13/tx/tmpwH3Anq/syn3-13_0_31036104-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:35Z] INFO  23:35:19,408 HelpFormatter - Date/Time: 2015/09/30 23:35:19
[2015-09-30T22:35Z] INFO  23:35:19,408 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:35Z] INFO  23:35:19,408 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:35Z] INFO  23:35:19,436 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:35Z] INFO  23:35:19,440 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:35Z] INFO  23:35:19,490 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:35Z] INFO  23:35:19,539 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:35Z] INFO  23:35:19,546 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:35Z] INFO  23:35:19,685 MuTect - [MUTECT] Processed 205011043 reads in 622 ms
[2015-09-30T22:35Z] INFO  23:35:19,698 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
[2015-09-30T22:35Z] INFO  23:35:19,737 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:19,807 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:35Z] INFO  23:35:19,885 MuTect - [MUTECT] Processed 121005712 reads in 646 ms
[2015-09-30T22:35Z] INFO  23:35:19,974 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:19,986 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:35Z] INFO  23:35:20,062 IntervalUtils - Processing 578686 bp from intervals
[2015-09-30T22:35Z] INFO  23:35:20,066 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:35Z] INFO  23:35:20,066 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:35Z] INFO  23:35:20,120 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:35Z] INFO  23:35:20,285 MuTect - [MUTECT] Processed 206011072 reads in 600 ms
[2015-09-30T22:35Z] INFO  23:35:20,305 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:35Z] INFO  23:35:20,305 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:35Z] INFO  23:35:20,305 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:35Z] INFO  23:35:20,306 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:35Z] INFO  23:35:20,522 MuTect - [MUTECT] Processed 122005723 reads in 637 ms
[2015-09-30T22:35Z] INFO  23:35:20,886 MuTect - [MUTECT] Processed 207011144 reads in 601 ms
[2015-09-30T22:35Z] INFO  23:35:21,193 MuTect - [MUTECT] Processed 123005785 reads in 671 ms
[2015-09-30T22:35Z] INFO  23:35:21,488 MuTect - [MUTECT] Processed 208011201 reads in 602 ms
[2015-09-30T22:35Z] INFO  23:35:21,851 MuTect - [MUTECT] Processed 124005791 reads in 658 ms
[2015-09-30T22:35Z] INFO  23:35:21,885 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:21,975 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:22,119 MuTect - [MUTECT] Processed 209011271 reads in 631 ms
[2015-09-30T22:35Z] INFO  23:35:22,480 MuTect - [MUTECT] Processed 125005821 reads in 629 ms
[2015-09-30T22:35Z] INFO  23:35:22,737 MuTect - [MUTECT] Processed 210011360 reads in 618 ms
[2015-09-30T22:35Z] INFO  23:35:22,999 MuTect - [MUTECT] Processed 1000001 reads in 2646 ms
[2015-09-30T22:35Z] INFO  23:35:23,225 MuTect - [MUTECT] Processed 126005867 reads in 745 ms
[2015-09-30T22:35Z] INFO  23:35:23,398 MuTect - [MUTECT] Processed 211011370 reads in 661 ms
[2015-09-30T22:35Z] INFO  23:35:23,733 MuTect - [MUTECT] Processed 2000074 reads in 734 ms
[2015-09-30T22:35Z] INFO  23:35:23,966 MuTect - [MUTECT] Processed 127005868 reads in 741 ms
[2015-09-30T22:35Z] INFO  23:35:23,988 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:35Z] INFO  23:35:23,993 ProgressMeter -            done        6.63e+06    2.3 m       20.0 s    100.0%         2.3 m     0.0 s
[2015-09-30T22:35Z] INFO  23:35:23,993 ProgressMeter - Total runtime 138.32 secs, 2.31 min, 0.04 hours
[2015-09-30T22:35Z] INFO  23:35:24,061 MicroScheduler - 162300 reads were filtered out during the traversal out of approximately 2476056 total reads (6.55%)
[2015-09-30T22:35Z] INFO  23:35:24,061 MicroScheduler -   -> 120801 reads (4.88% of total) failing DuplicateReadFilter
[2015-09-30T22:35Z] INFO  23:35:24,061 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:35Z] INFO  23:35:24,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:35Z] INFO  23:35:24,062 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:35Z] INFO  23:35:24,062 MicroScheduler -   -> 41499 reads (1.68% of total) failing UnmappedReadFilter
[2015-09-30T22:35Z] INFO  23:35:24,404 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:24,522 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:24,614 MuTect - [MUTECT] Processed 3000100 reads in 881 ms
[2015-09-30T22:35Z] INFO  23:35:24,662 MuTect - [MUTECT] Processed 128005932 reads in 696 ms
[2015-09-30T22:35Z] INFO  23:35:25,067 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:35Z] bgzip syn3-12_31116488_62142833-raw-mutect.vcf
[2015-09-30T22:35Z] tabix index syn3-12_31116488_62142833-raw-mutect.vcf.gz
[2015-09-30T22:35Z] INFO  23:35:25,345 MuTect - [MUTECT] Processed 129005947 reads in 683 ms
[2015-09-30T22:35Z] INFO  23:35:25,375 MuTect - [MUTECT] Processed 4000182 reads in 761 ms
[2015-09-30T22:35Z] INFO  23:35:26,002 MuTect - [MUTECT] Processed 130005958 reads in 657 ms
[2015-09-30T22:35Z] INFO  23:35:26,084 MuTect - [MUTECT] Processed 5000215 reads in 709 ms
[2015-09-30T22:35Z] INFO  23:35:26,501 ProgressMeter -    12:117178101        4.53e+06   90.0 s       19.0 s     68.7%         2.2 m    41.0 s
[2015-09-30T22:35Z] INFO  23:35:26,744 MuTect - [MUTECT] Processed 131006038 reads in 742 ms
[2015-09-30T22:35Z] INFO  23:35:26,823 MuTect - [MUTECT] Processed 6000242 reads in 739 ms
[2015-09-30T22:35Z] INFO  23:35:26,900 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:35Z] MuTect: MuTect
[2015-09-30T22:35Z] INFO  23:35:27,244 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:27,457 MuTect - [MUTECT] Processed 132006042 reads in 713 ms
[2015-09-30T22:35Z] INFO  23:35:27,556 MuTect - [MUTECT] Processed 7000286 reads in 732 ms
[2015-09-30T22:35Z] INFO  23:35:28,139 MuTect - [MUTECT] Processed 133006131 reads in 682 ms
[2015-09-30T22:35Z] INFO  23:35:28,295 MuTect - [MUTECT] Processed 8000288 reads in 740 ms
[2015-09-30T22:35Z] INFO  23:35:28,816 MuTect - [MUTECT] Processed 134006250 reads in 677 ms
[2015-09-30T22:35Z] INFO  23:35:29,006 MuTect - [MUTECT] Processed 9000299 reads in 711 ms
[2015-09-30T22:35Z] INFO  23:35:29,158 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/13/syn3-13_31036377_62334609-raw-mutect-regions.bed to be BED
[2015-09-30T22:35Z] INFO  23:35:29,209 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:35Z] INFO  23:35:29,210 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:35Z] INFO  23:35:29,210 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:35Z] INFO  23:35:29,210 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:35Z] INFO  23:35:29,213 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/13/syn3-13_31036377_62334609-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/13/tx/tmpWJ7S7F/syn3-13_31036377_62334609-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:35Z] INFO  23:35:29,213 HelpFormatter - Date/Time: 2015/09/30 23:35:29
[2015-09-30T22:35Z] INFO  23:35:29,213 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:35Z] INFO  23:35:29,213 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:35Z] INFO  23:35:29,239 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:35Z] INFO  23:35:29,243 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:35Z] INFO  23:35:29,290 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:35Z] INFO  23:35:29,334 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:35Z] INFO  23:35:29,337 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:29,341 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:35Z] INFO  23:35:29,381 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T22:35Z] INFO  23:35:29,405 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:35Z] INFO  23:35:29,534 MuTect - [MUTECT] Processed 135006307 reads in 718 ms
[2015-09-30T22:35Z] INFO  23:35:29,572 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:35Z] INFO  23:35:29,665 IntervalUtils - Processing 1124551 bp from intervals
[2015-09-30T22:35Z] INFO  23:35:29,669 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:35Z] INFO  23:35:29,669 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:35Z] INFO  23:35:29,728 MuTect - [MUTECT] Processed 10000384 reads in 722 ms
[2015-09-30T22:35Z] INFO  23:35:29,817 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:35Z] INFO  23:35:29,880 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:29,955 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:35Z] INFO  23:35:29,955 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:35Z] INFO  23:35:29,955 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:35Z] INFO  23:35:29,956 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:35Z] INFO  23:35:30,246 MuTect - [MUTECT] Processed 136006373 reads in 712 ms
[2015-09-30T22:35Z] INFO  23:35:30,476 MuTect - [MUTECT] Processed 11000423 reads in 748 ms
[2015-09-30T22:35Z] INFO  23:35:30,960 MuTect - [MUTECT] Processed 137006468 reads in 714 ms
[2015-09-30T22:35Z] INFO  23:35:31,237 MuTect - [MUTECT] Processed 12000469 reads in 761 ms
[2015-09-30T22:35Z] INFO  23:35:31,642 MuTect - [MUTECT] Processed 138006541 reads in 682 ms
[2015-09-30T22:35Z] INFO  23:35:31,737 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:31,996 MuTect - [MUTECT] Processed 13000520 reads in 759 ms
[2015-09-30T22:35Z] INFO  23:35:32,351 MuTect - [MUTECT] Processed 139006630 reads in 709 ms
[2015-09-30T22:35Z] INFO  23:35:32,352 MuTect - [MUTECT] Processed 1000047 reads in 2352 ms
[2015-09-30T22:35Z] INFO  23:35:32,539 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:32,728 MuTect - [MUTECT] Processed 14000571 reads in 732 ms
[2015-09-30T22:35Z] INFO  23:35:33,037 MuTect - [MUTECT] Processed 140006679 reads in 686 ms
[2015-09-30T22:35Z] INFO  23:35:33,151 MuTect - [MUTECT] Processed 2000089 reads in 799 ms
[2015-09-30T22:35Z] INFO  23:35:33,359 MuTect - [MUTECT] Processed 15000572 reads in 631 ms
[2015-09-30T22:35Z] INFO  23:35:33,670 MuTect - [MUTECT] Processed 141006703 reads in 633 ms
[2015-09-30T22:35Z] INFO  23:35:33,857 MuTect - [MUTECT] Processed 3000104 reads in 706 ms
[2015-09-30T22:35Z] INFO  23:35:33,991 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:34,080 MuTect - [MUTECT] Processed 16000620 reads in 721 ms
[2015-09-30T22:35Z] INFO  23:35:34,330 MuTect - [MUTECT] Processed 142006776 reads in 660 ms
[2015-09-30T22:35Z] INFO  23:35:34,465 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:34,689 MuTect - [MUTECT] Processed 4000165 reads in 832 ms
[2015-09-30T22:35Z] INFO  23:35:34,781 MuTect - [MUTECT] Processed 17000639 reads in 701 ms
[2015-09-30T22:35Z] INFO  23:35:34,973 MuTect - [MUTECT] Processed 143006855 reads in 643 ms
[2015-09-30T22:35Z] INFO  23:35:35,092 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:35,386 MuTect - [MUTECT] Processed 5000169 reads in 697 ms
[2015-09-30T22:35Z] INFO  23:35:35,459 MuTect - [MUTECT] Processed 18000701 reads in 678 ms
[2015-09-30T22:35Z] INFO  23:35:35,618 MuTect - [MUTECT] Processed 144006896 reads in 645 ms
[2015-09-30T22:35Z] INFO  23:35:36,079 MuTect - [MUTECT] Processed 6000193 reads in 692 ms
[2015-09-30T22:35Z] INFO  23:35:36,089 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:36,115 MuTect - [MUTECT] Processed 19000708 reads in 656 ms
[2015-09-30T22:35Z] INFO  23:35:36,237 MuTect - [MUTECT] Processed 145006975 reads in 618 ms
[2015-09-30T22:35Z] INFO  23:35:36,760 MuTect - [MUTECT] Processed 7000223 reads in 682 ms
[2015-09-30T22:35Z] INFO  23:35:36,877 MuTect - [MUTECT] Processed 146007098 reads in 641 ms
[2015-09-30T22:35Z] INFO  23:35:36,942 MuTect - [MUTECT] Processed 20000795 reads in 827 ms
[2015-09-30T22:35Z] INFO  23:35:36,990 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:37,418 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:37,447 MuTect - [MUTECT] Processed 8000260 reads in 687 ms
[2015-09-30T22:35Z] INFO  23:35:37,520 MuTect - [MUTECT] Processed 147007165 reads in 643 ms
[2015-09-30T22:35Z] INFO  23:35:37,697 MuTect - [MUTECT] Processed 21000854 reads in 755 ms
[2015-09-30T22:35Z] INFO  23:35:38,149 MuTect - [MUTECT] Processed 148007249 reads in 629 ms
[2015-09-30T22:35Z] INFO  23:35:38,177 MuTect - [MUTECT] Processed 9000309 reads in 729 ms
[2015-09-30T22:35Z] INFO  23:35:38,291 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:38,414 MuTect - [MUTECT] Processed 22000903 reads in 717 ms
[2015-09-30T22:35Z] INFO  23:35:38,971 MuTect - [MUTECT] Processed 149007365 reads in 822 ms
[2015-09-30T22:35Z] INFO  23:35:39,065 MuTect - [MUTECT] Processed 10000328 reads in 889 ms
[2015-09-30T22:35Z] INFO  23:35:39,084 MuTect - [MUTECT] Processed 23000967 reads in 670 ms
[2015-09-30T22:35Z] INFO  23:35:39,578 MuTect - [MUTECT] Processed 150007406 reads in 607 ms
[2015-09-30T22:35Z] INFO  23:35:39,654 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:39,771 MuTect - [MUTECT] Processed 24001015 reads in 687 ms
[2015-09-30T22:35Z] INFO  23:35:39,845 MuTect - [MUTECT] Processed 11000404 reads in 780 ms
[2015-09-30T22:35Z] INFO  23:35:39,910 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:40,207 MuTect - [MUTECT] Processed 151007445 reads in 629 ms
[2015-09-30T22:35Z] INFO  23:35:40,454 MuTect - [MUTECT] Processed 25001057 reads in 683 ms
[2015-09-30T22:35Z] INFO  23:35:40,511 MuTect - [MUTECT] Processed 12000424 reads in 666 ms
[2015-09-30T22:35Z] INFO  23:35:40,574 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:40,861 MuTect - [MUTECT] Processed 152007501 reads in 654 ms
[2015-09-30T22:35Z] INFO  23:35:41,144 MuTect - [MUTECT] Processed 13000433 reads in 633 ms
[2015-09-30T22:35Z] INFO  23:35:41,361 MuTect - [MUTECT] Processed 26001161 reads in 907 ms
[2015-09-30T22:35Z] INFO  23:35:41,520 MuTect - [MUTECT] Processed 153007515 reads in 659 ms
[2015-09-30T22:35Z] INFO  23:35:41,781 MuTect - [MUTECT] Processed 14000456 reads in 637 ms
[2015-09-30T22:35Z] INFO  23:35:42,075 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:42,159 MuTect - [MUTECT] Processed 154007563 reads in 639 ms
[2015-09-30T22:35Z] INFO  23:35:42,161 MuTect - [MUTECT] Processed 27001171 reads in 800 ms
[2015-09-30T22:35Z] INFO  23:35:42,411 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:42,498 MuTect - [MUTECT] Processed 15000523 reads in 717 ms
[2015-09-30T22:35Z] INFO  23:35:42,642 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:42,827 MuTect - [MUTECT] Processed 155007624 reads in 667 ms
[2015-09-30T22:35Z] INFO  23:35:42,861 MuTect - [MUTECT] Processed 28001177 reads in 700 ms
[2015-09-30T22:35Z] INFO  23:35:43,165 MuTect - [MUTECT] Processed 16000572 reads in 667 ms
[2015-09-30T22:35Z] INFO  23:35:43,540 MuTect - [MUTECT] Processed 156007640 reads in 714 ms
[2015-09-30T22:35Z] INFO  23:35:43,655 MuTect - [MUTECT] Processed 29001182 reads in 794 ms
[2015-09-30T22:35Z] INFO  23:35:43,931 MuTect - [MUTECT] Processed 17000605 reads in 766 ms
[2015-09-30T22:35Z] INFO  23:35:44,225 MuTect - [MUTECT] Processed 157007678 reads in 685 ms
[2015-09-30T22:35Z] INFO  23:35:44,513 MuTect - [MUTECT] Processed 30001224 reads in 858 ms
[2015-09-30T22:35Z] INFO  23:35:44,745 MuTect - [MUTECT] Processed 18000618 reads in 814 ms
[2015-09-30T22:35Z] INFO  23:35:44,888 MuTect - [MUTECT] Processed 158007735 reads in 663 ms
[2015-09-30T22:35Z] INFO  23:35:44,933 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:44,975 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:45,004 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:45,267 MuTect - [MUTECT] Processed 31001272 reads in 754 ms
[2015-09-30T22:35Z] INFO  23:35:45,406 MuTect - [MUTECT] Processed 19000668 reads in 661 ms
[2015-09-30T22:35Z] INFO  23:35:45,540 MuTect - [MUTECT] Processed 159007760 reads in 652 ms
[2015-09-30T22:35Z] INFO  23:35:45,931 MuTect - [MUTECT] Processed 32001317 reads in 664 ms
[2015-09-30T22:35Z] INFO  23:35:46,049 MuTect - [MUTECT] Processed 20000714 reads in 643 ms
[2015-09-30T22:35Z] INFO  23:35:46,192 MuTect - [MUTECT] Processed 160007863 reads in 652 ms
[2015-09-30T22:35Z] INFO  23:35:46,597 MuTect - [MUTECT] Processed 33001324 reads in 666 ms
[2015-09-30T22:35Z] INFO  23:35:46,703 MuTect - [MUTECT] Processed 21000785 reads in 654 ms
[2015-09-30T22:35Z] INFO  23:35:46,874 MuTect - [MUTECT] Processed 161007886 reads in 682 ms
[2015-09-30T22:35Z] INFO  23:35:47,252 MuTect - [MUTECT] Processed 34001410 reads in 655 ms
[2015-09-30T22:35Z] INFO  23:35:47,319 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:47,376 MuTect - [MUTECT] Processed 22000810 reads in 673 ms
[2015-09-30T22:35Z] INFO  23:35:47,379 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:47,382 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:47,587 MuTect - [MUTECT] Processed 162007913 reads in 713 ms
[2015-09-30T22:35Z] INFO  23:35:47,920 MuTect - [MUTECT] Processed 35001461 reads in 668 ms
[2015-09-30T22:35Z] INFO  23:35:48,051 MuTect - [MUTECT] Processed 23000883 reads in 675 ms
[2015-09-30T22:35Z] INFO  23:35:48,261 MuTect - [MUTECT] Processed 163007954 reads in 674 ms
[2015-09-30T22:35Z] INFO  23:35:48,578 MuTect - [MUTECT] Processed 36001520 reads in 657 ms
[2015-09-30T22:35Z] INFO  23:35:48,674 MuTect - [MUTECT] Processed 24000953 reads in 623 ms
[2015-09-30T22:35Z] INFO  23:35:48,953 MuTect - [MUTECT] Processed 164008024 reads in 692 ms
[2015-09-30T22:35Z] INFO  23:35:49,269 MuTect - [MUTECT] Processed 37001578 reads in 692 ms
[2015-09-30T22:35Z] INFO  23:35:49,353 MuTect - [MUTECT] Processed 25000990 reads in 679 ms
[2015-09-30T22:35Z] INFO  23:35:49,429 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:49,607 MuTect - [MUTECT] Processed 165008025 reads in 654 ms
[2015-09-30T22:35Z] INFO  23:35:49,616 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:49,939 MuTect - [MUTECT] Processed 38001674 reads in 670 ms
[2015-09-30T22:35Z] INFO  23:35:49,981 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:50,022 MuTect - [MUTECT] Processed 26001049 reads in 669 ms
[2015-09-30T22:35Z] INFO  23:35:50,263 MuTect - [MUTECT] Processed 166008034 reads in 656 ms
[2015-09-30T22:35Z] INFO  23:35:50,308 ProgressMeter -     13:28897029        1.24e+06   30.0 s       24.0 s     88.5%        33.0 s     3.0 s
[2015-09-30T22:35Z] INFO  23:35:50,600 MuTect - [MUTECT] Processed 39001687 reads in 661 ms
[2015-09-30T22:35Z] INFO  23:35:50,712 MuTect - [MUTECT] Processed 27001050 reads in 690 ms
[2015-09-30T22:35Z] INFO  23:35:50,921 MuTect - [MUTECT] Processed 167008049 reads in 658 ms
[2015-09-30T22:35Z] INFO  23:35:51,258 MuTect - [MUTECT] Processed 40001692 reads in 658 ms
[2015-09-30T22:35Z] INFO  23:35:51,382 MuTect - [MUTECT] Processed 28001114 reads in 670 ms
[2015-09-30T22:35Z] INFO  23:35:51,557 MuTect - [MUTECT] Processed 168008078 reads in 636 ms
[2015-09-30T22:35Z] INFO  23:35:51,770 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:51,903 MuTect - [MUTECT] Processed 41001713 reads in 645 ms
[2015-09-30T22:35Z] INFO  23:35:51,971 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:52,001 MuTect - [MUTECT] Processed 29001201 reads in 619 ms
[2015-09-30T22:35Z] INFO  23:35:52,193 MuTect - [MUTECT] Processed 169008120 reads in 636 ms
[2015-09-30T22:35Z] INFO  23:35:52,411 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:52,564 MuTect - [MUTECT] Processed 42001739 reads in 661 ms
[2015-09-30T22:35Z] INFO  23:35:52,652 MuTect - [MUTECT] Processed 30001320 reads in 651 ms
[2015-09-30T22:35Z] INFO  23:35:52,868 MuTect - [MUTECT] Processed 170008164 reads in 675 ms
[2015-09-30T22:35Z] INFO  23:35:53,234 MuTect - [MUTECT] Processed 43001753 reads in 670 ms
[2015-09-30T22:35Z] INFO  23:35:53,274 MuTect - [MUTECT] Processed 31001424 reads in 622 ms
[2015-09-30T22:35Z] INFO  23:35:53,518 MuTect - [MUTECT] Processed 171008254 reads in 650 ms
[2015-09-30T22:35Z] INFO  23:35:53,837 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:53,914 MuTect - [MUTECT] Processed 44001759 reads in 680 ms
[2015-09-30T22:35Z] INFO  23:35:53,929 MuTect - [MUTECT] Processed 32001490 reads in 655 ms
[2015-09-30T22:35Z] INFO  23:35:54,084 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:35Z] INFO  23:35:54,088 ProgressMeter -            done        1.40e+06   33.0 s       24.0 s    100.0%        33.0 s     0.0 s
[2015-09-30T22:35Z] INFO  23:35:54,088 ProgressMeter - Total runtime 33.78 secs, 0.56 min, 0.01 hours
[2015-09-30T22:35Z] INFO  23:35:54,151 MicroScheduler - 31320 reads were filtered out during the traversal out of approximately 530132 total reads (5.91%)
[2015-09-30T22:35Z] INFO  23:35:54,151 MicroScheduler -   -> 22964 reads (4.33% of total) failing DuplicateReadFilter
[2015-09-30T22:35Z] INFO  23:35:54,151 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:35Z] INFO  23:35:54,152 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:35Z] INFO  23:35:54,152 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:35Z] INFO  23:35:54,152 MicroScheduler -   -> 8356 reads (1.58% of total) failing UnmappedReadFilter
[2015-09-30T22:35Z] INFO  23:35:54,156 MuTect - [MUTECT] Processed 172008281 reads in 638 ms
[2015-09-30T22:35Z] INFO  23:35:54,580 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:54,638 MuTect - [MUTECT] Processed 33001559 reads in 709 ms
[2015-09-30T22:35Z] INFO  23:35:54,845 MuTect - [MUTECT] Processed 173008339 reads in 689 ms
[2015-09-30T22:35Z] INFO  23:35:55,136 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:35Z] bgzip syn3-13_0_31036104-raw-mutect.vcf
[2015-09-30T22:35Z] tabix index syn3-13_0_31036104-raw-mutect.vcf.gz
[2015-09-30T22:35Z] INFO  23:35:55,299 MuTect - [MUTECT] Processed 34001610 reads in 661 ms
[2015-09-30T22:35Z] INFO  23:35:55,510 MuTect - [MUTECT] Processed 174008374 reads in 665 ms
[2015-09-30T22:35Z] INFO  23:35:55,977 MuTect - [MUTECT] Processed 35001660 reads in 677 ms
[2015-09-30T22:35Z] INFO  23:35:56,082 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:56,172 MuTect - [MUTECT] Processed 175008459 reads in 662 ms
[2015-09-30T22:35Z] INFO  23:35:56,502 ProgressMeter -    12:122492906        5.79e+06  120.0 s       20.0 s     88.1%         2.3 m    16.0 s
[2015-09-30T22:35Z] INFO  23:35:56,657 MuTect - [MUTECT] Processed 36001688 reads in 681 ms
[2015-09-30T22:35Z] INFO  23:35:56,842 MuTect - [MUTECT] Processed 176008545 reads in 670 ms
[2015-09-30T22:35Z] INFO  23:35:57,044 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:57,357 MuTect - [MUTECT] Processed 37001757 reads in 700 ms
[2015-09-30T22:35Z] INFO  23:35:57,514 MuTect - [MUTECT] Processed 177008591 reads in 672 ms
[2015-09-30T22:35Z] MuTect: MuTect
[2015-09-30T22:35Z] INFO  23:35:58,040 MuTect - [MUTECT] Processed 38001827 reads in 683 ms
[2015-09-30T22:35Z] INFO  23:35:58,185 MuTect - [MUTECT] Processed 178008716 reads in 671 ms
[2015-09-30T22:35Z] INFO  23:35:58,395 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:58,736 MuTect - [MUTECT] Processed 39001926 reads in 696 ms
[2015-09-30T22:35Z] INFO  23:35:58,831 MuTect - [MUTECT] Processed 179008798 reads in 646 ms
[2015-09-30T22:35Z] INFO  23:35:59,420 MuTect - [MUTECT] Processed 40001961 reads in 684 ms
[2015-09-30T22:35Z] INFO  23:35:59,473 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:35Z] INFO  23:35:59,515 MuTect - [MUTECT] Processed 180008862 reads in 684 ms
[2015-09-30T22:35Z] INFO  23:35:59,806 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/13/syn3-13_63745563_94765401-raw-mutect-regions.bed to be BED
[2015-09-30T22:35Z] INFO  23:35:59,862 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:35Z] INFO  23:35:59,862 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:35Z] INFO  23:35:59,862 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:35Z] INFO  23:35:59,862 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:35Z] INFO  23:35:59,866 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/13/syn3-13_63745563_94765401-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/13/tx/tmppSiK35/syn3-13_63745563_94765401-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:35Z] INFO  23:35:59,866 HelpFormatter - Date/Time: 2015/09/30 23:35:59
[2015-09-30T22:35Z] INFO  23:35:59,866 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:35Z] INFO  23:35:59,866 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:35Z] INFO  23:35:59,894 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:35Z] INFO  23:35:59,898 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:35Z] INFO  23:35:59,952 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:35Z] INFO  23:35:59,957 ProgressMeter -     13:45008425        1.45e+06   30.0 s       20.0 s     52.7%        56.0 s    26.0 s
[2015-09-30T22:36Z] INFO  23:36:00,001 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:36Z] INFO  23:36:00,008 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:36Z] INFO  23:36:00,032 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:36Z] INFO  23:36:00,052 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:36Z] INFO  23:36:00,099 MuTect - [MUTECT] Processed 41001973 reads in 679 ms
[2015-09-30T22:36Z] INFO  23:36:00,181 MuTect - [MUTECT] Processed 181008937 reads in 666 ms
[2015-09-30T22:36Z] INFO  23:36:00,230 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:36Z] INFO  23:36:00,294 IntervalUtils - Processing 325612 bp from intervals
[2015-09-30T22:36Z] INFO  23:36:00,298 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:36Z] INFO  23:36:00,298 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:36Z] INFO  23:36:00,352 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:36Z] INFO  23:36:00,547 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:36Z] INFO  23:36:00,548 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:36Z] INFO  23:36:00,548 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:36Z] INFO  23:36:00,549 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:36Z] INFO  23:36:00,729 MuTect - [MUTECT] Processed 42002056 reads in 630 ms
[2015-09-30T22:36Z] INFO  23:36:00,749 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:00,857 MuTect - [MUTECT] Processed 182008954 reads in 676 ms
[2015-09-30T22:36Z] INFO  23:36:01,379 MuTect - [MUTECT] Processed 43002173 reads in 650 ms
[2015-09-30T22:36Z] INFO  23:36:01,544 MuTect - [MUTECT] Processed 183008990 reads in 687 ms
[2015-09-30T22:36Z] INFO  23:36:01,981 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:02,011 MuTect - [MUTECT] Processed 44002218 reads in 632 ms
[2015-09-30T22:36Z] INFO  23:36:02,236 MuTect - [MUTECT] Processed 184009011 reads in 692 ms
[2015-09-30T22:36Z] INFO  23:36:02,650 MuTect - [MUTECT] Processed 45002241 reads in 639 ms
[2015-09-30T22:36Z] INFO  23:36:02,966 MuTect - [MUTECT] Processed 185009012 reads in 730 ms
[2015-09-30T22:36Z] INFO  23:36:03,098 MuTect - [MUTECT] Processed 1000003 reads in 2501 ms
[2015-09-30T22:36Z] INFO  23:36:03,257 MuTect - [MUTECT] Processed 46002262 reads in 607 ms
[2015-09-30T22:36Z] INFO  23:36:03,398 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:03,677 MuTect - [MUTECT] Processed 186009014 reads in 711 ms
[2015-09-30T22:36Z] INFO  23:36:03,889 MuTect - [MUTECT] Processed 47002292 reads in 631 ms
[2015-09-30T22:36Z] INFO  23:36:03,974 MuTect - [MUTECT] Processed 2000038 reads in 876 ms
[2015-09-30T22:36Z] INFO  23:36:04,336 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:04,342 MuTect - [MUTECT] Processed 187009059 reads in 665 ms
[2015-09-30T22:36Z] INFO  23:36:04,569 MuTect - [MUTECT] Processed 48002355 reads in 681 ms
[2015-09-30T22:36Z] INFO  23:36:04,766 MuTect - [MUTECT] Processed 3000090 reads in 792 ms
[2015-09-30T22:36Z] INFO  23:36:04,963 MuTect - [MUTECT] Processed 188009133 reads in 621 ms
[2015-09-30T22:36Z] INFO  23:36:05,228 MuTect - [MUTECT] Processed 49002413 reads in 659 ms
[2015-09-30T22:36Z] INFO  23:36:05,399 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:05,521 MuTect - [MUTECT] Processed 4000131 reads in 755 ms
[2015-09-30T22:36Z] INFO  23:36:05,526 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:05,565 MuTect - [MUTECT] Processed 189009240 reads in 602 ms
[2015-09-30T22:36Z] INFO  23:36:05,900 MuTect - [MUTECT] Processed 50002417 reads in 672 ms
[2015-09-30T22:36Z] INFO  23:36:06,173 MuTect - [MUTECT] Processed 190009256 reads in 608 ms
[2015-09-30T22:36Z] INFO  23:36:06,271 MuTect - [MUTECT] Processed 5000133 reads in 750 ms
[2015-09-30T22:36Z] INFO  23:36:06,578 MuTect - [MUTECT] Processed 51002488 reads in 678 ms
[2015-09-30T22:36Z] INFO  23:36:06,779 MuTect - [MUTECT] Processed 191009404 reads in 606 ms
[2015-09-30T22:36Z] INFO  23:36:06,927 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:06,948 MuTect - [MUTECT] Processed 6000197 reads in 677 ms
[2015-09-30T22:36Z] INFO  23:36:07,250 MuTect - [MUTECT] Processed 52002522 reads in 672 ms
[2015-09-30T22:36Z] INFO  23:36:07,399 MuTect - [MUTECT] Processed 192009416 reads in 620 ms
[2015-09-30T22:36Z] INFO  23:36:07,543 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:07,658 MuTect - [MUTECT] Processed 7000228 reads in 710 ms
[2015-09-30T22:36Z] INFO  23:36:08,034 MuTect - [MUTECT] Processed 53002558 reads in 784 ms
[2015-09-30T22:36Z] INFO  23:36:08,050 MuTect - [MUTECT] Processed 193009485 reads in 651 ms
[2015-09-30T22:36Z] INFO  23:36:08,127 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:08,349 MuTect - [MUTECT] Processed 8000297 reads in 691 ms
[2015-09-30T22:36Z] INFO  23:36:08,778 MuTect - [MUTECT] Processed 194009538 reads in 728 ms
[2015-09-30T22:36Z] INFO  23:36:08,874 MuTect - [MUTECT] Processed 54002627 reads in 840 ms
[2015-09-30T22:36Z] INFO  23:36:09,039 MuTect - [MUTECT] Processed 9000354 reads in 690 ms
[2015-09-30T22:36Z] INFO  23:36:09,456 MuTect - [MUTECT] Processed 195009575 reads in 678 ms
[2015-09-30T22:36Z] INFO  23:36:09,504 MuTect - [MUTECT] Processed 55002650 reads in 630 ms
[2015-09-30T22:36Z] INFO  23:36:09,671 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:09,762 MuTect - [MUTECT] Processed 10000410 reads in 723 ms
[2015-09-30T22:36Z] INFO  23:36:10,117 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:10,130 MuTect - [MUTECT] Processed 56002707 reads in 626 ms
[2015-09-30T22:36Z] INFO  23:36:10,153 MuTect - [MUTECT] Processed 196009586 reads in 697 ms
[2015-09-30T22:36Z] INFO  23:36:10,418 MuTect - [MUTECT] Processed 11000429 reads in 656 ms
[2015-09-30T22:36Z] INFO  23:36:10,626 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:10,777 MuTect - [MUTECT] Processed 57002737 reads in 647 ms
[2015-09-30T22:36Z] INFO  23:36:10,808 MuTect - [MUTECT] Processed 197009659 reads in 655 ms
[2015-09-30T22:36Z] INFO  23:36:11,092 MuTect - [MUTECT] Processed 12000457 reads in 674 ms
[2015-09-30T22:36Z] INFO  23:36:11,446 MuTect - [MUTECT] Processed 58002752 reads in 669 ms
[2015-09-30T22:36Z] INFO  23:36:11,482 MuTect - [MUTECT] Processed 198009722 reads in 674 ms
[2015-09-30T22:36Z] INFO  23:36:11,750 MuTect - [MUTECT] Processed 13000500 reads in 658 ms
[2015-09-30T22:36Z] INFO  23:36:11,948 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:12,105 MuTect - [MUTECT] Processed 199009807 reads in 623 ms
[2015-09-30T22:36Z] INFO  23:36:12,174 MuTect - [MUTECT] Processed 59002816 reads in 728 ms
[2015-09-30T22:36Z] INFO  23:36:12,260 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:12,460 MuTect - [MUTECT] Processed 14000560 reads in 710 ms
[2015-09-30T22:36Z] INFO  23:36:12,739 MuTect - [MUTECT] Processed 200009869 reads in 634 ms
[2015-09-30T22:36Z] INFO  23:36:12,793 MuTect - [MUTECT] Processed 60002849 reads in 619 ms
[2015-09-30T22:36Z] INFO  23:36:12,995 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:36Z] INFO  23:36:12,999 ProgressMeter -            done        6.70e+06    2.3 m       20.0 s    100.0%         2.3 m     0.0 s
[2015-09-30T22:36Z] INFO  23:36:12,999 ProgressMeter - Total runtime 136.50 secs, 2.28 min, 0.04 hours
[2015-09-30T22:36Z] INFO  23:36:13,062 MicroScheduler - 151291 reads were filtered out during the traversal out of approximately 2410887 total reads (6.28%)
[2015-09-30T22:36Z] INFO  23:36:13,063 MicroScheduler -   -> 113255 reads (4.70% of total) failing DuplicateReadFilter
[2015-09-30T22:36Z] INFO  23:36:13,063 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:36Z] INFO  23:36:13,063 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:36Z] INFO  23:36:13,063 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:36Z] INFO  23:36:13,063 MicroScheduler -   -> 38036 reads (1.58% of total) failing UnmappedReadFilter
[2015-09-30T22:36Z] INFO  23:36:13,150 MuTect - [MUTECT] Processed 15000573 reads in 690 ms
[2015-09-30T22:36Z] INFO  23:36:13,263 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:13,473 MuTect - [MUTECT] Processed 61002885 reads in 680 ms
[2015-09-30T22:36Z] INFO  23:36:13,876 MuTect - [MUTECT] Processed 16000613 reads in 726 ms
[2015-09-30T22:36Z] INFO  23:36:14,080 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:36Z] INFO  23:36:14,113 MuTect - [MUTECT] Processed 62002938 reads in 640 ms
[2015-09-30T22:36Z] INFO  23:36:14,373 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:14,577 MuTect - [MUTECT] Processed 17000618 reads in 701 ms
[2015-09-30T22:36Z] INFO  23:36:14,801 MuTect - [MUTECT] Processed 63003008 reads in 688 ms
[2015-09-30T22:36Z] INFO  23:36:15,305 MuTect - [MUTECT] Processed 18000663 reads in 728 ms
[2015-09-30T22:36Z] INFO  23:36:15,444 MuTect - [MUTECT] Processed 64003078 reads in 643 ms
[2015-09-30T22:36Z] INFO  23:36:16,041 MuTect - [MUTECT] Processed 65003103 reads in 597 ms
[2015-09-30T22:36Z] INFO  23:36:16,923 MuTect - [MUTECT] Processed 66003159 reads in 882 ms
[2015-09-30T22:36Z] INFO  23:36:16,956 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:36Z] bgzip syn3-12_93169109_124189486-raw-mutect.vcf
[2015-09-30T22:36Z] tabix index syn3-12_93169109_124189486-raw-mutect.vcf.gz
[2015-09-30T22:36Z] INFO  23:36:17,560 MuTect - [MUTECT] Processed 67003228 reads in 637 ms
[2015-09-30T22:36Z] INFO  23:36:18,193 MuTect - [MUTECT] Processed 68003257 reads in 633 ms
[2015-09-30T22:36Z] INFO  23:36:18,668 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:18,712 MuTect - [MUTECT] Processed 19000669 reads in 3407 ms
[2015-09-30T22:36Z] INFO  23:36:18,842 MuTect - [MUTECT] Processed 69003357 reads in 649 ms
[2015-09-30T22:36Z] INFO  23:36:19,269 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:19,452 MuTect - [MUTECT] Processed 70003366 reads in 610 ms
[2015-09-30T22:36Z] INFO  23:36:19,552 MuTect - [MUTECT] Processed 20000695 reads in 840 ms
[2015-09-30T22:36Z] INFO  23:36:20,253 MuTect - [MUTECT] Processed 21000713 reads in 701 ms
[2015-09-30T22:36Z] INFO  23:36:20,265 MuTect - [MUTECT] Processed 71003378 reads in 813 ms
[2015-09-30T22:36Z] INFO  23:36:20,329 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:36Z] INFO  23:36:20,334 ProgressMeter -            done        7.81e+05   19.0 s       25.0 s    100.0%        19.0 s     0.0 s
[2015-09-30T22:36Z] INFO  23:36:20,335 ProgressMeter - Total runtime 19.79 secs, 0.33 min, 0.01 hours
[2015-09-30T22:36Z] INFO  23:36:20,400 MicroScheduler - 13637 reads were filtered out during the traversal out of approximately 249607 total reads (5.46%)
[2015-09-30T22:36Z] INFO  23:36:20,401 MicroScheduler -   -> 9706 reads (3.89% of total) failing DuplicateReadFilter
[2015-09-30T22:36Z] INFO  23:36:20,401 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:36Z] INFO  23:36:20,401 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:36Z] INFO  23:36:20,401 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:36Z] INFO  23:36:20,401 MicroScheduler -   -> 3931 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:36Z] MuTect: MuTect
[2015-09-30T22:36Z] INFO  23:36:20,932 MuTect - [MUTECT] Processed 72003386 reads in 667 ms
[2015-09-30T22:36Z] INFO  23:36:21,417 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:36Z] bgzip syn3-13_63745563_94765401-raw-mutect.vcf
[2015-09-30T22:36Z] tabix index syn3-13_63745563_94765401-raw-mutect.vcf.gz
[2015-09-30T22:36Z] INFO  23:36:21,623 MuTect - [MUTECT] Processed 73003435 reads in 691 ms
[2015-09-30T22:36Z] INFO  23:36:21,956 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:22,325 MuTect - [MUTECT] Processed 74003458 reads in 702 ms
[2015-09-30T22:36Z] INFO  23:36:22,493 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/13/syn3-13_94938309_115169878-raw-mutect-regions.bed to be BED
[2015-09-30T22:36Z] INFO  23:36:22,546 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:36Z] INFO  23:36:22,547 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:36Z] INFO  23:36:22,547 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:36Z] INFO  23:36:22,547 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:36Z] INFO  23:36:22,550 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/13/syn3-13_94938309_115169878-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/13/tx/tmpfsWa_1/syn3-13_94938309_115169878-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:36Z] INFO  23:36:22,551 HelpFormatter - Date/Time: 2015/09/30 23:36:22
[2015-09-30T22:36Z] INFO  23:36:22,551 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:36Z] INFO  23:36:22,551 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:36Z] INFO  23:36:22,578 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:36Z] INFO  23:36:22,582 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:36Z] INFO  23:36:22,630 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:36Z] INFO  23:36:22,676 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:36Z] INFO  23:36:22,683 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:36Z] INFO  23:36:22,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:36Z] INFO  23:36:22,714 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:36Z] INFO  23:36:22,896 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:36Z] INFO  23:36:22,980 IntervalUtils - Processing 830267 bp from intervals
[2015-09-30T22:36Z] INFO  23:36:22,984 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:36Z] INFO  23:36:22,984 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:36Z] INFO  23:36:23,030 MuTect - [MUTECT] Processed 75003510 reads in 705 ms
[2015-09-30T22:36Z] INFO  23:36:23,036 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:36Z] INFO  23:36:23,270 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:36Z] INFO  23:36:23,271 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:36Z] INFO  23:36:23,271 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:36Z] INFO  23:36:23,272 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:36Z] INFO  23:36:23,708 MuTect - [MUTECT] Processed 76003591 reads in 678 ms
[2015-09-30T22:36Z] MuTect: MuTect
[2015-09-30T22:36Z] INFO  23:36:24,289 MuTect - [MUTECT] Processed 77003662 reads in 581 ms
[2015-09-30T22:36Z] INFO  23:36:24,883 MuTect - [MUTECT] Processed 78003723 reads in 594 ms
[2015-09-30T22:36Z] INFO  23:36:25,402 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:25,547 MuTect - [MUTECT] Processed 79003761 reads in 664 ms
[2015-09-30T22:36Z] INFO  23:36:26,226 MuTect - [MUTECT] Processed 80003868 reads in 679 ms
[2015-09-30T22:36Z] INFO  23:36:26,233 MuTect - [MUTECT] Processed 1000046 reads in 2917 ms
[2015-09-30T22:36Z] INFO  23:36:26,291 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:36Z] INFO  23:36:26,295 ProgressMeter -            done        2.71e+06   56.0 s       20.0 s    100.0%        56.0 s     0.0 s
[2015-09-30T22:36Z] INFO  23:36:26,295 ProgressMeter - Total runtime 56.34 secs, 0.94 min, 0.02 hours
[2015-09-30T22:36Z] INFO  23:36:26,302 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/14/syn3-14_0_31050569-raw-mutect-regions.bed to be BED
[2015-09-30T22:36Z] INFO  23:36:26,357 MicroScheduler - 54386 reads were filtered out during the traversal out of approximately 955064 total reads (5.69%)
[2015-09-30T22:36Z] INFO  23:36:26,357 MicroScheduler -   -> 39212 reads (4.11% of total) failing DuplicateReadFilter
[2015-09-30T22:36Z] INFO  23:36:26,357 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:36Z] INFO  23:36:26,357 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:36Z] INFO  23:36:26,357 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:36Z] INFO  23:36:26,357 MicroScheduler -   -> 15174 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:36Z] INFO  23:36:26,359 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:36Z] INFO  23:36:26,359 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:36Z] INFO  23:36:26,359 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:36Z] INFO  23:36:26,359 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:36Z] INFO  23:36:26,363 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/14/syn3-14_0_31050569-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/14/tx/tmpQ4AENb/syn3-14_0_31050569-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:36Z] INFO  23:36:26,363 HelpFormatter - Date/Time: 2015/09/30 23:36:26
[2015-09-30T22:36Z] INFO  23:36:26,363 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:36Z] INFO  23:36:26,363 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:36Z] INFO  23:36:26,392 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:36Z] INFO  23:36:26,396 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:36Z] INFO  23:36:26,449 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:36Z] INFO  23:36:26,499 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:36Z] INFO  23:36:26,507 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:36Z] INFO  23:36:26,530 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:36Z] INFO  23:36:26,542 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:36Z] INFO  23:36:26,719 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:36Z] INFO  23:36:26,797 IntervalUtils - Processing 839940 bp from intervals
[2015-09-30T22:36Z] INFO  23:36:26,801 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:36Z] INFO  23:36:26,801 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:36Z] INFO  23:36:26,856 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:36Z] INFO  23:36:27,020 MuTect - [MUTECT] Processed 2000141 reads in 787 ms
[2015-09-30T22:36Z] INFO  23:36:27,100 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:36Z] INFO  23:36:27,101 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:36Z] INFO  23:36:27,101 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:36Z] INFO  23:36:27,102 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:36Z] INFO  23:36:27,336 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:36Z] bgzip syn3-13_31036377_62334609-raw-mutect.vcf
[2015-09-30T22:36Z] tabix index syn3-13_31036377_62334609-raw-mutect.vcf.gz
[2015-09-30T22:36Z] INFO  23:36:27,946 MuTect - [MUTECT] Processed 3000248 reads in 926 ms
[2015-09-30T22:36Z] INFO  23:36:28,314 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:28,747 MuTect - [MUTECT] Processed 4000308 reads in 801 ms
[2015-09-30T22:36Z] INFO  23:36:29,481 MuTect - [MUTECT] Processed 5000364 reads in 734 ms
[2015-09-30T22:36Z] MuTect: MuTect
[2015-09-30T22:36Z] INFO  23:36:29,948 MuTect - [MUTECT] Processed 1000019 reads in 2546 ms
[2015-09-30T22:36Z] INFO  23:36:30,220 MuTect - [MUTECT] Processed 6000438 reads in 739 ms
[2015-09-30T22:36Z] INFO  23:36:30,673 MuTect - [MUTECT] Processed 2000056 reads in 725 ms
[2015-09-30T22:36Z] INFO  23:36:31,010 MuTect - [MUTECT] Processed 7000497 reads in 790 ms
[2015-09-30T22:36Z] INFO  23:36:31,179 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:31,384 MuTect - [MUTECT] Processed 3000176 reads in 711 ms
[2015-09-30T22:36Z] INFO  23:36:31,725 MuTect - [MUTECT] Processed 8000566 reads in 715 ms
[2015-09-30T22:36Z] INFO  23:36:31,809 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/14/syn3-14_31055710_62162825-raw-mutect-regions.bed to be BED
[2015-09-30T22:36Z] INFO  23:36:31,866 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:36Z] INFO  23:36:31,866 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:36Z] INFO  23:36:31,866 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:36Z] INFO  23:36:31,866 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:36Z] INFO  23:36:31,870 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/14/syn3-14_31055710_62162825-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/14/tx/tmp3gnU3f/syn3-14_31055710_62162825-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:36Z] INFO  23:36:31,870 HelpFormatter - Date/Time: 2015/09/30 23:36:31
[2015-09-30T22:36Z] INFO  23:36:31,870 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:36Z] INFO  23:36:31,870 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:36Z] INFO  23:36:31,898 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:36Z] INFO  23:36:31,902 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:36Z] INFO  23:36:31,956 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:36Z] INFO  23:36:32,005 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:36Z] INFO  23:36:32,013 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:36Z] INFO  23:36:32,036 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:36Z] INFO  23:36:32,048 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:36Z] INFO  23:36:32,082 MuTect - [MUTECT] Processed 4000277 reads in 698 ms
[2015-09-30T22:36Z] INFO  23:36:32,230 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:36Z] INFO  23:36:32,329 IntervalUtils - Processing 1235919 bp from intervals
[2015-09-30T22:36Z] INFO  23:36:32,333 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:36Z] INFO  23:36:32,333 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:36Z] INFO  23:36:32,484 MuTect - [MUTECT] Processed 9000614 reads in 759 ms
[2015-09-30T22:36Z] INFO  23:36:32,613 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:32,632 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:36Z] INFO  23:36:32,796 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:36Z] INFO  23:36:32,796 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:36Z] INFO  23:36:32,796 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:36Z] INFO  23:36:32,797 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:36Z] INFO  23:36:32,883 MuTect - [MUTECT] Processed 5000287 reads in 801 ms
[2015-09-30T22:36Z] INFO  23:36:33,258 MuTect - [MUTECT] Processed 10000635 reads in 774 ms
[2015-09-30T22:36Z] INFO  23:36:33,637 MuTect - [MUTECT] Processed 6000308 reads in 754 ms
[2015-09-30T22:36Z] INFO  23:36:33,898 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:33,974 MuTect - [MUTECT] Processed 11000710 reads in 716 ms
[2015-09-30T22:36Z] INFO  23:36:34,398 MuTect - [MUTECT] Processed 7000362 reads in 761 ms
[2015-09-30T22:36Z] INFO  23:36:34,740 MuTect - [MUTECT] Processed 12000800 reads in 766 ms
[2015-09-30T22:36Z] INFO  23:36:35,152 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:35,164 MuTect - [MUTECT] Processed 1000037 reads in 2319 ms
[2015-09-30T22:36Z] INFO  23:36:35,186 MuTect - [MUTECT] Processed 8000379 reads in 788 ms
[2015-09-30T22:36Z] INFO  23:36:35,495 MuTect - [MUTECT] Processed 13000827 reads in 755 ms
[2015-09-30T22:36Z] INFO  23:36:35,895 MuTect - [MUTECT] Processed 9000458 reads in 709 ms
[2015-09-30T22:36Z] INFO  23:36:36,204 MuTect - [MUTECT] Processed 14000897 reads in 709 ms
[2015-09-30T22:36Z] INFO  23:36:36,218 MuTect - [MUTECT] Processed 2000086 reads in 1055 ms
[2015-09-30T22:36Z] INFO  23:36:36,460 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:36,505 MuTect - [MUTECT] Processed 10000470 reads in 610 ms
[2015-09-30T22:36Z] INFO  23:36:36,931 MuTect - [MUTECT] Processed 15000959 reads in 727 ms
[2015-09-30T22:36Z] INFO  23:36:37,039 MuTect - [MUTECT] Processed 3000123 reads in 821 ms
[2015-09-30T22:36Z] INFO  23:36:37,135 MuTect - [MUTECT] Processed 11000482 reads in 630 ms
[2015-09-30T22:36Z] INFO  23:36:37,393 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:37,617 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:37,651 MuTect - [MUTECT] Processed 16000984 reads in 720 ms
[2015-09-30T22:36Z] INFO  23:36:37,771 MuTect - [MUTECT] Processed 4000179 reads in 732 ms
[2015-09-30T22:36Z] INFO  23:36:37,782 MuTect - [MUTECT] Processed 12000525 reads in 647 ms
[2015-09-30T22:36Z] INFO  23:36:38,384 MuTect - [MUTECT] Processed 17000989 reads in 733 ms
[2015-09-30T22:36Z] INFO  23:36:38,488 MuTect - [MUTECT] Processed 13000589 reads in 706 ms
[2015-09-30T22:36Z] INFO  23:36:38,583 MuTect - [MUTECT] Processed 5000240 reads in 812 ms
[2015-09-30T22:36Z] INFO  23:36:38,768 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:39,104 MuTect - [MUTECT] Processed 18001068 reads in 720 ms
[2015-09-30T22:36Z] INFO  23:36:39,194 MuTect - [MUTECT] Processed 14000610 reads in 706 ms
[2015-09-30T22:36Z] INFO  23:36:39,356 MuTect - [MUTECT] Processed 6000276 reads in 773 ms
[2015-09-30T22:36Z] INFO  23:36:39,685 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:39,833 MuTect - [MUTECT] Processed 19001098 reads in 728 ms
[2015-09-30T22:36Z] INFO  23:36:39,884 MuTect - [MUTECT] Processed 15000666 reads in 690 ms
[2015-09-30T22:36Z] INFO  23:36:40,051 MuTect - [MUTECT] Processed 7000329 reads in 695 ms
[2015-09-30T22:36Z] INFO  23:36:40,502 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:40,546 MuTect - [MUTECT] Processed 20001231 reads in 714 ms
[2015-09-30T22:36Z] INFO  23:36:40,608 MuTect - [MUTECT] Processed 16000734 reads in 724 ms
[2015-09-30T22:36Z] INFO  23:36:40,709 MuTect - [MUTECT] Processed 8000357 reads in 658 ms
[2015-09-30T22:36Z] INFO  23:36:41,268 MuTect - [MUTECT] Processed 21001308 reads in 722 ms
[2015-09-30T22:36Z] INFO  23:36:41,293 MuTect - [MUTECT] Processed 17000762 reads in 685 ms
[2015-09-30T22:36Z] INFO  23:36:41,421 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:41,425 MuTect - [MUTECT] Processed 9000389 reads in 716 ms
[2015-09-30T22:36Z] INFO  23:36:41,959 MuTect - [MUTECT] Processed 18000790 reads in 666 ms
[2015-09-30T22:36Z] INFO  23:36:41,969 MuTect - [MUTECT] Processed 22001320 reads in 701 ms
[2015-09-30T22:36Z] INFO  23:36:41,974 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:42,118 MuTect - [MUTECT] Processed 10000444 reads in 693 ms
[2015-09-30T22:36Z] INFO  23:36:42,622 MuTect - [MUTECT] Processed 19000897 reads in 663 ms
[2015-09-30T22:36Z] INFO  23:36:42,700 MuTect - [MUTECT] Processed 23001371 reads in 731 ms
[2015-09-30T22:36Z] INFO  23:36:42,846 MuTect - [MUTECT] Processed 11000458 reads in 728 ms
[2015-09-30T22:36Z] INFO  23:36:43,092 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:43,367 MuTect - [MUTECT] Processed 20000937 reads in 745 ms
[2015-09-30T22:36Z] INFO  23:36:43,416 MuTect - [MUTECT] Processed 24001413 reads in 716 ms
[2015-09-30T22:36Z] INFO  23:36:43,554 MuTect - [MUTECT] Processed 12000476 reads in 707 ms
[2015-09-30T22:36Z] INFO  23:36:43,938 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:44,058 MuTect - [MUTECT] Processed 21000994 reads in 691 ms
[2015-09-30T22:36Z] INFO  23:36:44,232 MuTect - [MUTECT] Processed 25001516 reads in 816 ms
[2015-09-30T22:36Z] INFO  23:36:44,275 MuTect - [MUTECT] Processed 13000481 reads in 722 ms
[2015-09-30T22:36Z] INFO  23:36:44,278 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:44,758 MuTect - [MUTECT] Processed 22000995 reads in 700 ms
[2015-09-30T22:36Z] INFO  23:36:44,984 MuTect - [MUTECT] Processed 26001544 reads in 752 ms
[2015-09-30T22:36Z] INFO  23:36:45,034 MuTect - [MUTECT] Processed 14000481 reads in 759 ms
[2015-09-30T22:36Z] INFO  23:36:45,432 MuTect - [MUTECT] Processed 23001019 reads in 674 ms
[2015-09-30T22:36Z] INFO  23:36:45,696 MuTect - [MUTECT] Processed 27001607 reads in 712 ms
[2015-09-30T22:36Z] INFO  23:36:45,717 MuTect - [MUTECT] Processed 15000492 reads in 683 ms
[2015-09-30T22:36Z] INFO  23:36:45,824 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:46,075 MuTect - [MUTECT] Processed 24001021 reads in 643 ms
[2015-09-30T22:36Z] INFO  23:36:46,339 MuTect - [MUTECT] Processed 28001622 reads in 643 ms
[2015-09-30T22:36Z] INFO  23:36:46,384 MuTect - [MUTECT] Processed 16000506 reads in 666 ms
[2015-09-30T22:36Z] INFO  23:36:46,542 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:46,715 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:46,729 MuTect - [MUTECT] Processed 25001059 reads in 654 ms
[2015-09-30T22:36Z] INFO  23:36:47,010 MuTect - [MUTECT] Processed 29001642 reads in 671 ms
[2015-09-30T22:36Z] INFO  23:36:47,105 MuTect - [MUTECT] Processed 17000519 reads in 722 ms
[2015-09-30T22:36Z] INFO  23:36:47,399 MuTect - [MUTECT] Processed 26001059 reads in 670 ms
[2015-09-30T22:36Z] INFO  23:36:47,705 MuTect - [MUTECT] Processed 30001645 reads in 695 ms
[2015-09-30T22:36Z] INFO  23:36:47,831 MuTect - [MUTECT] Processed 18000562 reads in 725 ms
[2015-09-30T22:36Z] INFO  23:36:48,072 MuTect - [MUTECT] Processed 27001085 reads in 673 ms
[2015-09-30T22:36Z] INFO  23:36:48,415 MuTect - [MUTECT] Processed 31001664 reads in 710 ms
[2015-09-30T22:36Z] INFO  23:36:48,485 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:48,522 MuTect - [MUTECT] Processed 19000614 reads in 692 ms
[2015-09-30T22:36Z] INFO  23:36:48,758 MuTect - [MUTECT] Processed 28001129 reads in 686 ms
[2015-09-30T22:36Z] INFO  23:36:48,975 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:48,976 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:49,125 MuTect - [MUTECT] Processed 32001667 reads in 710 ms
[2015-09-30T22:36Z] INFO  23:36:49,248 MuTect - [MUTECT] Processed 20000642 reads in 726 ms
[2015-09-30T22:36Z] INFO  23:36:49,511 MuTect - [MUTECT] Processed 29001131 reads in 753 ms
[2015-09-30T22:36Z] INFO  23:36:49,771 MuTect - [MUTECT] Processed 33001746 reads in 645 ms
[2015-09-30T22:36Z] INFO  23:36:49,972 MuTect - [MUTECT] Processed 21000722 reads in 724 ms
[2015-09-30T22:36Z] INFO  23:36:50,250 MuTect - [MUTECT] Processed 30001131 reads in 739 ms
[2015-09-30T22:36Z] INFO  23:36:50,486 MuTect - [MUTECT] Processed 34001775 reads in 716 ms
[2015-09-30T22:36Z] INFO  23:36:50,701 MuTect - [MUTECT] Processed 22000755 reads in 729 ms
[2015-09-30T22:36Z] INFO  23:36:50,958 MuTect - [MUTECT] Processed 31001199 reads in 708 ms
[2015-09-30T22:36Z] INFO  23:36:51,063 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:51,170 MuTect - [MUTECT] Processed 35001786 reads in 684 ms
[2015-09-30T22:36Z] INFO  23:36:51,391 MuTect - [MUTECT] Processed 23000785 reads in 690 ms
[2015-09-30T22:36Z] INFO  23:36:51,403 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:51,465 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:51,687 MuTect - [MUTECT] Processed 32001287 reads in 729 ms
[2015-09-30T22:36Z] INFO  23:36:51,847 MuTect - [MUTECT] Processed 36001929 reads in 677 ms
[2015-09-30T22:36Z] INFO  23:36:52,148 MuTect - [MUTECT] Processed 24000829 reads in 757 ms
[2015-09-30T22:36Z] INFO  23:36:52,332 MuTect - [MUTECT] Processed 33001372 reads in 645 ms
[2015-09-30T22:36Z] INFO  23:36:52,549 MuTect - [MUTECT] Processed 37001994 reads in 702 ms
[2015-09-30T22:36Z] INFO  23:36:52,831 MuTect - [MUTECT] Processed 25000847 reads in 683 ms
[2015-09-30T22:36Z] INFO  23:36:52,997 MuTect - [MUTECT] Processed 34001411 reads in 665 ms
[2015-09-30T22:36Z] INFO  23:36:53,274 ProgressMeter -    13:110959256        1.25e+06   30.0 s       24.0 s     61.0%        49.0 s    19.0 s
[2015-09-30T22:36Z] INFO  23:36:53,278 MuTect - [MUTECT] Processed 38001997 reads in 729 ms
[2015-09-30T22:36Z] INFO  23:36:53,497 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:53,562 MuTect - [MUTECT] Processed 26000887 reads in 731 ms
[2015-09-30T22:36Z] INFO  23:36:53,726 MuTect - [MUTECT] Processed 35001453 reads in 729 ms
[2015-09-30T22:36Z] INFO  23:36:53,794 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:53,828 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:53,981 MuTect - [MUTECT] Processed 39002027 reads in 703 ms
[2015-09-30T22:36Z] INFO  23:36:54,255 MuTect - [MUTECT] Processed 27000957 reads in 693 ms
[2015-09-30T22:36Z] INFO  23:36:54,422 MuTect - [MUTECT] Processed 36001520 reads in 696 ms
[2015-09-30T22:36Z] INFO  23:36:54,753 MuTect - [MUTECT] Processed 40002044 reads in 772 ms
[2015-09-30T22:36Z] INFO  23:36:54,952 MuTect - [MUTECT] Processed 28000994 reads in 697 ms
[2015-09-30T22:36Z] INFO  23:36:55,164 MuTect - [MUTECT] Processed 37001548 reads in 741 ms
[2015-09-30T22:36Z] INFO  23:36:55,497 MuTect - [MUTECT] Processed 41002138 reads in 744 ms
[2015-09-30T22:36Z] INFO  23:36:55,726 MuTect - [MUTECT] Processed 29001003 reads in 774 ms
[2015-09-30T22:36Z] INFO  23:36:55,832 MuTect - [MUTECT] Processed 38001610 reads in 668 ms
[2015-09-30T22:36Z] INFO  23:36:55,953 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:56,067 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:56,169 MuTect - [MUTECT] Processed 42002250 reads in 672 ms
[2015-09-30T22:36Z] INFO  23:36:56,198 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:56,489 MuTect - [MUTECT] Processed 39001693 reads in 658 ms
[2015-09-30T22:36Z] INFO  23:36:56,514 MuTect - [MUTECT] Processed 30001050 reads in 788 ms
[2015-09-30T22:36Z] INFO  23:36:56,845 MuTect - [MUTECT] Processed 43002302 reads in 676 ms
[2015-09-30T22:36Z] INFO  23:36:57,103 ProgressMeter -     14:23346737        1.18e+06   30.0 s       25.0 s     50.0%        60.0 s    30.0 s
[2015-09-30T22:36Z] INFO  23:36:57,125 MuTect - [MUTECT] Processed 40001714 reads in 636 ms
[2015-09-30T22:36Z] INFO  23:36:57,224 MuTect - [MUTECT] Processed 31001108 reads in 710 ms
[2015-09-30T22:36Z] INFO  23:36:57,485 MuTect - [MUTECT] Processed 44002304 reads in 640 ms
[2015-09-30T22:36Z] INFO  23:36:57,773 MuTect - [MUTECT] Processed 41001775 reads in 648 ms
[2015-09-30T22:36Z] INFO  23:36:57,974 MuTect - [MUTECT] Processed 32001150 reads in 750 ms
[2015-09-30T22:36Z] INFO  23:36:58,167 MuTect - [MUTECT] Processed 45002391 reads in 682 ms
[2015-09-30T22:36Z] INFO  23:36:58,198 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:58,242 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:58,426 MuTect - [MUTECT] Processed 42001794 reads in 653 ms
[2015-09-30T22:36Z] INFO  23:36:58,650 MuTect - [MUTECT] Processed 33001215 reads in 676 ms
[2015-09-30T22:36Z] INFO  23:36:58,818 MuTect - [MUTECT] Processed 46002521 reads in 651 ms
[2015-09-30T22:36Z] INFO  23:36:59,036 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:36Z] INFO  23:36:59,066 MuTect - [MUTECT] Processed 43001878 reads in 640 ms
[2015-09-30T22:36Z] INFO  23:36:59,340 MuTect - [MUTECT] Processed 34001223 reads in 690 ms
[2015-09-30T22:36Z] INFO  23:36:59,506 MuTect - [MUTECT] Processed 47002530 reads in 688 ms
[2015-09-30T22:36Z] INFO  23:36:59,682 MuTect - [MUTECT] Processed 44001898 reads in 616 ms
[2015-09-30T22:37Z] INFO  23:37:00,063 MuTect - [MUTECT] Processed 35001230 reads in 723 ms
[2015-09-30T22:37Z] INFO  23:37:00,232 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:00,262 MuTect - [MUTECT] Processed 48002580 reads in 756 ms
[2015-09-30T22:37Z] INFO  23:37:00,298 MuTect - [MUTECT] Processed 45001991 reads in 616 ms
[2015-09-30T22:37Z] INFO  23:37:00,355 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:00,767 MuTect - [MUTECT] Processed 36001253 reads in 704 ms
[2015-09-30T22:37Z] INFO  23:37:00,936 MuTect - [MUTECT] Processed 46002024 reads in 638 ms
[2015-09-30T22:37Z] INFO  23:37:00,952 MuTect - [MUTECT] Processed 49002614 reads in 690 ms
[2015-09-30T22:37Z] INFO  23:37:01,396 MuTect - [MUTECT] Processed 37001268 reads in 629 ms
[2015-09-30T22:37Z] INFO  23:37:01,511 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:01,610 MuTect - [MUTECT] Processed 47002112 reads in 674 ms
[2015-09-30T22:37Z] INFO  23:37:01,654 MuTect - [MUTECT] Processed 50002697 reads in 702 ms
[2015-09-30T22:37Z] INFO  23:37:02,114 MuTect - [MUTECT] Processed 38001342 reads in 718 ms
[2015-09-30T22:37Z] INFO  23:37:02,269 MuTect - [MUTECT] Processed 48002210 reads in 659 ms
[2015-09-30T22:37Z] INFO  23:37:02,427 MuTect - [MUTECT] Processed 51002710 reads in 773 ms
[2015-09-30T22:37Z] INFO  23:37:02,473 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:02,795 MuTect - [MUTECT] Processed 39001366 reads in 680 ms
[2015-09-30T22:37Z] INFO  23:37:02,800 ProgressMeter -     14:50797037        1.47e+06   30.0 s       20.0 s     48.9%        61.0 s    31.0 s
[2015-09-30T22:37Z] INFO  23:37:02,947 MuTect - [MUTECT] Processed 49002291 reads in 678 ms
[2015-09-30T22:37Z] INFO  23:37:03,021 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:03,171 MuTect - [MUTECT] Processed 52002815 reads in 744 ms
[2015-09-30T22:37Z] INFO  23:37:03,459 MuTect - [MUTECT] Processed 40001413 reads in 665 ms
[2015-09-30T22:37Z] INFO  23:37:03,598 MuTect - [MUTECT] Processed 50002315 reads in 651 ms
[2015-09-30T22:37Z] INFO  23:37:03,893 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:03,931 MuTect - [MUTECT] Processed 53002877 reads in 760 ms
[2015-09-30T22:37Z] INFO  23:37:04,132 MuTect - [MUTECT] Processed 41001451 reads in 673 ms
[2015-09-30T22:37Z] INFO  23:37:04,253 MuTect - [MUTECT] Processed 51002378 reads in 655 ms
[2015-09-30T22:37Z] INFO  23:37:04,637 MuTect - [MUTECT] Processed 54002881 reads in 706 ms
[2015-09-30T22:37Z] INFO  23:37:04,661 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:04,806 MuTect - [MUTECT] Processed 42001463 reads in 674 ms
[2015-09-30T22:37Z] INFO  23:37:04,894 MuTect - [MUTECT] Processed 52002430 reads in 641 ms
[2015-09-30T22:37Z] INFO  23:37:05,339 MuTect - [MUTECT] Processed 55002897 reads in 702 ms
[2015-09-30T22:37Z] INFO  23:37:05,480 MuTect - [MUTECT] Processed 43001537 reads in 674 ms
[2015-09-30T22:37Z] INFO  23:37:05,484 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:05,566 MuTect - [MUTECT] Processed 53002462 reads in 672 ms
[2015-09-30T22:37Z] INFO  23:37:06,068 MuTect - [MUTECT] Processed 56002957 reads in 729 ms
[2015-09-30T22:37Z] INFO  23:37:06,124 MuTect - [MUTECT] Processed 44001590 reads in 644 ms
[2015-09-30T22:37Z] INFO  23:37:06,236 MuTect - [MUTECT] Processed 54002557 reads in 670 ms
[2015-09-30T22:37Z] INFO  23:37:06,378 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:06,726 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:06,769 MuTect - [MUTECT] Processed 45001650 reads in 645 ms
[2015-09-30T22:37Z] INFO  23:37:06,816 MuTect - [MUTECT] Processed 57003072 reads in 748 ms
[2015-09-30T22:37Z] INFO  23:37:06,928 MuTect - [MUTECT] Processed 55002683 reads in 692 ms
[2015-09-30T22:37Z] INFO  23:37:07,421 MuTect - [MUTECT] Processed 46001671 reads in 652 ms
[2015-09-30T22:37Z] INFO  23:37:07,523 MuTect - [MUTECT] Processed 58003124 reads in 707 ms
[2015-09-30T22:37Z] INFO  23:37:07,631 MuTect - [MUTECT] Processed 56002689 reads in 703 ms
[2015-09-30T22:37Z] INFO  23:37:07,778 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:08,058 MuTect - [MUTECT] Processed 47001763 reads in 637 ms
[2015-09-30T22:37Z] INFO  23:37:08,229 MuTect - [MUTECT] Processed 59003131 reads in 706 ms
[2015-09-30T22:37Z] INFO  23:37:08,333 MuTect - [MUTECT] Processed 57002720 reads in 702 ms
[2015-09-30T22:37Z] INFO  23:37:08,723 MuTect - [MUTECT] Processed 48001800 reads in 665 ms
[2015-09-30T22:37Z] INFO  23:37:08,786 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:08,926 MuTect - [MUTECT] Processed 60003208 reads in 697 ms
[2015-09-30T22:37Z] INFO  23:37:08,960 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:08,988 MuTect - [MUTECT] Processed 58002729 reads in 655 ms
[2015-09-30T22:37Z] INFO  23:37:09,377 MuTect - [MUTECT] Processed 49001804 reads in 654 ms
[2015-09-30T22:37Z] INFO  23:37:09,634 MuTect - [MUTECT] Processed 61003285 reads in 708 ms
[2015-09-30T22:37Z] INFO  23:37:09,634 MuTect - [MUTECT] Processed 59002796 reads in 646 ms
[2015-09-30T22:37Z] INFO  23:37:10,074 MuTect - [MUTECT] Processed 50001879 reads in 697 ms
[2015-09-30T22:37Z] INFO  23:37:10,214 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:10,284 MuTect - [MUTECT] Processed 60002811 reads in 650 ms
[2015-09-30T22:37Z] INFO  23:37:10,358 MuTect - [MUTECT] Processed 62003356 reads in 724 ms
[2015-09-30T22:37Z] INFO  23:37:10,737 MuTect - [MUTECT] Processed 51001920 reads in 663 ms
[2015-09-30T22:37Z] INFO  23:37:11,025 MuTect - [MUTECT] Processed 61002869 reads in 741 ms
[2015-09-30T22:37Z] INFO  23:37:11,050 MuTect - [MUTECT] Processed 63003436 reads in 692 ms
[2015-09-30T22:37Z] INFO  23:37:11,189 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:11,282 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:11,414 MuTect - [MUTECT] Processed 52001937 reads in 677 ms
[2015-09-30T22:37Z] INFO  23:37:11,726 MuTect - [MUTECT] Processed 64003496 reads in 676 ms
[2015-09-30T22:37Z] INFO  23:37:11,781 MuTect - [MUTECT] Processed 62002951 reads in 756 ms
[2015-09-30T22:37Z] INFO  23:37:12,068 MuTect - [MUTECT] Processed 53001984 reads in 654 ms
[2015-09-30T22:37Z] INFO  23:37:12,395 MuTect - [MUTECT] Processed 65003611 reads in 669 ms
[2015-09-30T22:37Z] INFO  23:37:12,442 MuTect - [MUTECT] Processed 63002955 reads in 661 ms
[2015-09-30T22:37Z] INFO  23:37:12,532 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:12,724 MuTect - [MUTECT] Processed 54001994 reads in 656 ms
[2015-09-30T22:37Z] INFO  23:37:13,101 MuTect - [MUTECT] Processed 64003004 reads in 659 ms
[2015-09-30T22:37Z] INFO  23:37:13,118 MuTect - [MUTECT] Processed 66003648 reads in 723 ms
[2015-09-30T22:37Z] INFO  23:37:13,365 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:13,434 MuTect - [MUTECT] Processed 55002000 reads in 710 ms
[2015-09-30T22:37Z] INFO  23:37:13,745 MuTect - [MUTECT] Processed 65003108 reads in 644 ms
[2015-09-30T22:37Z] INFO  23:37:13,850 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:13,912 MuTect - [MUTECT] Processed 67003653 reads in 794 ms
[2015-09-30T22:37Z] INFO  23:37:14,143 MuTect - [MUTECT] Processed 56002017 reads in 709 ms
[2015-09-30T22:37Z] INFO  23:37:14,371 MuTect - [MUTECT] Processed 66003153 reads in 626 ms
[2015-09-30T22:37Z] INFO  23:37:14,845 MuTect - [MUTECT] Processed 57002099 reads in 702 ms
[2015-09-30T22:37Z] INFO  23:37:14,987 MuTect - [MUTECT] Processed 67003238 reads in 615 ms
[2015-09-30T22:37Z] INFO  23:37:15,202 MuTect - [MUTECT] Processed 68003715 reads in 1290 ms
[2015-09-30T22:37Z] INFO  23:37:15,399 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:15,417 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:15,542 MuTect - [MUTECT] Processed 58002141 reads in 697 ms
[2015-09-30T22:37Z] INFO  23:37:15,606 MuTect - [MUTECT] Processed 68003325 reads in 620 ms
[2015-09-30T22:37Z] INFO  23:37:15,894 MuTect - [MUTECT] Processed 69003780 reads in 692 ms
[2015-09-30T22:37Z] INFO  23:37:16,230 MuTect - [MUTECT] Processed 69003354 reads in 624 ms
[2015-09-30T22:37Z] INFO  23:37:16,232 MuTect - [MUTECT] Processed 59002171 reads in 690 ms
[2015-09-30T22:37Z] INFO  23:37:16,443 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:16,627 MuTect - [MUTECT] Processed 70003822 reads in 733 ms
[2015-09-30T22:37Z] INFO  23:37:16,853 MuTect - [MUTECT] Processed 70003487 reads in 623 ms
[2015-09-30T22:37Z] INFO  23:37:16,916 MuTect - [MUTECT] Processed 60002175 reads in 684 ms
[2015-09-30T22:37Z] INFO  23:37:17,367 MuTect - [MUTECT] Processed 71003865 reads in 740 ms
[2015-09-30T22:37Z] INFO  23:37:17,438 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:17,472 MuTect - [MUTECT] Processed 71003577 reads in 619 ms
[2015-09-30T22:37Z] INFO  23:37:17,599 MuTect - [MUTECT] Processed 61002193 reads in 683 ms
[2015-09-30T22:37Z] INFO  23:37:17,814 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:18,030 MuTect - [MUTECT] Processed 72003956 reads in 663 ms
[2015-09-30T22:37Z] INFO  23:37:18,100 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:37Z] INFO  23:37:18,105 ProgressMeter -            done        2.21e+06   54.0 s       24.0 s    100.0%        54.0 s     0.0 s
[2015-09-30T22:37Z] INFO  23:37:18,105 ProgressMeter - Total runtime 54.83 secs, 0.91 min, 0.02 hours
[2015-09-30T22:37Z] INFO  23:37:18,129 MuTect - [MUTECT] Processed 72003614 reads in 656 ms
[2015-09-30T22:37Z] INFO  23:37:18,170 MicroScheduler - 55664 reads were filtered out during the traversal out of approximately 871751 total reads (6.39%)
[2015-09-30T22:37Z] INFO  23:37:18,170 MicroScheduler -   -> 41461 reads (4.76% of total) failing DuplicateReadFilter
[2015-09-30T22:37Z] INFO  23:37:18,170 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:37Z] INFO  23:37:18,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:37Z] INFO  23:37:18,170 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:37Z] INFO  23:37:18,170 MicroScheduler -   -> 14203 reads (1.63% of total) failing UnmappedReadFilter
[2015-09-30T22:37Z] INFO  23:37:18,281 MuTect - [MUTECT] Processed 62002205 reads in 682 ms
[2015-09-30T22:37Z] INFO  23:37:18,805 MuTect - [MUTECT] Processed 73003714 reads in 677 ms
[2015-09-30T22:37Z] INFO  23:37:18,948 MuTect - [MUTECT] Processed 63002233 reads in 667 ms
[2015-09-30T22:37Z] INFO  23:37:19,036 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:19,132 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:37Z] INFO  23:37:19,509 MuTect - [MUTECT] Processed 74003775 reads in 704 ms
[2015-09-30T22:37Z] INFO  23:37:19,632 MuTect - [MUTECT] Processed 64002255 reads in 684 ms
[2015-09-30T22:37Z] INFO  23:37:19,669 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:37Z] bgzip syn3-13_94938309_115169878-raw-mutect.vcf
[2015-09-30T22:37Z] tabix index syn3-13_94938309_115169878-raw-mutect.vcf.gz
[2015-09-30T22:37Z] INFO  23:37:20,175 MuTect - [MUTECT] Processed 75003830 reads in 666 ms
[2015-09-30T22:37Z] INFO  23:37:20,327 MuTect - [MUTECT] Processed 65002268 reads in 695 ms
[2015-09-30T22:37Z] INFO  23:37:20,840 MuTect - [MUTECT] Processed 76003833 reads in 665 ms
[2015-09-30T22:37Z] INFO  23:37:21,023 MuTect - [MUTECT] Processed 66002293 reads in 696 ms
[2015-09-30T22:37Z] INFO  23:37:21,475 MuTect - [MUTECT] Processed 77003863 reads in 635 ms
[2015-09-30T22:37Z] INFO  23:37:21,651 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:21,698 MuTect - [MUTECT] Processed 67002316 reads in 675 ms
[2015-09-30T22:37Z] INFO  23:37:21,890 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:22,120 MuTect - [MUTECT] Processed 78003981 reads in 645 ms
[2015-09-30T22:37Z] MuTect: MuTect
[2015-09-30T22:37Z] INFO  23:37:22,411 MuTect - [MUTECT] Processed 68002356 reads in 713 ms
[2015-09-30T22:37Z] INFO  23:37:22,781 MuTect - [MUTECT] Processed 79004095 reads in 661 ms
[2015-09-30T22:37Z] INFO  23:37:23,108 MuTect - [MUTECT] Processed 69002415 reads in 697 ms
[2015-09-30T22:37Z] INFO  23:37:23,450 MuTect - [MUTECT] Processed 80004122 reads in 669 ms
[2015-09-30T22:37Z] INFO  23:37:23,797 MuTect - [MUTECT] Processed 70002437 reads in 689 ms
[2015-09-30T22:37Z] INFO  23:37:23,929 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:24,111 MuTect - [MUTECT] Processed 81004124 reads in 661 ms
[2015-09-30T22:37Z] INFO  23:37:24,254 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:24,497 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/14/syn3-14_62186823_93262365-raw-mutect-regions.bed to be BED
[2015-09-30T22:37Z] INFO  23:37:24,504 MuTect - [MUTECT] Processed 71002467 reads in 707 ms
[2015-09-30T22:37Z] INFO  23:37:24,554 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:37Z] INFO  23:37:24,554 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:37Z] INFO  23:37:24,554 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:37Z] INFO  23:37:24,554 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:37Z] INFO  23:37:24,558 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/14/syn3-14_62186823_93262365-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/14/tx/tmpAM7zuO/syn3-14_62186823_93262365-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:37Z] INFO  23:37:24,558 HelpFormatter - Date/Time: 2015/09/30 23:37:24
[2015-09-30T22:37Z] INFO  23:37:24,558 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:37Z] INFO  23:37:24,558 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:37Z] INFO  23:37:24,586 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:37Z] INFO  23:37:24,591 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:37Z] INFO  23:37:24,646 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:37Z] INFO  23:37:24,696 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:37Z] INFO  23:37:24,703 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:37Z] INFO  23:37:24,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:37Z] INFO  23:37:24,738 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:37Z] INFO  23:37:24,913 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:37Z] INFO  23:37:25,024 IntervalUtils - Processing 1557127 bp from intervals
[2015-09-30T22:37Z] INFO  23:37:25,028 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:37Z] INFO  23:37:25,028 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:37Z] INFO  23:37:25,190 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:37Z] INFO  23:37:25,202 MuTect - [MUTECT] Processed 72002477 reads in 698 ms
[2015-09-30T22:37Z] INFO  23:37:25,714 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:37Z] INFO  23:37:25,714 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:37Z] INFO  23:37:25,714 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:37Z] INFO  23:37:25,715 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:37Z] INFO  23:37:25,875 MuTect - [MUTECT] Processed 82004192 reads in 1764 ms
[2015-09-30T22:37Z] INFO  23:37:25,890 MuTect - [MUTECT] Processed 73002539 reads in 688 ms
[2015-09-30T22:37Z] INFO  23:37:26,565 MuTect - [MUTECT] Processed 74002580 reads in 674 ms
[2015-09-30T22:37Z] INFO  23:37:26,603 MuTect - [MUTECT] Processed 83004263 reads in 728 ms
[2015-09-30T22:37Z] INFO  23:37:26,912 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:27,104 ProgressMeter -     14:25325936        2.41e+06   60.0 s       24.0 s     95.8%        62.0 s     2.0 s
[2015-09-30T22:37Z] INFO  23:37:27,271 MuTect - [MUTECT] Processed 75002581 reads in 707 ms
[2015-09-30T22:37Z] INFO  23:37:27,301 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:27,338 MuTect - [MUTECT] Processed 84004270 reads in 735 ms
[2015-09-30T22:37Z] INFO  23:37:28,030 MuTect - [MUTECT] Processed 76002605 reads in 759 ms
[2015-09-30T22:37Z] INFO  23:37:28,087 MuTect - [MUTECT] Processed 85004281 reads in 749 ms
[2015-09-30T22:37Z] INFO  23:37:28,360 MuTect - [MUTECT] Processed 1000009 reads in 2597 ms
[2015-09-30T22:37Z] INFO  23:37:28,611 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:37Z] INFO  23:37:28,615 ProgressMeter -            done        2.47e+06   61.0 s       24.0 s    100.0%        61.0 s     0.0 s
[2015-09-30T22:37Z] INFO  23:37:28,615 ProgressMeter - Total runtime 61.51 secs, 1.03 min, 0.02 hours
[2015-09-30T22:37Z] INFO  23:37:28,677 MicroScheduler - 65274 reads were filtered out during the traversal out of approximately 993514 total reads (6.57%)
[2015-09-30T22:37Z] INFO  23:37:28,677 MicroScheduler -   -> 48642 reads (4.90% of total) failing DuplicateReadFilter
[2015-09-30T22:37Z] INFO  23:37:28,677 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:37Z] INFO  23:37:28,677 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:37Z] INFO  23:37:28,677 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:37Z] INFO  23:37:28,678 MicroScheduler -   -> 16632 reads (1.67% of total) failing UnmappedReadFilter
[2015-09-30T22:37Z] INFO  23:37:28,746 MuTect - [MUTECT] Processed 77002628 reads in 716 ms
[2015-09-30T22:37Z] INFO  23:37:29,124 MuTect - [MUTECT] Processed 2000019 reads in 764 ms
[2015-09-30T22:37Z] INFO  23:37:29,444 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:29,469 MuTect - [MUTECT] Processed 78002646 reads in 723 ms
[2015-09-30T22:37Z] INFO  23:37:29,687 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:37Z] bgzip syn3-14_0_31050569-raw-mutect.vcf
[2015-09-30T22:37Z] tabix index syn3-14_0_31050569-raw-mutect.vcf.gz
[2015-09-30T22:37Z] INFO  23:37:29,882 MuTect - [MUTECT] Processed 3000029 reads in 758 ms
[2015-09-30T22:37Z] INFO  23:37:30,190 MuTect - [MUTECT] Processed 79002658 reads in 721 ms
[2015-09-30T22:37Z] INFO  23:37:30,502 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:30,652 MuTect - [MUTECT] Processed 4000068 reads in 770 ms
[2015-09-30T22:37Z] INFO  23:37:30,913 MuTect - [MUTECT] Processed 80002714 reads in 723 ms
[2015-09-30T22:37Z] INFO  23:37:31,366 MuTect - [MUTECT] Processed 5000171 reads in 714 ms
[2015-09-30T22:37Z] INFO  23:37:31,576 MuTect - [MUTECT] Processed 81002719 reads in 663 ms
[2015-09-30T22:37Z] INFO  23:37:31,971 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:32,068 MuTect - [MUTECT] Processed 6000180 reads in 702 ms
[2015-09-30T22:37Z] MuTect: MuTect
[2015-09-30T22:37Z] INFO  23:37:32,310 MuTect - [MUTECT] Processed 82002744 reads in 734 ms
[2015-09-30T22:37Z] INFO  23:37:32,795 MuTect - [MUTECT] Processed 7000230 reads in 727 ms
[2015-09-30T22:37Z] INFO  23:37:32,801 ProgressMeter -     14:61923718        3.15e+06   60.0 s       19.0 s     99.5%        60.0 s     0.0 s
[2015-09-30T22:37Z] INFO  23:37:33,004 MuTect - [MUTECT] Processed 83002804 reads in 694 ms
[2015-09-30T22:37Z] INFO  23:37:33,196 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:37Z] INFO  23:37:33,200 ProgressMeter -            done        3.16e+06   60.0 s       19.0 s    100.0%        60.0 s     0.0 s
[2015-09-30T22:37Z] INFO  23:37:33,200 ProgressMeter - Total runtime 60.40 secs, 1.01 min, 0.02 hours
[2015-09-30T22:37Z] INFO  23:37:33,202 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:33,267 MicroScheduler - 55859 reads were filtered out during the traversal out of approximately 993287 total reads (5.62%)
[2015-09-30T22:37Z] INFO  23:37:33,268 MicroScheduler -   -> 40261 reads (4.05% of total) failing DuplicateReadFilter
[2015-09-30T22:37Z] INFO  23:37:33,268 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:37Z] INFO  23:37:33,268 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:37Z] INFO  23:37:33,268 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:37Z] INFO  23:37:33,268 MicroScheduler -   -> 15598 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:37Z] INFO  23:37:33,474 MuTect - [MUTECT] Processed 8000301 reads in 679 ms
[2015-09-30T22:37Z] INFO  23:37:34,256 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:37Z] bgzip syn3-14_31055710_62162825-raw-mutect.vcf
[2015-09-30T22:37Z] tabix index syn3-14_31055710_62162825-raw-mutect.vcf.gz
[2015-09-30T22:37Z] INFO  23:37:34,372 MuTect - [MUTECT] Processed 9000362 reads in 898 ms
[2015-09-30T22:37Z] INFO  23:37:34,508 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/14/syn3-14_93263525_107349540-raw-mutect-regions.bed to be BED
[2015-09-30T22:37Z] INFO  23:37:34,564 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:37Z] INFO  23:37:34,564 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:37Z] INFO  23:37:34,564 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:37Z] INFO  23:37:34,565 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:37Z] INFO  23:37:34,568 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/14/syn3-14_93263525_107349540-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/14/tx/tmpY0Nx3k/syn3-14_93263525_107349540-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:37Z] INFO  23:37:34,568 HelpFormatter - Date/Time: 2015/09/30 23:37:34
[2015-09-30T22:37Z] INFO  23:37:34,568 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:37Z] INFO  23:37:34,568 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:37Z] INFO  23:37:34,597 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:37Z] INFO  23:37:34,601 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:37Z] INFO  23:37:34,657 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:37Z] INFO  23:37:34,706 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:37Z] INFO  23:37:34,714 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:37Z] INFO  23:37:34,762 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T22:37Z] INFO  23:37:34,773 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:37Z] INFO  23:37:34,950 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:37Z] INFO  23:37:35,047 IntervalUtils - Processing 1055285 bp from intervals
[2015-09-30T22:37Z] INFO  23:37:35,050 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:37Z] INFO  23:37:35,051 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:37Z] INFO  23:37:35,054 MuTect - [MUTECT] Processed 10000378 reads in 682 ms
[2015-09-30T22:37Z] INFO  23:37:35,105 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:37Z] INFO  23:37:35,342 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:37Z] INFO  23:37:35,342 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:37Z] INFO  23:37:35,343 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:37Z] INFO  23:37:35,344 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:37Z] INFO  23:37:35,663 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:35,728 MuTect - [MUTECT] Processed 11000379 reads in 674 ms
[2015-09-30T22:37Z] INFO  23:37:36,411 MuTect - [MUTECT] Processed 12000416 reads in 683 ms
[2015-09-30T22:37Z] MuTect: MuTect
[2015-09-30T22:37Z] INFO  23:37:37,079 MuTect - [MUTECT] Processed 13000438 reads in 668 ms
[2015-09-30T22:37Z] INFO  23:37:37,745 MuTect - [MUTECT] Processed 14000491 reads in 666 ms
[2015-09-30T22:37Z] INFO  23:37:37,760 MuTect - [MUTECT] Processed 1000049 reads in 2370 ms
[2015-09-30T22:37Z] INFO  23:37:38,152 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:38,387 MuTect - [MUTECT] Processed 15000529 reads in 642 ms
[2015-09-30T22:37Z] INFO  23:37:38,513 MuTect - [MUTECT] Processed 2000080 reads in 753 ms
[2015-09-30T22:37Z] INFO  23:37:38,652 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/15/syn3-15_0_31041107-raw-mutect-regions.bed to be BED
[2015-09-30T22:37Z] INFO  23:37:38,708 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:37Z] INFO  23:37:38,709 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:37Z] INFO  23:37:38,709 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:37Z] INFO  23:37:38,709 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:37Z] INFO  23:37:38,713 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/15/syn3-15_0_31041107-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/15/tx/tmp_fluNp/syn3-15_0_31041107-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:37Z] INFO  23:37:38,713 HelpFormatter - Date/Time: 2015/09/30 23:37:38
[2015-09-30T22:37Z] INFO  23:37:38,713 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:37Z] INFO  23:37:38,713 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:37Z] INFO  23:37:38,741 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:37Z] INFO  23:37:38,745 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:37Z] INFO  23:37:38,796 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:37Z] INFO  23:37:38,844 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:37Z] INFO  23:37:38,852 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:37Z] INFO  23:37:38,875 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:37Z] INFO  23:37:38,886 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:37Z] INFO  23:37:39,015 MuTect - [MUTECT] Processed 16000535 reads in 627 ms
[2015-09-30T22:37Z] INFO  23:37:39,066 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:37Z] INFO  23:37:39,144 IntervalUtils - Processing 659213 bp from intervals
[2015-09-30T22:37Z] INFO  23:37:39,148 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:37Z] INFO  23:37:39,148 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:37Z] INFO  23:37:39,203 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:37Z] INFO  23:37:39,216 MuTect - [MUTECT] Processed 3000081 reads in 703 ms
[2015-09-30T22:37Z] INFO  23:37:39,445 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:37Z] INFO  23:37:39,445 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:37Z] INFO  23:37:39,445 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:37Z] INFO  23:37:39,446 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:37Z] INFO  23:37:39,477 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:39,649 MuTect - [MUTECT] Processed 17000541 reads in 635 ms
[2015-09-30T22:37Z] INFO  23:37:39,928 MuTect - [MUTECT] Processed 4000122 reads in 712 ms
[2015-09-30T22:37Z] INFO  23:37:40,283 MuTect - [MUTECT] Processed 18000598 reads in 634 ms
[2015-09-30T22:37Z] INFO  23:37:40,372 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:40,680 MuTect - [MUTECT] Processed 5000202 reads in 752 ms
[2015-09-30T22:37Z] INFO  23:37:40,963 MuTect - [MUTECT] Processed 19000611 reads in 680 ms
[2015-09-30T22:37Z] INFO  23:37:41,416 MuTect - [MUTECT] Processed 6000218 reads in 736 ms
[2015-09-30T22:37Z] INFO  23:37:41,630 MuTect - [MUTECT] Processed 20000643 reads in 667 ms
[2015-09-30T22:37Z] INFO  23:37:42,049 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:42,146 MuTect - [MUTECT] Processed 7000240 reads in 730 ms
[2015-09-30T22:37Z] INFO  23:37:42,279 MuTect - [MUTECT] Processed 21000758 reads in 649 ms
[2015-09-30T22:37Z] INFO  23:37:42,446 MuTect - [MUTECT] Processed 1000037 reads in 2953 ms
[2015-09-30T22:37Z] INFO  23:37:42,604 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:42,814 MuTect - [MUTECT] Processed 8000248 reads in 668 ms
[2015-09-30T22:37Z] INFO  23:37:42,973 MuTect - [MUTECT] Processed 22000822 reads in 694 ms
[2015-09-30T22:37Z] INFO  23:37:43,375 MuTect - [MUTECT] Processed 2000329 reads in 929 ms
[2015-09-30T22:37Z] INFO  23:37:43,486 MuTect - [MUTECT] Processed 9000326 reads in 672 ms
[2015-09-30T22:37Z] INFO  23:37:43,626 MuTect - [MUTECT] Processed 23000859 reads in 653 ms
[2015-09-30T22:37Z] INFO  23:37:44,176 MuTect - [MUTECT] Processed 10000410 reads in 689 ms
[2015-09-30T22:37Z] INFO  23:37:44,296 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:44,309 MuTect - [MUTECT] Processed 24000949 reads in 683 ms
[2015-09-30T22:37Z] INFO  23:37:44,824 MuTect - [MUTECT] Processed 3000581 reads in 1449 ms
[2015-09-30T22:37Z] INFO  23:37:44,837 MuTect - [MUTECT] Processed 11000434 reads in 662 ms
[2015-09-30T22:37Z] INFO  23:37:44,994 MuTect - [MUTECT] Processed 25000954 reads in 685 ms
[2015-09-30T22:37Z] INFO  23:37:45,047 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:45,152 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:45,519 MuTect - [MUTECT] Processed 12000504 reads in 682 ms
[2015-09-30T22:37Z] INFO  23:37:45,666 MuTect - [MUTECT] Processed 26000995 reads in 672 ms
[2015-09-30T22:37Z] INFO  23:37:45,936 MuTect - [MUTECT] Processed 4000634 reads in 1112 ms
[2015-09-30T22:37Z] INFO  23:37:46,206 MuTect - [MUTECT] Processed 13000570 reads in 687 ms
[2015-09-30T22:37Z] INFO  23:37:46,355 MuTect - [MUTECT] Processed 27001001 reads in 689 ms
[2015-09-30T22:37Z] INFO  23:37:46,680 MuTect - [MUTECT] Processed 5000651 reads in 743 ms
[2015-09-30T22:37Z] INFO  23:37:46,685 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:47,029 MuTect - [MUTECT] Processed 28001049 reads in 674 ms
[2015-09-30T22:37Z] INFO  23:37:47,046 MuTect - [MUTECT] Processed 14000613 reads in 840 ms
[2015-09-30T22:37Z] INFO  23:37:47,307 MuTect - [MUTECT] Processed 6000689 reads in 628 ms
[2015-09-30T22:37Z] INFO  23:37:47,393 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:47,695 MuTect - [MUTECT] Processed 29001140 reads in 666 ms
[2015-09-30T22:37Z] INFO  23:37:47,751 MuTect - [MUTECT] Processed 15000641 reads in 705 ms
[2015-09-30T22:37Z] INFO  23:37:47,933 MuTect - [MUTECT] Processed 7000702 reads in 626 ms
[2015-09-30T22:37Z] INFO  23:37:48,355 MuTect - [MUTECT] Processed 30001207 reads in 660 ms
[2015-09-30T22:37Z] INFO  23:37:48,569 MuTect - [MUTECT] Processed 16000660 reads in 818 ms
[2015-09-30T22:37Z] INFO  23:37:48,678 MuTect - [MUTECT] Processed 8000724 reads in 745 ms
[2015-09-30T22:37Z] INFO  23:37:49,011 MuTect - [MUTECT] Processed 31001225 reads in 656 ms
[2015-09-30T22:37Z] INFO  23:37:49,142 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:49,248 MuTect - [MUTECT] Processed 17000744 reads in 679 ms
[2015-09-30T22:37Z] INFO  23:37:49,384 MuTect - [MUTECT] Processed 9000733 reads in 706 ms
[2015-09-30T22:37Z] INFO  23:37:49,569 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:49,680 MuTect - [MUTECT] Processed 32001289 reads in 669 ms
[2015-09-30T22:37Z] INFO  23:37:49,829 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:49,890 MuTect - [MUTECT] Processed 18000793 reads in 642 ms
[2015-09-30T22:37Z] INFO  23:37:50,157 MuTect - [MUTECT] Processed 10000807 reads in 773 ms
[2015-09-30T22:37Z] INFO  23:37:50,326 MuTect - [MUTECT] Processed 33001336 reads in 646 ms
[2015-09-30T22:37Z] INFO  23:37:50,567 MuTect - [MUTECT] Processed 19000830 reads in 677 ms
[2015-09-30T22:37Z] INFO  23:37:50,936 MuTect - [MUTECT] Processed 11000874 reads in 779 ms
[2015-09-30T22:37Z] INFO  23:37:51,031 MuTect - [MUTECT] Processed 34001374 reads in 705 ms
[2015-09-30T22:37Z] INFO  23:37:51,238 MuTect - [MUTECT] Processed 20000869 reads in 671 ms
[2015-09-30T22:37Z] INFO  23:37:51,572 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:51,712 MuTect - [MUTECT] Processed 35001441 reads in 681 ms
[2015-09-30T22:37Z] INFO  23:37:51,762 MuTect - [MUTECT] Processed 12000983 reads in 826 ms
[2015-09-30T22:37Z] INFO  23:37:51,853 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:51,954 MuTect - [MUTECT] Processed 21000945 reads in 716 ms
[2015-09-30T22:37Z] INFO  23:37:52,342 MuTect - [MUTECT] Processed 36001445 reads in 630 ms
[2015-09-30T22:37Z] INFO  23:37:52,629 MuTect - [MUTECT] Processed 22000962 reads in 675 ms
[2015-09-30T22:37Z] INFO  23:37:52,638 MuTect - [MUTECT] Processed 13001186 reads in 876 ms
[2015-09-30T22:37Z] INFO  23:37:53,003 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:53,018 MuTect - [MUTECT] Processed 37001498 reads in 676 ms
[2015-09-30T22:37Z] INFO  23:37:53,278 MuTect - [MUTECT] Processed 23001022 reads in 649 ms
[2015-09-30T22:37Z] INFO  23:37:53,423 MuTect - [MUTECT] Processed 14001270 reads in 785 ms
[2015-09-30T22:37Z] INFO  23:37:53,688 MuTect - [MUTECT] Processed 38001501 reads in 670 ms
[2015-09-30T22:37Z] INFO  23:37:53,844 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:53,951 MuTect - [MUTECT] Processed 24001083 reads in 673 ms
[2015-09-30T22:37Z] INFO  23:37:54,046 MuTect - [MUTECT] Processed 15001375 reads in 623 ms
[2015-09-30T22:37Z] INFO  23:37:54,072 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:54,356 MuTect - [MUTECT] Processed 39001536 reads in 668 ms
[2015-09-30T22:37Z] INFO  23:37:54,615 MuTect - [MUTECT] Processed 25001121 reads in 664 ms
[2015-09-30T22:37Z] INFO  23:37:54,733 MuTect - [MUTECT] Processed 16001432 reads in 687 ms
[2015-09-30T22:37Z] INFO  23:37:55,017 MuTect - [MUTECT] Processed 40001571 reads in 661 ms
[2015-09-30T22:37Z] INFO  23:37:55,259 MuTect - [MUTECT] Processed 26001135 reads in 644 ms
[2015-09-30T22:37Z] INFO  23:37:55,433 MuTect - [MUTECT] Processed 17001542 reads in 700 ms
[2015-09-30T22:37Z] INFO  23:37:55,667 MuTect - [MUTECT] Processed 41001577 reads in 650 ms
[2015-09-30T22:37Z] INFO  23:37:55,717 ProgressMeter -     14:69993653        1.37e+06   30.0 s       21.0 s     30.0%       100.0 s    70.0 s
[2015-09-30T22:37Z] INFO  23:37:55,917 MuTect - [MUTECT] Processed 27001223 reads in 658 ms
[2015-09-30T22:37Z] INFO  23:37:56,129 MuTect - [MUTECT] Processed 18001626 reads in 696 ms
[2015-09-30T22:37Z] INFO  23:37:56,173 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:56,185 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:56,293 MuTect - [MUTECT] Processed 42001643 reads in 626 ms
[2015-09-30T22:37Z] INFO  23:37:56,349 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:56,560 MuTect - [MUTECT] Processed 28001276 reads in 643 ms
[2015-09-30T22:37Z] INFO  23:37:56,824 MuTect - [MUTECT] Processed 19001676 reads in 695 ms
[2015-09-30T22:37Z] INFO  23:37:56,941 MuTect - [MUTECT] Processed 43001652 reads in 648 ms
[2015-09-30T22:37Z] INFO  23:37:57,218 MuTect - [MUTECT] Processed 29001366 reads in 658 ms
[2015-09-30T22:37Z] INFO  23:37:57,581 MuTect - [MUTECT] Processed 44001699 reads in 640 ms
[2015-09-30T22:37Z] INFO  23:37:57,808 MuTect - [MUTECT] Processed 20001695 reads in 984 ms
[2015-09-30T22:37Z] INFO  23:37:57,857 MuTect - [MUTECT] Processed 30001406 reads in 639 ms
[2015-09-30T22:37Z] INFO  23:37:58,296 MuTect - [MUTECT] Processed 45001717 reads in 715 ms
[2015-09-30T22:37Z] INFO  23:37:58,421 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:58,495 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:58,536 MuTect - [MUTECT] Processed 21001728 reads in 728 ms
[2015-09-30T22:37Z] INFO  23:37:58,576 MuTect - [MUTECT] Processed 31001501 reads in 719 ms
[2015-09-30T22:37Z] INFO  23:37:58,971 MuTect - [MUTECT] Processed 46001741 reads in 675 ms
[2015-09-30T22:37Z] INFO  23:37:59,233 MuTect - [MUTECT] Processed 22001849 reads in 697 ms
[2015-09-30T22:37Z] INFO  23:37:59,260 MuTect - [MUTECT] Processed 32001585 reads in 684 ms
[2015-09-30T22:37Z] INFO  23:37:59,608 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:37Z] INFO  23:37:59,612 MuTect - [MUTECT] Processed 47001793 reads in 641 ms
[2015-09-30T22:37Z] INFO  23:37:59,868 MuTect - [MUTECT] Processed 23001874 reads in 635 ms
[2015-09-30T22:37Z] INFO  23:37:59,910 MuTect - [MUTECT] Processed 33001614 reads in 650 ms
[2015-09-30T22:38Z] INFO  23:38:00,273 MuTect - [MUTECT] Processed 48001797 reads in 660 ms
[2015-09-30T22:38Z] INFO  23:38:00,517 MuTect - [MUTECT] Processed 24001925 reads in 649 ms
[2015-09-30T22:38Z] INFO  23:38:00,576 MuTect - [MUTECT] Processed 34001673 reads in 666 ms
[2015-09-30T22:38Z] INFO  23:38:00,630 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:00,633 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:00,935 MuTect - [MUTECT] Processed 49001820 reads in 663 ms
[2015-09-30T22:38Z] INFO  23:38:01,140 MuTect - [MUTECT] Processed 25001984 reads in 623 ms
[2015-09-30T22:38Z] INFO  23:38:01,235 MuTect - [MUTECT] Processed 35001735 reads in 659 ms
[2015-09-30T22:38Z] INFO  23:38:01,572 MuTect - [MUTECT] Processed 50001873 reads in 637 ms
[2015-09-30T22:38Z] INFO  23:38:01,835 MuTect - [MUTECT] Processed 26002113 reads in 695 ms
[2015-09-30T22:38Z] INFO  23:38:01,880 MuTect - [MUTECT] Processed 36001784 reads in 645 ms
[2015-09-30T22:38Z] INFO  23:38:02,273 MuTect - [MUTECT] Processed 51001911 reads in 701 ms
[2015-09-30T22:38Z] INFO  23:38:02,461 MuTect - [MUTECT] Processed 27002154 reads in 626 ms
[2015-09-30T22:38Z] INFO  23:38:02,558 MuTect - [MUTECT] Processed 37001785 reads in 677 ms
[2015-09-30T22:38Z] INFO  23:38:02,936 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:02,947 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:02,980 MuTect - [MUTECT] Processed 52001949 reads in 707 ms
[2015-09-30T22:38Z] INFO  23:38:03,254 MuTect - [MUTECT] Processed 38001878 reads in 697 ms
[2015-09-30T22:38Z] INFO  23:38:03,320 MuTect - [MUTECT] Processed 28002194 reads in 859 ms
[2015-09-30T22:38Z] INFO  23:38:03,487 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:03,662 MuTect - [MUTECT] Processed 53002042 reads in 682 ms
[2015-09-30T22:38Z] INFO  23:38:03,949 MuTect - [MUTECT] Processed 39001924 reads in 695 ms
[2015-09-30T22:38Z] INFO  23:38:03,950 MuTect - [MUTECT] Processed 29002201 reads in 630 ms
[2015-09-30T22:38Z] INFO  23:38:04,376 MuTect - [MUTECT] Processed 54002103 reads in 714 ms
[2015-09-30T22:38Z] INFO  23:38:04,563 MuTect - [MUTECT] Processed 30002247 reads in 613 ms
[2015-09-30T22:38Z] INFO  23:38:04,654 MuTect - [MUTECT] Processed 40001983 reads in 704 ms
[2015-09-30T22:38Z] INFO  23:38:05,059 MuTect - [MUTECT] Processed 55002130 reads in 683 ms
[2015-09-30T22:38Z] INFO  23:38:05,130 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:05,257 MuTect - [MUTECT] Processed 31002264 reads in 694 ms
[2015-09-30T22:38Z] INFO  23:38:05,326 MuTect - [MUTECT] Processed 41002070 reads in 672 ms
[2015-09-30T22:38Z] INFO  23:38:05,336 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:05,345 ProgressMeter -    14:101349703        1.19e+06   30.0 s       25.0 s     42.1%        71.0 s    41.0 s
[2015-09-30T22:38Z] INFO  23:38:05,708 MuTect - [MUTECT] Processed 56002165 reads in 649 ms
[2015-09-30T22:38Z] INFO  23:38:05,867 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:05,909 MuTect - [MUTECT] Processed 32002287 reads in 652 ms
[2015-09-30T22:38Z] INFO  23:38:06,029 MuTect - [MUTECT] Processed 42002109 reads in 704 ms
[2015-09-30T22:38Z] INFO  23:38:06,356 MuTect - [MUTECT] Processed 57002264 reads in 648 ms
[2015-09-30T22:38Z] INFO  23:38:06,561 MuTect - [MUTECT] Processed 33002289 reads in 652 ms
[2015-09-30T22:38Z] INFO  23:38:06,722 MuTect - [MUTECT] Processed 43002240 reads in 693 ms
[2015-09-30T22:38Z] INFO  23:38:06,992 MuTect - [MUTECT] Processed 58002355 reads in 636 ms
[2015-09-30T22:38Z] INFO  23:38:07,229 MuTect - [MUTECT] Processed 34002337 reads in 668 ms
[2015-09-30T22:38Z] INFO  23:38:07,394 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:07,421 MuTect - [MUTECT] Processed 44002340 reads in 699 ms
[2015-09-30T22:38Z] INFO  23:38:07,630 MuTect - [MUTECT] Processed 59002440 reads in 638 ms
[2015-09-30T22:38Z] INFO  23:38:07,647 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:07,880 MuTect - [MUTECT] Processed 35002402 reads in 651 ms
[2015-09-30T22:38Z] INFO  23:38:08,091 MuTect - [MUTECT] Processed 45002444 reads in 670 ms
[2015-09-30T22:38Z] INFO  23:38:08,261 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:08,315 MuTect - [MUTECT] Processed 60002453 reads in 685 ms
[2015-09-30T22:38Z] INFO  23:38:08,575 MuTect - [MUTECT] Processed 36002490 reads in 695 ms
[2015-09-30T22:38Z] INFO  23:38:08,729 MuTect - [MUTECT] Processed 46002469 reads in 638 ms
[2015-09-30T22:38Z] INFO  23:38:08,966 MuTect - [MUTECT] Processed 61002543 reads in 651 ms
[2015-09-30T22:38Z] INFO  23:38:09,268 MuTect - [MUTECT] Processed 37002510 reads in 693 ms
[2015-09-30T22:38Z] INFO  23:38:09,370 MuTect - [MUTECT] Processed 47002539 reads in 641 ms
[2015-09-30T22:38Z] INFO  23:38:09,447 ProgressMeter -     15:26107642        9.83e+05   30.0 s       30.0 s     54.0%        55.0 s    25.0 s
[2015-09-30T22:38Z] INFO  23:38:09,625 MuTect - [MUTECT] Processed 62002554 reads in 659 ms
[2015-09-30T22:38Z] INFO  23:38:09,909 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:09,936 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:09,944 MuTect - [MUTECT] Processed 38002613 reads in 676 ms
[2015-09-30T22:38Z] INFO  23:38:09,994 MuTect - [MUTECT] Processed 48002551 reads in 624 ms
[2015-09-30T22:38Z] INFO  23:38:10,277 MuTect - [MUTECT] Processed 63002629 reads in 652 ms
[2015-09-30T22:38Z] INFO  23:38:10,615 MuTect - [MUTECT] Processed 49002571 reads in 621 ms
[2015-09-30T22:38Z] INFO  23:38:10,637 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:10,667 MuTect - [MUTECT] Processed 39002643 reads in 723 ms
[2015-09-30T22:38Z] INFO  23:38:10,948 MuTect - [MUTECT] Processed 64002657 reads in 671 ms
[2015-09-30T22:38Z] INFO  23:38:11,246 MuTect - [MUTECT] Processed 50002678 reads in 631 ms
[2015-09-30T22:38Z] INFO  23:38:11,365 MuTect - [MUTECT] Processed 40002740 reads in 698 ms
[2015-09-30T22:38Z] INFO  23:38:11,644 MuTect - [MUTECT] Processed 65002726 reads in 696 ms
[2015-09-30T22:38Z] INFO  23:38:11,899 MuTect - [MUTECT] Processed 51002690 reads in 653 ms
[2015-09-30T22:38Z] INFO  23:38:12,088 MuTect - [MUTECT] Processed 41002852 reads in 722 ms
[2015-09-30T22:38Z] INFO  23:38:12,125 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:12,135 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:12,271 MuTect - [MUTECT] Processed 66002733 reads in 627 ms
[2015-09-30T22:38Z] INFO  23:38:12,555 MuTect - [MUTECT] Processed 52002707 reads in 656 ms
[2015-09-30T22:38Z] INFO  23:38:12,786 MuTect - [MUTECT] Processed 42002872 reads in 699 ms
[2015-09-30T22:38Z] INFO  23:38:12,901 MuTect - [MUTECT] Processed 67002744 reads in 630 ms
[2015-09-30T22:38Z] INFO  23:38:13,065 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:13,220 MuTect - [MUTECT] Processed 53002718 reads in 665 ms
[2015-09-30T22:38Z] INFO  23:38:13,487 MuTect - [MUTECT] Processed 43002961 reads in 701 ms
[2015-09-30T22:38Z] INFO  23:38:13,574 MuTect - [MUTECT] Processed 68002828 reads in 673 ms
[2015-09-30T22:38Z] INFO  23:38:13,901 MuTect - [MUTECT] Processed 54002814 reads in 681 ms
[2015-09-30T22:38Z] INFO  23:38:14,204 MuTect - [MUTECT] Processed 44003051 reads in 717 ms
[2015-09-30T22:38Z] INFO  23:38:14,438 MuTect - [MUTECT] Processed 69002858 reads in 864 ms
[2015-09-30T22:38Z] INFO  23:38:14,469 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:14,560 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:14,598 MuTect - [MUTECT] Processed 55002953 reads in 697 ms
[2015-09-30T22:38Z] INFO  23:38:14,927 MuTect - [MUTECT] Processed 45003070 reads in 723 ms
[2015-09-30T22:38Z] INFO  23:38:15,299 MuTect - [MUTECT] Processed 56002955 reads in 701 ms
[2015-09-30T22:38Z] INFO  23:38:15,619 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:15,795 MuTect - [MUTECT] Processed 46003136 reads in 868 ms
[2015-09-30T22:38Z] INFO  23:38:15,890 MuTect - [MUTECT] Processed 70002860 reads in 1452 ms
[2015-09-30T22:38Z] INFO  23:38:15,977 MuTect - [MUTECT] Processed 57003013 reads in 678 ms
[2015-09-30T22:38Z] INFO  23:38:16,453 MuTect - [MUTECT] Processed 47003191 reads in 658 ms
[2015-09-30T22:38Z] INFO  23:38:16,575 MuTect - [MUTECT] Processed 71002961 reads in 685 ms
[2015-09-30T22:38Z] INFO  23:38:16,653 MuTect - [MUTECT] Processed 58003102 reads in 675 ms
[2015-09-30T22:38Z] INFO  23:38:16,964 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:17,065 MuTect - [MUTECT] Processed 48003312 reads in 612 ms
[2015-09-30T22:38Z] INFO  23:38:17,255 MuTect - [MUTECT] Processed 72003076 reads in 680 ms
[2015-09-30T22:38Z] INFO  23:38:17,317 MuTect - [MUTECT] Processed 59003162 reads in 665 ms
[2015-09-30T22:38Z] INFO  23:38:17,579 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:17,682 MuTect - [MUTECT] Processed 49003500 reads in 616 ms
[2015-09-30T22:38Z] INFO  23:38:17,931 MuTect - [MUTECT] Processed 73003096 reads in 676 ms
[2015-09-30T22:38Z] INFO  23:38:17,960 MuTect - [MUTECT] Processed 60003169 reads in 643 ms
[2015-09-30T22:38Z] INFO  23:38:18,250 MuTect - [MUTECT] Processed 50003511 reads in 569 ms
[2015-09-30T22:38Z] INFO  23:38:18,597 MuTect - [MUTECT] Processed 74003150 reads in 666 ms
[2015-09-30T22:38Z] INFO  23:38:18,631 MuTect - [MUTECT] Processed 61003169 reads in 671 ms
[2015-09-30T22:38Z] INFO  23:38:18,881 MuTect - [MUTECT] Processed 51003660 reads in 631 ms
[2015-09-30T22:38Z] INFO  23:38:19,133 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:19,257 MuTect - [MUTECT] Processed 75003217 reads in 660 ms
[2015-09-30T22:38Z] INFO  23:38:19,317 MuTect - [MUTECT] Processed 62003249 reads in 686 ms
[2015-09-30T22:38Z] INFO  23:38:19,561 MuTect - [MUTECT] Processed 52003764 reads in 680 ms
[2015-09-30T22:38Z] INFO  23:38:19,900 MuTect - [MUTECT] Processed 76003260 reads in 643 ms
[2015-09-30T22:38Z] INFO  23:38:19,907 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:20,015 MuTect - [MUTECT] Processed 63003312 reads in 698 ms
[2015-09-30T22:38Z] INFO  23:38:20,281 MuTect - [MUTECT] Processed 53003772 reads in 720 ms
[2015-09-30T22:38Z] INFO  23:38:20,543 MuTect - [MUTECT] Processed 77003277 reads in 643 ms
[2015-09-30T22:38Z] INFO  23:38:20,670 MuTect - [MUTECT] Processed 64003340 reads in 655 ms
[2015-09-30T22:38Z] INFO  23:38:20,844 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:20,950 MuTect - [MUTECT] Processed 54003839 reads in 669 ms
[2015-09-30T22:38Z] INFO  23:38:21,212 MuTect - [MUTECT] Processed 78003293 reads in 669 ms
[2015-09-30T22:38Z] INFO  23:38:21,316 MuTect - [MUTECT] Processed 65003406 reads in 646 ms
[2015-09-30T22:38Z] INFO  23:38:21,611 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:21,647 MuTect - [MUTECT] Processed 55003893 reads in 697 ms
[2015-09-30T22:38Z] INFO  23:38:21,867 MuTect - [MUTECT] Processed 79003361 reads in 655 ms
[2015-09-30T22:38Z] INFO  23:38:21,957 MuTect - [MUTECT] Processed 66003490 reads in 641 ms
[2015-09-30T22:38Z] INFO  23:38:22,077 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:22,282 MuTect - [MUTECT] Processed 56003911 reads in 635 ms
[2015-09-30T22:38Z] INFO  23:38:22,526 MuTect - [MUTECT] Processed 80003382 reads in 659 ms
[2015-09-30T22:38Z] INFO  23:38:22,601 MuTect - [MUTECT] Processed 67003595 reads in 644 ms
[2015-09-30T22:38Z] INFO  23:38:22,928 MuTect - [MUTECT] Processed 57003947 reads in 646 ms
[2015-09-30T22:38Z] INFO  23:38:23,175 MuTect - [MUTECT] Processed 81003435 reads in 649 ms
[2015-09-30T22:38Z] INFO  23:38:23,254 MuTect - [MUTECT] Processed 68003610 reads in 653 ms
[2015-09-30T22:38Z] INFO  23:38:23,527 MuTect - [MUTECT] Processed 58004052 reads in 599 ms
[2015-09-30T22:38Z] INFO  23:38:23,612 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:23,835 MuTect - [MUTECT] Processed 82003485 reads in 660 ms
[2015-09-30T22:38Z] INFO  23:38:23,849 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:23,936 MuTect - [MUTECT] Processed 69003616 reads in 682 ms
[2015-09-30T22:38Z] INFO  23:38:24,136 MuTect - [MUTECT] Processed 59004116 reads in 609 ms
[2015-09-30T22:38Z] INFO  23:38:24,387 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:24,480 MuTect - [MUTECT] Processed 83003499 reads in 645 ms
[2015-09-30T22:38Z] INFO  23:38:24,624 MuTect - [MUTECT] Processed 70003705 reads in 688 ms
[2015-09-30T22:38Z] INFO  23:38:24,737 MuTect - [MUTECT] Processed 60004183 reads in 601 ms
[2015-09-30T22:38Z] INFO  23:38:25,152 MuTect - [MUTECT] Processed 84003559 reads in 672 ms
[2015-09-30T22:38Z] INFO  23:38:25,291 MuTect - [MUTECT] Processed 71003794 reads in 667 ms
[2015-09-30T22:38Z] INFO  23:38:25,372 MuTect - [MUTECT] Processed 61004264 reads in 635 ms
[2015-09-30T22:38Z] INFO  23:38:25,718 ProgressMeter -     14:76123522        2.63e+06   60.0 s       22.0 s     60.0%       100.0 s    40.0 s
[2015-09-30T22:38Z] INFO  23:38:25,796 MuTect - [MUTECT] Processed 85003603 reads in 644 ms
[2015-09-30T22:38Z] INFO  23:38:25,925 MuTect - [MUTECT] Processed 72003797 reads in 634 ms
[2015-09-30T22:38Z] INFO  23:38:25,983 MuTect - [MUTECT] Processed 62004327 reads in 611 ms
[2015-09-30T22:38Z] INFO  23:38:26,191 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:26,473 MuTect - [MUTECT] Processed 86003664 reads in 677 ms
[2015-09-30T22:38Z] INFO  23:38:26,599 MuTect - [MUTECT] Processed 73003924 reads in 674 ms
[2015-09-30T22:38Z] INFO  23:38:26,613 MuTect - [MUTECT] Processed 63004364 reads in 630 ms
[2015-09-30T22:38Z] INFO  23:38:26,732 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:27,144 MuTect - [MUTECT] Processed 87003762 reads in 671 ms
[2015-09-30T22:38Z] INFO  23:38:27,215 MuTect - [MUTECT] Processed 64004392 reads in 602 ms
[2015-09-30T22:38Z] INFO  23:38:27,266 MuTect - [MUTECT] Processed 74003947 reads in 667 ms
[2015-09-30T22:38Z] INFO  23:38:27,819 MuTect - [MUTECT] Processed 88003763 reads in 675 ms
[2015-09-30T22:38Z] INFO  23:38:27,859 MuTect - [MUTECT] Processed 65004481 reads in 644 ms
[2015-09-30T22:38Z] INFO  23:38:27,929 MuTect - [MUTECT] Processed 75003969 reads in 663 ms
[2015-09-30T22:38Z] INFO  23:38:28,160 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:38Z] INFO  23:38:28,163 ProgressMeter -            done        1.83e+06   48.0 s       26.0 s    100.0%        48.0 s     0.0 s
[2015-09-30T22:38Z] INFO  23:38:28,163 ProgressMeter - Total runtime 48.72 secs, 0.81 min, 0.01 hours
[2015-09-30T22:38Z] INFO  23:38:28,227 MicroScheduler - 43927 reads were filtered out during the traversal out of approximately 773274 total reads (5.68%)
[2015-09-30T22:38Z] INFO  23:38:28,227 MicroScheduler -   -> 31798 reads (4.11% of total) failing DuplicateReadFilter
[2015-09-30T22:38Z] INFO  23:38:28,228 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:38Z] INFO  23:38:28,228 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:38Z] INFO  23:38:28,228 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:38Z] INFO  23:38:28,228 MicroScheduler -   -> 12129 reads (1.57% of total) failing UnmappedReadFilter
[2015-09-30T22:38Z] INFO  23:38:28,398 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:28,535 MuTect - [MUTECT] Processed 89003794 reads in 716 ms
[2015-09-30T22:38Z] INFO  23:38:28,604 MuTect - [MUTECT] Processed 76003975 reads in 675 ms
[2015-09-30T22:38Z] INFO  23:38:28,967 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:29,185 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:38Z] INFO  23:38:29,260 MuTect - [MUTECT] Processed 90003870 reads in 725 ms
[2015-09-30T22:38Z] bgzip syn3-15_0_31041107-raw-mutect.vcf
[2015-09-30T22:38Z] INFO  23:38:29,305 MuTect - [MUTECT] Processed 77003990 reads in 701 ms
[2015-09-30T22:38Z] tabix index syn3-15_0_31041107-raw-mutect.vcf.gz
[2015-09-30T22:38Z] INFO  23:38:29,926 MuTect - [MUTECT] Processed 91003901 reads in 666 ms
[2015-09-30T22:38Z] INFO  23:38:29,995 MuTect - [MUTECT] Processed 78004002 reads in 689 ms
[2015-09-30T22:38Z] INFO  23:38:30,550 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:30,601 MuTect - [MUTECT] Processed 92004036 reads in 675 ms
[2015-09-30T22:38Z] INFO  23:38:30,656 MuTect - [MUTECT] Processed 79004047 reads in 662 ms
[2015-09-30T22:38Z] INFO  23:38:31,107 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:31,232 MuTect - [MUTECT] Processed 93004116 reads in 631 ms
[2015-09-30T22:38Z] INFO  23:38:31,349 MuTect - [MUTECT] Processed 80004154 reads in 693 ms
[2015-09-30T22:38Z] INFO  23:38:31,887 MuTect - [MUTECT] Processed 94004181 reads in 655 ms
[2015-09-30T22:38Z] MuTect: MuTect
[2015-09-30T22:38Z] INFO  23:38:32,004 MuTect - [MUTECT] Processed 81004268 reads in 655 ms
[2015-09-30T22:38Z] INFO  23:38:32,529 MuTect - [MUTECT] Processed 95004229 reads in 642 ms
[2015-09-30T22:38Z] INFO  23:38:32,550 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:32,603 MuTect - [MUTECT] Processed 82004384 reads in 599 ms
[2015-09-30T22:38Z] INFO  23:38:33,180 MuTect - [MUTECT] Processed 96004233 reads in 651 ms
[2015-09-30T22:38Z] INFO  23:38:33,209 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:33,236 MuTect - [MUTECT] Processed 83004400 reads in 632 ms
[2015-09-30T22:38Z] INFO  23:38:33,814 MuTect - [MUTECT] Processed 97004305 reads in 634 ms
[2015-09-30T22:38Z] INFO  23:38:33,888 MuTect - [MUTECT] Processed 84004420 reads in 653 ms
[2015-09-30T22:38Z] INFO  23:38:34,020 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/15/syn3-15_31042312_62147370-raw-mutect-regions.bed to be BED
[2015-09-30T22:38Z] INFO  23:38:34,077 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:38Z] INFO  23:38:34,077 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:38Z] INFO  23:38:34,077 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:38Z] INFO  23:38:34,077 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:38Z] INFO  23:38:34,081 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/15/syn3-15_31042312_62147370-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/15/tx/tmp9Ffm1q/syn3-15_31042312_62147370-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:38Z] INFO  23:38:34,081 HelpFormatter - Date/Time: 2015/09/30 23:38:34
[2015-09-30T22:38Z] INFO  23:38:34,081 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:38Z] INFO  23:38:34,081 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:38Z] INFO  23:38:34,109 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:38Z] INFO  23:38:34,113 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:38Z] INFO  23:38:34,165 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:38Z] INFO  23:38:34,213 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:38Z] INFO  23:38:34,221 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:38Z] INFO  23:38:34,244 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:38Z] INFO  23:38:34,255 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:38Z] INFO  23:38:34,434 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:38Z] INFO  23:38:34,470 MuTect - [MUTECT] Processed 98004345 reads in 656 ms
[2015-09-30T22:38Z] INFO  23:38:34,547 MuTect - [MUTECT] Processed 85004429 reads in 659 ms
[2015-09-30T22:38Z] INFO  23:38:34,559 IntervalUtils - Processing 2237327 bp from intervals
[2015-09-30T22:38Z] INFO  23:38:34,563 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:38Z] INFO  23:38:34,563 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:38Z] INFO  23:38:34,728 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:38Z] INFO  23:38:34,795 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:34,951 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:38Z] INFO  23:38:34,951 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:38Z] INFO  23:38:34,951 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:38Z] INFO  23:38:34,952 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:38Z] INFO  23:38:35,141 MuTect - [MUTECT] Processed 99004463 reads in 671 ms
[2015-09-30T22:38Z] INFO  23:38:35,205 MuTect - [MUTECT] Processed 86004434 reads in 658 ms
[2015-09-30T22:38Z] INFO  23:38:35,347 ProgressMeter -    14:105617868        2.51e+06   60.0 s       23.0 s     82.6%        72.0 s    12.0 s
[2015-09-30T22:38Z] INFO  23:38:35,401 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:35,831 MuTect - [MUTECT] Processed 100004576 reads in 690 ms
[2015-09-30T22:38Z] INFO  23:38:35,860 MuTect - [MUTECT] Processed 87004466 reads in 655 ms
[2015-09-30T22:38Z] INFO  23:38:36,500 MuTect - [MUTECT] Processed 101004642 reads in 669 ms
[2015-09-30T22:38Z] INFO  23:38:36,518 MuTect - [MUTECT] Processed 88004483 reads in 657 ms
[2015-09-30T22:38Z] INFO  23:38:37,035 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:37,177 MuTect - [MUTECT] Processed 102004649 reads in 677 ms
[2015-09-30T22:38Z] INFO  23:38:37,196 MuTect - [MUTECT] Processed 89004557 reads in 679 ms
[2015-09-30T22:38Z] INFO  23:38:37,561 MuTect - [MUTECT] Processed 1000017 reads in 2561 ms
[2015-09-30T22:38Z] INFO  23:38:37,767 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:37,849 MuTect - [MUTECT] Processed 103004752 reads in 672 ms
[2015-09-30T22:38Z] INFO  23:38:37,866 MuTect - [MUTECT] Processed 90004668 reads in 670 ms
[2015-09-30T22:38Z] INFO  23:38:38,329 MuTect - [MUTECT] Processed 2000025 reads in 769 ms
[2015-09-30T22:38Z] INFO  23:38:38,488 MuTect - [MUTECT] Processed 91004744 reads in 622 ms
[2015-09-30T22:38Z] INFO  23:38:38,529 MuTect - [MUTECT] Processed 104004759 reads in 680 ms
[2015-09-30T22:38Z] INFO  23:38:39,077 MuTect - [MUTECT] Processed 3000027 reads in 748 ms
[2015-09-30T22:38Z] INFO  23:38:39,132 MuTect - [MUTECT] Processed 92004842 reads in 644 ms
[2015-09-30T22:38Z] INFO  23:38:39,193 MuTect - [MUTECT] Processed 105004787 reads in 664 ms
[2015-09-30T22:38Z] INFO  23:38:39,217 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:39,469 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:39,792 MuTect - [MUTECT] Processed 4000096 reads in 715 ms
[2015-09-30T22:38Z] INFO  23:38:39,802 MuTect - [MUTECT] Processed 93004973 reads in 670 ms
[2015-09-30T22:38Z] INFO  23:38:39,829 MuTect - [MUTECT] Processed 106004817 reads in 636 ms
[2015-09-30T22:38Z] INFO  23:38:40,049 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:40,430 MuTect - [MUTECT] Processed 94004975 reads in 628 ms
[2015-09-30T22:38Z] INFO  23:38:40,504 MuTect - [MUTECT] Processed 5000185 reads in 711 ms
[2015-09-30T22:38Z] INFO  23:38:40,506 MuTect - [MUTECT] Processed 107004881 reads in 677 ms
[2015-09-30T22:38Z] INFO  23:38:41,152 MuTect - [MUTECT] Processed 95005114 reads in 722 ms
[2015-09-30T22:38Z] INFO  23:38:41,164 MuTect - [MUTECT] Processed 108004935 reads in 658 ms
[2015-09-30T22:38Z] INFO  23:38:41,196 MuTect - [MUTECT] Processed 6000186 reads in 693 ms
[2015-09-30T22:38Z] INFO  23:38:41,396 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:41,799 MuTect - [MUTECT] Processed 109004954 reads in 635 ms
[2015-09-30T22:38Z] INFO  23:38:41,919 MuTect - [MUTECT] Processed 7000213 reads in 723 ms
[2015-09-30T22:38Z] INFO  23:38:41,927 MuTect - [MUTECT] Processed 96005175 reads in 775 ms
[2015-09-30T22:38Z] INFO  23:38:42,068 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:42,437 MuTect - [MUTECT] Processed 110005022 reads in 638 ms
[2015-09-30T22:38Z] INFO  23:38:42,496 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:42,590 MuTect - [MUTECT] Processed 8000297 reads in 671 ms
[2015-09-30T22:38Z] INFO  23:38:42,681 MuTect - [MUTECT] Processed 97005182 reads in 754 ms
[2015-09-30T22:38Z] INFO  23:38:43,116 MuTect - [MUTECT] Processed 111005038 reads in 679 ms
[2015-09-30T22:38Z] INFO  23:38:43,256 MuTect - [MUTECT] Processed 9000370 reads in 666 ms
[2015-09-30T22:38Z] INFO  23:38:43,328 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:43,772 MuTect - [MUTECT] Processed 112005050 reads in 656 ms
[2015-09-30T22:38Z] INFO  23:38:43,898 MuTect - [MUTECT] Processed 10000383 reads in 642 ms
[2015-09-30T22:38Z] INFO  23:38:43,925 MuTect - [MUTECT] Processed 98005270 reads in 1244 ms
[2015-09-30T22:38Z] INFO  23:38:44,705 MuTect - [MUTECT] Processed 113005146 reads in 933 ms
[2015-09-30T22:38Z] INFO  23:38:44,778 MuTect - [MUTECT] Processed 11000416 reads in 880 ms
[2015-09-30T22:38Z] INFO  23:38:45,007 MuTect - [MUTECT] Processed 99005324 reads in 1082 ms
[2015-09-30T22:38Z] INFO  23:38:45,109 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:45,425 MuTect - [MUTECT] Processed 114005194 reads in 720 ms
[2015-09-30T22:38Z] INFO  23:38:45,437 MuTect - [MUTECT] Processed 12000571 reads in 659 ms
[2015-09-30T22:38Z] INFO  23:38:45,578 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:46,112 MuTect - [MUTECT] Processed 115005222 reads in 687 ms
[2015-09-30T22:38Z] INFO  23:38:46,158 MuTect - [MUTECT] Processed 13000582 reads in 720 ms
[2015-09-30T22:38Z] INFO  23:38:46,203 MuTect - [MUTECT] Processed 100005331 reads in 1196 ms
[2015-09-30T22:38Z] INFO  23:38:46,823 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:46,825 MuTect - [MUTECT] Processed 14000639 reads in 668 ms
[2015-09-30T22:38Z] INFO  23:38:46,833 MuTect - [MUTECT] Processed 116005248 reads in 721 ms
[2015-09-30T22:38Z] INFO  23:38:47,022 MuTect - [MUTECT] Processed 101005434 reads in 819 ms
[2015-09-30T22:38Z] INFO  23:38:47,468 MuTect - [MUTECT] Processed 15000696 reads in 643 ms
[2015-09-30T22:38Z] INFO  23:38:47,547 MuTect - [MUTECT] Processed 117005384 reads in 714 ms
[2015-09-30T22:38Z] INFO  23:38:47,721 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:48,097 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:48,130 MuTect - [MUTECT] Processed 102005486 reads in 1108 ms
[2015-09-30T22:38Z] INFO  23:38:48,137 MuTect - [MUTECT] Processed 16000735 reads in 669 ms
[2015-09-30T22:38Z] INFO  23:38:48,255 MuTect - [MUTECT] Processed 118005422 reads in 708 ms
[2015-09-30T22:38Z] INFO  23:38:48,873 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:38Z] INFO  23:38:48,876 ProgressMeter -            done        2.99e+06   73.0 s       24.0 s    100.0%        73.0 s     0.0 s
[2015-09-30T22:38Z] INFO  23:38:48,876 ProgressMeter - Total runtime 73.53 secs, 1.23 min, 0.02 hours
[2015-09-30T22:38Z] INFO  23:38:48,884 MuTect - [MUTECT] Processed 17000743 reads in 747 ms
[2015-09-30T22:38Z] INFO  23:38:48,937 MuTect - [MUTECT] Processed 119005519 reads in 682 ms
[2015-09-30T22:38Z] INFO  23:38:48,942 MicroScheduler - 85057 reads were filtered out during the traversal out of approximately 1231463 total reads (6.91%)
[2015-09-30T22:38Z] INFO  23:38:48,943 MicroScheduler -   -> 64267 reads (5.22% of total) failing DuplicateReadFilter
[2015-09-30T22:38Z] INFO  23:38:48,943 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:38Z] INFO  23:38:48,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:38Z] INFO  23:38:48,943 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:38Z] INFO  23:38:48,943 MicroScheduler -   -> 20790 reads (1.69% of total) failing UnmappedReadFilter
[2015-09-30T22:38Z] INFO  23:38:49,073 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:49,618 MuTect - [MUTECT] Processed 18000751 reads in 734 ms
[2015-09-30T22:38Z] INFO  23:38:49,654 MuTect - [MUTECT] Processed 120005583 reads in 717 ms
[2015-09-30T22:38Z] INFO  23:38:49,953 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:38Z] bgzip syn3-14_93263525_107349540-raw-mutect.vcf
[2015-09-30T22:38Z] tabix index syn3-14_93263525_107349540-raw-mutect.vcf.gz
[2015-09-30T22:38Z] INFO  23:38:50,095 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:50,319 MuTect - [MUTECT] Processed 19000764 reads in 701 ms
[2015-09-30T22:38Z] INFO  23:38:50,355 MuTect - [MUTECT] Processed 121005658 reads in 701 ms
[2015-09-30T22:38Z] INFO  23:38:51,012 MuTect - [MUTECT] Processed 20000825 reads in 693 ms
[2015-09-30T22:38Z] INFO  23:38:51,022 MuTect - [MUTECT] Processed 122005727 reads in 667 ms
[2015-09-30T22:38Z] INFO  23:38:51,574 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:51,701 MuTect - [MUTECT] Processed 21000905 reads in 689 ms
[2015-09-30T22:38Z] INFO  23:38:51,720 MuTect - [MUTECT] Processed 123005801 reads in 698 ms
[2015-09-30T22:38Z] MuTect: MuTect
[2015-09-30T22:38Z] INFO  23:38:52,398 MuTect - [MUTECT] Processed 22000911 reads in 696 ms
[2015-09-30T22:38Z] INFO  23:38:52,421 MuTect - [MUTECT] Processed 124005809 reads in 701 ms
[2015-09-30T22:38Z] INFO  23:38:52,718 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:53,073 MuTect - [MUTECT] Processed 23000981 reads in 676 ms
[2015-09-30T22:38Z] INFO  23:38:53,111 MuTect - [MUTECT] Processed 125005908 reads in 690 ms
[2015-09-30T22:38Z] INFO  23:38:53,750 MuTect - [MUTECT] Processed 24000985 reads in 677 ms
[2015-09-30T22:38Z] INFO  23:38:53,775 MuTect - [MUTECT] Processed 126005910 reads in 664 ms
[2015-09-30T22:38Z] INFO  23:38:54,029 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:54,332 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/15/syn3-15_62148224_93170844-raw-mutect-regions.bed to be BED
[2015-09-30T22:38Z] INFO  23:38:54,387 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:38Z] INFO  23:38:54,387 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:38Z] INFO  23:38:54,387 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:38Z] INFO  23:38:54,387 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:38Z] INFO  23:38:54,391 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/15/syn3-15_62148224_93170844-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/15/tx/tmpEA8dBA/syn3-15_62148224_93170844-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:38Z] INFO  23:38:54,391 HelpFormatter - Date/Time: 2015/09/30 23:38:54
[2015-09-30T22:38Z] INFO  23:38:54,391 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:38Z] INFO  23:38:54,391 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:38Z] INFO  23:38:54,419 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:38Z] INFO  23:38:54,423 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:38Z] INFO  23:38:54,426 MuTect - [MUTECT] Processed 25001001 reads in 676 ms
[2015-09-30T22:38Z] INFO  23:38:54,440 MuTect - [MUTECT] Processed 127005951 reads in 665 ms
[2015-09-30T22:38Z] INFO  23:38:54,477 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:38Z] INFO  23:38:54,526 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:38Z] INFO  23:38:54,533 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:38Z] INFO  23:38:54,585 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T22:38Z] INFO  23:38:54,622 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:38Z] INFO  23:38:54,804 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:38Z] INFO  23:38:54,942 IntervalUtils - Processing 2371101 bp from intervals
[2015-09-30T22:38Z] INFO  23:38:54,946 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:38Z] INFO  23:38:54,946 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:38Z] INFO  23:38:54,975 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:55,097 MuTect - [MUTECT] Processed 128005952 reads in 657 ms
[2015-09-30T22:38Z] INFO  23:38:55,121 MuTect - [MUTECT] Processed 26001034 reads in 695 ms
[2015-09-30T22:38Z] INFO  23:38:55,124 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:38Z] INFO  23:38:55,300 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:38Z] INFO  23:38:55,300 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:38Z] INFO  23:38:55,300 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:38Z] INFO  23:38:55,301 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:38Z] INFO  23:38:55,719 ProgressMeter -     14:91943304        3.91e+06   90.0 s       23.0 s     93.0%        96.0 s     6.0 s
[2015-09-30T22:38Z] INFO  23:38:55,789 MuTect - [MUTECT] Processed 129005964 reads in 692 ms
[2015-09-30T22:38Z] INFO  23:38:55,808 MuTect - [MUTECT] Processed 27001041 reads in 687 ms
[2015-09-30T22:38Z] INFO  23:38:56,453 MuTect - [MUTECT] Processed 28001182 reads in 645 ms
[2015-09-30T22:38Z] INFO  23:38:56,488 MuTect - [MUTECT] Processed 130006035 reads in 699 ms
[2015-09-30T22:38Z] INFO  23:38:57,132 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:57,140 MuTect - [MUTECT] Processed 29001232 reads in 687 ms
[2015-09-30T22:38Z] INFO  23:38:57,223 MuTect - [MUTECT] Processed 131006098 reads in 735 ms
[2015-09-30T22:38Z] INFO  23:38:57,484 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:57,801 MuTect - [MUTECT] Processed 1000016 reads in 2452 ms
[2015-09-30T22:38Z] INFO  23:38:57,830 MuTect - [MUTECT] Processed 30001281 reads in 690 ms
[2015-09-30T22:38Z] INFO  23:38:57,905 MuTect - [MUTECT] Processed 132006154 reads in 682 ms
[2015-09-30T22:38Z] INFO  23:38:58,540 MuTect - [MUTECT] Processed 31001345 reads in 710 ms
[2015-09-30T22:38Z] INFO  23:38:58,616 MuTect - [MUTECT] Processed 133006174 reads in 711 ms
[2015-09-30T22:38Z] INFO  23:38:58,939 MuTect - [MUTECT] Processed 2000041 reads in 1139 ms
[2015-09-30T22:38Z] INFO  23:38:59,248 MuTect - [MUTECT] Processed 32001378 reads in 708 ms
[2015-09-30T22:38Z] INFO  23:38:59,348 MuTect - [MUTECT] Processed 134006188 reads in 732 ms
[2015-09-30T22:38Z] INFO  23:38:59,681 MuTect - [MUTECT] Processed 3000051 reads in 742 ms
[2015-09-30T22:38Z] INFO  23:38:59,729 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:59,897 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:38Z] INFO  23:38:59,908 MuTect - [MUTECT] Processed 33001448 reads in 660 ms
[2015-09-30T22:39Z] INFO  23:39:00,010 MuTect - [MUTECT] Processed 135006257 reads in 662 ms
[2015-09-30T22:39Z] INFO  23:39:00,033 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:00,412 MuTect - [MUTECT] Processed 4000143 reads in 730 ms
[2015-09-30T22:39Z] INFO  23:39:00,569 MuTect - [MUTECT] Processed 34001528 reads in 661 ms
[2015-09-30T22:39Z] INFO  23:39:00,664 MuTect - [MUTECT] Processed 136006260 reads in 654 ms
[2015-09-30T22:39Z] INFO  23:39:01,164 MuTect - [MUTECT] Processed 5000154 reads in 753 ms
[2015-09-30T22:39Z] INFO  23:39:01,239 MuTect - [MUTECT] Processed 35001530 reads in 670 ms
[2015-09-30T22:39Z] INFO  23:39:01,384 MuTect - [MUTECT] Processed 137006295 reads in 720 ms
[2015-09-30T22:39Z] INFO  23:39:01,804 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:39Z] INFO  23:39:01,807 ProgressMeter -            done        4.20e+06   96.0 s       22.0 s    100.0%        96.0 s     0.0 s
[2015-09-30T22:39Z] INFO  23:39:01,808 ProgressMeter - Total runtime 96.09 secs, 1.60 min, 0.03 hours
[2015-09-30T22:39Z] INFO  23:39:01,874 MicroScheduler - 103323 reads were filtered out during the traversal out of approximately 1645925 total reads (6.28%)
[2015-09-30T22:39Z] INFO  23:39:01,874 MicroScheduler -   -> 76781 reads (4.66% of total) failing DuplicateReadFilter
[2015-09-30T22:39Z] INFO  23:39:01,874 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:39Z] INFO  23:39:01,875 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:39Z] INFO  23:39:01,875 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:39Z] INFO  23:39:01,875 MicroScheduler -   -> 26542 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:39Z] INFO  23:39:01,880 MuTect - [MUTECT] Processed 36001594 reads in 641 ms
[2015-09-30T22:39Z] INFO  23:39:01,890 MuTect - [MUTECT] Processed 6000244 reads in 726 ms
[2015-09-30T22:39Z] INFO  23:39:02,183 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:02,470 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:02,547 MuTect - [MUTECT] Processed 37001615 reads in 666 ms
[2015-09-30T22:39Z] INFO  23:39:02,600 MuTect - [MUTECT] Processed 7000298 reads in 710 ms
[2015-09-30T22:39Z] INFO  23:39:02,892 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:39Z] bgzip syn3-14_62186823_93262365-raw-mutect.vcf
[2015-09-30T22:39Z] tabix index syn3-14_62186823_93262365-raw-mutect.vcf.gz
[2015-09-30T22:39Z] INFO  23:39:03,209 MuTect - [MUTECT] Processed 38001620 reads in 663 ms
[2015-09-30T22:39Z] INFO  23:39:03,353 MuTect - [MUTECT] Processed 8000339 reads in 753 ms
[2015-09-30T22:39Z] INFO  23:39:03,889 MuTect - [MUTECT] Processed 39001662 reads in 680 ms
[2015-09-30T22:39Z] INFO  23:39:04,075 MuTect - [MUTECT] Processed 9000362 reads in 722 ms
[2015-09-30T22:39Z] INFO  23:39:04,562 MuTect - [MUTECT] Processed 40001723 reads in 673 ms
[2015-09-30T22:39Z] INFO  23:39:04,671 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:04,805 MuTect - [MUTECT] Processed 10000444 reads in 730 ms
[2015-09-30T22:39Z] INFO  23:39:04,954 ProgressMeter -     15:40322619        1.42e+06   30.0 s       21.0 s     21.3%         2.4 m   111.0 s
[2015-09-30T22:39Z] INFO  23:39:05,054 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:05,240 MuTect - [MUTECT] Processed 41001747 reads in 678 ms
[2015-09-30T22:39Z] MuTect: MuTect
[2015-09-30T22:39Z] INFO  23:39:05,494 MuTect - [MUTECT] Processed 11000512 reads in 689 ms
[2015-09-30T22:39Z] INFO  23:39:05,885 MuTect - [MUTECT] Processed 42001750 reads in 645 ms
[2015-09-30T22:39Z] INFO  23:39:06,233 MuTect - [MUTECT] Processed 12000586 reads in 738 ms
[2015-09-30T22:39Z] INFO  23:39:06,543 MuTect - [MUTECT] Processed 43001825 reads in 658 ms
[2015-09-30T22:39Z] INFO  23:39:06,907 MuTect - [MUTECT] Processed 13000685 reads in 675 ms
[2015-09-30T22:39Z] INFO  23:39:06,999 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:07,174 MuTect - [MUTECT] Processed 44001853 reads in 631 ms
[2015-09-30T22:39Z] INFO  23:39:07,232 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/15/syn3-15_93173163_102531392-raw-mutect-regions.bed to be BED
[2015-09-30T22:39Z] INFO  23:39:07,286 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:39Z] INFO  23:39:07,286 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:39Z] INFO  23:39:07,286 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:39Z] INFO  23:39:07,286 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:39Z] INFO  23:39:07,290 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/15/syn3-15_93173163_102531392-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/15/tx/tmp1OE9Rw/syn3-15_93173163_102531392-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:39Z] INFO  23:39:07,290 HelpFormatter - Date/Time: 2015/09/30 23:39:07
[2015-09-30T22:39Z] INFO  23:39:07,290 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:39Z] INFO  23:39:07,290 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:39Z] INFO  23:39:07,318 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:39Z] INFO  23:39:07,322 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:39Z] INFO  23:39:07,378 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:39Z] INFO  23:39:07,425 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:39Z] INFO  23:39:07,432 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:39Z] INFO  23:39:07,454 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:39Z] INFO  23:39:07,465 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:39Z] INFO  23:39:07,560 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:07,615 MuTect - [MUTECT] Processed 14000770 reads in 708 ms
[2015-09-30T22:39Z] INFO  23:39:07,634 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:39Z] INFO  23:39:07,696 IntervalUtils - Processing 301747 bp from intervals
[2015-09-30T22:39Z] INFO  23:39:07,700 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:39Z] INFO  23:39:07,700 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:39Z] INFO  23:39:07,751 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:39Z] INFO  23:39:07,840 MuTect - [MUTECT] Processed 45001923 reads in 666 ms
[2015-09-30T22:39Z] INFO  23:39:07,998 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:39Z] INFO  23:39:07,998 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:39Z] INFO  23:39:07,999 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:39Z] INFO  23:39:08,000 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:39Z] INFO  23:39:08,318 MuTect - [MUTECT] Processed 15000788 reads in 703 ms
[2015-09-30T22:39Z] INFO  23:39:08,539 MuTect - [MUTECT] Processed 46001938 reads in 699 ms
[2015-09-30T22:39Z] INFO  23:39:09,015 MuTect - [MUTECT] Processed 16000851 reads in 697 ms
[2015-09-30T22:39Z] INFO  23:39:09,210 MuTect - [MUTECT] Processed 47001950 reads in 671 ms
[2015-09-30T22:39Z] INFO  23:39:09,292 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:09,738 MuTect - [MUTECT] Processed 17000936 reads in 723 ms
[2015-09-30T22:39Z] INFO  23:39:09,857 MuTect - [MUTECT] Processed 48001979 reads in 647 ms
[2015-09-30T22:39Z] INFO  23:39:10,273 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:10,379 MuTect - [MUTECT] Processed 1000066 reads in 2335 ms
[2015-09-30T22:39Z] INFO  23:39:10,413 MuTect - [MUTECT] Processed 18000997 reads in 675 ms
[2015-09-30T22:39Z] INFO  23:39:10,542 MuTect - [MUTECT] Processed 49002000 reads in 685 ms
[2015-09-30T22:39Z] INFO  23:39:11,070 MuTect - [MUTECT] Processed 19001040 reads in 657 ms
[2015-09-30T22:39Z] INFO  23:39:11,114 MuTect - [MUTECT] Processed 2000101 reads in 735 ms
[2015-09-30T22:39Z] INFO  23:39:11,177 MuTect - [MUTECT] Processed 50002078 reads in 635 ms
[2015-09-30T22:39Z] INFO  23:39:11,477 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:11,760 MuTect - [MUTECT] Processed 20001123 reads in 690 ms
[2015-09-30T22:39Z] INFO  23:39:11,864 MuTect - [MUTECT] Processed 51002084 reads in 687 ms
[2015-09-30T22:39Z] INFO  23:39:11,932 MuTect - [MUTECT] Processed 3000108 reads in 817 ms
[2015-09-30T22:39Z] INFO  23:39:12,424 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:12,434 MuTect - [MUTECT] Processed 21001195 reads in 674 ms
[2015-09-30T22:39Z] INFO  23:39:12,556 MuTect - [MUTECT] Processed 52002138 reads in 692 ms
[2015-09-30T22:39Z] INFO  23:39:12,736 MuTect - [MUTECT] Processed 4000114 reads in 805 ms
[2015-09-30T22:39Z] INFO  23:39:12,755 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:13,077 MuTect - [MUTECT] Processed 22001281 reads in 643 ms
[2015-09-30T22:39Z] INFO  23:39:13,213 MuTect - [MUTECT] Processed 53002196 reads in 657 ms
[2015-09-30T22:39Z] INFO  23:39:13,522 MuTect - [MUTECT] Processed 5000116 reads in 786 ms
[2015-09-30T22:39Z] INFO  23:39:13,731 MuTect - [MUTECT] Processed 23001290 reads in 654 ms
[2015-09-30T22:39Z] INFO  23:39:13,815 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:13,864 MuTect - [MUTECT] Processed 54002238 reads in 651 ms
[2015-09-30T22:39Z] INFO  23:39:14,227 MuTect - [MUTECT] Processed 6000133 reads in 705 ms
[2015-09-30T22:39Z] INFO  23:39:14,415 MuTect - [MUTECT] Processed 24001311 reads in 684 ms
[2015-09-30T22:39Z] INFO  23:39:14,506 MuTect - [MUTECT] Processed 55002323 reads in 642 ms
[2015-09-30T22:39Z] INFO  23:39:15,009 MuTect - [MUTECT] Processed 7000142 reads in 782 ms
[2015-09-30T22:39Z] INFO  23:39:15,029 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:15,078 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:15,132 MuTect - [MUTECT] Processed 25001365 reads in 717 ms
[2015-09-30T22:39Z] INFO  23:39:15,186 MuTect - [MUTECT] Processed 56002387 reads in 680 ms
[2015-09-30T22:39Z] INFO  23:39:15,799 MuTect - [MUTECT] Processed 8000243 reads in 790 ms
[2015-09-30T22:39Z] INFO  23:39:15,867 MuTect - [MUTECT] Processed 26001387 reads in 735 ms
[2015-09-30T22:39Z] INFO  23:39:15,866 MuTect - [MUTECT] Processed 57002475 reads in 680 ms
[2015-09-30T22:39Z] INFO  23:39:16,135 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:16,507 MuTect - [MUTECT] Processed 58002509 reads in 641 ms
[2015-09-30T22:39Z] INFO  23:39:16,547 MuTect - [MUTECT] Processed 9000276 reads in 748 ms
[2015-09-30T22:39Z] INFO  23:39:16,561 MuTect - [MUTECT] Processed 27001407 reads in 694 ms
[2015-09-30T22:39Z] INFO  23:39:17,153 MuTect - [MUTECT] Processed 59002550 reads in 646 ms
[2015-09-30T22:39Z] INFO  23:39:17,204 MuTect - [MUTECT] Processed 28001454 reads in 643 ms
[2015-09-30T22:39Z] INFO  23:39:17,208 MuTect - [MUTECT] Processed 10000281 reads in 661 ms
[2015-09-30T22:39Z] INFO  23:39:17,307 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:17,599 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:17,817 MuTect - [MUTECT] Processed 60002565 reads in 664 ms
[2015-09-30T22:39Z] INFO  23:39:17,862 MuTect - [MUTECT] Processed 29001539 reads in 658 ms
[2015-09-30T22:39Z] INFO  23:39:17,883 MuTect - [MUTECT] Processed 11000302 reads in 675 ms
[2015-09-30T22:39Z] INFO  23:39:18,386 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:18,503 MuTect - [MUTECT] Processed 30001560 reads in 641 ms
[2015-09-30T22:39Z] INFO  23:39:18,513 MuTect - [MUTECT] Processed 61002598 reads in 696 ms
[2015-09-30T22:39Z] INFO  23:39:18,880 MuTect - [MUTECT] Processed 12000304 reads in 997 ms
[2015-09-30T22:39Z] INFO  23:39:19,187 MuTect - [MUTECT] Processed 62002674 reads in 674 ms
[2015-09-30T22:39Z] INFO  23:39:19,192 MuTect - [MUTECT] Processed 31001582 reads in 689 ms
[2015-09-30T22:39Z] INFO  23:39:19,466 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:19,586 MuTect - [MUTECT] Processed 13000384 reads in 706 ms
[2015-09-30T22:39Z] INFO  23:39:19,827 MuTect - [MUTECT] Processed 63002709 reads in 640 ms
[2015-09-30T22:39Z] INFO  23:39:19,853 MuTect - [MUTECT] Processed 32001687 reads in 661 ms
[2015-09-30T22:39Z] INFO  23:39:20,313 MuTect - [MUTECT] Processed 14000429 reads in 727 ms
[2015-09-30T22:39Z] INFO  23:39:20,373 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:20,445 MuTect - [MUTECT] Processed 64002753 reads in 618 ms
[2015-09-30T22:39Z] INFO  23:39:20,507 MuTect - [MUTECT] Processed 33001736 reads in 654 ms
[2015-09-30T22:39Z] INFO  23:39:20,688 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:21,027 MuTect - [MUTECT] Processed 15000546 reads in 714 ms
[2015-09-30T22:39Z] INFO  23:39:21,068 MuTect - [MUTECT] Processed 65002846 reads in 622 ms
[2015-09-30T22:39Z] INFO  23:39:21,209 MuTect - [MUTECT] Processed 34001807 reads in 702 ms
[2015-09-30T22:39Z] INFO  23:39:21,691 MuTect - [MUTECT] Processed 66002879 reads in 624 ms
[2015-09-30T22:39Z] INFO  23:39:21,756 MuTect - [MUTECT] Processed 16000595 reads in 729 ms
[2015-09-30T22:39Z] INFO  23:39:21,898 MuTect - [MUTECT] Processed 35001824 reads in 689 ms
[2015-09-30T22:39Z] INFO  23:39:21,920 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:22,333 MuTect - [MUTECT] Processed 67002896 reads in 642 ms
[2015-09-30T22:39Z] INFO  23:39:22,428 MuTect - [MUTECT] Processed 17000712 reads in 672 ms
[2015-09-30T22:39Z] INFO  23:39:22,567 MuTect - [MUTECT] Processed 36001855 reads in 669 ms
[2015-09-30T22:39Z] INFO  23:39:22,647 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:22,737 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:22,962 MuTect - [MUTECT] Processed 68002927 reads in 629 ms
[2015-09-30T22:39Z] INFO  23:39:23,102 MuTect - [MUTECT] Processed 18000715 reads in 673 ms
[2015-09-30T22:39Z] INFO  23:39:23,214 MuTect - [MUTECT] Processed 37001868 reads in 647 ms
[2015-09-30T22:39Z] INFO  23:39:23,595 MuTect - [MUTECT] Processed 69003008 reads in 633 ms
[2015-09-30T22:39Z] INFO  23:39:23,766 MuTect - [MUTECT] Processed 19000786 reads in 665 ms
[2015-09-30T22:39Z] INFO  23:39:23,879 MuTect - [MUTECT] Processed 38001887 reads in 665 ms
[2015-09-30T22:39Z] INFO  23:39:24,232 MuTect - [MUTECT] Processed 70003050 reads in 637 ms
[2015-09-30T22:39Z] INFO  23:39:24,340 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:24,461 MuTect - [MUTECT] Processed 20000812 reads in 695 ms
[2015-09-30T22:39Z] INFO  23:39:24,515 MuTect - [MUTECT] Processed 39001945 reads in 636 ms
[2015-09-30T22:39Z] INFO  23:39:24,850 MuTect - [MUTECT] Processed 71003068 reads in 618 ms
[2015-09-30T22:39Z] INFO  23:39:24,911 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:24,959 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:25,171 MuTect - [MUTECT] Processed 21000854 reads in 710 ms
[2015-09-30T22:39Z] INFO  23:39:25,185 MuTect - [MUTECT] Processed 40001950 reads in 670 ms
[2015-09-30T22:39Z] INFO  23:39:25,303 ProgressMeter -     15:66420837        1.48e+06   30.0 s       20.0 s     19.7%         2.5 m     2.0 m
[2015-09-30T22:39Z] INFO  23:39:25,505 MuTect - [MUTECT] Processed 72003166 reads in 655 ms
[2015-09-30T22:39Z] INFO  23:39:25,892 MuTect - [MUTECT] Processed 41001971 reads in 707 ms
[2015-09-30T22:39Z] INFO  23:39:25,897 MuTect - [MUTECT] Processed 22000954 reads in 726 ms
[2015-09-30T22:39Z] INFO  23:39:26,186 MuTect - [MUTECT] Processed 73003179 reads in 681 ms
[2015-09-30T22:39Z] INFO  23:39:26,582 MuTect - [MUTECT] Processed 23001014 reads in 685 ms
[2015-09-30T22:39Z] INFO  23:39:26,607 MuTect - [MUTECT] Processed 42002032 reads in 715 ms
[2015-09-30T22:39Z] INFO  23:39:26,691 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:26,839 MuTect - [MUTECT] Processed 74003299 reads in 653 ms
[2015-09-30T22:39Z] INFO  23:39:27,086 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:27,271 MuTect - [MUTECT] Processed 43002066 reads in 664 ms
[2015-09-30T22:39Z] INFO  23:39:27,293 MuTect - [MUTECT] Processed 24001025 reads in 711 ms
[2015-09-30T22:39Z] INFO  23:39:27,486 MuTect - [MUTECT] Processed 75003400 reads in 647 ms
[2015-09-30T22:39Z] INFO  23:39:27,493 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:27,937 MuTect - [MUTECT] Processed 44002109 reads in 666 ms
[2015-09-30T22:39Z] INFO  23:39:28,018 MuTect - [MUTECT] Processed 25001103 reads in 725 ms
[2015-09-30T22:39Z] INFO  23:39:28,100 MuTect - [MUTECT] Processed 76003432 reads in 614 ms
[2015-09-30T22:39Z] INFO  23:39:28,599 MuTect - [MUTECT] Processed 45002150 reads in 662 ms
[2015-09-30T22:39Z] INFO  23:39:28,720 MuTect - [MUTECT] Processed 77003537 reads in 620 ms
[2015-09-30T22:39Z] INFO  23:39:28,924 MuTect - [MUTECT] Processed 26001162 reads in 906 ms
[2015-09-30T22:39Z] INFO  23:39:28,966 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:29,120 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:29,262 MuTect - [MUTECT] Processed 46002169 reads in 663 ms
[2015-09-30T22:39Z] INFO  23:39:29,354 MuTect - [MUTECT] Processed 78003566 reads in 634 ms
[2015-09-30T22:39Z] INFO  23:39:29,551 MuTect - [MUTECT] Processed 27001193 reads in 627 ms
[2015-09-30T22:39Z] INFO  23:39:29,921 MuTect - [MUTECT] Processed 47002225 reads in 659 ms
[2015-09-30T22:39Z] INFO  23:39:29,992 MuTect - [MUTECT] Processed 79003578 reads in 638 ms
[2015-09-30T22:39Z] INFO  23:39:30,041 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:30,254 MuTect - [MUTECT] Processed 28001236 reads in 703 ms
[2015-09-30T22:39Z] INFO  23:39:30,608 MuTect - [MUTECT] Processed 48002241 reads in 687 ms
[2015-09-30T22:39Z] INFO  23:39:30,670 MuTect - [MUTECT] Processed 80003626 reads in 678 ms
[2015-09-30T22:39Z] INFO  23:39:30,766 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:39Z] INFO  23:39:30,769 ProgressMeter -            done        7.55e+05   22.0 s       30.0 s    100.0%        22.0 s     0.0 s
[2015-09-30T22:39Z] INFO  23:39:30,769 ProgressMeter - Total runtime 22.77 secs, 0.38 min, 0.01 hours
[2015-09-30T22:39Z] INFO  23:39:30,834 MicroScheduler - 21961 reads were filtered out during the traversal out of approximately 344170 total reads (6.38%)
[2015-09-30T22:39Z] INFO  23:39:30,834 MicroScheduler -   -> 16625 reads (4.83% of total) failing DuplicateReadFilter
[2015-09-30T22:39Z] INFO  23:39:30,834 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:39Z] INFO  23:39:30,834 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:39Z] INFO  23:39:30,834 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:39Z] INFO  23:39:30,834 MicroScheduler -   -> 5336 reads (1.55% of total) failing UnmappedReadFilter
[2015-09-30T22:39Z] INFO  23:39:31,311 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:31,314 MuTect - [MUTECT] Processed 49002263 reads in 706 ms
[2015-09-30T22:39Z] INFO  23:39:31,326 MuTect - [MUTECT] Processed 81003671 reads in 656 ms
[2015-09-30T22:39Z] INFO  23:39:31,526 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:31,897 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:39Z] bgzip syn3-15_93173163_102531392-raw-mutect.vcf
[2015-09-30T22:39Z] INFO  23:39:31,976 MuTect - [MUTECT] Processed 82003684 reads in 650 ms
[2015-09-30T22:39Z] INFO  23:39:31,992 MuTect - [MUTECT] Processed 50002370 reads in 678 ms
[2015-09-30T22:39Z] tabix index syn3-15_93173163_102531392-raw-mutect.vcf.gz
[2015-09-30T22:39Z] INFO  23:39:32,609 MuTect - [MUTECT] Processed 83003751 reads in 633 ms
[2015-09-30T22:39Z] INFO  23:39:32,680 MuTect - [MUTECT] Processed 51002456 reads in 688 ms
[2015-09-30T22:39Z] INFO  23:39:33,270 MuTect - [MUTECT] Processed 84003783 reads in 661 ms
[2015-09-30T22:39Z] INFO  23:39:33,324 MuTect - [MUTECT] Processed 52002545 reads in 644 ms
[2015-09-30T22:39Z] INFO  23:39:33,572 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:33,658 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:34,005 MuTect - [MUTECT] Processed 53002569 reads in 681 ms
[2015-09-30T22:39Z] INFO  23:39:34,011 MuTect - [MUTECT] Processed 85003804 reads in 741 ms
[2015-09-30T22:39Z] MuTect: MuTect
[2015-09-30T22:39Z] INFO  23:39:34,680 MuTect - [MUTECT] Processed 54002617 reads in 675 ms
[2015-09-30T22:39Z] INFO  23:39:34,681 MuTect - [MUTECT] Processed 86003823 reads in 670 ms
[2015-09-30T22:39Z] INFO  23:39:34,955 ProgressMeter -     15:42681875        2.86e+06   60.0 s       20.0 s     41.1%         2.4 m    85.0 s
[2015-09-30T22:39Z] INFO  23:39:35,334 MuTect - [MUTECT] Processed 87003870 reads in 653 ms
[2015-09-30T22:39Z] INFO  23:39:35,378 MuTect - [MUTECT] Processed 55002680 reads in 698 ms
[2015-09-30T22:39Z] INFO  23:39:35,888 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:35,957 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:35,967 MuTect - [MUTECT] Processed 88003943 reads in 633 ms
[2015-09-30T22:39Z] INFO  23:39:36,035 MuTect - [MUTECT] Processed 56002760 reads in 657 ms
[2015-09-30T22:39Z] INFO  23:39:36,606 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/16/syn3-16_0_31021934-raw-mutect-regions.bed to be BED
[2015-09-30T22:39Z] INFO  23:39:36,640 MuTect - [MUTECT] Processed 89004011 reads in 673 ms
[2015-09-30T22:39Z] INFO  23:39:36,662 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:39Z] INFO  23:39:36,662 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:39Z] INFO  23:39:36,662 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:39Z] INFO  23:39:36,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:39Z] INFO  23:39:36,666 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/16/syn3-16_0_31021934-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/16/tx/tmpy5arzY/syn3-16_0_31021934-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:39Z] INFO  23:39:36,666 HelpFormatter - Date/Time: 2015/09/30 23:39:36
[2015-09-30T22:39Z] INFO  23:39:36,666 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:39Z] INFO  23:39:36,666 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:39Z] INFO  23:39:36,694 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:39Z] INFO  23:39:36,699 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:39Z] INFO  23:39:36,706 MuTect - [MUTECT] Processed 57002833 reads in 671 ms
[2015-09-30T22:39Z] INFO  23:39:36,749 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:39Z] INFO  23:39:36,798 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:39Z] INFO  23:39:36,805 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:39Z] INFO  23:39:36,853 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T22:39Z] INFO  23:39:36,886 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:39Z] INFO  23:39:37,065 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:39Z] INFO  23:39:37,317 MuTect - [MUTECT] Processed 90004023 reads in 677 ms
[2015-09-30T22:39Z] INFO  23:39:37,324 IntervalUtils - Processing 3098080 bp from intervals
[2015-09-30T22:39Z] INFO  23:39:37,328 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:39Z] INFO  23:39:37,328 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:39Z] INFO  23:39:37,381 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:39Z] INFO  23:39:37,409 MuTect - [MUTECT] Processed 58002940 reads in 703 ms
[2015-09-30T22:39Z] INFO  23:39:37,558 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:39Z] INFO  23:39:37,558 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:39Z] INFO  23:39:37,559 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:39Z] INFO  23:39:37,560 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:39Z] INFO  23:39:37,981 MuTect - [MUTECT] Processed 91004090 reads in 664 ms
[2015-09-30T22:39Z] INFO  23:39:38,050 MuTect - [MUTECT] Processed 59002998 reads in 641 ms
[2015-09-30T22:39Z] INFO  23:39:38,257 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:38,293 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:38,611 MuTect - [MUTECT] Processed 92004186 reads in 630 ms
[2015-09-30T22:39Z] INFO  23:39:38,706 MuTect - [MUTECT] Processed 60003062 reads in 656 ms
[2015-09-30T22:39Z] INFO  23:39:39,255 MuTect - [MUTECT] Processed 93004282 reads in 644 ms
[2015-09-30T22:39Z] INFO  23:39:39,340 MuTect - [MUTECT] Processed 61003079 reads in 634 ms
[2015-09-30T22:39Z] INFO  23:39:39,853 MuTect - [MUTECT] Processed 1000118 reads in 2249 ms
[2015-09-30T22:39Z] INFO  23:39:39,905 MuTect - [MUTECT] Processed 94004393 reads in 650 ms
[2015-09-30T22:39Z] INFO  23:39:40,004 MuTect - [MUTECT] Processed 62003114 reads in 664 ms
[2015-09-30T22:39Z] INFO  23:39:40,565 MuTect - [MUTECT] Processed 95004417 reads in 660 ms
[2015-09-30T22:39Z] INFO  23:39:40,576 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:40,591 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:40,661 MuTect - [MUTECT] Processed 63003160 reads in 657 ms
[2015-09-30T22:39Z] INFO  23:39:40,715 MuTect - [MUTECT] Processed 2000208 reads in 862 ms
[2015-09-30T22:39Z] INFO  23:39:41,268 MuTect - [MUTECT] Processed 96004423 reads in 703 ms
[2015-09-30T22:39Z] INFO  23:39:41,340 MuTect - [MUTECT] Processed 64003168 reads in 679 ms
[2015-09-30T22:39Z] INFO  23:39:41,407 MuTect - [MUTECT] Processed 3000329 reads in 692 ms
[2015-09-30T22:39Z] INFO  23:39:41,767 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:41,973 MuTect - [MUTECT] Processed 97004458 reads in 705 ms
[2015-09-30T22:39Z] INFO  23:39:42,032 MuTect - [MUTECT] Processed 65003281 reads in 692 ms
[2015-09-30T22:39Z] INFO  23:39:42,062 MuTect - [MUTECT] Processed 4000337 reads in 655 ms
[2015-09-30T22:39Z] INFO  23:39:42,642 MuTect - [MUTECT] Processed 98004496 reads in 669 ms
[2015-09-30T22:39Z] INFO  23:39:42,669 MuTect - [MUTECT] Processed 66003320 reads in 637 ms
[2015-09-30T22:39Z] INFO  23:39:42,831 MuTect - [MUTECT] Processed 5000424 reads in 769 ms
[2015-09-30T22:39Z] INFO  23:39:43,004 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:43,188 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:43,307 MuTect - [MUTECT] Processed 99004594 reads in 665 ms
[2015-09-30T22:39Z] INFO  23:39:43,345 MuTect - [MUTECT] Processed 67003320 reads in 676 ms
[2015-09-30T22:39Z] INFO  23:39:43,527 MuTect - [MUTECT] Processed 6000442 reads in 696 ms
[2015-09-30T22:39Z] INFO  23:39:43,978 MuTect - [MUTECT] Processed 100004617 reads in 671 ms
[2015-09-30T22:39Z] INFO  23:39:43,981 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:44,000 MuTect - [MUTECT] Processed 68003390 reads in 655 ms
[2015-09-30T22:39Z] INFO  23:39:44,164 MuTect - [MUTECT] Processed 7000574 reads in 637 ms
[2015-09-30T22:39Z] INFO  23:39:44,646 MuTect - [MUTECT] Processed 101004640 reads in 668 ms
[2015-09-30T22:39Z] INFO  23:39:44,660 MuTect - [MUTECT] Processed 69003403 reads in 660 ms
[2015-09-30T22:39Z] INFO  23:39:44,832 MuTect - [MUTECT] Processed 8000644 reads in 668 ms
[2015-09-30T22:39Z] INFO  23:39:45,298 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:45,333 MuTect - [MUTECT] Processed 70003415 reads in 673 ms
[2015-09-30T22:39Z] INFO  23:39:45,342 MuTect - [MUTECT] Processed 102004684 reads in 696 ms
[2015-09-30T22:39Z] INFO  23:39:45,539 MuTect - [MUTECT] Processed 9000652 reads in 707 ms
[2015-09-30T22:39Z] INFO  23:39:45,547 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:46,011 MuTect - [MUTECT] Processed 71003419 reads in 677 ms
[2015-09-30T22:39Z] INFO  23:39:46,032 MuTect - [MUTECT] Processed 103004760 reads in 690 ms
[2015-09-30T22:39Z] INFO  23:39:46,267 MuTect - [MUTECT] Processed 10000773 reads in 728 ms
[2015-09-30T22:39Z] INFO  23:39:46,283 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:46,701 MuTect - [MUTECT] Processed 72003437 reads in 691 ms
[2015-09-30T22:39Z] INFO  23:39:46,706 MuTect - [MUTECT] Processed 104004830 reads in 674 ms
[2015-09-30T22:39Z] INFO  23:39:46,979 MuTect - [MUTECT] Processed 11000881 reads in 712 ms
[2015-09-30T22:39Z] INFO  23:39:47,386 MuTect - [MUTECT] Processed 73003474 reads in 685 ms
[2015-09-30T22:39Z] INFO  23:39:47,410 MuTect - [MUTECT] Processed 105004869 reads in 704 ms
[2015-09-30T22:39Z] INFO  23:39:47,649 MuTect - [MUTECT] Processed 12000934 reads in 670 ms
[2015-09-30T22:39Z] INFO  23:39:47,737 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:48,010 MuTect - [MUTECT] Processed 74003524 reads in 623 ms
[2015-09-30T22:39Z] INFO  23:39:48,043 MuTect - [MUTECT] Processed 106004912 reads in 633 ms
[2015-09-30T22:39Z] INFO  23:39:48,303 MuTect - [MUTECT] Processed 13001057 reads in 654 ms
[2015-09-30T22:39Z] INFO  23:39:48,405 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:48,479 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:48,647 MuTect - [MUTECT] Processed 107005056 reads in 604 ms
[2015-09-30T22:39Z] INFO  23:39:48,648 MuTect - [MUTECT] Processed 75003691 reads in 639 ms
[2015-09-30T22:39Z] INFO  23:39:49,062 MuTect - [MUTECT] Processed 14001087 reads in 759 ms
[2015-09-30T22:39Z] INFO  23:39:49,199 MuTect - [MUTECT] Processed 108005078 reads in 552 ms
[2015-09-30T22:39Z] INFO  23:39:49,307 MuTect - [MUTECT] Processed 76003732 reads in 659 ms
[2015-09-30T22:39Z] INFO  23:39:49,687 MuTect - [MUTECT] Processed 15001122 reads in 625 ms
[2015-09-30T22:39Z] INFO  23:39:49,786 MuTect - [MUTECT] Processed 109005127 reads in 587 ms
[2015-09-30T22:39Z] INFO  23:39:49,950 MuTect - [MUTECT] Processed 77003792 reads in 643 ms
[2015-09-30T22:39Z] INFO  23:39:50,337 MuTect - [MUTECT] Processed 16001259 reads in 650 ms
[2015-09-30T22:39Z] INFO  23:39:50,389 MuTect - [MUTECT] Processed 110005199 reads in 603 ms
[2015-09-30T22:39Z] INFO  23:39:50,587 MuTect - [MUTECT] Processed 78003829 reads in 637 ms
[2015-09-30T22:39Z] INFO  23:39:50,607 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:50,877 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:50,971 MuTect - [MUTECT] Processed 17001280 reads in 634 ms
[2015-09-30T22:39Z] INFO  23:39:51,004 MuTect - [MUTECT] Processed 111005225 reads in 615 ms
[2015-09-30T22:39Z] INFO  23:39:51,127 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:51,226 MuTect - [MUTECT] Processed 79003866 reads in 639 ms
[2015-09-30T22:39Z] INFO  23:39:51,578 MuTect - [MUTECT] Processed 112005235 reads in 574 ms
[2015-09-30T22:39Z] INFO  23:39:51,625 MuTect - [MUTECT] Processed 18001401 reads in 654 ms
[2015-09-30T22:39Z] INFO  23:39:51,863 MuTect - [MUTECT] Processed 80004011 reads in 637 ms
[2015-09-30T22:39Z] INFO  23:39:52,155 MuTect - [MUTECT] Processed 113005308 reads in 577 ms
[2015-09-30T22:39Z] INFO  23:39:52,291 MuTect - [MUTECT] Processed 19001503 reads in 666 ms
[2015-09-30T22:39Z] INFO  23:39:52,493 MuTect - [MUTECT] Processed 81004060 reads in 630 ms
[2015-09-30T22:39Z] INFO  23:39:52,783 MuTect - [MUTECT] Processed 114005380 reads in 628 ms
[2015-09-30T22:39Z] INFO  23:39:52,882 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:53,013 MuTect - [MUTECT] Processed 20001596 reads in 722 ms
[2015-09-30T22:39Z] INFO  23:39:53,090 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:53,158 MuTect - [MUTECT] Processed 82004188 reads in 665 ms
[2015-09-30T22:39Z] INFO  23:39:53,398 MuTect - [MUTECT] Processed 115005425 reads in 615 ms
[2015-09-30T22:39Z] INFO  23:39:53,632 MuTect - [MUTECT] Processed 21001654 reads in 619 ms
[2015-09-30T22:39Z] INFO  23:39:53,807 MuTect - [MUTECT] Processed 83004235 reads in 649 ms
[2015-09-30T22:39Z] INFO  23:39:54,080 MuTect - [MUTECT] Processed 116005433 reads in 682 ms
[2015-09-30T22:39Z] INFO  23:39:54,232 MuTect - [MUTECT] Processed 22001658 reads in 600 ms
[2015-09-30T22:39Z] INFO  23:39:54,443 MuTect - [MUTECT] Processed 84004355 reads in 636 ms
[2015-09-30T22:39Z] INFO  23:39:54,727 MuTect - [MUTECT] Processed 117005506 reads in 647 ms
[2015-09-30T22:39Z] INFO  23:39:54,778 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:54,845 MuTect - [MUTECT] Processed 23001722 reads in 613 ms
[2015-09-30T22:39Z] INFO  23:39:54,855 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:55,172 MuTect - [MUTECT] Processed 85004576 reads in 729 ms
[2015-09-30T22:39Z] INFO  23:39:55,303 ProgressMeter -     15:74366915        2.84e+06   60.0 s       21.0 s     40.0%         2.5 m    89.0 s
[2015-09-30T22:39Z] INFO  23:39:55,395 MuTect - [MUTECT] Processed 118005539 reads in 668 ms
[2015-09-30T22:39Z] INFO  23:39:55,481 MuTect - [MUTECT] Processed 24001813 reads in 636 ms
[2015-09-30T22:39Z] INFO  23:39:55,789 MuTect - [MUTECT] Processed 86004622 reads in 617 ms
[2015-09-30T22:39Z] INFO  23:39:56,041 MuTect - [MUTECT] Processed 119005607 reads in 646 ms
[2015-09-30T22:39Z] INFO  23:39:56,099 MuTect - [MUTECT] Processed 25001854 reads in 617 ms
[2015-09-30T22:39Z] INFO  23:39:56,199 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:56,407 MuTect - [MUTECT] Processed 87004656 reads in 618 ms
[2015-09-30T22:39Z] INFO  23:39:56,669 MuTect - [MUTECT] Processed 120005639 reads in 628 ms
[2015-09-30T22:39Z] INFO  23:39:56,769 MuTect - [MUTECT] Processed 26001958 reads in 671 ms
[2015-09-30T22:39Z] INFO  23:39:56,998 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:57,032 MuTect - [MUTECT] Processed 88004760 reads in 625 ms
[2015-09-30T22:39Z] INFO  23:39:57,242 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:57,308 MuTect - [MUTECT] Processed 121005765 reads in 639 ms
[2015-09-30T22:39Z] INFO  23:39:57,439 MuTect - [MUTECT] Processed 27001965 reads in 670 ms
[2015-09-30T22:39Z] INFO  23:39:57,687 MuTect - [MUTECT] Processed 89004782 reads in 655 ms
[2015-09-30T22:39Z] INFO  23:39:57,934 MuTect - [MUTECT] Processed 122005782 reads in 626 ms
[2015-09-30T22:39Z] INFO  23:39:58,079 MuTect - [MUTECT] Processed 28002015 reads in 640 ms
[2015-09-30T22:39Z] INFO  23:39:58,366 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:58,373 MuTect - [MUTECT] Processed 90004858 reads in 686 ms
[2015-09-30T22:39Z] INFO  23:39:58,564 MuTect - [MUTECT] Processed 123005842 reads in 630 ms
[2015-09-30T22:39Z] INFO  23:39:58,748 MuTect - [MUTECT] Processed 29002042 reads in 669 ms
[2015-09-30T22:39Z] INFO  23:39:58,985 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:59,045 MuTect - [MUTECT] Processed 91004916 reads in 672 ms
[2015-09-30T22:39Z] INFO  23:39:59,182 MuTect - [MUTECT] Processed 124005888 reads in 618 ms
[2015-09-30T22:39Z] INFO  23:39:59,469 MuTect - [MUTECT] Processed 30002069 reads in 721 ms
[2015-09-30T22:39Z] INFO  23:39:59,533 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:39Z] INFO  23:39:59,694 MuTect - [MUTECT] Processed 92004964 reads in 649 ms
[2015-09-30T22:39Z] INFO  23:39:59,842 MuTect - [MUTECT] Processed 125005933 reads in 660 ms
[2015-09-30T22:40Z] INFO  23:40:00,154 MuTect - [MUTECT] Processed 31002153 reads in 685 ms
[2015-09-30T22:40Z] INFO  23:40:00,345 MuTect - [MUTECT] Processed 93005045 reads in 651 ms
[2015-09-30T22:40Z] INFO  23:40:00,502 MuTect - [MUTECT] Processed 126005971 reads in 660 ms
[2015-09-30T22:40Z] INFO  23:40:00,818 MuTect - [MUTECT] Processed 32002301 reads in 664 ms
[2015-09-30T22:40Z] INFO  23:40:00,912 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:01,010 MuTect - [MUTECT] Processed 94005138 reads in 665 ms
[2015-09-30T22:40Z] INFO  23:40:01,195 MuTect - [MUTECT] Processed 127006044 reads in 693 ms
[2015-09-30T22:40Z] INFO  23:40:01,260 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:01,513 MuTect - [MUTECT] Processed 33002358 reads in 695 ms
[2015-09-30T22:40Z] INFO  23:40:01,633 MuTect - [MUTECT] Processed 95005208 reads in 623 ms
[2015-09-30T22:40Z] INFO  23:40:01,812 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:01,848 MuTect - [MUTECT] Processed 128006161 reads in 653 ms
[2015-09-30T22:40Z] INFO  23:40:02,263 MuTect - [MUTECT] Processed 34002449 reads in 750 ms
[2015-09-30T22:40Z] INFO  23:40:02,264 MuTect - [MUTECT] Processed 96005220 reads in 631 ms
[2015-09-30T22:40Z] INFO  23:40:02,508 MuTect - [MUTECT] Processed 129006181 reads in 660 ms
[2015-09-30T22:40Z] INFO  23:40:02,906 MuTect - [MUTECT] Processed 97005223 reads in 642 ms
[2015-09-30T22:40Z] INFO  23:40:03,045 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:03,082 MuTect - [MUTECT] Processed 35002456 reads in 819 ms
[2015-09-30T22:40Z] INFO  23:40:03,181 MuTect - [MUTECT] Processed 130006254 reads in 673 ms
[2015-09-30T22:40Z] INFO  23:40:03,489 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:03,568 MuTect - [MUTECT] Processed 98005265 reads in 662 ms
[2015-09-30T22:40Z] INFO  23:40:03,796 MuTect - [MUTECT] Processed 36002544 reads in 714 ms
[2015-09-30T22:40Z] INFO  23:40:03,861 MuTect - [MUTECT] Processed 131006308 reads in 680 ms
[2015-09-30T22:40Z] INFO  23:40:03,916 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:04,222 MuTect - [MUTECT] Processed 99005331 reads in 654 ms
[2015-09-30T22:40Z] INFO  23:40:04,416 MuTect - [MUTECT] Processed 37002574 reads in 620 ms
[2015-09-30T22:40Z] INFO  23:40:04,541 MuTect - [MUTECT] Processed 132006334 reads in 680 ms
[2015-09-30T22:40Z] INFO  23:40:04,864 MuTect - [MUTECT] Processed 100005442 reads in 642 ms
[2015-09-30T22:40Z] INFO  23:40:04,956 ProgressMeter -     15:45658316        4.48e+06   90.0 s       20.0 s     63.2%         2.4 m    52.0 s
[2015-09-30T22:40Z] INFO  23:40:05,023 MuTect - [MUTECT] Processed 38002574 reads in 607 ms
[2015-09-30T22:40Z] INFO  23:40:05,142 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:05,239 MuTect - [MUTECT] Processed 133006355 reads in 698 ms
[2015-09-30T22:40Z] INFO  23:40:05,519 MuTect - [MUTECT] Processed 101005500 reads in 655 ms
[2015-09-30T22:40Z] INFO  23:40:05,667 MuTect - [MUTECT] Processed 39002653 reads in 644 ms
[2015-09-30T22:40Z] INFO  23:40:05,829 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:05,922 MuTect - [MUTECT] Processed 134006412 reads in 683 ms
[2015-09-30T22:40Z] INFO  23:40:06,199 MuTect - [MUTECT] Processed 102005505 reads in 680 ms
[2015-09-30T22:40Z] INFO  23:40:06,302 MuTect - [MUTECT] Processed 40002759 reads in 635 ms
[2015-09-30T22:40Z] INFO  23:40:06,494 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:06,664 MuTect - [MUTECT] Processed 135006434 reads in 742 ms
[2015-09-30T22:40Z] INFO  23:40:06,854 MuTect - [MUTECT] Processed 103005637 reads in 655 ms
[2015-09-30T22:40Z] INFO  23:40:06,965 MuTect - [MUTECT] Processed 41002814 reads in 663 ms
[2015-09-30T22:40Z] INFO  23:40:07,335 MuTect - [MUTECT] Processed 136006438 reads in 671 ms
[2015-09-30T22:40Z] INFO  23:40:07,474 MuTect - [MUTECT] Processed 104005697 reads in 620 ms
[2015-09-30T22:40Z] INFO  23:40:07,561 ProgressMeter -      16:1500714        1.12e+06   30.0 s       26.0 s     10.6%         4.7 m     4.2 m
[2015-09-30T22:40Z] INFO  23:40:07,594 MuTect - [MUTECT] Processed 42002825 reads in 629 ms
[2015-09-30T22:40Z] INFO  23:40:07,920 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:08,002 MuTect - [MUTECT] Processed 137006504 reads in 667 ms
[2015-09-30T22:40Z] INFO  23:40:08,082 MuTect - [MUTECT] Processed 105005849 reads in 608 ms
[2015-09-30T22:40Z] INFO  23:40:08,291 MuTect - [MUTECT] Processed 43002894 reads in 697 ms
[2015-09-30T22:40Z] INFO  23:40:08,678 MuTect - [MUTECT] Processed 138006529 reads in 676 ms
[2015-09-30T22:40Z] INFO  23:40:08,738 MuTect - [MUTECT] Processed 106005896 reads in 656 ms
[2015-09-30T22:40Z] INFO  23:40:08,824 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:08,968 MuTect - [MUTECT] Processed 44002969 reads in 677 ms
[2015-09-30T22:40Z] INFO  23:40:09,159 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:09,377 MuTect - [MUTECT] Processed 107005907 reads in 639 ms
[2015-09-30T22:40Z] INFO  23:40:09,403 MuTect - [MUTECT] Processed 139006597 reads in 725 ms
[2015-09-30T22:40Z] INFO  23:40:09,625 MuTect - [MUTECT] Processed 45002970 reads in 657 ms
[2015-09-30T22:40Z] INFO  23:40:10,016 MuTect - [MUTECT] Processed 108005970 reads in 639 ms
[2015-09-30T22:40Z] INFO  23:40:10,117 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:10,136 MuTect - [MUTECT] Processed 140006630 reads in 733 ms
[2015-09-30T22:40Z] INFO  23:40:10,287 MuTect - [MUTECT] Processed 46002983 reads in 662 ms
[2015-09-30T22:40Z] INFO  23:40:10,670 MuTect - [MUTECT] Processed 109006045 reads in 654 ms
[2015-09-30T22:40Z] INFO  23:40:10,835 MuTect - [MUTECT] Processed 141006731 reads in 699 ms
[2015-09-30T22:40Z] INFO  23:40:10,915 MuTect - [MUTECT] Processed 47003051 reads in 628 ms
[2015-09-30T22:40Z] INFO  23:40:11,083 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:11,343 MuTect - [MUTECT] Processed 110006098 reads in 673 ms
[2015-09-30T22:40Z] INFO  23:40:11,531 MuTect - [MUTECT] Processed 142006741 reads in 696 ms
[2015-09-30T22:40Z] INFO  23:40:11,541 MuTect - [MUTECT] Processed 48003073 reads in 626 ms
[2015-09-30T22:40Z] INFO  23:40:11,922 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:12,023 MuTect - [MUTECT] Processed 111006102 reads in 680 ms
[2015-09-30T22:40Z] INFO  23:40:12,151 MuTect - [MUTECT] Processed 49003164 reads in 610 ms
[2015-09-30T22:40Z] INFO  23:40:12,217 MuTect - [MUTECT] Processed 143006764 reads in 686 ms
[2015-09-30T22:40Z] INFO  23:40:12,444 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:12,667 MuTect - [MUTECT] Processed 112006190 reads in 643 ms
[2015-09-30T22:40Z] INFO  23:40:12,792 MuTect - [MUTECT] Processed 50003227 reads in 641 ms
[2015-09-30T22:40Z] INFO  23:40:12,895 MuTect - [MUTECT] Processed 144006764 reads in 678 ms
[2015-09-30T22:40Z] INFO  23:40:13,370 MuTect - [MUTECT] Processed 113006247 reads in 704 ms
[2015-09-30T22:40Z] INFO  23:40:13,449 MuTect - [MUTECT] Processed 51003236 reads in 657 ms
[2015-09-30T22:40Z] INFO  23:40:13,548 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:13,597 MuTect - [MUTECT] Processed 145006783 reads in 701 ms
[2015-09-30T22:40Z] INFO  23:40:14,073 MuTect - [MUTECT] Processed 114006329 reads in 703 ms
[2015-09-30T22:40Z] INFO  23:40:14,118 MuTect - [MUTECT] Processed 52003262 reads in 669 ms
[2015-09-30T22:40Z] INFO  23:40:14,249 MuTect - [MUTECT] Processed 146006807 reads in 653 ms
[2015-09-30T22:40Z] INFO  23:40:14,417 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:14,783 MuTect - [MUTECT] Processed 53003298 reads in 665 ms
[2015-09-30T22:40Z] INFO  23:40:14,788 MuTect - [MUTECT] Processed 115006351 reads in 715 ms
[2015-09-30T22:40Z] INFO  23:40:14,824 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:14,956 MuTect - [MUTECT] Processed 147006855 reads in 707 ms
[2015-09-30T22:40Z] INFO  23:40:15,501 MuTect - [MUTECT] Processed 116006409 reads in 713 ms
[2015-09-30T22:40Z] INFO  23:40:15,510 MuTect - [MUTECT] Processed 54003359 reads in 727 ms
[2015-09-30T22:40Z] INFO  23:40:15,634 MuTect - [MUTECT] Processed 148006892 reads in 678 ms
[2015-09-30T22:40Z] INFO  23:40:16,040 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:16,186 MuTect - [MUTECT] Processed 117006445 reads in 685 ms
[2015-09-30T22:40Z] INFO  23:40:16,286 MuTect - [MUTECT] Processed 149006953 reads in 652 ms
[2015-09-30T22:40Z] INFO  23:40:16,313 MuTect - [MUTECT] Processed 55003407 reads in 803 ms
[2015-09-30T22:40Z] INFO  23:40:16,892 MuTect - [MUTECT] Processed 118006530 reads in 706 ms
[2015-09-30T22:40Z] INFO  23:40:17,046 MuTect - [MUTECT] Processed 56003487 reads in 733 ms
[2015-09-30T22:40Z] INFO  23:40:17,121 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:17,418 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:17,558 MuTect - [MUTECT] Processed 150007022 reads in 1272 ms
[2015-09-30T22:40Z] INFO  23:40:17,649 MuTect - [MUTECT] Processed 119006535 reads in 757 ms
[2015-09-30T22:40Z] INFO  23:40:17,757 MuTect - [MUTECT] Processed 57003531 reads in 711 ms
[2015-09-30T22:40Z] INFO  23:40:18,198 MuTect - [MUTECT] Processed 151007083 reads in 640 ms
[2015-09-30T22:40Z] INFO  23:40:18,361 MuTect - [MUTECT] Processed 120006578 reads in 712 ms
[2015-09-30T22:40Z] INFO  23:40:18,415 MuTect - [MUTECT] Processed 58003570 reads in 658 ms
[2015-09-30T22:40Z] INFO  23:40:18,641 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:18,897 MuTect - [MUTECT] Processed 152007118 reads in 699 ms
[2015-09-30T22:40Z] INFO  23:40:19,039 MuTect - [MUTECT] Processed 121006663 reads in 678 ms
[2015-09-30T22:40Z] INFO  23:40:19,095 MuTect - [MUTECT] Processed 59003726 reads in 680 ms
[2015-09-30T22:40Z] INFO  23:40:19,374 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:19,573 MuTect - [MUTECT] Processed 153007128 reads in 676 ms
[2015-09-30T22:40Z] INFO  23:40:19,689 MuTect - [MUTECT] Processed 122006709 reads in 650 ms
[2015-09-30T22:40Z] INFO  23:40:19,757 MuTect - [MUTECT] Processed 60003756 reads in 662 ms
[2015-09-30T22:40Z] INFO  23:40:19,917 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:20,266 MuTect - [MUTECT] Processed 154007205 reads in 693 ms
[2015-09-30T22:40Z] INFO  23:40:20,365 MuTect - [MUTECT] Processed 123006776 reads in 676 ms
[2015-09-30T22:40Z] INFO  23:40:20,395 MuTect - [MUTECT] Processed 61003757 reads in 638 ms
[2015-09-30T22:40Z] INFO  23:40:20,940 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:20,943 MuTect - [MUTECT] Processed 155007267 reads in 677 ms
[2015-09-30T22:40Z] INFO  23:40:21,008 MuTect - [MUTECT] Processed 62003867 reads in 613 ms
[2015-09-30T22:40Z] INFO  23:40:21,061 MuTect - [MUTECT] Processed 124006849 reads in 696 ms
[2015-09-30T22:40Z] INFO  23:40:21,474 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:21,603 MuTect - [MUTECT] Processed 156007279 reads in 660 ms
[2015-09-30T22:40Z] INFO  23:40:21,637 MuTect - [MUTECT] Processed 63003937 reads in 629 ms
[2015-09-30T22:40Z] INFO  23:40:21,808 MuTect - [MUTECT] Processed 125006906 reads in 747 ms
[2015-09-30T22:40Z] INFO  23:40:22,261 MuTect - [MUTECT] Processed 64003996 reads in 624 ms
[2015-09-30T22:40Z] INFO  23:40:22,261 MuTect - [MUTECT] Processed 157007286 reads in 658 ms
[2015-09-30T22:40Z] INFO  23:40:22,452 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:22,590 MuTect - [MUTECT] Processed 126007048 reads in 782 ms
[2015-09-30T22:40Z] INFO  23:40:22,900 MuTect - [MUTECT] Processed 65004086 reads in 639 ms
[2015-09-30T22:40Z] INFO  23:40:22,969 MuTect - [MUTECT] Processed 158007340 reads in 708 ms
[2015-09-30T22:40Z] INFO  23:40:23,230 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:23,230 MuTect - [MUTECT] Processed 127007105 reads in 640 ms
[2015-09-30T22:40Z] INFO  23:40:23,562 MuTect - [MUTECT] Processed 66004186 reads in 662 ms
[2015-09-30T22:40Z] INFO  23:40:23,633 MuTect - [MUTECT] Processed 159007392 reads in 664 ms
[2015-09-30T22:40Z] INFO  23:40:23,681 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:23,853 MuTect - [MUTECT] Processed 128007135 reads in 623 ms
[2015-09-30T22:40Z] INFO  23:40:24,216 MuTect - [MUTECT] Processed 67004351 reads in 654 ms
[2015-09-30T22:40Z] INFO  23:40:24,316 MuTect - [MUTECT] Processed 160007455 reads in 683 ms
[2015-09-30T22:40Z] INFO  23:40:24,501 MuTect - [MUTECT] Processed 129007191 reads in 648 ms
[2015-09-30T22:40Z] INFO  23:40:24,873 MuTect - [MUTECT] Processed 68004425 reads in 657 ms
[2015-09-30T22:40Z] INFO  23:40:24,933 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:24,977 MuTect - [MUTECT] Processed 161007495 reads in 661 ms
[2015-09-30T22:40Z] INFO  23:40:25,153 MuTect - [MUTECT] Processed 130007251 reads in 652 ms
[2015-09-30T22:40Z] INFO  23:40:25,305 ProgressMeter -     15:78578142        4.03e+06   90.0 s       22.0 s     57.3%         2.6 m    67.0 s
[2015-09-30T22:40Z] INFO  23:40:25,393 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:25,517 MuTect - [MUTECT] Processed 69004473 reads in 644 ms
[2015-09-30T22:40Z] INFO  23:40:25,698 MuTect - [MUTECT] Processed 162007538 reads in 720 ms
[2015-09-30T22:40Z] INFO  23:40:25,798 MuTect - [MUTECT] Processed 131007292 reads in 645 ms
[2015-09-30T22:40Z] INFO  23:40:25,955 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:26,212 MuTect - [MUTECT] Processed 70004586 reads in 695 ms
[2015-09-30T22:40Z] INFO  23:40:26,418 MuTect - [MUTECT] Processed 163007548 reads in 721 ms
[2015-09-30T22:40Z] INFO  23:40:26,467 MuTect - [MUTECT] Processed 132007308 reads in 669 ms
[2015-09-30T22:40Z] INFO  23:40:26,829 MuTect - [MUTECT] Processed 71004712 reads in 617 ms
[2015-09-30T22:40Z] INFO  23:40:27,050 MuTect - [MUTECT] Processed 164007548 reads in 632 ms
[2015-09-30T22:40Z] INFO  23:40:27,140 MuTect - [MUTECT] Processed 133007398 reads in 673 ms
[2015-09-30T22:40Z] INFO  23:40:27,172 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:27,473 MuTect - [MUTECT] Processed 72004747 reads in 644 ms
[2015-09-30T22:40Z] INFO  23:40:27,708 MuTect - [MUTECT] Processed 165007579 reads in 657 ms
[2015-09-30T22:40Z] INFO  23:40:27,725 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:27,833 MuTect - [MUTECT] Processed 134007477 reads in 693 ms
[2015-09-30T22:40Z] INFO  23:40:28,184 MuTect - [MUTECT] Processed 73004811 reads in 711 ms
[2015-09-30T22:40Z] INFO  23:40:28,249 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:28,332 MuTect - [MUTECT] Processed 166007584 reads in 625 ms
[2015-09-30T22:40Z] INFO  23:40:28,548 MuTect - [MUTECT] Processed 135007558 reads in 715 ms
[2015-09-30T22:40Z] INFO  23:40:28,843 MuTect - [MUTECT] Processed 74004838 reads in 659 ms
[2015-09-30T22:40Z] INFO  23:40:28,964 MuTect - [MUTECT] Processed 167007628 reads in 632 ms
[2015-09-30T22:40Z] INFO  23:40:29,292 MuTect - [MUTECT] Processed 136007566 reads in 744 ms
[2015-09-30T22:40Z] INFO  23:40:29,507 MuTect - [MUTECT] Processed 75004859 reads in 664 ms
[2015-09-30T22:40Z] INFO  23:40:29,533 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:29,631 MuTect - [MUTECT] Processed 168007660 reads in 667 ms
[2015-09-30T22:40Z] INFO  23:40:29,952 MuTect - [MUTECT] Processed 137007689 reads in 660 ms
[2015-09-30T22:40Z] INFO  23:40:29,997 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:30,193 MuTect - [MUTECT] Processed 76004984 reads in 686 ms
[2015-09-30T22:40Z] INFO  23:40:30,332 MuTect - [MUTECT] Processed 169007661 reads in 701 ms
[2015-09-30T22:40Z] INFO  23:40:30,475 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:30,638 MuTect - [MUTECT] Processed 138007789 reads in 686 ms
[2015-09-30T22:40Z] INFO  23:40:30,817 MuTect - [MUTECT] Processed 77005072 reads in 624 ms
[2015-09-30T22:40Z] INFO  23:40:31,064 MuTect - [MUTECT] Processed 170007661 reads in 732 ms
[2015-09-30T22:40Z] INFO  23:40:31,336 MuTect - [MUTECT] Processed 139007914 reads in 698 ms
[2015-09-30T22:40Z] INFO  23:40:31,478 MuTect - [MUTECT] Processed 78005156 reads in 661 ms
[2015-09-30T22:40Z] INFO  23:40:31,740 MuTect - [MUTECT] Processed 171007740 reads in 676 ms
[2015-09-30T22:40Z] INFO  23:40:32,005 MuTect - [MUTECT] Processed 140007954 reads in 669 ms
[2015-09-30T22:40Z] INFO  23:40:32,101 MuTect - [MUTECT] Processed 79005161 reads in 623 ms
[2015-09-30T22:40Z] INFO  23:40:32,208 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:32,298 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:32,451 MuTect - [MUTECT] Processed 172007764 reads in 711 ms
[2015-09-30T22:40Z] INFO  23:40:32,556 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:32,670 MuTect - [MUTECT] Processed 141008050 reads in 665 ms
[2015-09-30T22:40Z] INFO  23:40:32,732 MuTect - [MUTECT] Processed 80005289 reads in 631 ms
[2015-09-30T22:40Z] INFO  23:40:33,176 MuTect - [MUTECT] Processed 173007793 reads in 725 ms
[2015-09-30T22:40Z] INFO  23:40:33,321 MuTect - [MUTECT] Processed 81005327 reads in 589 ms
[2015-09-30T22:40Z] INFO  23:40:33,374 MuTect - [MUTECT] Processed 142008086 reads in 704 ms
[2015-09-30T22:40Z] INFO  23:40:33,837 MuTect - [MUTECT] Processed 174007856 reads in 661 ms
[2015-09-30T22:40Z] INFO  23:40:33,910 MuTect - [MUTECT] Processed 82005359 reads in 589 ms
[2015-09-30T22:40Z] INFO  23:40:34,148 MuTect - [MUTECT] Processed 143008105 reads in 774 ms
[2015-09-30T22:40Z] INFO  23:40:34,503 MuTect - [MUTECT] Processed 83005444 reads in 593 ms
[2015-09-30T22:40Z] INFO  23:40:34,584 MuTect - [MUTECT] Processed 175007898 reads in 747 ms
[2015-09-30T22:40Z] INFO  23:40:34,662 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:34,853 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:34,857 MuTect - [MUTECT] Processed 144008182 reads in 709 ms
[2015-09-30T22:40Z] INFO  23:40:34,948 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:34,957 ProgressMeter -     15:56969728        6.10e+06  120.0 s       19.0 s     91.0%         2.2 m    11.0 s
[2015-09-30T22:40Z] INFO  23:40:35,089 MuTect - [MUTECT] Processed 84005446 reads in 586 ms
[2015-09-30T22:40Z] INFO  23:40:35,312 MuTect - [MUTECT] Processed 176007938 reads in 728 ms
[2015-09-30T22:40Z] INFO  23:40:35,546 MuTect - [MUTECT] Processed 145008214 reads in 689 ms
[2015-09-30T22:40Z] INFO  23:40:35,649 MuTect - [MUTECT] Processed 85005450 reads in 560 ms
[2015-09-30T22:40Z] INFO  23:40:36,004 MuTect - [MUTECT] Processed 177007985 reads in 692 ms
[2015-09-30T22:40Z] INFO  23:40:36,225 MuTect - [MUTECT] Processed 146008328 reads in 679 ms
[2015-09-30T22:40Z] INFO  23:40:36,247 MuTect - [MUTECT] Processed 86005554 reads in 598 ms
[2015-09-30T22:40Z] INFO  23:40:36,690 MuTect - [MUTECT] Processed 178008049 reads in 686 ms
[2015-09-30T22:40Z] INFO  23:40:36,870 MuTect - [MUTECT] Processed 87005638 reads in 623 ms
[2015-09-30T22:40Z] INFO  23:40:36,881 MuTect - [MUTECT] Processed 147008336 reads in 656 ms
[2015-09-30T22:40Z] INFO  23:40:37,073 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:37,268 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:37,371 MuTect - [MUTECT] Processed 179008081 reads in 681 ms
[2015-09-30T22:40Z] INFO  23:40:37,489 MuTect - [MUTECT] Processed 88005684 reads in 619 ms
[2015-09-30T22:40Z] INFO  23:40:37,509 MuTect - [MUTECT] Processed 148008368 reads in 628 ms
[2015-09-30T22:40Z] INFO  23:40:37,551 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:37,562 ProgressMeter -      16:2819449        2.37e+06   60.0 s       25.0 s     22.8%         4.4 m     3.4 m
[2015-09-30T22:40Z] INFO  23:40:38,072 MuTect - [MUTECT] Processed 180008184 reads in 701 ms
[2015-09-30T22:40Z] INFO  23:40:38,157 MuTect - [MUTECT] Processed 89005748 reads in 667 ms
[2015-09-30T22:40Z] INFO  23:40:38,192 MuTect - [MUTECT] Processed 149008433 reads in 683 ms
[2015-09-30T22:40Z] INFO  23:40:38,793 MuTect - [MUTECT] Processed 181008197 reads in 721 ms
[2015-09-30T22:40Z] INFO  23:40:38,808 MuTect - [MUTECT] Processed 90005771 reads in 652 ms
[2015-09-30T22:40Z] INFO  23:40:38,856 MuTect - [MUTECT] Processed 150008487 reads in 664 ms
[2015-09-30T22:40Z] INFO  23:40:39,340 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:39,493 MuTect - [MUTECT] Processed 91005833 reads in 685 ms
[2015-09-30T22:40Z] INFO  23:40:39,541 MuTect - [MUTECT] Processed 182008199 reads in 748 ms
[2015-09-30T22:40Z] INFO  23:40:39,550 MuTect - [MUTECT] Processed 151008571 reads in 694 ms
[2015-09-30T22:40Z] INFO  23:40:39,603 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:39,929 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:40,197 MuTect - [MUTECT] Processed 152008571 reads in 647 ms
[2015-09-30T22:40Z] INFO  23:40:40,209 MuTect - [MUTECT] Processed 92005925 reads in 716 ms
[2015-09-30T22:40Z] INFO  23:40:40,275 MuTect - [MUTECT] Processed 183008281 reads in 734 ms
[2015-09-30T22:40Z] INFO  23:40:40,851 MuTect - [MUTECT] Processed 153008590 reads in 654 ms
[2015-09-30T22:40Z] INFO  23:40:40,870 MuTect - [MUTECT] Processed 93005946 reads in 661 ms
[2015-09-30T22:40Z] INFO  23:40:40,961 MuTect - [MUTECT] Processed 184008345 reads in 686 ms
[2015-09-30T22:40Z] INFO  23:40:41,468 MuTect - [MUTECT] Processed 154008605 reads in 617 ms
[2015-09-30T22:40Z] INFO  23:40:41,526 MuTect - [MUTECT] Processed 94006089 reads in 655 ms
[2015-09-30T22:40Z] INFO  23:40:41,669 MuTect - [MUTECT] Processed 185008400 reads in 708 ms
[2015-09-30T22:40Z] INFO  23:40:42,053 MuTect - [MUTECT] Processed 155008696 reads in 585 ms
[2015-09-30T22:40Z] INFO  23:40:42,084 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:42,170 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:42,182 MuTect - [MUTECT] Processed 95006167 reads in 657 ms
[2015-09-30T22:40Z] INFO  23:40:42,321 MuTect - [MUTECT] Processed 186008469 reads in 652 ms
[2015-09-30T22:40Z] INFO  23:40:42,692 MuTect - [MUTECT] Processed 156008720 reads in 639 ms
[2015-09-30T22:40Z] INFO  23:40:42,802 MuTect - [MUTECT] Processed 96006225 reads in 620 ms
[2015-09-30T22:40Z] INFO  23:40:42,998 MuTect - [MUTECT] Processed 187008487 reads in 677 ms
[2015-09-30T22:40Z] INFO  23:40:43,319 MuTect - [MUTECT] Processed 157008727 reads in 627 ms
[2015-09-30T22:40Z] INFO  23:40:43,449 MuTect - [MUTECT] Processed 97006230 reads in 647 ms
[2015-09-30T22:40Z] INFO  23:40:43,667 MuTect - [MUTECT] Processed 188008492 reads in 669 ms
[2015-09-30T22:40Z] INFO  23:40:43,930 MuTect - [MUTECT] Processed 158008744 reads in 611 ms
[2015-09-30T22:40Z] INFO  23:40:44,098 MuTect - [MUTECT] Processed 98006312 reads in 649 ms
[2015-09-30T22:40Z] INFO  23:40:44,102 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:44,377 MuTect - [MUTECT] Processed 189008529 reads in 710 ms
[2015-09-30T22:40Z] INFO  23:40:44,539 MuTect - [MUTECT] Processed 159008779 reads in 609 ms
[2015-09-30T22:40Z] INFO  23:40:44,561 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:44,707 MuTect - [MUTECT] Processed 99006346 reads in 609 ms
[2015-09-30T22:40Z] INFO  23:40:45,084 MuTect - [MUTECT] Processed 190008553 reads in 707 ms
[2015-09-30T22:40Z] INFO  23:40:45,162 MuTect - [MUTECT] Processed 160008810 reads in 622 ms
[2015-09-30T22:40Z] INFO  23:40:45,361 MuTect - [MUTECT] Processed 100006394 reads in 654 ms
[2015-09-30T22:40Z] INFO  23:40:45,619 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:45,740 MuTect - [MUTECT] Processed 191008556 reads in 656 ms
[2015-09-30T22:40Z] INFO  23:40:45,805 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:40Z] INFO  23:40:45,832 MuTect - [MUTECT] Processed 161008850 reads in 671 ms
[2015-09-30T22:40Z] INFO  23:40:46,008 MuTect - [MUTECT] Processed 101006404 reads in 647 ms
[2015-09-30T22:40Z] INFO  23:40:46,201 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:46,243 ProgressMeter -            done        6.57e+06    2.2 m       19.0 s    100.0%         2.2 m     0.0 s
[2015-09-30T22:40Z] INFO  23:40:46,243 ProgressMeter - Total runtime 131.29 secs, 2.19 min, 0.04 hours
[2015-09-30T22:40Z] INFO  23:40:46,316 MicroScheduler - 137490 reads were filtered out during the traversal out of approximately 2255362 total reads (6.10%)
[2015-09-30T22:40Z] INFO  23:40:46,316 MicroScheduler -   -> 101269 reads (4.49% of total) failing DuplicateReadFilter
[2015-09-30T22:40Z] INFO  23:40:46,316 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:40Z] INFO  23:40:46,316 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:40Z] INFO  23:40:46,316 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:40Z] INFO  23:40:46,317 MicroScheduler -   -> 36221 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:40Z] INFO  23:40:46,488 MuTect - [MUTECT] Processed 162008875 reads in 656 ms
[2015-09-30T22:40Z] INFO  23:40:46,655 MuTect - [MUTECT] Processed 102006422 reads in 647 ms
[2015-09-30T22:40Z] INFO  23:40:47,123 MuTect - [MUTECT] Processed 163008947 reads in 635 ms
[2015-09-30T22:40Z] INFO  23:40:47,341 MuTect - [MUTECT] Processed 103006465 reads in 685 ms
[2015-09-30T22:40Z] INFO  23:40:47,700 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:47,712 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:40Z] INFO  23:40:47,784 MuTect - [MUTECT] Processed 164008964 reads in 661 ms
[2015-09-30T22:40Z] bgzip syn3-15_31042312_62147370-raw-mutect.vcf
[2015-09-30T22:40Z] tabix index syn3-15_31042312_62147370-raw-mutect.vcf.gz
[2015-09-30T22:40Z] INFO  23:40:48,004 MuTect - [MUTECT] Processed 104006472 reads in 664 ms
[2015-09-30T22:40Z] INFO  23:40:48,465 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:48,494 MuTect - [MUTECT] Processed 165008965 reads in 710 ms
[2015-09-30T22:40Z] INFO  23:40:48,652 MuTect - [MUTECT] Processed 105006551 reads in 648 ms
[2015-09-30T22:40Z] INFO  23:40:49,173 MuTect - [MUTECT] Processed 166009018 reads in 679 ms
[2015-09-30T22:40Z] INFO  23:40:49,276 MuTect - [MUTECT] Processed 106006606 reads in 624 ms
[2015-09-30T22:40Z] INFO  23:40:49,822 MuTect - [MUTECT] Processed 167009086 reads in 649 ms
[2015-09-30T22:40Z] INFO  23:40:49,907 MuTect - [MUTECT] Processed 107006624 reads in 631 ms
[2015-09-30T22:40Z] INFO  23:40:50,184 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:40Z] MuTect: MuTect
[2015-09-30T22:40Z] INFO  23:40:50,502 MuTect - [MUTECT] Processed 168009094 reads in 680 ms
[2015-09-30T22:40Z] INFO  23:40:50,545 MuTect - [MUTECT] Processed 108006731 reads in 637 ms
[2015-09-30T22:40Z] INFO  23:40:50,666 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:51,189 MuTect - [MUTECT] Processed 109006765 reads in 645 ms
[2015-09-30T22:40Z] INFO  23:40:51,205 MuTect - [MUTECT] Processed 169009121 reads in 703 ms
[2015-09-30T22:40Z] INFO  23:40:51,828 MuTect - [MUTECT] Processed 110006855 reads in 639 ms
[2015-09-30T22:40Z] INFO  23:40:51,896 MuTect - [MUTECT] Processed 170009124 reads in 691 ms
[2015-09-30T22:40Z] INFO  23:40:52,283 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/16/syn3-16_31044089_62860191-raw-mutect-regions.bed to be BED
[2015-09-30T22:40Z] INFO  23:40:52,340 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:40Z] INFO  23:40:52,340 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:40Z] INFO  23:40:52,340 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:40Z] INFO  23:40:52,340 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:40Z] INFO  23:40:52,344 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/16/syn3-16_31044089_62860191-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/16/tx/tmpp4IXNW/syn3-16_31044089_62860191-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:40Z] INFO  23:40:52,344 HelpFormatter - Date/Time: 2015/09/30 23:40:52
[2015-09-30T22:40Z] INFO  23:40:52,344 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:40Z] INFO  23:40:52,344 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:40Z] INFO  23:40:52,373 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:40Z] INFO  23:40:52,377 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:40Z] INFO  23:40:52,427 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:40Z] INFO  23:40:52,466 MuTect - [MUTECT] Processed 111006856 reads in 638 ms
[2015-09-30T22:40Z] INFO  23:40:52,477 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:40Z] INFO  23:40:52,485 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:40Z] INFO  23:40:52,546 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2015-09-30T22:40Z] INFO  23:40:52,573 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:40Z] INFO  23:40:52,710 MuTect - [MUTECT] Processed 171009325 reads in 814 ms
[2015-09-30T22:40Z] INFO  23:40:52,754 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:40Z] INFO  23:40:52,848 IntervalUtils - Processing 1115296 bp from intervals
[2015-09-30T22:40Z] INFO  23:40:52,852 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:40Z] INFO  23:40:52,852 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:40Z] INFO  23:40:52,858 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:52,951 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:53,025 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:40Z] INFO  23:40:53,103 MuTect - [MUTECT] Processed 112006863 reads in 637 ms
[2015-09-30T22:40Z] INFO  23:40:53,157 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:40Z] INFO  23:40:53,158 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:40Z] INFO  23:40:53,158 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:40Z] INFO  23:40:53,159 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:40Z] INFO  23:40:53,448 MuTect - [MUTECT] Processed 172009350 reads in 738 ms
[2015-09-30T22:40Z] INFO  23:40:53,784 MuTect - [MUTECT] Processed 113006921 reads in 681 ms
[2015-09-30T22:40Z] INFO  23:40:54,100 MuTect - [MUTECT] Processed 173009449 reads in 652 ms
[2015-09-30T22:40Z] INFO  23:40:54,466 MuTect - [MUTECT] Processed 114006986 reads in 682 ms
[2015-09-30T22:40Z] INFO  23:40:54,803 MuTect - [MUTECT] Processed 174009480 reads in 703 ms
[2015-09-30T22:40Z] INFO  23:40:55,116 MuTect - [MUTECT] Processed 115007014 reads in 650 ms
[2015-09-30T22:40Z] INFO  23:40:55,306 ProgressMeter -     15:85055681        5.44e+06  120.0 s       22.0 s     78.1%         2.6 m    33.0 s
[2015-09-30T22:40Z] INFO  23:40:55,332 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:55,428 MuTect - [MUTECT] Processed 1000068 reads in 2206 ms
[2015-09-30T22:40Z] INFO  23:40:55,496 MuTect - [MUTECT] Processed 175009596 reads in 692 ms
[2015-09-30T22:40Z] INFO  23:40:55,776 MuTect - [MUTECT] Processed 116007119 reads in 660 ms
[2015-09-30T22:40Z] INFO  23:40:56,155 MuTect - [MUTECT] Processed 176009640 reads in 660 ms
[2015-09-30T22:40Z] INFO  23:40:56,277 MuTect - [MUTECT] Processed 2000167 reads in 849 ms
[2015-09-30T22:40Z] INFO  23:40:56,398 MuTect - [MUTECT] Processed 117007209 reads in 622 ms
[2015-09-30T22:40Z] INFO  23:40:56,478 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:56,807 MuTect - [MUTECT] Processed 177009659 reads in 652 ms
[2015-09-30T22:40Z] INFO  23:40:56,975 MuTect - [MUTECT] Processed 3000227 reads in 697 ms
[2015-09-30T22:40Z] INFO  23:40:57,057 MuTect - [MUTECT] Processed 118007273 reads in 659 ms
[2015-09-30T22:40Z] INFO  23:40:57,096 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:57,440 MuTect - [MUTECT] Processed 178009760 reads in 633 ms
[2015-09-30T22:40Z] INFO  23:40:57,582 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:57,661 MuTect - [MUTECT] Processed 4000282 reads in 687 ms
[2015-09-30T22:40Z] INFO  23:40:57,741 MuTect - [MUTECT] Processed 119007338 reads in 684 ms
[2015-09-30T22:40Z] INFO  23:40:58,083 MuTect - [MUTECT] Processed 179009775 reads in 643 ms
[2015-09-30T22:40Z] INFO  23:40:58,352 MuTect - [MUTECT] Processed 5000375 reads in 691 ms
[2015-09-30T22:40Z] INFO  23:40:58,403 MuTect - [MUTECT] Processed 120007342 reads in 662 ms
[2015-09-30T22:40Z] INFO  23:40:58,585 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:58,706 MuTect - [MUTECT] Processed 180009811 reads in 623 ms
[2015-09-30T22:40Z] INFO  23:40:59,061 MuTect - [MUTECT] Processed 121007396 reads in 658 ms
[2015-09-30T22:40Z] INFO  23:40:59,077 MuTect - [MUTECT] Processed 6000497 reads in 725 ms
[2015-09-30T22:40Z] INFO  23:40:59,350 MuTect - [MUTECT] Processed 181009833 reads in 644 ms
[2015-09-30T22:40Z] INFO  23:40:59,363 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:40Z] INFO  23:40:59,782 MuTect - [MUTECT] Processed 7000562 reads in 705 ms
[2015-09-30T22:40Z] INFO  23:40:59,782 MuTect - [MUTECT] Processed 122007406 reads in 721 ms
[2015-09-30T22:40Z] INFO  23:40:59,805 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:00,011 MuTect - [MUTECT] Processed 182009892 reads in 661 ms
[2015-09-30T22:41Z] INFO  23:41:00,435 MuTect - [MUTECT] Processed 123007511 reads in 653 ms
[2015-09-30T22:41Z] INFO  23:41:00,479 MuTect - [MUTECT] Processed 8000590 reads in 697 ms
[2015-09-30T22:41Z] INFO  23:41:00,611 MuTect - [MUTECT] Processed 183009967 reads in 600 ms
[2015-09-30T22:41Z] INFO  23:41:01,097 MuTect - [MUTECT] Processed 124007536 reads in 662 ms
[2015-09-30T22:41Z] INFO  23:41:01,173 MuTect - [MUTECT] Processed 9000633 reads in 693 ms
[2015-09-30T22:41Z] INFO  23:41:01,189 MuTect - [MUTECT] Processed 184010000 reads in 578 ms
[2015-09-30T22:41Z] INFO  23:41:01,563 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:01,719 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:01,787 MuTect - [MUTECT] Processed 125007537 reads in 690 ms
[2015-09-30T22:41Z] INFO  23:41:01,835 MuTect - [MUTECT] Processed 185010064 reads in 646 ms
[2015-09-30T22:41Z] INFO  23:41:01,894 MuTect - [MUTECT] Processed 10000637 reads in 722 ms
[2015-09-30T22:41Z] INFO  23:41:02,128 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:02,498 MuTect - [MUTECT] Processed 186010077 reads in 663 ms
[2015-09-30T22:41Z] INFO  23:41:02,538 MuTect - [MUTECT] Processed 126007538 reads in 751 ms
[2015-09-30T22:41Z] INFO  23:41:02,583 MuTect - [MUTECT] Processed 11000671 reads in 689 ms
[2015-09-30T22:41Z] INFO  23:41:03,115 MuTect - [MUTECT] Processed 187010141 reads in 617 ms
[2015-09-30T22:41Z] INFO  23:41:03,217 MuTect - [MUTECT] Processed 127007557 reads in 679 ms
[2015-09-30T22:41Z] INFO  23:41:03,252 MuTect - [MUTECT] Processed 12000697 reads in 668 ms
[2015-09-30T22:41Z] INFO  23:41:03,761 MuTect - [MUTECT] Processed 188010236 reads in 646 ms
[2015-09-30T22:41Z] INFO  23:41:03,830 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:03,863 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:03,903 MuTect - [MUTECT] Processed 13000792 reads in 651 ms
[2015-09-30T22:41Z] INFO  23:41:03,908 MuTect - [MUTECT] Processed 128007614 reads in 691 ms
[2015-09-30T22:41Z] INFO  23:41:04,413 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:04,438 MuTect - [MUTECT] Processed 189010294 reads in 677 ms
[2015-09-30T22:41Z] INFO  23:41:04,582 MuTect - [MUTECT] Processed 14000893 reads in 680 ms
[2015-09-30T22:41Z] INFO  23:41:04,594 MuTect - [MUTECT] Processed 129007694 reads in 685 ms
[2015-09-30T22:41Z] INFO  23:41:05,100 MuTect - [MUTECT] Processed 190010318 reads in 662 ms
[2015-09-30T22:41Z] INFO  23:41:05,275 MuTect - [MUTECT] Processed 15000948 reads in 693 ms
[2015-09-30T22:41Z] INFO  23:41:05,322 MuTect - [MUTECT] Processed 130007804 reads in 729 ms
[2015-09-30T22:41Z] INFO  23:41:05,734 MuTect - [MUTECT] Processed 191010326 reads in 634 ms
[2015-09-30T22:41Z] INFO  23:41:06,005 MuTect - [MUTECT] Processed 131007920 reads in 683 ms
[2015-09-30T22:41Z] INFO  23:41:06,032 MuTect - [MUTECT] Processed 16001005 reads in 757 ms
[2015-09-30T22:41Z] INFO  23:41:06,061 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:06,399 MuTect - [MUTECT] Processed 192010333 reads in 665 ms
[2015-09-30T22:41Z] INFO  23:41:06,510 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:06,644 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:06,723 MuTect - [MUTECT] Processed 132008042 reads in 718 ms
[2015-09-30T22:41Z] INFO  23:41:06,897 MuTect - [MUTECT] Processed 17001017 reads in 865 ms
[2015-09-30T22:41Z] INFO  23:41:07,147 MuTect - [MUTECT] Processed 193010346 reads in 748 ms
[2015-09-30T22:41Z] INFO  23:41:07,415 MuTect - [MUTECT] Processed 133008080 reads in 692 ms
[2015-09-30T22:41Z] INFO  23:41:07,635 MuTect - [MUTECT] Processed 18001166 reads in 738 ms
[2015-09-30T22:41Z] INFO  23:41:07,836 MuTect - [MUTECT] Processed 194010412 reads in 689 ms
[2015-09-30T22:41Z] INFO  23:41:08,139 MuTect - [MUTECT] Processed 134008149 reads in 724 ms
[2015-09-30T22:41Z] INFO  23:41:08,167 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:08,521 MuTect - [MUTECT] Processed 195010508 reads in 685 ms
[2015-09-30T22:41Z] INFO  23:41:08,685 MuTect - [MUTECT] Processed 19001214 reads in 1050 ms
[2015-09-30T22:41Z] INFO  23:41:08,853 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:08,899 MuTect - [MUTECT] Processed 135008177 reads in 760 ms
[2015-09-30T22:41Z] INFO  23:41:09,207 MuTect - [MUTECT] Processed 196010578 reads in 686 ms
[2015-09-30T22:41Z] INFO  23:41:09,362 MuTect - [MUTECT] Processed 20001262 reads in 677 ms
[2015-09-30T22:41Z] INFO  23:41:09,578 MuTect - [MUTECT] Processed 136008236 reads in 679 ms
[2015-09-30T22:41Z] INFO  23:41:09,871 MuTect - [MUTECT] Processed 197010581 reads in 664 ms
[2015-09-30T22:41Z] INFO  23:41:10,030 MuTect - [MUTECT] Processed 21001364 reads in 668 ms
[2015-09-30T22:41Z] INFO  23:41:10,331 MuTect - [MUTECT] Processed 137008317 reads in 753 ms
[2015-09-30T22:41Z] INFO  23:41:10,412 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:10,449 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:10,517 MuTect - [MUTECT] Processed 198010688 reads in 646 ms
[2015-09-30T22:41Z] INFO  23:41:10,728 MuTect - [MUTECT] Processed 22001463 reads in 698 ms
[2015-09-30T22:41Z] INFO  23:41:10,998 MuTect - [MUTECT] Processed 138008360 reads in 667 ms
[2015-09-30T22:41Z] INFO  23:41:11,086 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:11,171 MuTect - [MUTECT] Processed 199010726 reads in 654 ms
[2015-09-30T22:41Z] INFO  23:41:11,462 MuTect - [MUTECT] Processed 23001486 reads in 734 ms
[2015-09-30T22:41Z] INFO  23:41:11,662 MuTect - [MUTECT] Processed 139008391 reads in 664 ms
[2015-09-30T22:41Z] INFO  23:41:11,831 MuTect - [MUTECT] Processed 200010764 reads in 660 ms
[2015-09-30T22:41Z] INFO  23:41:12,102 MuTect - [MUTECT] Processed 24001560 reads in 640 ms
[2015-09-30T22:41Z] INFO  23:41:12,325 MuTect - [MUTECT] Processed 140008423 reads in 663 ms
[2015-09-30T22:41Z] INFO  23:41:12,450 MuTect - [MUTECT] Processed 201010767 reads in 618 ms
[2015-09-30T22:41Z] INFO  23:41:12,665 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:12,841 MuTect - [MUTECT] Processed 25001900 reads in 739 ms
[2015-09-30T22:41Z] INFO  23:41:12,980 MuTect - [MUTECT] Processed 141008491 reads in 654 ms
[2015-09-30T22:41Z] INFO  23:41:13,141 MuTect - [MUTECT] Processed 202010796 reads in 692 ms
[2015-09-30T22:41Z] INFO  23:41:13,358 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:13,676 MuTect - [MUTECT] Processed 142008504 reads in 697 ms
[2015-09-30T22:41Z] INFO  23:41:13,821 MuTect - [MUTECT] Processed 203010851 reads in 680 ms
[2015-09-30T22:41Z] INFO  23:41:13,836 MuTect - [MUTECT] Processed 26002013 reads in 995 ms
[2015-09-30T22:41Z] INFO  23:41:14,195 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:14,405 MuTect - [MUTECT] Processed 143008552 reads in 729 ms
[2015-09-30T22:41Z] INFO  23:41:14,506 MuTect - [MUTECT] Processed 204010910 reads in 685 ms
[2015-09-30T22:41Z] INFO  23:41:14,950 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:15,116 MuTect - [MUTECT] Processed 27002089 reads in 1280 ms
[2015-09-30T22:41Z] INFO  23:41:15,123 MuTect - [MUTECT] Processed 144008591 reads in 718 ms
[2015-09-30T22:41Z] INFO  23:41:15,223 MuTect - [MUTECT] Processed 205010926 reads in 717 ms
[2015-09-30T22:41Z] INFO  23:41:15,693 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:15,823 MuTect - [MUTECT] Processed 145008640 reads in 700 ms
[2015-09-30T22:41Z] INFO  23:41:15,891 MuTect - [MUTECT] Processed 28002109 reads in 775 ms
[2015-09-30T22:41Z] INFO  23:41:15,921 MuTect - [MUTECT] Processed 206010955 reads in 698 ms
[2015-09-30T22:41Z] INFO  23:41:16,528 MuTect - [MUTECT] Processed 146008754 reads in 705 ms
[2015-09-30T22:41Z] INFO  23:41:16,631 MuTect - [MUTECT] Processed 29002134 reads in 740 ms
[2015-09-30T22:41Z] INFO  23:41:16,637 MuTect - [MUTECT] Processed 207010955 reads in 716 ms
[2015-09-30T22:41Z] INFO  23:41:17,200 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:17,216 MuTect - [MUTECT] Processed 147008822 reads in 688 ms
[2015-09-30T22:41Z] INFO  23:41:17,257 MuTect - [MUTECT] Processed 30002192 reads in 626 ms
[2015-09-30T22:41Z] INFO  23:41:17,306 MuTect - [MUTECT] Processed 208011086 reads in 669 ms
[2015-09-30T22:41Z] INFO  23:41:17,535 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:17,563 ProgressMeter -     16:11136318        4.01e+06  100.0 s       24.0 s     40.2%         4.1 m     2.5 m
[2015-09-30T22:41Z] INFO  23:41:17,903 MuTect - [MUTECT] Processed 148008900 reads in 687 ms
[2015-09-30T22:41Z] INFO  23:41:17,914 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:17,957 MuTect - [MUTECT] Processed 209011199 reads in 651 ms
[2015-09-30T22:41Z] INFO  23:41:18,644 MuTect - [MUTECT] Processed 210011283 reads in 687 ms
[2015-09-30T22:41Z] INFO  23:41:19,190 MuTect - [MUTECT] Processed 149008934 reads in 1287 ms
[2015-09-30T22:41Z] INFO  23:41:19,312 MuTect - [MUTECT] Processed 211011325 reads in 668 ms
[2015-09-30T22:41Z] INFO  23:41:19,359 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:19,993 MuTect - [MUTECT] Processed 212011346 reads in 681 ms
[2015-09-30T22:41Z] INFO  23:41:20,076 MuTect - [MUTECT] Processed 31002211 reads in 2819 ms
[2015-09-30T22:41Z] INFO  23:41:20,471 MuTect - [MUTECT] Processed 150008993 reads in 1281 ms
[2015-09-30T22:41Z] INFO  23:41:20,677 MuTect - [MUTECT] Processed 213011368 reads in 684 ms
[2015-09-30T22:41Z] INFO  23:41:21,239 MuTect - [MUTECT] Processed 32002328 reads in 1163 ms
[2015-09-30T22:41Z] INFO  23:41:21,343 MuTect - [MUTECT] Processed 214011373 reads in 666 ms
[2015-09-30T22:41Z] INFO  23:41:21,597 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:21,850 MuTect - [MUTECT] Processed 151009015 reads in 1379 ms
[2015-09-30T22:41Z] INFO  23:41:22,002 MuTect - [MUTECT] Processed 33002375 reads in 763 ms
[2015-09-30T22:41Z] INFO  23:41:22,022 MuTect - [MUTECT] Processed 215011438 reads in 679 ms
[2015-09-30T22:41Z] INFO  23:41:22,139 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:22,202 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:22,584 MuTect - [MUTECT] Processed 152009036 reads in 734 ms
[2015-09-30T22:41Z] INFO  23:41:22,645 MuTect - [MUTECT] Processed 34002452 reads in 643 ms
[2015-09-30T22:41Z] INFO  23:41:22,719 MuTect - [MUTECT] Processed 216011452 reads in 697 ms
[2015-09-30T22:41Z] INFO  23:41:23,160 ProgressMeter -     16:46726328        8.22e+05   30.0 s       36.0 s     28.0%       107.0 s    77.0 s
[2015-09-30T22:41Z] INFO  23:41:23,292 MuTect - [MUTECT] Processed 153009162 reads in 708 ms
[2015-09-30T22:41Z] INFO  23:41:23,293 MuTect - [MUTECT] Processed 35002532 reads in 648 ms
[2015-09-30T22:41Z] INFO  23:41:23,406 MuTect - [MUTECT] Processed 217011511 reads in 687 ms
[2015-09-30T22:41Z] INFO  23:41:23,931 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:23,937 MuTect - [MUTECT] Processed 36002585 reads in 644 ms
[2015-09-30T22:41Z] INFO  23:41:24,006 MuTect - [MUTECT] Processed 154009212 reads in 714 ms
[2015-09-30T22:41Z] INFO  23:41:24,088 MuTect - [MUTECT] Processed 218011529 reads in 682 ms
[2015-09-30T22:41Z] INFO  23:41:24,457 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:24,527 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:24,563 MuTect - [MUTECT] Processed 37002635 reads in 626 ms
[2015-09-30T22:41Z] INFO  23:41:24,686 MuTect - [MUTECT] Processed 155009247 reads in 680 ms
[2015-09-30T22:41Z] INFO  23:41:24,745 MuTect - [MUTECT] Processed 219011570 reads in 657 ms
[2015-09-30T22:41Z] INFO  23:41:25,183 MuTect - [MUTECT] Processed 38002651 reads in 620 ms
[2015-09-30T22:41Z] INFO  23:41:25,307 ProgressMeter -     15:91459258        6.76e+06    2.5 m       22.0 s     96.9%         2.6 m     4.0 s
[2015-09-30T22:41Z] INFO  23:41:25,436 MuTect - [MUTECT] Processed 220011616 reads in 691 ms
[2015-09-30T22:41Z] INFO  23:41:25,441 MuTect - [MUTECT] Processed 156009269 reads in 755 ms
[2015-09-30T22:41Z] INFO  23:41:25,838 MuTect - [MUTECT] Processed 39002725 reads in 655 ms
[2015-09-30T22:41Z] INFO  23:41:26,102 MuTect - [MUTECT] Processed 221011704 reads in 666 ms
[2015-09-30T22:41Z] INFO  23:41:26,154 MuTect - [MUTECT] Processed 157009279 reads in 713 ms
[2015-09-30T22:41Z] INFO  23:41:26,245 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:26,518 MuTect - [MUTECT] Processed 40002761 reads in 680 ms
[2015-09-30T22:41Z] INFO  23:41:26,765 MuTect - [MUTECT] Processed 222011794 reads in 663 ms
[2015-09-30T22:41Z] INFO  23:41:26,833 MuTect - [MUTECT] Processed 158009366 reads in 679 ms
[2015-09-30T22:41Z] INFO  23:41:26,994 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:27,203 MuTect - [MUTECT] Processed 41002791 reads in 685 ms
[2015-09-30T22:41Z] INFO  23:41:27,235 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:27,446 MuTect - [MUTECT] Processed 223011880 reads in 681 ms
[2015-09-30T22:41Z] INFO  23:41:27,506 MuTect - [MUTECT] Processed 159009459 reads in 673 ms
[2015-09-30T22:41Z] INFO  23:41:27,870 MuTect - [MUTECT] Processed 42002874 reads in 667 ms
[2015-09-30T22:41Z] INFO  23:41:28,129 MuTect - [MUTECT] Processed 224011921 reads in 683 ms
[2015-09-30T22:41Z] INFO  23:41:28,326 MuTect - [MUTECT] Processed 160009506 reads in 820 ms
[2015-09-30T22:41Z] INFO  23:41:28,456 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:28,514 MuTect - [MUTECT] Processed 43002882 reads in 644 ms
[2015-09-30T22:41Z] INFO  23:41:28,776 MuTect - [MUTECT] Processed 225011930 reads in 647 ms
[2015-09-30T22:41Z] INFO  23:41:29,009 MuTect - [MUTECT] Processed 161009564 reads in 683 ms
[2015-09-30T22:41Z] INFO  23:41:29,155 MuTect - [MUTECT] Processed 44002942 reads in 641 ms
[2015-09-30T22:41Z] INFO  23:41:29,464 MuTect - [MUTECT] Processed 226012034 reads in 688 ms
[2015-09-30T22:41Z] INFO  23:41:29,493 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:29,585 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:29,667 MuTect - [MUTECT] Processed 162009607 reads in 658 ms
[2015-09-30T22:41Z] INFO  23:41:29,796 MuTect - [MUTECT] Processed 45003046 reads in 641 ms
[2015-09-30T22:41Z] INFO  23:41:30,134 MuTect - [MUTECT] Processed 227012089 reads in 669 ms
[2015-09-30T22:41Z] INFO  23:41:30,315 MuTect - [MUTECT] Processed 163009667 reads in 648 ms
[2015-09-30T22:41Z] INFO  23:41:30,433 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:41Z] INFO  23:41:30,437 ProgressMeter -            done        6.99e+06    2.6 m       22.0 s    100.0%         2.6 m     0.0 s
[2015-09-30T22:41Z] INFO  23:41:30,438 ProgressMeter - Total runtime 155.14 secs, 2.59 min, 0.04 hours
[2015-09-30T22:41Z] INFO  23:41:30,469 MuTect - [MUTECT] Processed 46003048 reads in 672 ms
[2015-09-30T22:41Z] INFO  23:41:30,505 MicroScheduler - 173221 reads were filtered out during the traversal out of approximately 2711672 total reads (6.39%)
[2015-09-30T22:41Z] INFO  23:41:30,505 MicroScheduler -   -> 129664 reads (4.78% of total) failing DuplicateReadFilter
[2015-09-30T22:41Z] INFO  23:41:30,505 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:41Z] INFO  23:41:30,506 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:41Z] INFO  23:41:30,506 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:41Z] INFO  23:41:30,506 MicroScheduler -   -> 43557 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:41Z] INFO  23:41:30,998 MuTect - [MUTECT] Processed 164009715 reads in 683 ms
[2015-09-30T22:41Z] INFO  23:41:31,190 MuTect - [MUTECT] Processed 47003070 reads in 722 ms
[2015-09-30T22:41Z] INFO  23:41:31,548 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:41Z] bgzip syn3-15_62148224_93170844-raw-mutect.vcf
[2015-09-30T22:41Z] INFO  23:41:31,613 MuTect - [MUTECT] Processed 165009818 reads in 615 ms
[2015-09-30T22:41Z] tabix index syn3-15_62148224_93170844-raw-mutect.vcf.gz
[2015-09-30T22:41Z] INFO  23:41:31,864 MuTect - [MUTECT] Processed 48003114 reads in 674 ms
[2015-09-30T22:41Z] INFO  23:41:31,970 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:32,257 MuTect - [MUTECT] Processed 166009879 reads in 644 ms
[2015-09-30T22:41Z] INFO  23:41:32,556 MuTect - [MUTECT] Processed 49003171 reads in 692 ms
[2015-09-30T22:41Z] INFO  23:41:32,849 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:32,921 MuTect - [MUTECT] Processed 167010056 reads in 664 ms
[2015-09-30T22:41Z] INFO  23:41:33,220 MuTect - [MUTECT] Processed 50003205 reads in 664 ms
[2015-09-30T22:41Z] INFO  23:41:33,522 MuTect - [MUTECT] Processed 168010252 reads in 601 ms
[2015-09-30T22:41Z] INFO  23:41:33,876 MuTect - [MUTECT] Processed 51003320 reads in 656 ms
[2015-09-30T22:41Z] MuTect: MuTect
[2015-09-30T22:41Z] INFO  23:41:34,113 MuTect - [MUTECT] Processed 169010425 reads in 591 ms
[2015-09-30T22:41Z] INFO  23:41:34,189 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:34,518 MuTect - [MUTECT] Processed 52003341 reads in 642 ms
[2015-09-30T22:41Z] INFO  23:41:34,737 MuTect - [MUTECT] Processed 170010556 reads in 624 ms
[2015-09-30T22:41Z] INFO  23:41:35,179 MuTect - [MUTECT] Processed 53003430 reads in 661 ms
[2015-09-30T22:41Z] INFO  23:41:35,383 MuTect - [MUTECT] Processed 171010663 reads in 646 ms
[2015-09-30T22:41Z] INFO  23:41:35,792 MuTect - [MUTECT] Processed 54003522 reads in 613 ms
[2015-09-30T22:41Z] INFO  23:41:36,042 MuTect - [MUTECT] Processed 172010713 reads in 659 ms
[2015-09-30T22:41Z] INFO  23:41:36,254 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:36,313 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/16/syn3-16_64294277_90354753-raw-mutect-regions.bed to be BED
[2015-09-30T22:41Z] INFO  23:41:36,370 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:41Z] INFO  23:41:36,371 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:41Z] INFO  23:41:36,371 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:41Z] INFO  23:41:36,371 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:41Z] INFO  23:41:36,375 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/16/syn3-16_64294277_90354753-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/16/tx/tmpIu7tG6/syn3-16_64294277_90354753-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:41Z] INFO  23:41:36,375 HelpFormatter - Date/Time: 2015/09/30 23:41:36
[2015-09-30T22:41Z] INFO  23:41:36,375 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:41Z] INFO  23:41:36,375 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:41Z] INFO  23:41:36,403 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:41Z] INFO  23:41:36,407 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:41Z] INFO  23:41:36,459 MuTect - [MUTECT] Processed 55003578 reads in 667 ms
[2015-09-30T22:41Z] INFO  23:41:36,460 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:41Z] INFO  23:41:36,510 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:41Z] INFO  23:41:36,517 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:41Z] INFO  23:41:36,559 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:36,570 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2015-09-30T22:41Z] INFO  23:41:36,593 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:41Z] INFO  23:41:36,731 MuTect - [MUTECT] Processed 173010763 reads in 689 ms
[2015-09-30T22:41Z] INFO  23:41:36,772 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:41Z] INFO  23:41:36,885 IntervalUtils - Processing 1897108 bp from intervals
[2015-09-30T22:41Z] INFO  23:41:36,889 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:41Z] INFO  23:41:36,890 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:41Z] INFO  23:41:37,069 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:41Z] INFO  23:41:37,147 MuTect - [MUTECT] Processed 56003624 reads in 688 ms
[2015-09-30T22:41Z] INFO  23:41:37,235 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:41Z] INFO  23:41:37,235 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:41Z] INFO  23:41:37,235 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:41Z] INFO  23:41:37,236 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:41Z] INFO  23:41:37,378 MuTect - [MUTECT] Processed 174010764 reads in 646 ms
[2015-09-30T22:41Z] INFO  23:41:37,835 MuTect - [MUTECT] Processed 57003639 reads in 688 ms
[2015-09-30T22:41Z] INFO  23:41:38,057 MuTect - [MUTECT] Processed 175010789 reads in 680 ms
[2015-09-30T22:41Z] INFO  23:41:38,585 MuTect - [MUTECT] Processed 58003667 reads in 750 ms
[2015-09-30T22:41Z] INFO  23:41:38,734 MuTect - [MUTECT] Processed 176010862 reads in 677 ms
[2015-09-30T22:41Z] INFO  23:41:38,810 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:39,293 MuTect - [MUTECT] Processed 59003738 reads in 708 ms
[2015-09-30T22:41Z] INFO  23:41:39,359 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:39,380 MuTect - [MUTECT] Processed 177010965 reads in 646 ms
[2015-09-30T22:41Z] INFO  23:41:39,736 MuTect - [MUTECT] Processed 1000060 reads in 2438 ms
[2015-09-30T22:41Z] INFO  23:41:40,004 MuTect - [MUTECT] Processed 60003744 reads in 710 ms
[2015-09-30T22:41Z] INFO  23:41:40,043 MuTect - [MUTECT] Processed 178011066 reads in 663 ms
[2015-09-30T22:41Z] INFO  23:41:40,629 MuTect - [MUTECT] Processed 2000066 reads in 893 ms
[2015-09-30T22:41Z] INFO  23:41:40,695 MuTect - [MUTECT] Processed 179011107 reads in 652 ms
[2015-09-30T22:41Z] INFO  23:41:40,701 MuTect - [MUTECT] Processed 61003811 reads in 697 ms
[2015-09-30T22:41Z] INFO  23:41:41,334 MuTect - [MUTECT] Processed 180011173 reads in 639 ms
[2015-09-30T22:41Z] INFO  23:41:41,350 MuTect - [MUTECT] Processed 3000153 reads in 721 ms
[2015-09-30T22:41Z] INFO  23:41:41,413 MuTect - [MUTECT] Processed 62003822 reads in 713 ms
[2015-09-30T22:41Z] INFO  23:41:41,607 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:41,699 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:41,713 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:41,985 MuTect - [MUTECT] Processed 181011244 reads in 651 ms
[2015-09-30T22:41Z] INFO  23:41:42,069 MuTect - [MUTECT] Processed 4000191 reads in 719 ms
[2015-09-30T22:41Z] INFO  23:41:42,107 MuTect - [MUTECT] Processed 63003880 reads in 694 ms
[2015-09-30T22:41Z] INFO  23:41:42,615 MuTect - [MUTECT] Processed 182011262 reads in 630 ms
[2015-09-30T22:41Z] INFO  23:41:42,789 MuTect - [MUTECT] Processed 5000235 reads in 720 ms
[2015-09-30T22:41Z] INFO  23:41:42,815 MuTect - [MUTECT] Processed 64003971 reads in 708 ms
[2015-09-30T22:41Z] INFO  23:41:43,258 MuTect - [MUTECT] Processed 183011321 reads in 643 ms
[2015-09-30T22:41Z] INFO  23:41:43,525 MuTect - [MUTECT] Processed 6000321 reads in 736 ms
[2015-09-30T22:41Z] INFO  23:41:43,562 MuTect - [MUTECT] Processed 65004015 reads in 747 ms
[2015-09-30T22:41Z] INFO  23:41:43,819 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:43,963 MuTect - [MUTECT] Processed 184011400 reads in 705 ms
[2015-09-30T22:41Z] INFO  23:41:43,972 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:44,249 MuTect - [MUTECT] Processed 7000404 reads in 724 ms
[2015-09-30T22:41Z] INFO  23:41:44,255 MuTect - [MUTECT] Processed 66004033 reads in 693 ms
[2015-09-30T22:41Z] INFO  23:41:44,313 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:44,622 MuTect - [MUTECT] Processed 185011459 reads in 659 ms
[2015-09-30T22:41Z] INFO  23:41:44,918 MuTect - [MUTECT] Processed 8000445 reads in 669 ms
[2015-09-30T22:41Z] INFO  23:41:44,946 MuTect - [MUTECT] Processed 67004163 reads in 691 ms
[2015-09-30T22:41Z] INFO  23:41:45,291 MuTect - [MUTECT] Processed 186011475 reads in 669 ms
[2015-09-30T22:41Z] INFO  23:41:45,584 MuTect - [MUTECT] Processed 9000460 reads in 666 ms
[2015-09-30T22:41Z] INFO  23:41:45,636 MuTect - [MUTECT] Processed 68004205 reads in 690 ms
[2015-09-30T22:41Z] INFO  23:41:45,977 MuTect - [MUTECT] Processed 187011507 reads in 686 ms
[2015-09-30T22:41Z] INFO  23:41:46,148 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:46,260 MuTect - [MUTECT] Processed 10000531 reads in 676 ms
[2015-09-30T22:41Z] INFO  23:41:46,385 MuTect - [MUTECT] Processed 69004287 reads in 749 ms
[2015-09-30T22:41Z] INFO  23:41:46,513 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:46,653 MuTect - [MUTECT] Processed 188011581 reads in 676 ms
[2015-09-30T22:41Z] INFO  23:41:46,742 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:46,978 MuTect - [MUTECT] Processed 11000565 reads in 718 ms
[2015-09-30T22:41Z] INFO  23:41:47,410 MuTect - [MUTECT] Processed 189011656 reads in 757 ms
[2015-09-30T22:41Z] INFO  23:41:47,515 MuTect - [MUTECT] Processed 70004332 reads in 1130 ms
[2015-09-30T22:41Z] INFO  23:41:47,651 MuTect - [MUTECT] Processed 12000605 reads in 673 ms
[2015-09-30T22:41Z] INFO  23:41:47,995 MuTect - [MUTECT] Processed 190011818 reads in 585 ms
[2015-09-30T22:41Z] INFO  23:41:48,168 MuTect - [MUTECT] Processed 71004433 reads in 653 ms
[2015-09-30T22:41Z] INFO  23:41:48,293 MuTect - [MUTECT] Processed 13000691 reads in 642 ms
[2015-09-30T22:41Z] INFO  23:41:48,539 MuTect - [MUTECT] Processed 191011913 reads in 544 ms
[2015-09-30T22:41Z] INFO  23:41:48,746 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:48,821 MuTect - [MUTECT] Processed 72004483 reads in 652 ms
[2015-09-30T22:41Z] INFO  23:41:49,023 MuTect - [MUTECT] Processed 14000767 reads in 730 ms
[2015-09-30T22:41Z] INFO  23:41:49,160 MuTect - [MUTECT] Processed 192012011 reads in 621 ms
[2015-09-30T22:41Z] INFO  23:41:49,450 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:49,470 MuTect - [MUTECT] Processed 73004573 reads in 650 ms
[2015-09-30T22:41Z] INFO  23:41:49,649 MuTect - [MUTECT] Processed 15000827 reads in 626 ms
[2015-09-30T22:41Z] INFO  23:41:49,719 MuTect - [MUTECT] Processed 193012043 reads in 559 ms
[2015-09-30T22:41Z] INFO  23:41:50,136 MuTect - [MUTECT] Processed 74004643 reads in 666 ms
[2015-09-30T22:41Z] INFO  23:41:50,267 MuTect - [MUTECT] Processed 16000907 reads in 618 ms
[2015-09-30T22:41Z] INFO  23:41:50,315 MuTect - [MUTECT] Processed 194012127 reads in 596 ms
[2015-09-30T22:41Z] INFO  23:41:50,827 MuTect - [MUTECT] Processed 75004699 reads in 691 ms
[2015-09-30T22:41Z] INFO  23:41:50,889 MuTect - [MUTECT] Processed 17000998 reads in 622 ms
[2015-09-30T22:41Z] INFO  23:41:50,896 MuTect - [MUTECT] Processed 195012231 reads in 581 ms
[2015-09-30T22:41Z] INFO  23:41:50,982 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:51,513 MuTect - [MUTECT] Processed 76004780 reads in 686 ms
[2015-09-30T22:41Z] INFO  23:41:51,537 MuTect - [MUTECT] Processed 18001112 reads in 648 ms
[2015-09-30T22:41Z] INFO  23:41:51,570 MuTect - [MUTECT] Processed 196012355 reads in 674 ms
[2015-09-30T22:41Z] INFO  23:41:51,704 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:52,158 MuTect - [MUTECT] Processed 19001223 reads in 621 ms
[2015-09-30T22:41Z] INFO  23:41:52,191 MuTect - [MUTECT] Processed 77004788 reads in 678 ms
[2015-09-30T22:41Z] INFO  23:41:52,258 MuTect - [MUTECT] Processed 197012375 reads in 688 ms
[2015-09-30T22:41Z] INFO  23:41:52,288 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:52,808 MuTect - [MUTECT] Processed 20001319 reads in 650 ms
[2015-09-30T22:41Z] INFO  23:41:52,823 MuTect - [MUTECT] Processed 78004831 reads in 632 ms
[2015-09-30T22:41Z] INFO  23:41:52,841 MuTect - [MUTECT] Processed 198012402 reads in 583 ms
[2015-09-30T22:41Z] INFO  23:41:53,079 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:53,161 ProgressMeter -     16:56913090        2.24e+06   60.0 s       26.0 s     73.1%        82.0 s    22.0 s
[2015-09-30T22:41Z] INFO  23:41:53,431 MuTect - [MUTECT] Processed 21001396 reads in 623 ms
[2015-09-30T22:41Z] INFO  23:41:53,457 MuTect - [MUTECT] Processed 199012446 reads in 616 ms
[2015-09-30T22:41Z] INFO  23:41:53,494 MuTect - [MUTECT] Processed 79004919 reads in 671 ms
[2015-09-30T22:41Z] INFO  23:41:54,049 MuTect - [MUTECT] Processed 22001497 reads in 618 ms
[2015-09-30T22:41Z] INFO  23:41:54,060 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:54,106 MuTect - [MUTECT] Processed 200012558 reads in 649 ms
[2015-09-30T22:41Z] INFO  23:41:54,188 MuTect - [MUTECT] Processed 80004967 reads in 694 ms
[2015-09-30T22:41Z] INFO  23:41:54,668 MuTect - [MUTECT] Processed 201012606 reads in 562 ms
[2015-09-30T22:41Z] INFO  23:41:54,677 MuTect - [MUTECT] Processed 23001566 reads in 628 ms
[2015-09-30T22:41Z] INFO  23:41:54,890 MuTect - [MUTECT] Processed 81005060 reads in 702 ms
[2015-09-30T22:41Z] INFO  23:41:55,248 MuTect - [MUTECT] Processed 202012716 reads in 580 ms
[2015-09-30T22:41Z] INFO  23:41:55,250 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:55,318 MuTect - [MUTECT] Processed 24001569 reads in 641 ms
[2015-09-30T22:41Z] INFO  23:41:55,584 MuTect - [MUTECT] Processed 82005107 reads in 694 ms
[2015-09-30T22:41Z] INFO  23:41:55,780 MuTect - [MUTECT] Processed 203012781 reads in 532 ms
[2015-09-30T22:41Z] INFO  23:41:55,941 MuTect - [MUTECT] Processed 25001586 reads in 622 ms
[2015-09-30T22:41Z] INFO  23:41:56,265 MuTect - [MUTECT] Processed 83005155 reads in 681 ms
[2015-09-30T22:41Z] INFO  23:41:56,320 MuTect - [MUTECT] Processed 204013042 reads in 540 ms
[2015-09-30T22:41Z] INFO  23:41:56,358 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:56,558 MuTect - [MUTECT] Processed 26001666 reads in 618 ms
[2015-09-30T22:41Z] INFO  23:41:56,892 MuTect - [MUTECT] Processed 205013141 reads in 572 ms
[2015-09-30T22:41Z] INFO  23:41:56,920 MuTect - [MUTECT] Processed 84005238 reads in 655 ms
[2015-09-30T22:41Z] INFO  23:41:57,175 MuTect - [MUTECT] Processed 27001715 reads in 616 ms
[2015-09-30T22:41Z] INFO  23:41:57,327 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:57,442 MuTect - [MUTECT] Processed 206013397 reads in 550 ms
[2015-09-30T22:41Z] INFO  23:41:57,564 ProgressMeter -     16:18487249        5.50e+06    2.3 m       25.0 s     56.4%         4.1 m   108.0 s
[2015-09-30T22:41Z] INFO  23:41:57,594 MuTect - [MUTECT] Processed 85005331 reads in 674 ms
[2015-09-30T22:41Z] INFO  23:41:57,797 MuTect - [MUTECT] Processed 28001793 reads in 623 ms
[2015-09-30T22:41Z] INFO  23:41:58,025 MuTect - [MUTECT] Processed 207013398 reads in 583 ms
[2015-09-30T22:41Z] INFO  23:41:58,252 MuTect - [MUTECT] Processed 86005354 reads in 658 ms
[2015-09-30T22:41Z] INFO  23:41:58,424 MuTect - [MUTECT] Processed 29001833 reads in 627 ms
[2015-09-30T22:41Z] INFO  23:41:58,447 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:58,601 MuTect - [MUTECT] Processed 208013428 reads in 576 ms
[2015-09-30T22:41Z] INFO  23:41:58,898 MuTect - [MUTECT] Processed 87005373 reads in 646 ms
[2015-09-30T22:41Z] INFO  23:41:59,053 MuTect - [MUTECT] Processed 30001939 reads in 629 ms
[2015-09-30T22:41Z] INFO  23:41:59,068 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:59,250 MuTect - [MUTECT] Processed 209013462 reads in 649 ms
[2015-09-30T22:41Z] INFO  23:41:59,465 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:41Z] INFO  23:41:59,544 MuTect - [MUTECT] Processed 88005473 reads in 646 ms
[2015-09-30T22:41Z] INFO  23:41:59,689 MuTect - [MUTECT] Processed 31001984 reads in 636 ms
[2015-09-30T22:41Z] INFO  23:41:59,908 MuTect - [MUTECT] Processed 210013511 reads in 657 ms
[2015-09-30T22:42Z] INFO  23:42:00,184 MuTect - [MUTECT] Processed 89005562 reads in 640 ms
[2015-09-30T22:42Z] INFO  23:42:00,318 MuTect - [MUTECT] Processed 32001995 reads in 628 ms
[2015-09-30T22:42Z] INFO  23:42:00,559 MuTect - [MUTECT] Processed 211013575 reads in 652 ms
[2015-09-30T22:42Z] INFO  23:42:00,705 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:00,863 MuTect - [MUTECT] Processed 90005613 reads in 679 ms
[2015-09-30T22:42Z] INFO  23:42:00,955 MuTect - [MUTECT] Processed 33001997 reads in 638 ms
[2015-09-30T22:42Z] INFO  23:42:01,229 MuTect - [MUTECT] Processed 212013586 reads in 670 ms
[2015-09-30T22:42Z] INFO  23:42:01,516 MuTect - [MUTECT] Processed 91005660 reads in 653 ms
[2015-09-30T22:42Z] INFO  23:42:01,562 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:01,581 MuTect - [MUTECT] Processed 34002062 reads in 626 ms
[2015-09-30T22:42Z] INFO  23:42:01,654 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:01,934 MuTect - [MUTECT] Processed 213013587 reads in 705 ms
[2015-09-30T22:42Z] INFO  23:42:02,155 MuTect - [MUTECT] Processed 92005745 reads in 639 ms
[2015-09-30T22:42Z] INFO  23:42:02,205 MuTect - [MUTECT] Processed 35002103 reads in 624 ms
[2015-09-30T22:42Z] INFO  23:42:02,613 MuTect - [MUTECT] Processed 214013684 reads in 679 ms
[2015-09-30T22:42Z] INFO  23:42:02,812 MuTect - [MUTECT] Processed 93005825 reads in 657 ms
[2015-09-30T22:42Z] INFO  23:42:02,823 MuTect - [MUTECT] Processed 36002138 reads in 618 ms
[2015-09-30T22:42Z] INFO  23:42:02,852 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:03,243 MuTect - [MUTECT] Processed 215013696 reads in 630 ms
[2015-09-30T22:42Z] INFO  23:42:03,434 MuTect - [MUTECT] Processed 37002178 reads in 611 ms
[2015-09-30T22:42Z] INFO  23:42:03,490 MuTect - [MUTECT] Processed 94005861 reads in 678 ms
[2015-09-30T22:42Z] INFO  23:42:03,686 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:03,886 MuTect - [MUTECT] Processed 216013770 reads in 643 ms
[2015-09-30T22:42Z] INFO  23:42:03,999 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:04,058 MuTect - [MUTECT] Processed 38002289 reads in 624 ms
[2015-09-30T22:42Z] INFO  23:42:04,169 MuTect - [MUTECT] Processed 95005867 reads in 679 ms
[2015-09-30T22:42Z] INFO  23:42:04,580 MuTect - [MUTECT] Processed 217013826 reads in 694 ms
[2015-09-30T22:42Z] INFO  23:42:04,708 MuTect - [MUTECT] Processed 39002402 reads in 650 ms
[2015-09-30T22:42Z] INFO  23:42:04,847 MuTect - [MUTECT] Processed 96005970 reads in 678 ms
[2015-09-30T22:42Z] INFO  23:42:05,028 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:05,276 MuTect - [MUTECT] Processed 218013875 reads in 696 ms
[2015-09-30T22:42Z] INFO  23:42:05,357 MuTect - [MUTECT] Processed 40002512 reads in 649 ms
[2015-09-30T22:42Z] INFO  23:42:05,493 MuTect - [MUTECT] Processed 97006129 reads in 646 ms
[2015-09-30T22:42Z] INFO  23:42:05,935 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:05,961 MuTect - [MUTECT] Processed 219013900 reads in 685 ms
[2015-09-30T22:42Z] INFO  23:42:06,019 MuTect - [MUTECT] Processed 41002626 reads in 662 ms
[2015-09-30T22:42Z] INFO  23:42:06,164 MuTect - [MUTECT] Processed 98006183 reads in 671 ms
[2015-09-30T22:42Z] INFO  23:42:06,405 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:06,661 MuTect - [MUTECT] Processed 220013905 reads in 700 ms
[2015-09-30T22:42Z] INFO  23:42:06,691 MuTect - [MUTECT] Processed 42002673 reads in 672 ms
[2015-09-30T22:42Z] INFO  23:42:06,800 MuTect - [MUTECT] Processed 99006241 reads in 636 ms
[2015-09-30T22:42Z] INFO  23:42:07,118 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:07,238 ProgressMeter -     16:68269253        1.16e+06   30.0 s       25.0 s     20.6%         2.4 m   115.0 s
[2015-09-30T22:42Z] INFO  23:42:07,339 MuTect - [MUTECT] Processed 43002720 reads in 648 ms
[2015-09-30T22:42Z] INFO  23:42:07,360 MuTect - [MUTECT] Processed 221013965 reads in 699 ms
[2015-09-30T22:42Z] INFO  23:42:07,483 MuTect - [MUTECT] Processed 100006253 reads in 683 ms
[2015-09-30T22:42Z] INFO  23:42:07,995 MuTect - [MUTECT] Processed 44002812 reads in 656 ms
[2015-09-30T22:42Z] INFO  23:42:08,028 MuTect - [MUTECT] Processed 222013982 reads in 668 ms
[2015-09-30T22:42Z] INFO  23:42:08,122 MuTect - [MUTECT] Processed 101006320 reads in 639 ms
[2015-09-30T22:42Z] INFO  23:42:08,199 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:08,632 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:08,673 MuTect - [MUTECT] Processed 45002874 reads in 678 ms
[2015-09-30T22:42Z] INFO  23:42:08,707 MuTect - [MUTECT] Processed 223014068 reads in 679 ms
[2015-09-30T22:42Z] INFO  23:42:08,764 MuTect - [MUTECT] Processed 102006396 reads in 642 ms
[2015-09-30T22:42Z] INFO  23:42:09,157 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:09,376 MuTect - [MUTECT] Processed 46002941 reads in 703 ms
[2015-09-30T22:42Z] INFO  23:42:09,394 MuTect - [MUTECT] Processed 103006405 reads in 630 ms
[2015-09-30T22:42Z] INFO  23:42:09,404 MuTect - [MUTECT] Processed 224014144 reads in 697 ms
[2015-09-30T22:42Z] INFO  23:42:10,021 MuTect - [MUTECT] Processed 104006414 reads in 627 ms
[2015-09-30T22:42Z] INFO  23:42:10,059 MuTect - [MUTECT] Processed 47002954 reads in 683 ms
[2015-09-30T22:42Z] INFO  23:42:10,148 MuTect - [MUTECT] Processed 225014224 reads in 744 ms
[2015-09-30T22:42Z] INFO  23:42:10,619 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:10,695 MuTect - [MUTECT] Processed 105006475 reads in 673 ms
[2015-09-30T22:42Z] INFO  23:42:10,723 MuTect - [MUTECT] Processed 48002959 reads in 664 ms
[2015-09-30T22:42Z] INFO  23:42:10,868 MuTect - [MUTECT] Processed 226014286 reads in 720 ms
[2015-09-30T22:42Z] INFO  23:42:11,097 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:11,333 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:11,346 MuTect - [MUTECT] Processed 106006480 reads in 652 ms
[2015-09-30T22:42Z] INFO  23:42:11,431 MuTect - [MUTECT] Processed 49002974 reads in 708 ms
[2015-09-30T22:42Z] INFO  23:42:11,593 MuTect - [MUTECT] Processed 227014378 reads in 725 ms
[2015-09-30T22:42Z] INFO  23:42:11,990 MuTect - [MUTECT] Processed 107006532 reads in 644 ms
[2015-09-30T22:42Z] INFO  23:42:12,136 MuTect - [MUTECT] Processed 50003030 reads in 705 ms
[2015-09-30T22:42Z] INFO  23:42:12,274 MuTect - [MUTECT] Processed 228014412 reads in 681 ms
[2015-09-30T22:42Z] INFO  23:42:12,643 MuTect - [MUTECT] Processed 108006565 reads in 653 ms
[2015-09-30T22:42Z] INFO  23:42:12,818 MuTect - [MUTECT] Processed 51003154 reads in 682 ms
[2015-09-30T22:42Z] INFO  23:42:12,953 MuTect - [MUTECT] Processed 229014427 reads in 679 ms
[2015-09-30T22:42Z] INFO  23:42:12,969 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:13,313 MuTect - [MUTECT] Processed 109006645 reads in 670 ms
[2015-09-30T22:42Z] INFO  23:42:13,458 MuTect - [MUTECT] Processed 52003162 reads in 640 ms
[2015-09-30T22:42Z] INFO  23:42:13,565 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:13,622 MuTect - [MUTECT] Processed 230014500 reads in 669 ms
[2015-09-30T22:42Z] INFO  23:42:13,803 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:14,056 MuTect - [MUTECT] Processed 110006685 reads in 743 ms
[2015-09-30T22:42Z] INFO  23:42:14,140 MuTect - [MUTECT] Processed 53003225 reads in 682 ms
[2015-09-30T22:42Z] INFO  23:42:14,291 MuTect - [MUTECT] Processed 231014553 reads in 669 ms
[2015-09-30T22:42Z] INFO  23:42:14,688 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:42Z] INFO  23:42:14,693 ProgressMeter -            done        3.26e+06   81.0 s       24.0 s    100.0%        81.0 s     0.0 s
[2015-09-30T22:42Z] INFO  23:42:14,693 ProgressMeter - Total runtime 81.54 secs, 1.36 min, 0.02 hours
[2015-09-30T22:42Z] INFO  23:42:14,757 MicroScheduler - 86736 reads were filtered out during the traversal out of approximately 1326671 total reads (6.54%)
[2015-09-30T22:42Z] INFO  23:42:14,757 MicroScheduler -   -> 65270 reads (4.92% of total) failing DuplicateReadFilter
[2015-09-30T22:42Z] INFO  23:42:14,757 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:42Z] INFO  23:42:14,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:42Z] INFO  23:42:14,757 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:42Z] INFO  23:42:14,758 MicroScheduler -   -> 21466 reads (1.62% of total) failing UnmappedReadFilter
[2015-09-30T22:42Z] INFO  23:42:14,805 MuTect - [MUTECT] Processed 54003297 reads in 664 ms
[2015-09-30T22:42Z] INFO  23:42:14,959 MuTect - [MUTECT] Processed 232014589 reads in 668 ms
[2015-09-30T22:42Z] INFO  23:42:15,435 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:15,498 MuTect - [MUTECT] Processed 55003375 reads in 694 ms
[2015-09-30T22:42Z] INFO  23:42:15,656 MuTect - [MUTECT] Processed 233014667 reads in 697 ms
[2015-09-30T22:42Z] INFO  23:42:15,710 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:42Z] INFO  23:42:15,919 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:16,179 MuTect - [MUTECT] Processed 56003413 reads in 681 ms
[2015-09-30T22:42Z] INFO  23:42:16,338 MuTect - [MUTECT] Processed 234014676 reads in 682 ms
[2015-09-30T22:42Z] bgzip syn3-16_31044089_62860191-raw-mutect.vcf
[2015-09-30T22:42Z] tabix index syn3-16_31044089_62860191-raw-mutect.vcf.gz
[2015-09-30T22:42Z] INFO  23:42:16,874 MuTect - [MUTECT] Processed 57003466 reads in 695 ms
[2015-09-30T22:42Z] INFO  23:42:16,998 MuTect - [MUTECT] Processed 235014736 reads in 660 ms
[2015-09-30T22:42Z] INFO  23:42:17,565 MuTect - [MUTECT] Processed 58003572 reads in 691 ms
[2015-09-30T22:42Z] INFO  23:42:17,642 MuTect - [MUTECT] Processed 236014743 reads in 644 ms
[2015-09-30T22:42Z] INFO  23:42:17,810 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:18,235 MuTect - [MUTECT] Processed 59003627 reads in 670 ms
[2015-09-30T22:42Z] INFO  23:42:18,259 MuTect - [MUTECT] Processed 237014744 reads in 617 ms
[2015-09-30T22:42Z] INFO  23:42:18,828 MuTect - [MUTECT] Processed 238014841 reads in 569 ms
[2015-09-30T22:42Z] INFO  23:42:18,924 MuTect - [MUTECT] Processed 60003754 reads in 689 ms
[2015-09-30T22:42Z] INFO  23:42:19,336 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:19,460 MuTect - [MUTECT] Processed 239014887 reads in 632 ms
[2015-09-30T22:42Z] INFO  23:42:19,559 MuTect - [MUTECT] Processed 61003873 reads in 635 ms
[2015-09-30T22:42Z] INFO  23:42:20,091 MuTect - [MUTECT] Processed 240014983 reads in 631 ms
[2015-09-30T22:42Z] INFO  23:42:20,282 MuTect - [MUTECT] Processed 62003955 reads in 723 ms
[2015-09-30T22:42Z] INFO  23:42:20,573 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:20,720 MuTect - [MUTECT] Processed 241015045 reads in 629 ms
[2015-09-30T22:42Z] INFO  23:42:20,996 MuTect - [MUTECT] Processed 63004007 reads in 714 ms
[2015-09-30T22:42Z] INFO  23:42:21,361 MuTect - [MUTECT] Processed 242015085 reads in 641 ms
[2015-09-30T22:42Z] INFO  23:42:21,707 MuTect - [MUTECT] Processed 64004083 reads in 711 ms
[2015-09-30T22:42Z] INFO  23:42:21,952 MuTect - [MUTECT] Processed 243015170 reads in 591 ms
[2015-09-30T22:42Z] MuTect: MuTect
[2015-09-30T22:42Z] INFO  23:42:22,325 MuTect - [MUTECT] Processed 65004168 reads in 618 ms
[2015-09-30T22:42Z] INFO  23:42:22,538 MuTect - [MUTECT] Processed 244015184 reads in 586 ms
[2015-09-30T22:42Z] INFO  23:42:22,669 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:23,001 MuTect - [MUTECT] Processed 66004203 reads in 676 ms
[2015-09-30T22:42Z] INFO  23:42:23,194 MuTect - [MUTECT] Processed 245015271 reads in 656 ms
[2015-09-30T22:42Z] INFO  23:42:23,519 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:23,670 MuTect - [MUTECT] Processed 67004293 reads in 669 ms
[2015-09-30T22:42Z] INFO  23:42:23,813 MuTect - [MUTECT] Processed 246015335 reads in 619 ms
[2015-09-30T22:42Z] INFO  23:42:24,347 MuTect - [MUTECT] Processed 68004329 reads in 677 ms
[2015-09-30T22:42Z] INFO  23:42:24,370 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/17/syn3-17_0_31039439-raw-mutect-regions.bed to be BED
[2015-09-30T22:42Z] INFO  23:42:24,426 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:42Z] INFO  23:42:24,426 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:42Z] INFO  23:42:24,426 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:42Z] INFO  23:42:24,426 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:42Z] INFO  23:42:24,430 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/17/syn3-17_0_31039439-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/17/tx/tmp0wKZvl/syn3-17_0_31039439-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:42Z] INFO  23:42:24,430 HelpFormatter - Date/Time: 2015/09/30 23:42:24
[2015-09-30T22:42Z] INFO  23:42:24,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:42Z] INFO  23:42:24,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:42Z] INFO  23:42:24,438 MuTect - [MUTECT] Processed 247015385 reads in 625 ms
[2015-09-30T22:42Z] INFO  23:42:24,458 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:42Z] INFO  23:42:24,462 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:42Z] INFO  23:42:24,512 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:42Z] INFO  23:42:24,561 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:42Z] INFO  23:42:24,568 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:42Z] INFO  23:42:24,591 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:42Z] INFO  23:42:24,602 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:42Z] INFO  23:42:24,782 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:42Z] INFO  23:42:24,888 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:24,919 IntervalUtils - Processing 3037033 bp from intervals
[2015-09-30T22:42Z] INFO  23:42:24,923 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:42Z] INFO  23:42:24,923 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:42Z] INFO  23:42:25,013 MuTect - [MUTECT] Processed 69004481 reads in 666 ms
[2015-09-30T22:42Z] INFO  23:42:25,079 MuTect - [MUTECT] Processed 248015406 reads in 641 ms
[2015-09-30T22:42Z] INFO  23:42:25,121 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:42Z] INFO  23:42:25,309 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:42Z] INFO  23:42:25,310 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:42Z] INFO  23:42:25,310 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:42Z] INFO  23:42:25,311 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:42Z] INFO  23:42:25,696 MuTect - [MUTECT] Processed 70004608 reads in 683 ms
[2015-09-30T22:42Z] INFO  23:42:25,742 MuTect - [MUTECT] Processed 249015493 reads in 663 ms
[2015-09-30T22:42Z] INFO  23:42:25,882 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:26,366 MuTect - [MUTECT] Processed 71004731 reads in 670 ms
[2015-09-30T22:42Z] INFO  23:42:26,408 MuTect - [MUTECT] Processed 250015607 reads in 666 ms
[2015-09-30T22:42Z] INFO  23:42:27,049 MuTect - [MUTECT] Processed 72004731 reads in 683 ms
[2015-09-30T22:42Z] INFO  23:42:27,060 MuTect - [MUTECT] Processed 251015632 reads in 652 ms
[2015-09-30T22:42Z] INFO  23:42:27,166 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:27,565 ProgressMeter -     16:22483042        7.10e+06    2.8 m       23.0 s     72.6%         3.9 m    64.0 s
[2015-09-30T22:42Z] INFO  23:42:27,681 MuTect - [MUTECT] Processed 1000003 reads in 2322 ms
[2015-09-30T22:42Z] INFO  23:42:27,705 MuTect - [MUTECT] Processed 252015688 reads in 645 ms
[2015-09-30T22:42Z] INFO  23:42:27,727 MuTect - [MUTECT] Processed 73004763 reads in 678 ms
[2015-09-30T22:42Z] INFO  23:42:28,192 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:28,299 MuTect - [MUTECT] Processed 253015694 reads in 594 ms
[2015-09-30T22:42Z] INFO  23:42:28,424 MuTect - [MUTECT] Processed 74004792 reads in 697 ms
[2015-09-30T22:42Z] INFO  23:42:28,510 MuTect - [MUTECT] Processed 2000032 reads in 829 ms
[2015-09-30T22:42Z] INFO  23:42:28,941 MuTect - [MUTECT] Processed 254015716 reads in 641 ms
[2015-09-30T22:42Z] INFO  23:42:29,088 MuTect - [MUTECT] Processed 75004896 reads in 664 ms
[2015-09-30T22:42Z] INFO  23:42:29,231 MuTect - [MUTECT] Processed 3000095 reads in 720 ms
[2015-09-30T22:42Z] INFO  23:42:29,380 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:29,608 MuTect - [MUTECT] Processed 255015770 reads in 668 ms
[2015-09-30T22:42Z] INFO  23:42:29,782 MuTect - [MUTECT] Processed 76004912 reads in 694 ms
[2015-09-30T22:42Z] INFO  23:42:29,950 MuTect - [MUTECT] Processed 4000189 reads in 720 ms
[2015-09-30T22:42Z] INFO  23:42:30,281 MuTect - [MUTECT] Processed 256015856 reads in 673 ms
[2015-09-30T22:42Z] INFO  23:42:30,407 MuTect - [MUTECT] Processed 77004975 reads in 625 ms
[2015-09-30T22:42Z] INFO  23:42:30,407 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:30,684 MuTect - [MUTECT] Processed 5000265 reads in 734 ms
[2015-09-30T22:42Z] INFO  23:42:30,753 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:30,932 MuTect - [MUTECT] Processed 257015894 reads in 651 ms
[2015-09-30T22:42Z] INFO  23:42:31,058 MuTect - [MUTECT] Processed 78005015 reads in 651 ms
[2015-09-30T22:42Z] INFO  23:42:31,436 MuTect - [MUTECT] Processed 6000276 reads in 752 ms
[2015-09-30T22:42Z] INFO  23:42:31,580 MuTect - [MUTECT] Processed 258015974 reads in 648 ms
[2015-09-30T22:42Z] INFO  23:42:31,741 MuTect - [MUTECT] Processed 79005015 reads in 682 ms
[2015-09-30T22:42Z] INFO  23:42:31,863 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:32,165 MuTect - [MUTECT] Processed 7000324 reads in 729 ms
[2015-09-30T22:42Z] INFO  23:42:32,201 MuTect - [MUTECT] Processed 259016070 reads in 621 ms
[2015-09-30T22:42Z] INFO  23:42:32,423 MuTect - [MUTECT] Processed 80005058 reads in 683 ms
[2015-09-30T22:42Z] INFO  23:42:32,760 MuTect - [MUTECT] Inspected 69000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:32,826 MuTect - [MUTECT] Processed 260016087 reads in 625 ms
[2015-09-30T22:42Z] INFO  23:42:32,946 MuTect - [MUTECT] Processed 8000378 reads in 780 ms
[2015-09-30T22:42Z] INFO  23:42:33,113 MuTect - [MUTECT] Processed 81005132 reads in 690 ms
[2015-09-30T22:42Z] INFO  23:42:33,282 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:33,473 MuTect - [MUTECT] Processed 261016159 reads in 647 ms
[2015-09-30T22:42Z] INFO  23:42:33,661 MuTect - [MUTECT] Processed 9000408 reads in 716 ms
[2015-09-30T22:42Z] INFO  23:42:33,790 MuTect - [MUTECT] Processed 82005179 reads in 677 ms
[2015-09-30T22:42Z] INFO  23:42:34,114 MuTect - [MUTECT] Processed 262016230 reads in 641 ms
[2015-09-30T22:42Z] INFO  23:42:34,156 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:34,345 MuTect - [MUTECT] Processed 10000502 reads in 684 ms
[2015-09-30T22:42Z] INFO  23:42:34,471 MuTect - [MUTECT] Processed 83005195 reads in 680 ms
[2015-09-30T22:42Z] INFO  23:42:34,746 MuTect - [MUTECT] Processed 263016256 reads in 632 ms
[2015-09-30T22:42Z] INFO  23:42:34,932 MuTect - [MUTECT] Inspected 70000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:35,067 MuTect - [MUTECT] Processed 11000553 reads in 722 ms
[2015-09-30T22:42Z] INFO  23:42:35,109 MuTect - [MUTECT] Processed 84005220 reads in 639 ms
[2015-09-30T22:42Z] INFO  23:42:35,370 MuTect - [MUTECT] Processed 264016341 reads in 624 ms
[2015-09-30T22:42Z] INFO  23:42:35,471 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:35,737 MuTect - [MUTECT] Processed 12000615 reads in 670 ms
[2015-09-30T22:42Z] INFO  23:42:35,767 MuTect - [MUTECT] Processed 85005265 reads in 658 ms
[2015-09-30T22:42Z] INFO  23:42:36,006 MuTect - [MUTECT] Processed 265016441 reads in 636 ms
[2015-09-30T22:42Z] INFO  23:42:36,333 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:36,423 MuTect - [MUTECT] Processed 86005346 reads in 656 ms
[2015-09-30T22:42Z] INFO  23:42:36,428 MuTect - [MUTECT] Processed 13000670 reads in 691 ms
[2015-09-30T22:42Z] INFO  23:42:36,654 MuTect - [MUTECT] Processed 266016454 reads in 648 ms
[2015-09-30T22:42Z] INFO  23:42:37,074 MuTect - [MUTECT] Processed 87005396 reads in 651 ms
[2015-09-30T22:42Z] INFO  23:42:37,148 MuTect - [MUTECT] Processed 14000740 reads in 720 ms
[2015-09-30T22:42Z] INFO  23:42:37,163 MuTect - [MUTECT] Inspected 71000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:37,239 ProgressMeter -     16:71783901        2.56e+06   60.0 s       23.0 s     44.1%         2.3 m    75.0 s
[2015-09-30T22:42Z] INFO  23:42:37,290 MuTect - [MUTECT] Processed 267016538 reads in 636 ms
[2015-09-30T22:42Z] INFO  23:42:37,743 MuTect - [MUTECT] Processed 88005402 reads in 669 ms
[2015-09-30T22:42Z] INFO  23:42:37,753 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:37,813 MuTect - [MUTECT] Processed 15000784 reads in 665 ms
[2015-09-30T22:42Z] INFO  23:42:37,949 MuTect - [MUTECT] Processed 268016563 reads in 659 ms
[2015-09-30T22:42Z] INFO  23:42:38,349 MuTect - [MUTECT] Processed 89005487 reads in 606 ms
[2015-09-30T22:42Z] INFO  23:42:38,417 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:38,461 MuTect - [MUTECT] Processed 16000849 reads in 648 ms
[2015-09-30T22:42Z] INFO  23:42:38,575 MuTect - [MUTECT] Processed 269016601 reads in 626 ms
[2015-09-30T22:42Z] INFO  23:42:39,024 MuTect - [MUTECT] Processed 90005535 reads in 675 ms
[2015-09-30T22:42Z] INFO  23:42:39,116 MuTect - [MUTECT] Processed 17000918 reads in 655 ms
[2015-09-30T22:42Z] INFO  23:42:39,222 MuTect - [MUTECT] Processed 270016619 reads in 647 ms
[2015-09-30T22:42Z] INFO  23:42:39,691 MuTect - [MUTECT] Processed 91005559 reads in 666 ms
[2015-09-30T22:42Z] INFO  23:42:39,768 MuTect - [MUTECT] Processed 18000997 reads in 652 ms
[2015-09-30T22:42Z] INFO  23:42:39,847 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:40,369 MuTect - [MUTECT] Processed 92005561 reads in 679 ms
[2015-09-30T22:42Z] INFO  23:42:40,453 MuTect - [MUTECT] Processed 19001050 reads in 685 ms
[2015-09-30T22:42Z] INFO  23:42:40,467 MuTect - [MUTECT] Inspected 72000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:40,605 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:40,945 MuTect - [MUTECT] Processed 271016668 reads in 1723 ms
[2015-09-30T22:42Z] INFO  23:42:41,039 MuTect - [MUTECT] Processed 93005670 reads in 670 ms
[2015-09-30T22:42Z] INFO  23:42:41,184 MuTect - [MUTECT] Processed 20001092 reads in 731 ms
[2015-09-30T22:42Z] INFO  23:42:41,594 MuTect - [MUTECT] Processed 272016800 reads in 649 ms
[2015-09-30T22:42Z] INFO  23:42:41,711 MuTect - [MUTECT] Processed 94005779 reads in 672 ms
[2015-09-30T22:42Z] INFO  23:42:41,903 MuTect - [MUTECT] Processed 21001135 reads in 719 ms
[2015-09-30T22:42Z] INFO  23:42:42,087 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:42,235 MuTect - [MUTECT] Processed 273016904 reads in 641 ms
[2015-09-30T22:42Z] INFO  23:42:42,350 MuTect - [MUTECT] Processed 95005797 reads in 639 ms
[2015-09-30T22:42Z] INFO  23:42:42,624 MuTect - [MUTECT] Inspected 73000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:42,692 MuTect - [MUTECT] Processed 22001224 reads in 789 ms
[2015-09-30T22:42Z] INFO  23:42:42,867 MuTect - [MUTECT] Processed 274016981 reads in 632 ms
[2015-09-30T22:42Z] INFO  23:42:42,926 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:42,994 MuTect - [MUTECT] Processed 96005818 reads in 644 ms
[2015-09-30T22:42Z] INFO  23:42:43,362 MuTect - [MUTECT] Processed 23001232 reads in 670 ms
[2015-09-30T22:42Z] INFO  23:42:43,494 MuTect - [MUTECT] Processed 275017017 reads in 627 ms
[2015-09-30T22:42Z] INFO  23:42:43,622 MuTect - [MUTECT] Processed 97005830 reads in 628 ms
[2015-09-30T22:42Z] INFO  23:42:44,019 MuTect - [MUTECT] Processed 24001273 reads in 657 ms
[2015-09-30T22:42Z] INFO  23:42:44,199 MuTect - [MUTECT] Processed 276017124 reads in 705 ms
[2015-09-30T22:42Z] INFO  23:42:44,215 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:44,250 MuTect - [MUTECT] Processed 98005879 reads in 628 ms
[2015-09-30T22:42Z] INFO  23:42:44,706 MuTect - [MUTECT] Processed 25001293 reads in 687 ms
[2015-09-30T22:42Z] INFO  23:42:44,822 MuTect - [MUTECT] Inspected 74000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:44,842 MuTect - [MUTECT] Processed 277017156 reads in 643 ms
[2015-09-30T22:42Z] INFO  23:42:44,932 MuTect - [MUTECT] Processed 99005981 reads in 682 ms
[2015-09-30T22:42Z] INFO  23:42:45,219 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:45,421 MuTect - [MUTECT] Processed 26001358 reads in 715 ms
[2015-09-30T22:42Z] INFO  23:42:45,489 MuTect - [MUTECT] Processed 278017203 reads in 647 ms
[2015-09-30T22:42Z] INFO  23:42:45,608 MuTect - [MUTECT] Processed 100005983 reads in 676 ms
[2015-09-30T22:42Z] INFO  23:42:46,088 MuTect - [MUTECT] Processed 27001400 reads in 667 ms
[2015-09-30T22:42Z] INFO  23:42:46,104 MuTect - [MUTECT] Processed 279017240 reads in 615 ms
[2015-09-30T22:42Z] INFO  23:42:46,336 MuTect - [MUTECT] Processed 101005996 reads in 728 ms
[2015-09-30T22:42Z] INFO  23:42:46,717 MuTect - [MUTECT] Processed 280017321 reads in 613 ms
[2015-09-30T22:42Z] INFO  23:42:46,748 MuTect - [MUTECT] Processed 28001510 reads in 660 ms
[2015-09-30T22:42Z] INFO  23:42:46,791 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:46,898 MuTect - [MUTECT] Inspected 75000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:47,036 MuTect - [MUTECT] Processed 102006091 reads in 700 ms
[2015-09-30T22:42Z] INFO  23:42:47,353 MuTect - [MUTECT] Processed 281017432 reads in 636 ms
[2015-09-30T22:42Z] INFO  23:42:47,425 MuTect - [MUTECT] Processed 29001562 reads in 677 ms
[2015-09-30T22:42Z] INFO  23:42:47,613 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:47,707 MuTect - [MUTECT] Processed 103006174 reads in 671 ms
[2015-09-30T22:42Z] INFO  23:42:47,966 MuTect - [MUTECT] Processed 282017463 reads in 613 ms
[2015-09-30T22:42Z] INFO  23:42:48,136 MuTect - [MUTECT] Processed 30001594 reads in 711 ms
[2015-09-30T22:42Z] INFO  23:42:48,377 MuTect - [MUTECT] Processed 104006195 reads in 670 ms
[2015-09-30T22:42Z] INFO  23:42:48,591 MuTect - [MUTECT] Processed 283017468 reads in 624 ms
[2015-09-30T22:42Z] INFO  23:42:48,807 MuTect - [MUTECT] Processed 31001690 reads in 671 ms
[2015-09-30T22:42Z] INFO  23:42:49,044 MuTect - [MUTECT] Processed 105006217 reads in 667 ms
[2015-09-30T22:42Z] INFO  23:42:49,076 MuTect - [MUTECT] Inspected 76000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:49,228 MuTect - [MUTECT] Processed 284017483 reads in 638 ms
[2015-09-30T22:42Z] INFO  23:42:49,238 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:49,504 MuTect - [MUTECT] Processed 32001713 reads in 697 ms
[2015-09-30T22:42Z] INFO  23:42:49,707 MuTect - [MUTECT] Processed 106006323 reads in 663 ms
[2015-09-30T22:42Z] INFO  23:42:49,873 MuTect - [MUTECT] Processed 285017543 reads in 645 ms
[2015-09-30T22:42Z] INFO  23:42:49,931 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:50,201 MuTect - [MUTECT] Processed 33001787 reads in 697 ms
[2015-09-30T22:42Z] INFO  23:42:50,377 MuTect - [MUTECT] Processed 107006380 reads in 670 ms
[2015-09-30T22:42Z] INFO  23:42:50,452 MuTect - [MUTECT] Processed 286017628 reads in 579 ms
[2015-09-30T22:42Z] INFO  23:42:50,913 MuTect - [MUTECT] Processed 34001814 reads in 712 ms
[2015-09-30T22:42Z] INFO  23:42:51,021 MuTect - [MUTECT] Processed 108006486 reads in 644 ms
[2015-09-30T22:42Z] INFO  23:42:51,037 MuTect - [MUTECT] Processed 287017632 reads in 585 ms
[2015-09-30T22:42Z] INFO  23:42:51,402 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:51,625 MuTect - [MUTECT] Processed 35001905 reads in 712 ms
[2015-09-30T22:42Z] INFO  23:42:51,655 MuTect - [MUTECT] Processed 109006551 reads in 634 ms
[2015-09-30T22:42Z] INFO  23:42:51,668 MuTect - [MUTECT] Processed 288017686 reads in 631 ms
[2015-09-30T22:42Z] INFO  23:42:52,044 MuTect - [MUTECT] Inspected 77000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:52,278 MuTect - [MUTECT] Processed 289017760 reads in 610 ms
[2015-09-30T22:42Z] INFO  23:42:52,282 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:52,291 MuTect - [MUTECT] Processed 110006565 reads in 636 ms
[2015-09-30T22:42Z] INFO  23:42:52,322 MuTect - [MUTECT] Processed 36001906 reads in 697 ms
[2015-09-30T22:42Z] INFO  23:42:52,903 MuTect - [MUTECT] Processed 290017772 reads in 624 ms
[2015-09-30T22:42Z] INFO  23:42:52,984 MuTect - [MUTECT] Processed 111006679 reads in 693 ms
[2015-09-30T22:42Z] INFO  23:42:53,041 MuTect - [MUTECT] Processed 37001995 reads in 719 ms
[2015-09-30T22:42Z] INFO  23:42:53,504 MuTect - [MUTECT] Processed 291017870 reads in 602 ms
[2015-09-30T22:42Z] INFO  23:42:53,656 MuTect - [MUTECT] Processed 112006765 reads in 672 ms
[2015-09-30T22:42Z] INFO  23:42:53,767 MuTect - [MUTECT] Processed 38002036 reads in 726 ms
[2015-09-30T22:42Z] INFO  23:42:53,852 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:54,062 MuTect - [MUTECT] Processed 292017903 reads in 558 ms
[2015-09-30T22:42Z] INFO  23:42:54,312 MuTect - [MUTECT] Processed 113006860 reads in 656 ms
[2015-09-30T22:42Z] INFO  23:42:54,463 MuTect - [MUTECT] Processed 39002090 reads in 696 ms
[2015-09-30T22:42Z] INFO  23:42:54,587 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:54,662 MuTect - [MUTECT] Processed 293018003 reads in 600 ms
[2015-09-30T22:42Z] INFO  23:42:54,943 MuTect - [MUTECT] Processed 114006894 reads in 631 ms
[2015-09-30T22:42Z] INFO  23:42:55,133 MuTect - [MUTECT] Inspected 78000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:55,164 MuTect - [MUTECT] Processed 40002128 reads in 701 ms
[2015-09-30T22:42Z] INFO  23:42:55,251 MuTect - [MUTECT] Processed 294018049 reads in 589 ms
[2015-09-30T22:42Z] INFO  23:42:55,312 ProgressMeter -      17:3558404        1.04e+06   30.0 s       28.0 s     12.4%         4.0 m     3.5 m
[2015-09-30T22:42Z] INFO  23:42:55,579 MuTect - [MUTECT] Processed 115006946 reads in 636 ms
[2015-09-30T22:42Z] INFO  23:42:55,875 MuTect - [MUTECT] Processed 295018102 reads in 624 ms
[2015-09-30T22:42Z] INFO  23:42:55,877 MuTect - [MUTECT] Processed 41002187 reads in 712 ms
[2015-09-30T22:42Z] INFO  23:42:56,228 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:56,320 MuTect - [MUTECT] Processed 116007007 reads in 741 ms
[2015-09-30T22:42Z] INFO  23:42:56,497 MuTect - [MUTECT] Processed 296018126 reads in 622 ms
[2015-09-30T22:42Z] INFO  23:42:56,539 MuTect - [MUTECT] Processed 42002188 reads in 663 ms
[2015-09-30T22:42Z] INFO  23:42:56,815 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:57,049 MuTect - [MUTECT] Processed 117007042 reads in 729 ms
[2015-09-30T22:42Z] INFO  23:42:57,131 MuTect - [MUTECT] Processed 297018203 reads in 634 ms
[2015-09-30T22:42Z] INFO  23:42:57,226 MuTect - [MUTECT] Processed 43002212 reads in 687 ms
[2015-09-30T22:42Z] INFO  23:42:57,240 MuTect - [MUTECT] Inspected 79000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:57,567 ProgressMeter -     16:28986546        8.38e+06    3.3 m       23.0 s     87.2%         3.8 m    29.0 s
[2015-09-30T22:42Z] INFO  23:42:57,766 MuTect - [MUTECT] Processed 298018323 reads in 635 ms
[2015-09-30T22:42Z] INFO  23:42:57,796 MuTect - [MUTECT] Processed 118007091 reads in 747 ms
[2015-09-30T22:42Z] INFO  23:42:57,886 MuTect - [MUTECT] Processed 44002295 reads in 660 ms
[2015-09-30T22:42Z] INFO  23:42:58,418 MuTect - [MUTECT] Processed 299018364 reads in 652 ms
[2015-09-30T22:42Z] INFO  23:42:58,514 MuTect - [MUTECT] Processed 119007166 reads in 718 ms
[2015-09-30T22:42Z] INFO  23:42:58,543 MuTect - [MUTECT] Processed 45002375 reads in 657 ms
[2015-09-30T22:42Z] INFO  23:42:58,626 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:59,089 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:59,103 MuTect - [MUTECT] Processed 300018415 reads in 685 ms
[2015-09-30T22:42Z] INFO  23:42:59,204 MuTect - [MUTECT] Processed 120007238 reads in 690 ms
[2015-09-30T22:42Z] INFO  23:42:59,265 MuTect - [MUTECT] Processed 46002449 reads in 722 ms
[2015-09-30T22:42Z] INFO  23:42:59,676 MuTect - [MUTECT] Inspected 80000 potential candidates
[2015-09-30T22:42Z] INFO  23:42:59,759 MuTect - [MUTECT] Processed 301018436 reads in 656 ms
[2015-09-30T22:42Z] INFO  23:42:59,888 MuTect - [MUTECT] Processed 121007289 reads in 683 ms
[2015-09-30T22:42Z] INFO  23:42:59,921 MuTect - [MUTECT] Processed 47002528 reads in 656 ms
[2015-09-30T22:43Z] INFO  23:43:00,348 MuTect - [MUTECT] Processed 302018539 reads in 589 ms
[2015-09-30T22:43Z] INFO  23:43:00,602 MuTect - [MUTECT] Processed 122007314 reads in 715 ms
[2015-09-30T22:43Z] INFO  23:43:00,604 MuTect - [MUTECT] Processed 48002547 reads in 683 ms
[2015-09-30T22:43Z] INFO  23:43:00,897 MuTect - [MUTECT] Processed 303018545 reads in 549 ms
[2015-09-30T22:43Z] INFO  23:43:00,999 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:01,256 MuTect - [MUTECT] Processed 49002601 reads in 652 ms
[2015-09-30T22:43Z] INFO  23:43:01,285 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:01,314 MuTect - [MUTECT] Processed 123007395 reads in 712 ms
[2015-09-30T22:43Z] INFO  23:43:01,454 MuTect - [MUTECT] Processed 304018685 reads in 557 ms
[2015-09-30T22:43Z] INFO  23:43:01,909 MuTect - [MUTECT] Processed 50002603 reads in 653 ms
[2015-09-30T22:43Z] INFO  23:43:02,021 MuTect - [MUTECT] Processed 305018688 reads in 567 ms
[2015-09-30T22:43Z] INFO  23:43:02,064 MuTect - [MUTECT] Processed 124007463 reads in 750 ms
[2015-09-30T22:43Z] INFO  23:43:02,569 MuTect - [MUTECT] Processed 51002605 reads in 660 ms
[2015-09-30T22:43Z] INFO  23:43:02,587 MuTect - [MUTECT] Processed 306018786 reads in 566 ms
[2015-09-30T22:43Z] INFO  23:43:02,833 MuTect - [MUTECT] Processed 125007572 reads in 769 ms
[2015-09-30T22:43Z] INFO  23:43:03,242 MuTect - [MUTECT] Processed 307018849 reads in 655 ms
[2015-09-30T22:43Z] INFO  23:43:03,262 MuTect - [MUTECT] Processed 52002610 reads in 693 ms
[2015-09-30T22:43Z] INFO  23:43:03,272 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:03,605 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:03,610 MuTect - [MUTECT] Processed 126007608 reads in 777 ms
[2015-09-30T22:43Z] INFO  23:43:03,874 MuTect - [MUTECT] Processed 308018938 reads in 632 ms
[2015-09-30T22:43Z] INFO  23:43:03,958 MuTect - [MUTECT] Processed 53002742 reads in 696 ms
[2015-09-30T22:43Z] INFO  23:43:04,022 MuTect - [MUTECT] Inspected 81000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:04,283 MuTect - [MUTECT] Processed 127007629 reads in 673 ms
[2015-09-30T22:43Z] INFO  23:43:04,485 MuTect - [MUTECT] Processed 309019036 reads in 611 ms
[2015-09-30T22:43Z] INFO  23:43:04,651 MuTect - [MUTECT] Processed 54002806 reads in 693 ms
[2015-09-30T22:43Z] INFO  23:43:04,969 MuTect - [MUTECT] Processed 128007635 reads in 686 ms
[2015-09-30T22:43Z] INFO  23:43:05,088 MuTect - [MUTECT] Processed 310019173 reads in 603 ms
[2015-09-30T22:43Z] INFO  23:43:05,324 MuTect - [MUTECT] Processed 55002827 reads in 673 ms
[2015-09-30T22:43Z] INFO  23:43:05,653 MuTect - [MUTECT] Processed 129007741 reads in 684 ms
[2015-09-30T22:43Z] INFO  23:43:05,663 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:05,698 MuTect - [MUTECT] Processed 311019273 reads in 610 ms
[2015-09-30T22:43Z] INFO  23:43:06,018 MuTect - [MUTECT] Inspected 82000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:06,048 MuTect - [MUTECT] Processed 56002902 reads in 724 ms
[2015-09-30T22:43Z] INFO  23:43:06,130 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:06,287 MuTect - [MUTECT] Processed 312019276 reads in 589 ms
[2015-09-30T22:43Z] INFO  23:43:06,404 MuTect - [MUTECT] Processed 130007790 reads in 751 ms
[2015-09-30T22:43Z] INFO  23:43:06,750 MuTect - [MUTECT] Processed 57002959 reads in 702 ms
[2015-09-30T22:43Z] INFO  23:43:06,911 MuTect - [MUTECT] Processed 313019381 reads in 624 ms
[2015-09-30T22:43Z] INFO  23:43:07,128 MuTect - [MUTECT] Processed 131007859 reads in 724 ms
[2015-09-30T22:43Z] INFO  23:43:07,240 ProgressMeter -     16:81970080        3.80e+06   90.0 s       23.0 s     68.1%         2.2 m    42.0 s
[2015-09-30T22:43Z] INFO  23:43:07,426 MuTect - [MUTECT] Processed 58003050 reads in 676 ms
[2015-09-30T22:43Z] INFO  23:43:07,535 MuTect - [MUTECT] Processed 314019407 reads in 624 ms
[2015-09-30T22:43Z] INFO  23:43:07,810 MuTect - [MUTECT] Processed 132007952 reads in 682 ms
[2015-09-30T22:43Z] INFO  23:43:08,044 MuTect - [MUTECT] Inspected 83000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:08,046 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:08,099 MuTect - [MUTECT] Processed 59003060 reads in 673 ms
[2015-09-30T22:43Z] INFO  23:43:08,139 MuTect - [MUTECT] Processed 315019444 reads in 604 ms
[2015-09-30T22:43Z] INFO  23:43:08,227 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:08,556 MuTect - [MUTECT] Processed 133007984 reads in 746 ms
[2015-09-30T22:43Z] INFO  23:43:08,755 MuTect - [MUTECT] Processed 316019539 reads in 616 ms
[2015-09-30T22:43Z] INFO  23:43:08,805 MuTect - [MUTECT] Processed 60003184 reads in 706 ms
[2015-09-30T22:43Z] INFO  23:43:09,274 MuTect - [MUTECT] Processed 134008039 reads in 718 ms
[2015-09-30T22:43Z] INFO  23:43:09,362 MuTect - [MUTECT] Processed 317019584 reads in 607 ms
[2015-09-30T22:43Z] INFO  23:43:09,483 MuTect - [MUTECT] Processed 61003257 reads in 678 ms
[2015-09-30T22:43Z] INFO  23:43:09,983 MuTect - [MUTECT] Processed 318019630 reads in 621 ms
[2015-09-30T22:43Z] INFO  23:43:10,016 MuTect - [MUTECT] Inspected 84000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:10,034 MuTect - [MUTECT] Processed 135008106 reads in 760 ms
[2015-09-30T22:43Z] INFO  23:43:10,177 MuTect - [MUTECT] Processed 62003259 reads in 694 ms
[2015-09-30T22:43Z] INFO  23:43:10,284 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:10,471 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:10,600 MuTect - [MUTECT] Processed 319019647 reads in 617 ms
[2015-09-30T22:43Z] INFO  23:43:10,745 MuTect - [MUTECT] Processed 136008168 reads in 711 ms
[2015-09-30T22:43Z] INFO  23:43:10,850 MuTect - [MUTECT] Processed 63003288 reads in 673 ms
[2015-09-30T22:43Z] INFO  23:43:11,247 MuTect - [MUTECT] Processed 320019694 reads in 647 ms
[2015-09-30T22:43Z] INFO  23:43:11,504 MuTect - [MUTECT] Processed 137008255 reads in 759 ms
[2015-09-30T22:43Z] INFO  23:43:11,557 MuTect - [MUTECT] Processed 64003291 reads in 707 ms
[2015-09-30T22:43Z] INFO  23:43:11,829 MuTect - [MUTECT] Processed 321019819 reads in 582 ms
[2015-09-30T22:43Z] INFO  23:43:12,241 MuTect - [MUTECT] Processed 138008372 reads in 737 ms
[2015-09-30T22:43Z] INFO  23:43:12,271 MuTect - [MUTECT] Processed 65003317 reads in 714 ms
[2015-09-30T22:43Z] INFO  23:43:12,379 MuTect - [MUTECT] Processed 322019819 reads in 550 ms
[2015-09-30T22:43Z] INFO  23:43:12,551 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:12,887 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:12,930 MuTect - [MUTECT] Processed 139008380 reads in 689 ms
[2015-09-30T22:43Z] INFO  23:43:12,940 MuTect - [MUTECT] Processed 66003350 reads in 669 ms
[2015-09-30T22:43Z] INFO  23:43:12,951 MuTect - [MUTECT] Processed 323019851 reads in 572 ms
[2015-09-30T22:43Z] INFO  23:43:13,544 MuTect - [MUTECT] Processed 324019908 reads in 593 ms
[2015-09-30T22:43Z] INFO  23:43:13,584 MuTect - [MUTECT] Processed 67003454 reads in 644 ms
[2015-09-30T22:43Z] INFO  23:43:13,677 MuTect - [MUTECT] Processed 140008459 reads in 747 ms
[2015-09-30T22:43Z] INFO  23:43:13,851 MuTect - [MUTECT] Inspected 85000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:14,162 MuTect - [MUTECT] Processed 325019980 reads in 618 ms
[2015-09-30T22:43Z] INFO  23:43:14,259 MuTect - [MUTECT] Processed 68003501 reads in 675 ms
[2015-09-30T22:43Z] INFO  23:43:14,387 MuTect - [MUTECT] Processed 141008510 reads in 710 ms
[2015-09-30T22:43Z] INFO  23:43:14,639 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:14,782 MuTect - [MUTECT] Processed 326020105 reads in 620 ms
[2015-09-30T22:43Z] INFO  23:43:14,904 MuTect - [MUTECT] Processed 69003526 reads in 645 ms
[2015-09-30T22:43Z] INFO  23:43:15,148 MuTect - [MUTECT] Processed 142008511 reads in 761 ms
[2015-09-30T22:43Z] INFO  23:43:15,171 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:15,395 MuTect - [MUTECT] Processed 327020186 reads in 613 ms
[2015-09-30T22:43Z] INFO  23:43:15,577 MuTect - [MUTECT] Processed 70003559 reads in 673 ms
[2015-09-30T22:43Z] INFO  23:43:15,928 MuTect - [MUTECT] Processed 143008527 reads in 780 ms
[2015-09-30T22:43Z] INFO  23:43:16,026 MuTect - [MUTECT] Processed 328020239 reads in 631 ms
[2015-09-30T22:43Z] INFO  23:43:16,054 MuTect - [MUTECT] Inspected 86000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:16,316 MuTect - [MUTECT] Processed 71003653 reads in 739 ms
[2015-09-30T22:43Z] INFO  23:43:16,639 MuTect - [MUTECT] Processed 329020289 reads in 613 ms
[2015-09-30T22:43Z] INFO  23:43:16,678 MuTect - [MUTECT] Processed 144008605 reads in 750 ms
[2015-09-30T22:43Z] INFO  23:43:16,759 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:16,996 MuTect - [MUTECT] Processed 72003698 reads in 680 ms
[2015-09-30T22:43Z] INFO  23:43:17,250 MuTect - [MUTECT] Processed 330020343 reads in 610 ms
[2015-09-30T22:43Z] INFO  23:43:17,378 MuTect - [MUTECT] Processed 145008626 reads in 700 ms
[2015-09-30T22:43Z] INFO  23:43:17,640 MuTect - [MUTECT] Processed 73003727 reads in 644 ms
[2015-09-30T22:43Z] INFO  23:43:17,695 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:17,850 MuTect - [MUTECT] Processed 331020345 reads in 601 ms
[2015-09-30T22:43Z] INFO  23:43:18,071 MuTect - [MUTECT] Inspected 87000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:18,098 MuTect - [MUTECT] Processed 146008679 reads in 720 ms
[2015-09-30T22:43Z] INFO  23:43:18,308 MuTect - [MUTECT] Processed 74003813 reads in 668 ms
[2015-09-30T22:43Z] INFO  23:43:18,451 MuTect - [MUTECT] Processed 332020389 reads in 601 ms
[2015-09-30T22:43Z] INFO  23:43:18,773 MuTect - [MUTECT] Processed 147008766 reads in 675 ms
[2015-09-30T22:43Z] INFO  23:43:18,927 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:19,071 MuTect - [MUTECT] Processed 333020464 reads in 620 ms
[2015-09-30T22:43Z] INFO  23:43:19,103 MuTect - [MUTECT] Processed 75003877 reads in 795 ms
[2015-09-30T22:43Z] INFO  23:43:19,448 MuTect - [MUTECT] Processed 148008859 reads in 675 ms
[2015-09-30T22:43Z] INFO  23:43:19,676 MuTect - [MUTECT] Processed 334020560 reads in 605 ms
[2015-09-30T22:43Z] INFO  23:43:19,781 MuTect - [MUTECT] Processed 76003887 reads in 678 ms
[2015-09-30T22:43Z] INFO  23:43:19,986 MuTect - [MUTECT] Inspected 88000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:20,048 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:20,118 MuTect - [MUTECT] Processed 149008950 reads in 670 ms
[2015-09-30T22:43Z] INFO  23:43:20,281 MuTect - [MUTECT] Processed 335020619 reads in 605 ms
[2015-09-30T22:43Z] INFO  23:43:20,438 MuTect - [MUTECT] Processed 77003918 reads in 657 ms
[2015-09-30T22:43Z] INFO  23:43:20,781 MuTect - [MUTECT] Processed 150008964 reads in 663 ms
[2015-09-30T22:43Z] INFO  23:43:20,914 MuTect - [MUTECT] Processed 336020689 reads in 633 ms
[2015-09-30T22:43Z] INFO  23:43:21,138 MuTect - [MUTECT] Processed 78003990 reads in 700 ms
[2015-09-30T22:43Z] INFO  23:43:21,160 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:21,493 MuTect - [MUTECT] Processed 151009043 reads in 712 ms
[2015-09-30T22:43Z] INFO  23:43:21,529 MuTect - [MUTECT] Processed 337020734 reads in 615 ms
[2015-09-30T22:43Z] INFO  23:43:21,906 MuTect - [MUTECT] Processed 79003996 reads in 768 ms
[2015-09-30T22:43Z] INFO  23:43:21,993 MuTect - [MUTECT] Inspected 89000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:22,153 MuTect - [MUTECT] Processed 338020822 reads in 624 ms
[2015-09-30T22:43Z] INFO  23:43:22,176 MuTect - [MUTECT] Processed 152009069 reads in 683 ms
[2015-09-30T22:43Z] INFO  23:43:22,417 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:22,587 MuTect - [MUTECT] Processed 80004100 reads in 681 ms
[2015-09-30T22:43Z] INFO  23:43:22,790 MuTect - [MUTECT] Processed 339020826 reads in 637 ms
[2015-09-30T22:43Z] INFO  23:43:22,892 MuTect - [MUTECT] Processed 153009221 reads in 716 ms
[2015-09-30T22:43Z] INFO  23:43:23,243 MuTect - [MUTECT] Processed 81004159 reads in 656 ms
[2015-09-30T22:43Z] INFO  23:43:23,409 MuTect - [MUTECT] Processed 340020878 reads in 619 ms
[2015-09-30T22:43Z] INFO  23:43:23,563 MuTect - [MUTECT] Processed 154009340 reads in 671 ms
[2015-09-30T22:43Z] INFO  23:43:23,569 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:23,907 MuTect - [MUTECT] Processed 82004196 reads in 663 ms
[2015-09-30T22:43Z] INFO  23:43:24,005 MuTect - [MUTECT] Processed 341020952 reads in 596 ms
[2015-09-30T22:43Z] INFO  23:43:24,148 MuTect - [MUTECT] Inspected 90000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:24,251 MuTect - [MUTECT] Processed 155009432 reads in 688 ms
[2015-09-30T22:43Z] INFO  23:43:24,601 MuTect - [MUTECT] Processed 83004246 reads in 695 ms
[2015-09-30T22:43Z] INFO  23:43:24,645 MuTect - [MUTECT] Processed 342021007 reads in 640 ms
[2015-09-30T22:43Z] INFO  23:43:24,773 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:24,911 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:43Z] INFO  23:43:24,915 ProgressMeter -            done        9.66e+06    3.8 m       23.0 s    100.0%         3.8 m     0.0 s
[2015-09-30T22:43Z] INFO  23:43:24,915 ProgressMeter - Total runtime 227.36 secs, 3.79 min, 0.06 hours
[2015-09-30T22:43Z] INFO  23:43:24,925 MuTect - [MUTECT] Processed 156009460 reads in 674 ms
[2015-09-30T22:43Z] INFO  23:43:24,981 MicroScheduler - 270450 reads were filtered out during the traversal out of approximately 4046488 total reads (6.68%)
[2015-09-30T22:43Z] INFO  23:43:24,981 MicroScheduler -   -> 203189 reads (5.02% of total) failing DuplicateReadFilter
[2015-09-30T22:43Z] INFO  23:43:24,981 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:43Z] INFO  23:43:24,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:43Z] INFO  23:43:24,981 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:43Z] INFO  23:43:24,981 MicroScheduler -   -> 67261 reads (1.66% of total) failing UnmappedReadFilter
[2015-09-30T22:43Z] INFO  23:43:25,274 MuTect - [MUTECT] Processed 84004264 reads in 673 ms
[2015-09-30T22:43Z] INFO  23:43:25,313 ProgressMeter -      17:6353586        2.33e+06   60.0 s       25.0 s     25.9%         3.9 m     2.9 m
[2015-09-30T22:43Z] INFO  23:43:25,610 MuTect - [MUTECT] Processed 157009524 reads in 685 ms
[2015-09-30T22:43Z] INFO  23:43:25,823 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:25,924 MuTect - [MUTECT] Processed 85004267 reads in 650 ms
[2015-09-30T22:43Z] INFO  23:43:25,954 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:43Z] bgzip syn3-16_0_31021934-raw-mutect.vcf
[2015-09-30T22:43Z] tabix index syn3-16_0_31021934-raw-mutect.vcf.gz
[2015-09-30T22:43Z] INFO  23:43:26,280 MuTect - [MUTECT] Processed 158009621 reads in 670 ms
[2015-09-30T22:43Z] INFO  23:43:26,605 MuTect - [MUTECT] Processed 86004311 reads in 681 ms
[2015-09-30T22:43Z] INFO  23:43:26,943 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:26,946 MuTect - [MUTECT] Processed 159009708 reads in 666 ms
[2015-09-30T22:43Z] INFO  23:43:27,294 MuTect - [MUTECT] Processed 87004385 reads in 688 ms
[2015-09-30T22:43Z] INFO  23:43:27,598 MuTect - [MUTECT] Processed 160009781 reads in 652 ms
[2015-09-30T22:43Z] INFO  23:43:27,983 MuTect - [MUTECT] Processed 88004404 reads in 690 ms
[2015-09-30T22:43Z] INFO  23:43:28,059 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:28,281 MuTect - [MUTECT] Processed 161009812 reads in 683 ms
[2015-09-30T22:43Z] MuTect: MuTect
[2015-09-30T22:43Z] INFO  23:43:28,642 MuTect - [MUTECT] Processed 89004421 reads in 659 ms
[2015-09-30T22:43Z] INFO  23:43:28,950 MuTect - [MUTECT] Processed 162009838 reads in 669 ms
[2015-09-30T22:43Z] INFO  23:43:29,226 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:29,316 MuTect - [MUTECT] Processed 90004478 reads in 674 ms
[2015-09-30T22:43Z] INFO  23:43:29,609 MuTect - [MUTECT] Processed 163009856 reads in 659 ms
[2015-09-30T22:43Z] INFO  23:43:29,977 MuTect - [MUTECT] Processed 91004531 reads in 661 ms
[2015-09-30T22:43Z] INFO  23:43:30,279 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:30,286 MuTect - [MUTECT] Processed 164009938 reads in 677 ms
[2015-09-30T22:43Z] INFO  23:43:30,618 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/17/syn3-17_31047756_62076645-raw-mutect-regions.bed to be BED
[2015-09-30T22:43Z] INFO  23:43:30,623 MuTect - [MUTECT] Processed 92004561 reads in 646 ms
[2015-09-30T22:43Z] INFO  23:43:30,672 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:43Z] INFO  23:43:30,673 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:43Z] INFO  23:43:30,673 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:43Z] INFO  23:43:30,673 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:43Z] INFO  23:43:30,677 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/17/syn3-17_31047756_62076645-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/17/tx/tmpGsH6nh/syn3-17_31047756_62076645-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:43Z] INFO  23:43:30,677 HelpFormatter - Date/Time: 2015/09/30 23:43:30
[2015-09-30T22:43Z] INFO  23:43:30,677 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:43Z] INFO  23:43:30,677 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:43Z] INFO  23:43:30,704 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:43Z] INFO  23:43:30,708 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:43Z] INFO  23:43:30,761 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:43Z] INFO  23:43:30,809 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:43Z] INFO  23:43:30,816 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:43Z] INFO  23:43:30,839 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:43Z] INFO  23:43:30,850 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:43Z] INFO  23:43:30,987 MuTect - [MUTECT] Processed 165009941 reads in 701 ms
[2015-09-30T22:43Z] INFO  23:43:31,023 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:43Z] INFO  23:43:31,292 MuTect - [MUTECT] Processed 93004632 reads in 669 ms
[2015-09-30T22:43Z] INFO  23:43:31,454 IntervalUtils - Processing 3219528 bp from intervals
[2015-09-30T22:43Z] INFO  23:43:31,459 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:43Z] INFO  23:43:31,459 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:43Z] INFO  23:43:31,511 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:43Z] INFO  23:43:31,536 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:31,675 MuTect - [MUTECT] Processed 166010008 reads in 688 ms
[2015-09-30T22:43Z] INFO  23:43:31,721 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:43Z] INFO  23:43:31,721 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:43Z] INFO  23:43:31,721 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:43Z] INFO  23:43:31,722 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:43Z] INFO  23:43:31,966 MuTect - [MUTECT] Processed 94004639 reads in 674 ms
[2015-09-30T22:43Z] INFO  23:43:32,397 MuTect - [MUTECT] Processed 167010072 reads in 721 ms
[2015-09-30T22:43Z] INFO  23:43:32,416 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:32,568 MuTect - [MUTECT] Processed 95004664 reads in 602 ms
[2015-09-30T22:43Z] INFO  23:43:33,083 MuTect - [MUTECT] Processed 168010188 reads in 687 ms
[2015-09-30T22:43Z] INFO  23:43:33,185 MuTect - [MUTECT] Processed 96004676 reads in 617 ms
[2015-09-30T22:43Z] INFO  23:43:33,704 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:33,791 MuTect - [MUTECT] Processed 97004800 reads in 606 ms
[2015-09-30T22:43Z] INFO  23:43:33,826 MuTect - [MUTECT] Processed 169010243 reads in 743 ms
[2015-09-30T22:43Z] INFO  23:43:34,294 MuTect - [MUTECT] Processed 1000057 reads in 2525 ms
[2015-09-30T22:43Z] INFO  23:43:34,311 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:34,417 MuTect - [MUTECT] Processed 98004839 reads in 626 ms
[2015-09-30T22:43Z] INFO  23:43:34,534 MuTect - [MUTECT] Processed 170010252 reads in 708 ms
[2015-09-30T22:43Z] INFO  23:43:35,028 MuTect - [MUTECT] Processed 99004911 reads in 611 ms
[2015-09-30T22:43Z] INFO  23:43:35,040 MuTect - [MUTECT] Processed 2000122 reads in 747 ms
[2015-09-30T22:43Z] INFO  23:43:35,236 MuTect - [MUTECT] Processed 171010398 reads in 702 ms
[2015-09-30T22:43Z] INFO  23:43:35,646 MuTect - [MUTECT] Processed 100004916 reads in 618 ms
[2015-09-30T22:43Z] INFO  23:43:35,820 MuTect - [MUTECT] Processed 3000163 reads in 780 ms
[2015-09-30T22:43Z] INFO  23:43:35,890 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:35,935 MuTect - [MUTECT] Processed 172010514 reads in 699 ms
[2015-09-30T22:43Z] INFO  23:43:36,002 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:36,211 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:36,268 MuTect - [MUTECT] Processed 101004945 reads in 622 ms
[2015-09-30T22:43Z] INFO  23:43:36,554 MuTect - [MUTECT] Processed 4000239 reads in 734 ms
[2015-09-30T22:43Z] INFO  23:43:36,610 MuTect - [MUTECT] Processed 173010614 reads in 675 ms
[2015-09-30T22:43Z] INFO  23:43:36,862 MuTect - [MUTECT] Processed 102004981 reads in 594 ms
[2015-09-30T22:43Z] INFO  23:43:37,241 ProgressMeter -     16:88907353        4.81e+06  120.0 s       24.0 s     88.1%         2.3 m    16.0 s
[2015-09-30T22:43Z] INFO  23:43:37,285 MuTect - [MUTECT] Processed 5000247 reads in 730 ms
[2015-09-30T22:43Z] INFO  23:43:37,351 MuTect - [MUTECT] Processed 174010704 reads in 741 ms
[2015-09-30T22:43Z] INFO  23:43:37,503 MuTect - [MUTECT] Processed 103005036 reads in 641 ms
[2015-09-30T22:43Z] INFO  23:43:37,978 MuTect - [MUTECT] Processed 175010713 reads in 627 ms
[2015-09-30T22:43Z] INFO  23:43:38,046 MuTect - [MUTECT] Processed 6000302 reads in 761 ms
[2015-09-30T22:43Z] INFO  23:43:38,087 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:38,160 MuTect - [MUTECT] Processed 104005101 reads in 657 ms
[2015-09-30T22:43Z] INFO  23:43:38,203 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:38,478 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:38,613 MuTect - [MUTECT] Processed 176010846 reads in 635 ms
[2015-09-30T22:43Z] INFO  23:43:38,745 MuTect - [MUTECT] Processed 7000324 reads in 700 ms
[2015-09-30T22:43Z] INFO  23:43:38,832 MuTect - [MUTECT] Processed 105005125 reads in 672 ms
[2015-09-30T22:43Z] INFO  23:43:39,299 MuTect - [MUTECT] Processed 177010916 reads in 686 ms
[2015-09-30T22:43Z] INFO  23:43:39,419 MuTect - [MUTECT] Processed 8000367 reads in 673 ms
[2015-09-30T22:43Z] INFO  23:43:39,513 MuTect - [MUTECT] Processed 106005149 reads in 680 ms
[2015-09-30T22:43Z] INFO  23:43:39,940 MuTect - [MUTECT] Processed 178010965 reads in 641 ms
[2015-09-30T22:43Z] INFO  23:43:40,102 MuTect - [MUTECT] Processed 9000407 reads in 684 ms
[2015-09-30T22:43Z] INFO  23:43:40,174 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:40,213 MuTect - [MUTECT] Processed 107005206 reads in 701 ms
[2015-09-30T22:43Z] INFO  23:43:40,351 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:40,607 MuTect - [MUTECT] Processed 179011020 reads in 667 ms
[2015-09-30T22:43Z] INFO  23:43:40,685 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:40,801 MuTect - [MUTECT] Processed 10000434 reads in 698 ms
[2015-09-30T22:43Z] INFO  23:43:40,870 MuTect - [MUTECT] Processed 108005242 reads in 657 ms
[2015-09-30T22:43Z] INFO  23:43:41,275 MuTect - [MUTECT] Processed 180011067 reads in 668 ms
[2015-09-30T22:43Z] INFO  23:43:41,510 MuTect - [MUTECT] Processed 11000464 reads in 710 ms
[2015-09-30T22:43Z] INFO  23:43:41,572 MuTect - [MUTECT] Processed 109005269 reads in 702 ms
[2015-09-30T22:43Z] INFO  23:43:41,937 MuTect - [MUTECT] Processed 181011079 reads in 662 ms
[2015-09-30T22:43Z] INFO  23:43:42,209 MuTect - [MUTECT] Processed 12000488 reads in 699 ms
[2015-09-30T22:43Z] INFO  23:43:42,236 MuTect - [MUTECT] Processed 110005353 reads in 664 ms
[2015-09-30T22:43Z] INFO  23:43:42,308 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:42,484 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:42,559 MuTect - [MUTECT] Processed 182011176 reads in 622 ms
[2015-09-30T22:43Z] INFO  23:43:42,867 MuTect - [MUTECT] Processed 111005394 reads in 631 ms
[2015-09-30T22:43Z] INFO  23:43:42,902 MuTect - [MUTECT] Processed 13000541 reads in 693 ms
[2015-09-30T22:43Z] INFO  23:43:43,166 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:43,258 MuTect - [MUTECT] Processed 183011192 reads in 699 ms
[2015-09-30T22:43Z] INFO  23:43:43,517 MuTect - [MUTECT] Processed 112005518 reads in 650 ms
[2015-09-30T22:43Z] INFO  23:43:43,580 MuTect - [MUTECT] Processed 14000586 reads in 678 ms
[2015-09-30T22:43Z] INFO  23:43:43,889 MuTect - [MUTECT] Processed 184011238 reads in 631 ms
[2015-09-30T22:43Z] INFO  23:43:44,161 MuTect - [MUTECT] Processed 113005577 reads in 644 ms
[2015-09-30T22:43Z] INFO  23:43:44,240 MuTect - [MUTECT] Processed 15000642 reads in 660 ms
[2015-09-30T22:43Z] INFO  23:43:44,462 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:44,462 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:44,559 MuTect - [MUTECT] Processed 185011331 reads in 670 ms
[2015-09-30T22:43Z] INFO  23:43:44,791 MuTect - [MUTECT] Processed 114005617 reads in 630 ms
[2015-09-30T22:43Z] INFO  23:43:44,892 MuTect - [MUTECT] Processed 16000716 reads in 652 ms
[2015-09-30T22:43Z] INFO  23:43:45,232 MuTect - [MUTECT] Processed 186011375 reads in 673 ms
[2015-09-30T22:43Z] INFO  23:43:45,451 MuTect - [MUTECT] Processed 115005686 reads in 660 ms
[2015-09-30T22:43Z] INFO  23:43:45,493 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:45,547 MuTect - [MUTECT] Processed 17000801 reads in 655 ms
[2015-09-30T22:43Z] INFO  23:43:45,910 MuTect - [MUTECT] Processed 187011434 reads in 678 ms
[2015-09-30T22:43Z] INFO  23:43:46,145 MuTect - [MUTECT] Processed 116005723 reads in 694 ms
[2015-09-30T22:43Z] INFO  23:43:46,263 MuTect - [MUTECT] Processed 18000840 reads in 716 ms
[2015-09-30T22:43Z] INFO  23:43:46,499 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:46,593 MuTect - [MUTECT] Processed 188011453 reads in 683 ms
[2015-09-30T22:43Z] INFO  23:43:46,677 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:46,795 MuTect - [MUTECT] Processed 117005786 reads in 650 ms
[2015-09-30T22:43Z] INFO  23:43:46,992 MuTect - [MUTECT] Processed 19000905 reads in 729 ms
[2015-09-30T22:43Z] INFO  23:43:47,339 MuTect - [MUTECT] Processed 189011514 reads in 746 ms
[2015-09-30T22:43Z] INFO  23:43:47,492 MuTect - [MUTECT] Processed 118005890 reads in 697 ms
[2015-09-30T22:43Z] INFO  23:43:47,680 MuTect - [MUTECT] Processed 20000999 reads in 688 ms
[2015-09-30T22:43Z] INFO  23:43:47,873 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:48,044 MuTect - [MUTECT] Processed 190011518 reads in 705 ms
[2015-09-30T22:43Z] INFO  23:43:48,154 MuTect - [MUTECT] Processed 119005903 reads in 662 ms
[2015-09-30T22:43Z] INFO  23:43:48,437 MuTect - [MUTECT] Processed 21001168 reads in 757 ms
[2015-09-30T22:43Z] INFO  23:43:48,793 MuTect - [MUTECT] Processed 191011537 reads in 749 ms
[2015-09-30T22:43Z] INFO  23:43:48,803 MuTect - [MUTECT] Processed 120005952 reads in 649 ms
[2015-09-30T22:43Z] INFO  23:43:48,821 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:49,050 MuTect - [MUTECT] Processed 22001282 reads in 613 ms
[2015-09-30T22:43Z] INFO  23:43:49,113 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:49,461 MuTect - [MUTECT] Processed 121005980 reads in 658 ms
[2015-09-30T22:43Z] INFO  23:43:49,513 MuTect - [MUTECT] Processed 192011670 reads in 720 ms
[2015-09-30T22:43Z] INFO  23:43:49,651 MuTect - [MUTECT] Processed 23001315 reads in 601 ms
[2015-09-30T22:43Z] INFO  23:43:50,121 MuTect - [MUTECT] Processed 122006059 reads in 660 ms
[2015-09-30T22:43Z] INFO  23:43:50,224 MuTect - [MUTECT] Processed 193011722 reads in 711 ms
[2015-09-30T22:43Z] INFO  23:43:50,280 MuTect - [MUTECT] Processed 24001369 reads in 629 ms
[2015-09-30T22:43Z] INFO  23:43:50,785 MuTect - [MUTECT] Processed 123006092 reads in 664 ms
[2015-09-30T22:43Z] INFO  23:43:50,855 MuTect - [MUTECT] Processed 25001404 reads in 575 ms
[2015-09-30T22:43Z] INFO  23:43:51,029 MuTect - [MUTECT] Processed 194011828 reads in 805 ms
[2015-09-30T22:43Z] INFO  23:43:51,047 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:51,307 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:51,424 MuTect - [MUTECT] Processed 124006127 reads in 639 ms
[2015-09-30T22:43Z] INFO  23:43:51,434 MuTect - [MUTECT] Processed 26001440 reads in 579 ms
[2015-09-30T22:43Z] INFO  23:43:51,830 MuTect - [MUTECT] Processed 195011894 reads in 801 ms
[2015-09-30T22:43Z] INFO  23:43:52,045 MuTect - [MUTECT] Processed 125006172 reads in 621 ms
[2015-09-30T22:43Z] INFO  23:43:52,088 MuTect - [MUTECT] Processed 27001516 reads in 654 ms
[2015-09-30T22:43Z] INFO  23:43:52,304 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:52,526 MuTect - [MUTECT] Processed 196011999 reads in 696 ms
[2015-09-30T22:43Z] INFO  23:43:52,666 MuTect - [MUTECT] Processed 126006264 reads in 621 ms
[2015-09-30T22:43Z] INFO  23:43:52,760 MuTect - [MUTECT] Processed 28001538 reads in 671 ms
[2015-09-30T22:43Z] INFO  23:43:53,167 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:53,196 MuTect - [MUTECT] Processed 197012010 reads in 670 ms
[2015-09-30T22:43Z] INFO  23:43:53,297 MuTect - [MUTECT] Processed 127006267 reads in 631 ms
[2015-09-30T22:43Z] INFO  23:43:53,450 MuTect - [MUTECT] Processed 29001568 reads in 691 ms
[2015-09-30T22:43Z] INFO  23:43:53,585 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:53,883 MuTect - [MUTECT] Processed 198012019 reads in 687 ms
[2015-09-30T22:43Z] INFO  23:43:53,907 MuTect - [MUTECT] Processed 128006370 reads in 610 ms
[2015-09-30T22:43Z] INFO  23:43:54,135 MuTect - [MUTECT] Processed 30001624 reads in 685 ms
[2015-09-30T22:43Z] INFO  23:43:54,540 MuTect - [MUTECT] Processed 199012090 reads in 657 ms
[2015-09-30T22:43Z] INFO  23:43:54,549 MuTect - [MUTECT] Processed 129006443 reads in 642 ms
[2015-09-30T22:43Z] INFO  23:43:54,652 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:54,815 MuTect - [MUTECT] Processed 31001688 reads in 680 ms
[2015-09-30T22:43Z] INFO  23:43:55,182 MuTect - [MUTECT] Processed 130006480 reads in 633 ms
[2015-09-30T22:43Z] INFO  23:43:55,205 MuTect - [MUTECT] Processed 200012107 reads in 665 ms
[2015-09-30T22:43Z] INFO  23:43:55,314 ProgressMeter -      17:8014075        3.65e+06   90.0 s       24.0 s     39.7%         3.8 m     2.3 m
[2015-09-30T22:43Z] INFO  23:43:55,324 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:55,488 MuTect - [MUTECT] Processed 32001765 reads in 673 ms
[2015-09-30T22:43Z] INFO  23:43:55,514 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:43Z] INFO  23:43:55,519 ProgressMeter -            done        5.58e+06    2.3 m       24.0 s    100.0%         2.3 m     0.0 s
[2015-09-30T22:43Z] INFO  23:43:55,519 ProgressMeter - Total runtime 138.28 secs, 2.30 min, 0.04 hours
[2015-09-30T22:43Z] INFO  23:43:55,586 MicroScheduler - 162495 reads were filtered out during the traversal out of approximately 2388254 total reads (6.80%)
[2015-09-30T22:43Z] INFO  23:43:55,586 MicroScheduler -   -> 122884 reads (5.15% of total) failing DuplicateReadFilter
[2015-09-30T22:43Z] INFO  23:43:55,586 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:43Z] INFO  23:43:55,586 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:43Z] INFO  23:43:55,587 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:43Z] INFO  23:43:55,587 MicroScheduler -   -> 39611 reads (1.66% of total) failing UnmappedReadFilter
[2015-09-30T22:43Z] INFO  23:43:55,798 MuTect - [MUTECT] Processed 131006485 reads in 616 ms
[2015-09-30T22:43Z] INFO  23:43:56,168 MuTect - [MUTECT] Processed 33001842 reads in 680 ms
[2015-09-30T22:43Z] INFO  23:43:56,451 MuTect - [MUTECT] Processed 132006630 reads in 652 ms
[2015-09-30T22:43Z] INFO  23:43:56,578 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:43Z] bgzip syn3-16_64294277_90354753-raw-mutect.vcf
[2015-09-30T22:43Z] tabix index syn3-16_64294277_90354753-raw-mutect.vcf.gz
[2015-09-30T22:43Z] INFO  23:43:56,824 MuTect - [MUTECT] Processed 34001928 reads in 656 ms
[2015-09-30T22:43Z] INFO  23:43:57,078 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:57,116 MuTect - [MUTECT] Processed 133006687 reads in 666 ms
[2015-09-30T22:43Z] INFO  23:43:57,517 MuTect - [MUTECT] Processed 35002002 reads in 693 ms
[2015-09-30T22:43Z] INFO  23:43:57,659 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:57,778 MuTect - [MUTECT] Processed 134006705 reads in 662 ms
[2015-09-30T22:43Z] INFO  23:43:58,174 MuTect - [MUTECT] Processed 36002069 reads in 657 ms
[2015-09-30T22:43Z] INFO  23:43:58,421 MuTect - [MUTECT] Processed 135006722 reads in 643 ms
[2015-09-30T22:43Z] INFO  23:43:58,902 MuTect - [MUTECT] Processed 37002117 reads in 728 ms
[2015-09-30T22:43Z] MuTect: MuTect
[2015-09-30T22:43Z] INFO  23:43:59,091 MuTect - [MUTECT] Processed 136006769 reads in 670 ms
[2015-09-30T22:43Z] INFO  23:43:59,640 MuTect - [MUTECT] Processed 38002120 reads in 738 ms
[2015-09-30T22:43Z] INFO  23:43:59,664 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:43Z] INFO  23:43:59,751 MuTect - [MUTECT] Processed 137006782 reads in 660 ms
[2015-09-30T22:43Z] INFO  23:43:59,796 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:00,317 MuTect - [MUTECT] Processed 39002216 reads in 677 ms
[2015-09-30T22:44Z] INFO  23:44:00,410 MuTect - [MUTECT] Processed 138006821 reads in 659 ms
[2015-09-30T22:44Z] INFO  23:44:00,971 MuTect - [MUTECT] Processed 40002387 reads in 654 ms
[2015-09-30T22:44Z] INFO  23:44:01,018 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/17/syn3-17_62078196_81195210-raw-mutect-regions.bed to be BED
[2015-09-30T22:44Z] INFO  23:44:01,070 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:44Z] INFO  23:44:01,071 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:44Z] INFO  23:44:01,071 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:44Z] INFO  23:44:01,071 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:44Z] INFO  23:44:01,074 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/17/syn3-17_62078196_81195210-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/17/tx/tmphMa4gZ/syn3-17_62078196_81195210-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:44Z] INFO  23:44:01,074 HelpFormatter - Date/Time: 2015/09/30 23:44:01
[2015-09-30T22:44Z] INFO  23:44:01,074 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:44Z] INFO  23:44:01,075 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:44Z] INFO  23:44:01,095 MuTect - [MUTECT] Processed 139006911 reads in 685 ms
[2015-09-30T22:44Z] INFO  23:44:01,101 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:44Z] INFO  23:44:01,105 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:44Z] INFO  23:44:01,158 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:44Z] INFO  23:44:01,204 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:44Z] INFO  23:44:01,211 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:44Z] INFO  23:44:01,299 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2015-09-30T22:44Z] INFO  23:44:01,310 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:44Z] INFO  23:44:01,485 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:44Z] INFO  23:44:01,595 IntervalUtils - Processing 1876990 bp from intervals
[2015-09-30T22:44Z] INFO  23:44:01,599 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:44Z] INFO  23:44:01,599 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:44Z] INFO  23:44:01,639 MuTect - [MUTECT] Processed 41002430 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:01,724 ProgressMeter -     17:36357165        1.23e+06   30.0 s       24.0 s     13.4%         3.7 m     3.2 m
[2015-09-30T22:44Z] INFO  23:44:01,746 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:44Z] INFO  23:44:01,799 MuTect - [MUTECT] Processed 140006963 reads in 704 ms
[2015-09-30T22:44Z] INFO  23:44:01,895 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:44Z] INFO  23:44:01,895 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:44Z] INFO  23:44:01,895 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:44Z] INFO  23:44:01,896 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:44Z] INFO  23:44:02,214 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:02,409 MuTect - [MUTECT] Processed 42002456 reads in 770 ms
[2015-09-30T22:44Z] INFO  23:44:02,498 MuTect - [MUTECT] Processed 141006974 reads in 699 ms
[2015-09-30T22:44Z] INFO  23:44:03,083 MuTect - [MUTECT] Processed 43002473 reads in 674 ms
[2015-09-30T22:44Z] INFO  23:44:03,201 MuTect - [MUTECT] Processed 142007063 reads in 702 ms
[2015-09-30T22:44Z] INFO  23:44:03,342 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:03,774 MuTect - [MUTECT] Processed 44002561 reads in 691 ms
[2015-09-30T22:44Z] INFO  23:44:03,889 MuTect - [MUTECT] Processed 143007110 reads in 689 ms
[2015-09-30T22:44Z] INFO  23:44:04,276 MuTect - [MUTECT] Processed 1000056 reads in 2336 ms
[2015-09-30T22:44Z] INFO  23:44:04,431 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:04,476 MuTect - [MUTECT] Processed 45002628 reads in 702 ms
[2015-09-30T22:44Z] INFO  23:44:04,604 MuTect - [MUTECT] Processed 144007115 reads in 715 ms
[2015-09-30T22:44Z] INFO  23:44:05,185 MuTect - [MUTECT] Processed 46002736 reads in 709 ms
[2015-09-30T22:44Z] INFO  23:44:05,225 MuTect - [MUTECT] Processed 2000130 reads in 949 ms
[2015-09-30T22:44Z] INFO  23:44:05,288 MuTect - [MUTECT] Processed 145007209 reads in 684 ms
[2015-09-30T22:44Z] INFO  23:44:05,606 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:05,862 MuTect - [MUTECT] Processed 47002867 reads in 677 ms
[2015-09-30T22:44Z] INFO  23:44:05,894 MuTect - [MUTECT] Processed 3000206 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:05,988 MuTect - [MUTECT] Processed 146007229 reads in 700 ms
[2015-09-30T22:44Z] INFO  23:44:06,148 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:06,538 MuTect - [MUTECT] Processed 48002956 reads in 676 ms
[2015-09-30T22:44Z] INFO  23:44:06,607 MuTect - [MUTECT] Processed 4000238 reads in 714 ms
[2015-09-30T22:44Z] INFO  23:44:06,688 MuTect - [MUTECT] Processed 147007245 reads in 700 ms
[2015-09-30T22:44Z] INFO  23:44:06,753 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:07,180 MuTect - [MUTECT] Processed 49003044 reads in 642 ms
[2015-09-30T22:44Z] INFO  23:44:07,316 MuTect - [MUTECT] Processed 5000252 reads in 709 ms
[2015-09-30T22:44Z] INFO  23:44:07,344 MuTect - [MUTECT] Processed 148007268 reads in 656 ms
[2015-09-30T22:44Z] INFO  23:44:07,829 MuTect - [MUTECT] Processed 50003052 reads in 649 ms
[2015-09-30T22:44Z] INFO  23:44:07,995 MuTect - [MUTECT] Processed 149007274 reads in 651 ms
[2015-09-30T22:44Z] INFO  23:44:08,005 MuTect - [MUTECT] Processed 6000279 reads in 689 ms
[2015-09-30T22:44Z] INFO  23:44:08,112 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:08,496 MuTect - [MUTECT] Processed 51003055 reads in 667 ms
[2015-09-30T22:44Z] INFO  23:44:08,664 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:08,682 MuTect - [MUTECT] Processed 7000281 reads in 677 ms
[2015-09-30T22:44Z] INFO  23:44:08,700 MuTect - [MUTECT] Processed 150007395 reads in 705 ms
[2015-09-30T22:44Z] INFO  23:44:08,996 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:09,148 MuTect - [MUTECT] Processed 52003129 reads in 652 ms
[2015-09-30T22:44Z] INFO  23:44:09,336 MuTect - [MUTECT] Processed 8000285 reads in 654 ms
[2015-09-30T22:44Z] INFO  23:44:09,372 MuTect - [MUTECT] Processed 151007463 reads in 672 ms
[2015-09-30T22:44Z] INFO  23:44:09,829 MuTect - [MUTECT] Processed 53003168 reads in 681 ms
[2015-09-30T22:44Z] INFO  23:44:10,024 MuTect - [MUTECT] Processed 9000287 reads in 688 ms
[2015-09-30T22:44Z] INFO  23:44:10,050 MuTect - [MUTECT] Processed 152007529 reads in 678 ms
[2015-09-30T22:44Z] INFO  23:44:10,278 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:10,465 MuTect - [MUTECT] Processed 54003217 reads in 636 ms
[2015-09-30T22:44Z] INFO  23:44:10,737 MuTect - [MUTECT] Processed 10000288 reads in 713 ms
[2015-09-30T22:44Z] INFO  23:44:10,739 MuTect - [MUTECT] Processed 153007536 reads in 689 ms
[2015-09-30T22:44Z] INFO  23:44:11,137 MuTect - [MUTECT] Processed 55003273 reads in 672 ms
[2015-09-30T22:44Z] INFO  23:44:11,303 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:11,359 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:11,403 MuTect - [MUTECT] Processed 11000313 reads in 666 ms
[2015-09-30T22:44Z] INFO  23:44:11,429 MuTect - [MUTECT] Processed 154007542 reads in 690 ms
[2015-09-30T22:44Z] INFO  23:44:11,801 MuTect - [MUTECT] Processed 56003279 reads in 664 ms
[2015-09-30T22:44Z] INFO  23:44:12,059 MuTect - [MUTECT] Processed 12000372 reads in 655 ms
[2015-09-30T22:44Z] INFO  23:44:12,118 MuTect - [MUTECT] Processed 155007586 reads in 689 ms
[2015-09-30T22:44Z] INFO  23:44:12,430 MuTect - [MUTECT] Processed 57003299 reads in 629 ms
[2015-09-30T22:44Z] INFO  23:44:12,494 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:12,744 MuTect - [MUTECT] Processed 13000388 reads in 686 ms
[2015-09-30T22:44Z] INFO  23:44:12,773 MuTect - [MUTECT] Processed 156007616 reads in 655 ms
[2015-09-30T22:44Z] INFO  23:44:13,036 MuTect - [MUTECT] Processed 58003307 reads in 606 ms
[2015-09-30T22:44Z] INFO  23:44:13,453 MuTect - [MUTECT] Processed 157007625 reads in 680 ms
[2015-09-30T22:44Z] INFO  23:44:13,502 MuTect - [MUTECT] Processed 14000418 reads in 758 ms
[2015-09-30T22:44Z] INFO  23:44:13,703 MuTect - [MUTECT] Processed 59003364 reads in 667 ms
[2015-09-30T22:44Z] INFO  23:44:13,762 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:13,796 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:14,132 MuTect - [MUTECT] Processed 158007646 reads in 679 ms
[2015-09-30T22:44Z] INFO  23:44:14,185 MuTect - [MUTECT] Processed 15000467 reads in 682 ms
[2015-09-30T22:44Z] INFO  23:44:14,368 MuTect - [MUTECT] Processed 60003402 reads in 665 ms
[2015-09-30T22:44Z] INFO  23:44:14,526 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:14,831 MuTect - [MUTECT] Processed 159007673 reads in 699 ms
[2015-09-30T22:44Z] INFO  23:44:14,853 MuTect - [MUTECT] Processed 16000501 reads in 669 ms
[2015-09-30T22:44Z] INFO  23:44:14,989 MuTect - [MUTECT] Processed 61003472 reads in 621 ms
[2015-09-30T22:44Z] INFO  23:44:15,516 MuTect - [MUTECT] Processed 17000527 reads in 663 ms
[2015-09-30T22:44Z] INFO  23:44:15,520 MuTect - [MUTECT] Processed 160007732 reads in 689 ms
[2015-09-30T22:44Z] INFO  23:44:15,617 MuTect - [MUTECT] Processed 62003505 reads in 628 ms
[2015-09-30T22:44Z] INFO  23:44:16,142 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:16,200 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:16,217 MuTect - [MUTECT] Processed 18000540 reads in 701 ms
[2015-09-30T22:44Z] INFO  23:44:16,225 MuTect - [MUTECT] Processed 161007802 reads in 705 ms
[2015-09-30T22:44Z] INFO  23:44:16,304 MuTect - [MUTECT] Processed 63003610 reads in 687 ms
[2015-09-30T22:44Z] INFO  23:44:16,684 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:16,938 MuTect - [MUTECT] Processed 162007839 reads in 713 ms
[2015-09-30T22:44Z] INFO  23:44:16,950 MuTect - [MUTECT] Processed 19000544 reads in 733 ms
[2015-09-30T22:44Z] INFO  23:44:16,976 MuTect - [MUTECT] Processed 64003622 reads in 672 ms
[2015-09-30T22:44Z] INFO  23:44:17,627 MuTect - [MUTECT] Processed 163007840 reads in 689 ms
[2015-09-30T22:44Z] INFO  23:44:17,632 MuTect - [MUTECT] Processed 20000640 reads in 682 ms
[2015-09-30T22:44Z] INFO  23:44:17,638 MuTect - [MUTECT] Processed 65003689 reads in 662 ms
[2015-09-30T22:44Z] INFO  23:44:18,264 MuTect - [MUTECT] Processed 66003740 reads in 625 ms
[2015-09-30T22:44Z] INFO  23:44:18,297 MuTect - [MUTECT] Processed 164007905 reads in 670 ms
[2015-09-30T22:44Z] INFO  23:44:18,324 MuTect - [MUTECT] Processed 21000729 reads in 692 ms
[2015-09-30T22:44Z] INFO  23:44:18,644 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:18,695 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:18,786 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:18,885 MuTect - [MUTECT] Processed 67003779 reads in 622 ms
[2015-09-30T22:44Z] INFO  23:44:19,005 MuTect - [MUTECT] Processed 165008028 reads in 708 ms
[2015-09-30T22:44Z] INFO  23:44:19,047 MuTect - [MUTECT] Processed 22000738 reads in 723 ms
[2015-09-30T22:44Z] INFO  23:44:19,518 MuTect - [MUTECT] Processed 68003799 reads in 633 ms
[2015-09-30T22:44Z] INFO  23:44:19,677 MuTect - [MUTECT] Processed 166008044 reads in 672 ms
[2015-09-30T22:44Z] INFO  23:44:19,711 MuTect - [MUTECT] Processed 23000752 reads in 664 ms
[2015-09-30T22:44Z] INFO  23:44:20,139 MuTect - [MUTECT] Processed 69003859 reads in 621 ms
[2015-09-30T22:44Z] INFO  23:44:20,370 MuTect - [MUTECT] Processed 167008087 reads in 693 ms
[2015-09-30T22:44Z] INFO  23:44:20,377 MuTect - [MUTECT] Processed 24000766 reads in 666 ms
[2015-09-30T22:44Z] INFO  23:44:20,777 MuTect - [MUTECT] Processed 70003932 reads in 638 ms
[2015-09-30T22:44Z] INFO  23:44:20,871 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:21,044 MuTect - [MUTECT] Processed 168008124 reads in 674 ms
[2015-09-30T22:44Z] INFO  23:44:21,068 MuTect - [MUTECT] Processed 25000815 reads in 691 ms
[2015-09-30T22:44Z] INFO  23:44:21,106 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:21,219 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:21,441 MuTect - [MUTECT] Processed 71004012 reads in 664 ms
[2015-09-30T22:44Z] INFO  23:44:21,714 MuTect - [MUTECT] Processed 169008149 reads in 670 ms
[2015-09-30T22:44Z] INFO  23:44:21,736 MuTect - [MUTECT] Processed 26000847 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:22,080 MuTect - [MUTECT] Processed 72004072 reads in 639 ms
[2015-09-30T22:44Z] INFO  23:44:22,394 MuTect - [MUTECT] Processed 27000930 reads in 658 ms
[2015-09-30T22:44Z] INFO  23:44:22,399 MuTect - [MUTECT] Processed 170008250 reads in 685 ms
[2015-09-30T22:44Z] INFO  23:44:22,711 MuTect - [MUTECT] Processed 73004139 reads in 631 ms
[2015-09-30T22:44Z] INFO  23:44:22,919 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:23,077 MuTect - [MUTECT] Processed 28000970 reads in 683 ms
[2015-09-30T22:44Z] INFO  23:44:23,099 MuTect - [MUTECT] Processed 171008333 reads in 700 ms
[2015-09-30T22:44Z] INFO  23:44:23,329 MuTect - [MUTECT] Processed 74004150 reads in 618 ms
[2015-09-30T22:44Z] INFO  23:44:23,458 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:23,469 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:23,753 MuTect - [MUTECT] Processed 29001037 reads in 676 ms
[2015-09-30T22:44Z] INFO  23:44:23,826 MuTect - [MUTECT] Processed 172008386 reads in 727 ms
[2015-09-30T22:44Z] INFO  23:44:23,938 MuTect - [MUTECT] Processed 75004190 reads in 609 ms
[2015-09-30T22:44Z] INFO  23:44:24,421 MuTect - [MUTECT] Processed 30001098 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:24,543 MuTect - [MUTECT] Processed 173008477 reads in 717 ms
[2015-09-30T22:44Z] INFO  23:44:24,546 MuTect - [MUTECT] Processed 76004230 reads in 608 ms
[2015-09-30T22:44Z] INFO  23:44:24,967 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:25,155 MuTect - [MUTECT] Processed 31001104 reads in 734 ms
[2015-09-30T22:44Z] INFO  23:44:25,202 MuTect - [MUTECT] Processed 77004266 reads in 656 ms
[2015-09-30T22:44Z] INFO  23:44:25,211 MuTect - [MUTECT] Processed 174008491 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:25,315 ProgressMeter -     17:15341062        5.09e+06  120.0 s       23.0 s     54.9%         3.6 m    98.0 s
[2015-09-30T22:44Z] INFO  23:44:25,768 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:25,870 MuTect - [MUTECT] Processed 78004356 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:25,872 MuTect - [MUTECT] Processed 32001142 reads in 717 ms
[2015-09-30T22:44Z] INFO  23:44:25,886 MuTect - [MUTECT] Processed 175008544 reads in 675 ms
[2015-09-30T22:44Z] INFO  23:44:26,115 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:26,507 MuTect - [MUTECT] Processed 79004485 reads in 637 ms
[2015-09-30T22:44Z] INFO  23:44:26,618 MuTect - [MUTECT] Processed 176008593 reads in 732 ms
[2015-09-30T22:44Z] INFO  23:44:26,627 MuTect - [MUTECT] Processed 33001153 reads in 755 ms
[2015-09-30T22:44Z] INFO  23:44:27,160 MuTect - [MUTECT] Processed 80004556 reads in 653 ms
[2015-09-30T22:44Z] INFO  23:44:27,263 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:27,324 MuTect - [MUTECT] Processed 177008610 reads in 706 ms
[2015-09-30T22:44Z] INFO  23:44:27,379 MuTect - [MUTECT] Processed 34001164 reads in 752 ms
[2015-09-30T22:44Z] INFO  23:44:27,826 MuTect - [MUTECT] Processed 81004570 reads in 666 ms
[2015-09-30T22:44Z] INFO  23:44:28,043 MuTect - [MUTECT] Processed 178008723 reads in 719 ms
[2015-09-30T22:44Z] INFO  23:44:28,158 MuTect - [MUTECT] Processed 35001207 reads in 779 ms
[2015-09-30T22:44Z] INFO  23:44:28,491 MuTect - [MUTECT] Processed 82004687 reads in 665 ms
[2015-09-30T22:44Z] INFO  23:44:28,495 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:28,730 MuTect - [MUTECT] Processed 179008775 reads in 686 ms
[2015-09-30T22:44Z] INFO  23:44:28,782 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:28,850 MuTect - [MUTECT] Processed 36001225 reads in 692 ms
[2015-09-30T22:44Z] INFO  23:44:29,184 MuTect - [MUTECT] Processed 83004790 reads in 693 ms
[2015-09-30T22:44Z] INFO  23:44:29,424 MuTect - [MUTECT] Processed 180008785 reads in 695 ms
[2015-09-30T22:44Z] INFO  23:44:29,512 MuTect - [MUTECT] Processed 37001251 reads in 662 ms
[2015-09-30T22:44Z] INFO  23:44:29,869 MuTect - [MUTECT] Processed 84004796 reads in 685 ms
[2015-09-30T22:44Z] INFO  23:44:29,891 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:30,174 MuTect - [MUTECT] Processed 181008845 reads in 750 ms
[2015-09-30T22:44Z] INFO  23:44:30,244 MuTect - [MUTECT] Processed 38001368 reads in 732 ms
[2015-09-30T22:44Z] INFO  23:44:30,543 MuTect - [MUTECT] Processed 85004854 reads in 674 ms
[2015-09-30T22:44Z] INFO  23:44:30,748 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:30,895 MuTect - [MUTECT] Processed 182008918 reads in 721 ms
[2015-09-30T22:44Z] INFO  23:44:30,912 MuTect - [MUTECT] Processed 39001379 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:31,238 MuTect - [MUTECT] Processed 86004931 reads in 695 ms
[2015-09-30T22:44Z] INFO  23:44:31,289 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:31,574 MuTect - [MUTECT] Processed 40001381 reads in 662 ms
[2015-09-30T22:44Z] INFO  23:44:31,585 MuTect - [MUTECT] Processed 183008997 reads in 690 ms
[2015-09-30T22:44Z] INFO  23:44:31,725 ProgressMeter -     17:39079480        2.65e+06   60.0 s       22.0 s     27.4%         3.6 m     2.6 m
[2015-09-30T22:44Z] INFO  23:44:31,898 ProgressMeter -     17:71205796        1.51e+06   30.0 s       19.0 s     27.3%       109.0 s    79.0 s
[2015-09-30T22:44Z] INFO  23:44:31,951 MuTect - [MUTECT] Processed 87004950 reads in 713 ms
[2015-09-30T22:44Z] INFO  23:44:32,238 MuTect - [MUTECT] Processed 184009001 reads in 652 ms
[2015-09-30T22:44Z] INFO  23:44:32,253 MuTect - [MUTECT] Processed 41001493 reads in 679 ms
[2015-09-30T22:44Z] INFO  23:44:32,462 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:32,731 MuTect - [MUTECT] Processed 88005043 reads in 780 ms
[2015-09-30T22:44Z] INFO  23:44:32,896 MuTect - [MUTECT] Processed 185009098 reads in 659 ms
[2015-09-30T22:44Z] INFO  23:44:32,921 MuTect - [MUTECT] Processed 42001567 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:33,065 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:33,446 MuTect - [MUTECT] Processed 89005198 reads in 715 ms
[2015-09-30T22:44Z] INFO  23:44:33,593 MuTect - [MUTECT] Processed 186009098 reads in 697 ms
[2015-09-30T22:44Z] INFO  23:44:33,634 MuTect - [MUTECT] Processed 43001696 reads in 713 ms
[2015-09-30T22:44Z] INFO  23:44:33,899 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:34,271 MuTect - [MUTECT] Processed 90005291 reads in 825 ms
[2015-09-30T22:44Z] INFO  23:44:34,287 MuTect - [MUTECT] Processed 44001793 reads in 653 ms
[2015-09-30T22:44Z] INFO  23:44:34,324 MuTect - [MUTECT] Processed 187009190 reads in 731 ms
[2015-09-30T22:44Z] INFO  23:44:34,752 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:34,974 MuTect - [MUTECT] Processed 45001850 reads in 687 ms
[2015-09-30T22:44Z] INFO  23:44:35,049 MuTect - [MUTECT] Processed 188009264 reads in 724 ms
[2015-09-30T22:44Z] INFO  23:44:35,138 MuTect - [MUTECT] Processed 91005329 reads in 867 ms
[2015-09-30T22:44Z] INFO  23:44:35,273 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:35,645 MuTect - [MUTECT] Processed 46001915 reads in 671 ms
[2015-09-30T22:44Z] INFO  23:44:35,730 MuTect - [MUTECT] Processed 189009396 reads in 682 ms
[2015-09-30T22:44Z] INFO  23:44:35,996 MuTect - [MUTECT] Processed 92005377 reads in 858 ms
[2015-09-30T22:44Z] INFO  23:44:36,274 MuTect - [MUTECT] Processed 47001937 reads in 629 ms
[2015-09-30T22:44Z] INFO  23:44:36,336 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:36,370 MuTect - [MUTECT] Processed 190009418 reads in 640 ms
[2015-09-30T22:44Z] INFO  23:44:36,664 MuTect - [MUTECT] Processed 93005377 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:36,959 MuTect - [MUTECT] Processed 48002031 reads in 685 ms
[2015-09-30T22:44Z] INFO  23:44:36,982 MuTect - [MUTECT] Processed 191009488 reads in 612 ms
[2015-09-30T22:44Z] INFO  23:44:37,228 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:37,317 MuTect - [MUTECT] Processed 94005502 reads in 653 ms
[2015-09-30T22:44Z] INFO  23:44:37,569 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:37,622 MuTect - [MUTECT] Processed 192009594 reads in 640 ms
[2015-09-30T22:44Z] INFO  23:44:37,638 MuTect - [MUTECT] Processed 49002110 reads in 679 ms
[2015-09-30T22:44Z] INFO  23:44:38,020 MuTect - [MUTECT] Processed 95005594 reads in 703 ms
[2015-09-30T22:44Z] INFO  23:44:38,259 MuTect - [MUTECT] Processed 193009634 reads in 637 ms
[2015-09-30T22:44Z] INFO  23:44:38,300 MuTect - [MUTECT] Processed 50002136 reads in 662 ms
[2015-09-30T22:44Z] INFO  23:44:38,444 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:38,710 MuTect - [MUTECT] Processed 96005701 reads in 690 ms
[2015-09-30T22:44Z] INFO  23:44:38,886 MuTect - [MUTECT] Processed 194009736 reads in 627 ms
[2015-09-30T22:44Z] INFO  23:44:38,964 MuTect - [MUTECT] Processed 51002182 reads in 664 ms
[2015-09-30T22:44Z] INFO  23:44:39,378 MuTect - [MUTECT] Processed 97005781 reads in 668 ms
[2015-09-30T22:44Z] INFO  23:44:39,491 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:39,512 MuTect - [MUTECT] Processed 195009863 reads in 626 ms
[2015-09-30T22:44Z] INFO  23:44:39,635 MuTect - [MUTECT] Processed 52002218 reads in 671 ms
[2015-09-30T22:44Z] INFO  23:44:39,749 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:40,048 MuTect - [MUTECT] Processed 98005787 reads in 670 ms
[2015-09-30T22:44Z] INFO  23:44:40,115 MuTect - [MUTECT] Processed 196009926 reads in 602 ms
[2015-09-30T22:44Z] INFO  23:44:40,315 MuTect - [MUTECT] Processed 53002232 reads in 680 ms
[2015-09-30T22:44Z] INFO  23:44:40,572 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:40,697 MuTect - [MUTECT] Processed 197009930 reads in 583 ms
[2015-09-30T22:44Z] INFO  23:44:40,738 MuTect - [MUTECT] Processed 99005907 reads in 690 ms
[2015-09-30T22:44Z] INFO  23:44:40,966 MuTect - [MUTECT] Processed 54002319 reads in 651 ms
[2015-09-30T22:44Z] INFO  23:44:41,301 MuTect - [MUTECT] Processed 198009939 reads in 604 ms
[2015-09-30T22:44Z] INFO  23:44:41,410 MuTect - [MUTECT] Processed 100006041 reads in 672 ms
[2015-09-30T22:44Z] INFO  23:44:41,608 MuTect - [MUTECT] Processed 55002336 reads in 641 ms
[2015-09-30T22:44Z] INFO  23:44:41,638 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:41,852 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:41,937 MuTect - [MUTECT] Processed 199009944 reads in 636 ms
[2015-09-30T22:44Z] INFO  23:44:42,119 MuTect - [MUTECT] Processed 101006044 reads in 709 ms
[2015-09-30T22:44Z] INFO  23:44:42,281 MuTect - [MUTECT] Processed 56002465 reads in 674 ms
[2015-09-30T22:44Z] INFO  23:44:42,568 MuTect - [MUTECT] Processed 200010050 reads in 631 ms
[2015-09-30T22:44Z] INFO  23:44:42,680 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:42,830 MuTect - [MUTECT] Processed 102006126 reads in 711 ms
[2015-09-30T22:44Z] INFO  23:44:42,919 MuTect - [MUTECT] Processed 57002568 reads in 638 ms
[2015-09-30T22:44Z] INFO  23:44:43,171 MuTect - [MUTECT] Processed 201010156 reads in 603 ms
[2015-09-30T22:44Z] INFO  23:44:43,521 MuTect - [MUTECT] Processed 103006212 reads in 691 ms
[2015-09-30T22:44Z] INFO  23:44:43,558 MuTect - [MUTECT] Processed 58002658 reads in 639 ms
[2015-09-30T22:44Z] INFO  23:44:43,792 MuTect - [MUTECT] Processed 202010242 reads in 621 ms
[2015-09-30T22:44Z] INFO  23:44:43,842 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:43,926 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:44,180 MuTect - [MUTECT] Processed 104006313 reads in 659 ms
[2015-09-30T22:44Z] INFO  23:44:44,260 MuTect - [MUTECT] Processed 59002708 reads in 702 ms
[2015-09-30T22:44Z] INFO  23:44:44,468 MuTect - [MUTECT] Processed 203010260 reads in 675 ms
[2015-09-30T22:44Z] INFO  23:44:44,842 MuTect - [MUTECT] Processed 105006408 reads in 662 ms
[2015-09-30T22:44Z] INFO  23:44:44,842 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:44,951 MuTect - [MUTECT] Processed 60002723 reads in 691 ms
[2015-09-30T22:44Z] INFO  23:44:45,123 MuTect - [MUTECT] Processed 204010266 reads in 656 ms
[2015-09-30T22:44Z] INFO  23:44:45,531 MuTect - [MUTECT] Processed 106006510 reads in 689 ms
[2015-09-30T22:44Z] INFO  23:44:45,629 MuTect - [MUTECT] Processed 61002832 reads in 678 ms
[2015-09-30T22:44Z] INFO  23:44:45,724 MuTect - [MUTECT] Processed 205010311 reads in 601 ms
[2015-09-30T22:44Z] INFO  23:44:46,113 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:46,219 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:46,223 MuTect - [MUTECT] Processed 107006535 reads in 692 ms
[2015-09-30T22:44Z] INFO  23:44:46,363 MuTect - [MUTECT] Processed 206010449 reads in 639 ms
[2015-09-30T22:44Z] INFO  23:44:46,386 MuTect - [MUTECT] Processed 62002865 reads in 757 ms
[2015-09-30T22:44Z] INFO  23:44:46,868 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:46,909 MuTect - [MUTECT] Processed 108006610 reads in 686 ms
[2015-09-30T22:44Z] INFO  23:44:47,040 MuTect - [MUTECT] Processed 207010535 reads in 676 ms
[2015-09-30T22:44Z] INFO  23:44:47,072 MuTect - [MUTECT] Processed 63002920 reads in 686 ms
[2015-09-30T22:44Z] INFO  23:44:47,604 MuTect - [MUTECT] Processed 109006669 reads in 695 ms
[2015-09-30T22:44Z] INFO  23:44:47,706 MuTect - [MUTECT] Processed 208010621 reads in 667 ms
[2015-09-30T22:44Z] INFO  23:44:47,802 MuTect - [MUTECT] Processed 64002950 reads in 730 ms
[2015-09-30T22:44Z] INFO  23:44:48,297 MuTect - [MUTECT] Processed 110006677 reads in 693 ms
[2015-09-30T22:44Z] INFO  23:44:48,356 MuTect - [MUTECT] Processed 209010745 reads in 650 ms
[2015-09-30T22:44Z] INFO  23:44:48,465 MuTect - [MUTECT] Processed 65003026 reads in 663 ms
[2015-09-30T22:44Z] INFO  23:44:48,534 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:48,642 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:48,869 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:48,960 MuTect - [MUTECT] Processed 111006680 reads in 663 ms
[2015-09-30T22:44Z] INFO  23:44:49,026 MuTect - [MUTECT] Processed 210010766 reads in 670 ms
[2015-09-30T22:44Z] INFO  23:44:49,132 MuTect - [MUTECT] Processed 66003035 reads in 667 ms
[2015-09-30T22:44Z] INFO  23:44:49,639 MuTect - [MUTECT] Processed 112006746 reads in 679 ms
[2015-09-30T22:44Z] INFO  23:44:49,697 MuTect - [MUTECT] Processed 211010768 reads in 670 ms
[2015-09-30T22:44Z] INFO  23:44:49,778 MuTect - [MUTECT] Processed 67003091 reads in 646 ms
[2015-09-30T22:44Z] INFO  23:44:50,272 MuTect - [MUTECT] Processed 113006808 reads in 633 ms
[2015-09-30T22:44Z] INFO  23:44:50,351 MuTect - [MUTECT] Processed 212010770 reads in 655 ms
[2015-09-30T22:44Z] INFO  23:44:50,464 MuTect - [MUTECT] Processed 68003127 reads in 686 ms
[2015-09-30T22:44Z] INFO  23:44:50,722 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:50,908 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:50,916 MuTect - [MUTECT] Processed 114006847 reads in 644 ms
[2015-09-30T22:44Z] INFO  23:44:51,017 MuTect - [MUTECT] Processed 213010854 reads in 666 ms
[2015-09-30T22:44Z] INFO  23:44:51,158 MuTect - [MUTECT] Processed 69003170 reads in 694 ms
[2015-09-30T22:44Z] INFO  23:44:51,253 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:51,558 MuTect - [MUTECT] Processed 115006870 reads in 642 ms
[2015-09-30T22:44Z] INFO  23:44:51,731 MuTect - [MUTECT] Processed 214010941 reads in 714 ms
[2015-09-30T22:44Z] INFO  23:44:51,821 MuTect - [MUTECT] Processed 70003212 reads in 663 ms
[2015-09-30T22:44Z] INFO  23:44:52,228 MuTect - [MUTECT] Processed 116006961 reads in 670 ms
[2015-09-30T22:44Z] INFO  23:44:52,409 MuTect - [MUTECT] Processed 215011047 reads in 678 ms
[2015-09-30T22:44Z] INFO  23:44:52,499 MuTect - [MUTECT] Processed 71003226 reads in 678 ms
[2015-09-30T22:44Z] INFO  23:44:52,859 MuTect - [MUTECT] Processed 117007055 reads in 631 ms
[2015-09-30T22:44Z] INFO  23:44:53,067 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:53,130 MuTect - [MUTECT] Processed 216011112 reads in 721 ms
[2015-09-30T22:44Z] INFO  23:44:53,162 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:53,193 MuTect - [MUTECT] Processed 72003261 reads in 694 ms
[2015-09-30T22:44Z] INFO  23:44:53,476 MuTect - [MUTECT] Processed 118007066 reads in 617 ms
[2015-09-30T22:44Z] INFO  23:44:53,816 MuTect - [MUTECT] Processed 217011177 reads in 686 ms
[2015-09-30T22:44Z] INFO  23:44:53,924 MuTect - [MUTECT] Processed 73003315 reads in 731 ms
[2015-09-30T22:44Z] INFO  23:44:54,099 MuTect - [MUTECT] Processed 119007146 reads in 623 ms
[2015-09-30T22:44Z] INFO  23:44:54,461 MuTect - [MUTECT] Processed 218011188 reads in 645 ms
[2015-09-30T22:44Z] INFO  23:44:54,634 MuTect - [MUTECT] Processed 74003408 reads in 710 ms
[2015-09-30T22:44Z] INFO  23:44:54,669 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:54,734 MuTect - [MUTECT] Processed 120007193 reads in 635 ms
[2015-09-30T22:44Z] INFO  23:44:55,117 MuTect - [MUTECT] Processed 219011189 reads in 656 ms
[2015-09-30T22:44Z] INFO  23:44:55,308 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:55,316 ProgressMeter -     17:18575802        6.44e+06    2.5 m       23.0 s     69.0%         3.6 m    67.0 s
[2015-09-30T22:44Z] INFO  23:44:55,332 MuTect - [MUTECT] Processed 75003557 reads in 698 ms
[2015-09-30T22:44Z] INFO  23:44:55,355 MuTect - [MUTECT] Processed 121007282 reads in 621 ms
[2015-09-30T22:44Z] INFO  23:44:55,422 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:55,763 MuTect - [MUTECT] Processed 220011212 reads in 646 ms
[2015-09-30T22:44Z] INFO  23:44:56,032 MuTect - [MUTECT] Processed 76003558 reads in 700 ms
[2015-09-30T22:44Z] INFO  23:44:56,055 MuTect - [MUTECT] Processed 122007388 reads in 700 ms
[2015-09-30T22:44Z] INFO  23:44:56,458 MuTect - [MUTECT] Processed 221011236 reads in 695 ms
[2015-09-30T22:44Z] INFO  23:44:56,714 MuTect - [MUTECT] Processed 123007403 reads in 659 ms
[2015-09-30T22:44Z] INFO  23:44:56,722 MuTect - [MUTECT] Processed 77003660 reads in 690 ms
[2015-09-30T22:44Z] INFO  23:44:57,129 MuTect - [MUTECT] Processed 222011308 reads in 671 ms
[2015-09-30T22:44Z] INFO  23:44:57,381 MuTect - [MUTECT] Processed 124007528 reads in 667 ms
[2015-09-30T22:44Z] INFO  23:44:57,385 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:57,415 MuTect - [MUTECT] Processed 78003669 reads in 693 ms
[2015-09-30T22:44Z] INFO  23:44:57,606 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:57,669 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:57,781 MuTect - [MUTECT] Processed 223011415 reads in 652 ms
[2015-09-30T22:44Z] INFO  23:44:58,029 MuTect - [MUTECT] Processed 125007634 reads in 647 ms
[2015-09-30T22:44Z] INFO  23:44:58,155 MuTect - [MUTECT] Processed 79003769 reads in 740 ms
[2015-09-30T22:44Z] INFO  23:44:58,412 MuTect - [MUTECT] Processed 224011509 reads in 631 ms
[2015-09-30T22:44Z] INFO  23:44:58,683 MuTect - [MUTECT] Processed 126007661 reads in 655 ms
[2015-09-30T22:44Z] INFO  23:44:58,848 MuTect - [MUTECT] Processed 80003795 reads in 693 ms
[2015-09-30T22:44Z] INFO  23:44:59,042 MuTect - [MUTECT] Processed 225011595 reads in 630 ms
[2015-09-30T22:44Z] INFO  23:44:59,332 MuTect - [MUTECT] Processed 127007734 reads in 649 ms
[2015-09-30T22:44Z] INFO  23:44:59,525 MuTect - [MUTECT] Processed 81003845 reads in 677 ms
[2015-09-30T22:44Z] INFO  23:44:59,665 MuTect - [MUTECT] Processed 226011627 reads in 623 ms
[2015-09-30T22:44Z] INFO  23:44:59,879 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:59,903 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:44Z] INFO  23:44:59,985 MuTect - [MUTECT] Processed 128007808 reads in 653 ms
[2015-09-30T22:45Z] INFO  23:45:00,200 MuTect - [MUTECT] Processed 82003845 reads in 675 ms
[2015-09-30T22:45Z] INFO  23:45:00,286 MuTect - [MUTECT] Processed 227011663 reads in 621 ms
[2015-09-30T22:45Z] INFO  23:45:00,327 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:00,651 MuTect - [MUTECT] Processed 129007849 reads in 666 ms
[2015-09-30T22:45Z] INFO  23:45:00,873 MuTect - [MUTECT] Processed 83003931 reads in 673 ms
[2015-09-30T22:45Z] INFO  23:45:00,898 MuTect - [MUTECT] Processed 228011671 reads in 612 ms
[2015-09-30T22:45Z] INFO  23:45:01,332 MuTect - [MUTECT] Processed 130007931 reads in 681 ms
[2015-09-30T22:45Z] INFO  23:45:01,553 MuTect - [MUTECT] Processed 84003934 reads in 680 ms
[2015-09-30T22:45Z] INFO  23:45:01,557 MuTect - [MUTECT] Processed 229011739 reads in 659 ms
[2015-09-30T22:45Z] INFO  23:45:01,726 ProgressMeter -     17:40946571        4.12e+06   90.0 s       21.0 s     39.9%         3.8 m     2.3 m
[2015-09-30T22:45Z] INFO  23:45:01,898 ProgressMeter -     17:73832950        2.69e+06   60.0 s       22.0 s     47.1%         2.1 m    67.0 s
[2015-09-30T22:45Z] INFO  23:45:02,009 MuTect - [MUTECT] Processed 131007960 reads in 677 ms
[2015-09-30T22:45Z] INFO  23:45:02,040 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:02,107 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:02,192 MuTect - [MUTECT] Processed 85003959 reads in 639 ms
[2015-09-30T22:45Z] INFO  23:45:02,257 MuTect - [MUTECT] Processed 230011805 reads in 700 ms
[2015-09-30T22:45Z] INFO  23:45:02,680 MuTect - [MUTECT] Processed 132008045 reads in 671 ms
[2015-09-30T22:45Z] INFO  23:45:02,724 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:02,833 MuTect - [MUTECT] Processed 86004030 reads in 641 ms
[2015-09-30T22:45Z] INFO  23:45:02,952 MuTect - [MUTECT] Processed 231011917 reads in 695 ms
[2015-09-30T22:45Z] INFO  23:45:03,339 MuTect - [MUTECT] Processed 133008133 reads in 659 ms
[2015-09-30T22:45Z] INFO  23:45:03,445 MuTect - [MUTECT] Processed 87004113 reads in 611 ms
[2015-09-30T22:45Z] INFO  23:45:03,613 MuTect - [MUTECT] Processed 232011944 reads in 661 ms
[2015-09-30T22:45Z] INFO  23:45:04,027 MuTect - [MUTECT] Processed 134008141 reads in 688 ms
[2015-09-30T22:45Z] INFO  23:45:04,061 MuTect - [MUTECT] Processed 88004156 reads in 617 ms
[2015-09-30T22:45Z] INFO  23:45:04,169 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:04,269 MuTect - [MUTECT] Processed 233011989 reads in 656 ms
[2015-09-30T22:45Z] INFO  23:45:04,340 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:04,664 MuTect - [MUTECT] Processed 89004168 reads in 603 ms
[2015-09-30T22:45Z] INFO  23:45:04,746 MuTect - [MUTECT] Processed 135008145 reads in 719 ms
[2015-09-30T22:45Z] INFO  23:45:04,962 MuTect - [MUTECT] Processed 234012030 reads in 693 ms
[2015-09-30T22:45Z] INFO  23:45:05,290 MuTect - [MUTECT] Processed 90004176 reads in 626 ms
[2015-09-30T22:45Z] INFO  23:45:05,373 MuTect - [MUTECT] Inspected 69000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:05,450 MuTect - [MUTECT] Processed 136008162 reads in 704 ms
[2015-09-30T22:45Z] INFO  23:45:05,632 MuTect - [MUTECT] Processed 235012115 reads in 670 ms
[2015-09-30T22:45Z] INFO  23:45:05,918 MuTect - [MUTECT] Processed 91004255 reads in 628 ms
[2015-09-30T22:45Z] INFO  23:45:06,132 MuTect - [MUTECT] Processed 137008213 reads in 682 ms
[2015-09-30T22:45Z] INFO  23:45:06,296 MuTect - [MUTECT] Processed 236012149 reads in 664 ms
[2015-09-30T22:45Z] INFO  23:45:06,454 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:06,535 MuTect - [MUTECT] Processed 92004325 reads in 617 ms
[2015-09-30T22:45Z] INFO  23:45:06,547 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:06,822 MuTect - [MUTECT] Processed 138008264 reads in 690 ms
[2015-09-30T22:45Z] INFO  23:45:06,997 MuTect - [MUTECT] Processed 237012209 reads in 701 ms
[2015-09-30T22:45Z] INFO  23:45:07,172 MuTect - [MUTECT] Processed 93004383 reads in 637 ms
[2015-09-30T22:45Z] INFO  23:45:07,561 MuTect - [MUTECT] Processed 139008350 reads in 739 ms
[2015-09-30T22:45Z] INFO  23:45:07,672 MuTect - [MUTECT] Processed 238012253 reads in 675 ms
[2015-09-30T22:45Z] INFO  23:45:07,807 MuTect - [MUTECT] Processed 94004400 reads in 635 ms
[2015-09-30T22:45Z] INFO  23:45:08,284 MuTect - [MUTECT] Processed 140008424 reads in 723 ms
[2015-09-30T22:45Z] INFO  23:45:08,390 MuTect - [MUTECT] Processed 239012281 reads in 718 ms
[2015-09-30T22:45Z] INFO  23:45:08,456 MuTect - [MUTECT] Processed 95004441 reads in 649 ms
[2015-09-30T22:45Z] INFO  23:45:08,490 MuTect - [MUTECT] Inspected 70000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:08,637 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:08,992 MuTect - [MUTECT] Processed 141008442 reads in 708 ms
[2015-09-30T22:45Z] INFO  23:45:09,065 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:09,072 MuTect - [MUTECT] Processed 240012426 reads in 682 ms
[2015-09-30T22:45Z] INFO  23:45:09,087 MuTect - [MUTECT] Processed 96004453 reads in 631 ms
[2015-09-30T22:45Z] INFO  23:45:09,717 MuTect - [MUTECT] Processed 97004494 reads in 630 ms
[2015-09-30T22:45Z] INFO  23:45:09,770 MuTect - [MUTECT] Processed 241012460 reads in 698 ms
[2015-09-30T22:45Z] INFO  23:45:10,359 MuTect - [MUTECT] Processed 98004544 reads in 642 ms
[2015-09-30T22:45Z] INFO  23:45:10,377 MuTect - [MUTECT] Processed 142009506 reads in 1385 ms
[2015-09-30T22:45Z] INFO  23:45:10,656 MuTect - [MUTECT] Processed 242012647 reads in 886 ms
[2015-09-30T22:45Z] INFO  23:45:10,807 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:11,023 MuTect - [MUTECT] Processed 99004563 reads in 664 ms
[2015-09-30T22:45Z] INFO  23:45:11,346 MuTect - [MUTECT] Processed 143009570 reads in 969 ms
[2015-09-30T22:45Z] INFO  23:45:11,415 MuTect - [MUTECT] Inspected 71000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:11,481 MuTect - [MUTECT] Processed 243012707 reads in 825 ms
[2015-09-30T22:45Z] INFO  23:45:11,651 MuTect - [MUTECT] Processed 100004654 reads in 628 ms
[2015-09-30T22:45Z] INFO  23:45:12,004 MuTect - [MUTECT] Processed 144009586 reads in 658 ms
[2015-09-30T22:45Z] INFO  23:45:12,185 MuTect - [MUTECT] Processed 244012804 reads in 704 ms
[2015-09-30T22:45Z] INFO  23:45:12,256 MuTect - [MUTECT] Processed 101004716 reads in 605 ms
[2015-09-30T22:45Z] INFO  23:45:12,665 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:12,687 MuTect - [MUTECT] Processed 145009640 reads in 683 ms
[2015-09-30T22:45Z] INFO  23:45:12,888 MuTect - [MUTECT] Processed 102004809 reads in 632 ms
[2015-09-30T22:45Z] INFO  23:45:13,017 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:13,031 MuTect - [MUTECT] Processed 245012943 reads in 846 ms
[2015-09-30T22:45Z] INFO  23:45:13,382 MuTect - [MUTECT] Processed 146009733 reads in 695 ms
[2015-09-30T22:45Z] INFO  23:45:13,538 MuTect - [MUTECT] Processed 103004875 reads in 650 ms
[2015-09-30T22:45Z] INFO  23:45:13,879 MuTect - [MUTECT] Inspected 72000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:14,010 MuTect - [MUTECT] Processed 147009813 reads in 628 ms
[2015-09-30T22:45Z] INFO  23:45:14,182 MuTect - [MUTECT] Processed 104004920 reads in 644 ms
[2015-09-30T22:45Z] INFO  23:45:14,184 MuTect - [MUTECT] Processed 246013125 reads in 1153 ms
[2015-09-30T22:45Z] INFO  23:45:14,650 MuTect - [MUTECT] Processed 148009842 reads in 640 ms
[2015-09-30T22:45Z] INFO  23:45:14,851 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:14,853 MuTect - [MUTECT] Processed 105004992 reads in 671 ms
[2015-09-30T22:45Z] INFO  23:45:15,169 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:15,316 MuTect - [MUTECT] Processed 149009959 reads in 666 ms
[2015-09-30T22:45Z] INFO  23:45:15,506 MuTect - [MUTECT] Processed 247013510 reads in 1322 ms
[2015-09-30T22:45Z] INFO  23:45:15,531 MuTect - [MUTECT] Processed 106005040 reads in 678 ms
[2015-09-30T22:45Z] INFO  23:45:15,970 MuTect - [MUTECT] Processed 150010022 reads in 654 ms
[2015-09-30T22:45Z] INFO  23:45:16,185 MuTect - [MUTECT] Processed 107005093 reads in 654 ms
[2015-09-30T22:45Z] INFO  23:45:16,646 MuTect - [MUTECT] Processed 151010098 reads in 676 ms
[2015-09-30T22:45Z] INFO  23:45:16,885 MuTect - [MUTECT] Processed 108005127 reads in 700 ms
[2015-09-30T22:45Z] INFO  23:45:16,940 MuTect - [MUTECT] Processed 248013537 reads in 1434 ms
[2015-09-30T22:45Z] INFO  23:45:17,068 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:17,159 MuTect - [MUTECT] Inspected 73000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:17,323 MuTect - [MUTECT] Processed 152010103 reads in 677 ms
[2015-09-30T22:45Z] INFO  23:45:17,663 MuTect - [MUTECT] Processed 109005242 reads in 778 ms
[2015-09-30T22:45Z] INFO  23:45:17,697 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:17,998 MuTect - [MUTECT] Processed 153010203 reads in 675 ms
[2015-09-30T22:45Z] INFO  23:45:18,211 MuTect - [MUTECT] Processed 249013634 reads in 1271 ms
[2015-09-30T22:45Z] INFO  23:45:18,361 MuTect - [MUTECT] Processed 110005281 reads in 698 ms
[2015-09-30T22:45Z] INFO  23:45:18,636 MuTect - [MUTECT] Processed 154010266 reads in 638 ms
[2015-09-30T22:45Z] INFO  23:45:18,942 MuTect - [MUTECT] Processed 250013700 reads in 731 ms
[2015-09-30T22:45Z] INFO  23:45:19,023 MuTect - [MUTECT] Processed 111005282 reads in 662 ms
[2015-09-30T22:45Z] INFO  23:45:19,194 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:19,276 MuTect - [MUTECT] Processed 155010324 reads in 640 ms
[2015-09-30T22:45Z] INFO  23:45:19,627 MuTect - [MUTECT] Processed 251013763 reads in 685 ms
[2015-09-30T22:45Z] INFO  23:45:19,701 MuTect - [MUTECT] Processed 112005395 reads in 678 ms
[2015-09-30T22:45Z] INFO  23:45:19,804 MuTect - [MUTECT] Inspected 74000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:19,896 MuTect - [MUTECT] Processed 156010331 reads in 620 ms
[2015-09-30T22:45Z] INFO  23:45:20,073 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:20,242 MuTect - [MUTECT] Processed 252013777 reads in 615 ms
[2015-09-30T22:45Z] INFO  23:45:20,389 MuTect - [MUTECT] Processed 113005444 reads in 688 ms
[2015-09-30T22:45Z] INFO  23:45:20,518 MuTect - [MUTECT] Processed 157010381 reads in 622 ms
[2015-09-30T22:45Z] INFO  23:45:20,893 MuTect - [MUTECT] Processed 253013792 reads in 651 ms
[2015-09-30T22:45Z] INFO  23:45:21,066 MuTect - [MUTECT] Processed 114005465 reads in 677 ms
[2015-09-30T22:45Z] INFO  23:45:21,119 MuTect - [MUTECT] Processed 158010514 reads in 601 ms
[2015-09-30T22:45Z] INFO  23:45:21,197 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:21,579 MuTect - [MUTECT] Processed 254013794 reads in 686 ms
[2015-09-30T22:45Z] INFO  23:45:21,735 MuTect - [MUTECT] Processed 159010534 reads in 616 ms
[2015-09-30T22:45Z] INFO  23:45:21,753 MuTect - [MUTECT] Processed 115005550 reads in 687 ms
[2015-09-30T22:45Z] INFO  23:45:21,984 MuTect - [MUTECT] Inspected 75000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:22,232 MuTect - [MUTECT] Processed 255013852 reads in 653 ms
[2015-09-30T22:45Z] INFO  23:45:22,339 MuTect - [MUTECT] Processed 160010611 reads in 604 ms
[2015-09-30T22:45Z] INFO  23:45:22,444 MuTect - [MUTECT] Processed 116005683 reads in 691 ms
[2015-09-30T22:45Z] INFO  23:45:22,477 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:22,864 MuTect - [MUTECT] Processed 256013926 reads in 632 ms
[2015-09-30T22:45Z] INFO  23:45:22,964 MuTect - [MUTECT] Processed 161010636 reads in 625 ms
[2015-09-30T22:45Z] INFO  23:45:23,146 MuTect - [MUTECT] Processed 117005745 reads in 702 ms
[2015-09-30T22:45Z] INFO  23:45:23,282 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:23,493 MuTect - [MUTECT] Processed 257013956 reads in 629 ms
[2015-09-30T22:45Z] INFO  23:45:23,596 MuTect - [MUTECT] Processed 162010701 reads in 632 ms
[2015-09-30T22:45Z] INFO  23:45:23,872 MuTect - [MUTECT] Processed 118005822 reads in 726 ms
[2015-09-30T22:45Z] INFO  23:45:24,108 MuTect - [MUTECT] Processed 258014022 reads in 615 ms
[2015-09-30T22:45Z] INFO  23:45:24,234 MuTect - [MUTECT] Processed 163010759 reads in 638 ms
[2015-09-30T22:45Z] INFO  23:45:24,278 MuTect - [MUTECT] Inspected 76000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:24,550 MuTect - [MUTECT] Processed 119005924 reads in 678 ms
[2015-09-30T22:45Z] INFO  23:45:24,698 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:24,744 MuTect - [MUTECT] Processed 259014073 reads in 636 ms
[2015-09-30T22:45Z] INFO  23:45:24,883 MuTect - [MUTECT] Processed 164010870 reads in 649 ms
[2015-09-30T22:45Z] INFO  23:45:25,226 MuTect - [MUTECT] Processed 120005943 reads in 675 ms
[2015-09-30T22:45Z] INFO  23:45:25,318 ProgressMeter -     17:26723976        7.54e+06    3.0 m       23.0 s     81.6%         3.7 m    40.0 s
[2015-09-30T22:45Z] INFO  23:45:25,377 MuTect - [MUTECT] Processed 260014132 reads in 633 ms
[2015-09-30T22:45Z] INFO  23:45:25,393 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:25,548 MuTect - [MUTECT] Processed 165010946 reads in 665 ms
[2015-09-30T22:45Z] INFO  23:45:26,009 MuTect - [MUTECT] Processed 121006021 reads in 784 ms
[2015-09-30T22:45Z] INFO  23:45:26,024 MuTect - [MUTECT] Processed 261014157 reads in 647 ms
[2015-09-30T22:45Z] INFO  23:45:26,189 MuTect - [MUTECT] Processed 166011019 reads in 641 ms
[2015-09-30T22:45Z] INFO  23:45:26,394 MuTect - [MUTECT] Inspected 77000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:26,655 MuTect - [MUTECT] Processed 262014189 reads in 630 ms
[2015-09-30T22:45Z] INFO  23:45:26,717 MuTect - [MUTECT] Processed 122006024 reads in 708 ms
[2015-09-30T22:45Z] INFO  23:45:26,830 MuTect - [MUTECT] Processed 167011047 reads in 641 ms
[2015-09-30T22:45Z] INFO  23:45:26,998 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:27,288 MuTect - [MUTECT] Processed 263014263 reads in 634 ms
[2015-09-30T22:45Z] INFO  23:45:27,392 MuTect - [MUTECT] Processed 123006066 reads in 675 ms
[2015-09-30T22:45Z] INFO  23:45:27,463 MuTect - [MUTECT] Processed 168011069 reads in 633 ms
[2015-09-30T22:45Z] INFO  23:45:27,599 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:27,884 MuTect - [MUTECT] Processed 264014350 reads in 596 ms
[2015-09-30T22:45Z] INFO  23:45:28,073 MuTect - [MUTECT] Processed 124006134 reads in 681 ms
[2015-09-30T22:45Z] INFO  23:45:28,089 MuTect - [MUTECT] Processed 169011136 reads in 626 ms
[2015-09-30T22:45Z] INFO  23:45:28,509 MuTect - [MUTECT] Processed 265014355 reads in 624 ms
[2015-09-30T22:45Z] INFO  23:45:28,559 MuTect - [MUTECT] Inspected 78000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:28,767 MuTect - [MUTECT] Processed 170011227 reads in 678 ms
[2015-09-30T22:45Z] INFO  23:45:28,836 MuTect - [MUTECT] Processed 125006171 reads in 763 ms
[2015-09-30T22:45Z] INFO  23:45:29,139 MuTect - [MUTECT] Processed 266014421 reads in 630 ms
[2015-09-30T22:45Z] INFO  23:45:29,280 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:29,446 MuTect - [MUTECT] Processed 171011239 reads in 678 ms
[2015-09-30T22:45Z] INFO  23:45:29,569 MuTect - [MUTECT] Processed 126006219 reads in 733 ms
[2015-09-30T22:45Z] INFO  23:45:29,773 MuTect - [MUTECT] Processed 267014503 reads in 635 ms
[2015-09-30T22:45Z] INFO  23:45:29,944 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:30,112 MuTect - [MUTECT] Processed 172011269 reads in 667 ms
[2015-09-30T22:45Z] INFO  23:45:30,252 MuTect - [MUTECT] Processed 127006320 reads in 683 ms
[2015-09-30T22:45Z] INFO  23:45:30,409 MuTect - [MUTECT] Processed 268014591 reads in 636 ms
[2015-09-30T22:45Z] INFO  23:45:30,708 MuTect - [MUTECT] Inspected 79000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:30,766 MuTect - [MUTECT] Processed 173011301 reads in 654 ms
[2015-09-30T22:45Z] INFO  23:45:30,919 MuTect - [MUTECT] Processed 128006399 reads in 667 ms
[2015-09-30T22:45Z] INFO  23:45:31,028 MuTect - [MUTECT] Processed 269014641 reads in 618 ms
[2015-09-30T22:45Z] INFO  23:45:31,409 MuTect - [MUTECT] Processed 174011344 reads in 643 ms
[2015-09-30T22:45Z] INFO  23:45:31,603 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:31,605 MuTect - [MUTECT] Processed 129006505 reads in 686 ms
[2015-09-30T22:45Z] INFO  23:45:31,676 MuTect - [MUTECT] Processed 270014736 reads in 649 ms
[2015-09-30T22:45Z] INFO  23:45:31,727 ProgressMeter -     17:43326001        5.47e+06  120.0 s       21.0 s     52.5%         3.8 m   108.0 s
[2015-09-30T22:45Z] INFO  23:45:31,899 ProgressMeter -     17:76888321        4.02e+06   90.0 s       22.0 s     68.5%         2.2 m    41.0 s
[2015-09-30T22:45Z] INFO  23:45:32,030 MuTect - [MUTECT] Processed 175011442 reads in 621 ms
[2015-09-30T22:45Z] INFO  23:45:32,274 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:32,277 MuTect - [MUTECT] Processed 130006633 reads in 672 ms
[2015-09-30T22:45Z] INFO  23:45:32,303 MuTect - [MUTECT] Processed 271014751 reads in 627 ms
[2015-09-30T22:45Z] INFO  23:45:32,661 MuTect - [MUTECT] Processed 176011512 reads in 631 ms
[2015-09-30T22:45Z] INFO  23:45:32,781 MuTect - [MUTECT] Inspected 80000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:32,932 MuTect - [MUTECT] Processed 131006675 reads in 655 ms
[2015-09-30T22:45Z] INFO  23:45:32,932 MuTect - [MUTECT] Processed 272014781 reads in 629 ms
[2015-09-30T22:45Z] INFO  23:45:33,304 MuTect - [MUTECT] Processed 177011526 reads in 643 ms
[2015-09-30T22:45Z] INFO  23:45:33,561 MuTect - [MUTECT] Processed 273014866 reads in 629 ms
[2015-09-30T22:45Z] INFO  23:45:33,606 MuTect - [MUTECT] Processed 132006778 reads in 674 ms
[2015-09-30T22:45Z] INFO  23:45:33,740 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:33,944 MuTect - [MUTECT] Processed 178011610 reads in 640 ms
[2015-09-30T22:45Z] INFO  23:45:34,188 MuTect - [MUTECT] Processed 274014905 reads in 626 ms
[2015-09-30T22:45Z] INFO  23:45:34,296 MuTect - [MUTECT] Processed 133006835 reads in 690 ms
[2015-09-30T22:45Z] INFO  23:45:34,504 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:34,603 MuTect - [MUTECT] Processed 179011650 reads in 659 ms
[2015-09-30T22:45Z] INFO  23:45:34,817 MuTect - [MUTECT] Processed 275014910 reads in 630 ms
[2015-09-30T22:45Z] INFO  23:45:34,896 MuTect - [MUTECT] Inspected 81000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:34,997 MuTect - [MUTECT] Processed 134006897 reads in 701 ms
[2015-09-30T22:45Z] INFO  23:45:35,230 MuTect - [MUTECT] Processed 180012055 reads in 627 ms
[2015-09-30T22:45Z] INFO  23:45:35,458 MuTect - [MUTECT] Processed 276014992 reads in 641 ms
[2015-09-30T22:45Z] INFO  23:45:35,684 MuTect - [MUTECT] Processed 135006986 reads in 687 ms
[2015-09-30T22:45Z] INFO  23:45:35,834 MuTect - [MUTECT] Processed 181012108 reads in 604 ms
[2015-09-30T22:45Z] INFO  23:45:36,000 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:36,115 MuTect - [MUTECT] Processed 277015023 reads in 657 ms
[2015-09-30T22:45Z] INFO  23:45:36,385 MuTect - [MUTECT] Processed 136007047 reads in 701 ms
[2015-09-30T22:45Z] INFO  23:45:36,496 MuTect - [MUTECT] Processed 182012179 reads in 662 ms
[2015-09-30T22:45Z] INFO  23:45:36,767 MuTect - [MUTECT] Processed 278015061 reads in 652 ms
[2015-09-30T22:45Z] INFO  23:45:37,096 MuTect - [MUTECT] Processed 137007095 reads in 711 ms
[2015-09-30T22:45Z] INFO  23:45:37,103 MuTect - [MUTECT] Processed 183012315 reads in 607 ms
[2015-09-30T22:45Z] INFO  23:45:37,103 MuTect - [MUTECT] Inspected 82000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:37,440 MuTect - [MUTECT] Processed 279015150 reads in 673 ms
[2015-09-30T22:45Z] INFO  23:45:37,580 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:37,754 MuTect - [MUTECT] Processed 184012419 reads in 651 ms
[2015-09-30T22:45Z] INFO  23:45:37,814 MuTect - [MUTECT] Processed 138007116 reads in 718 ms
[2015-09-30T22:45Z] INFO  23:45:38,101 MuTect - [MUTECT] Processed 280015150 reads in 661 ms
[2015-09-30T22:45Z] INFO  23:45:38,255 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:38,420 MuTect - [MUTECT] Processed 185012509 reads in 666 ms
[2015-09-30T22:45Z] INFO  23:45:38,587 MuTect - [MUTECT] Processed 139007167 reads in 773 ms
[2015-09-30T22:45Z] INFO  23:45:38,710 MuTect - [MUTECT] Processed 281015250 reads in 609 ms
[2015-09-30T22:45Z] INFO  23:45:39,068 MuTect - [MUTECT] Processed 186012511 reads in 648 ms
[2015-09-30T22:45Z] INFO  23:45:39,246 MuTect - [MUTECT] Processed 140007171 reads in 659 ms
[2015-09-30T22:45Z] INFO  23:45:39,342 MuTect - [MUTECT] Processed 282015331 reads in 632 ms
[2015-09-30T22:45Z] INFO  23:45:39,744 MuTect - [MUTECT] Processed 187012525 reads in 676 ms
[2015-09-30T22:45Z] INFO  23:45:39,911 MuTect - [MUTECT] Processed 141007185 reads in 665 ms
[2015-09-30T22:45Z] INFO  23:45:39,935 MuTect - [MUTECT] Inspected 83000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:39,999 MuTect - [MUTECT] Processed 283015375 reads in 657 ms
[2015-09-30T22:45Z] INFO  23:45:40,426 MuTect - [MUTECT] Processed 188012569 reads in 682 ms
[2015-09-30T22:45Z] INFO  23:45:40,528 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:40,564 MuTect - [MUTECT] Processed 142007192 reads in 653 ms
[2015-09-30T22:45Z] INFO  23:45:40,641 MuTect - [MUTECT] Processed 284015459 reads in 642 ms
[2015-09-30T22:45Z] INFO  23:45:41,063 MuTect - [MUTECT] Processed 189012570 reads in 637 ms
[2015-09-30T22:45Z] INFO  23:45:41,153 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:41,261 MuTect - [MUTECT] Processed 143007273 reads in 697 ms
[2015-09-30T22:45Z] INFO  23:45:41,275 MuTect - [MUTECT] Processed 285015554 reads in 634 ms
[2015-09-30T22:45Z] INFO  23:45:41,699 MuTect - [MUTECT] Processed 190012577 reads in 636 ms
[2015-09-30T22:45Z] INFO  23:45:41,916 MuTect - [MUTECT] Processed 286015558 reads in 641 ms
[2015-09-30T22:45Z] INFO  23:45:41,968 MuTect - [MUTECT] Processed 144007358 reads in 707 ms
[2015-09-30T22:45Z] INFO  23:45:42,224 MuTect - [MUTECT] Inspected 84000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:42,352 MuTect - [MUTECT] Processed 191012595 reads in 653 ms
[2015-09-30T22:45Z] INFO  23:45:42,530 MuTect - [MUTECT] Processed 287015584 reads in 614 ms
[2015-09-30T22:45Z] INFO  23:45:42,624 MuTect - [MUTECT] Processed 145007452 reads in 656 ms
[2015-09-30T22:45Z] INFO  23:45:42,829 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:43,003 MuTect - [MUTECT] Processed 192012741 reads in 651 ms
[2015-09-30T22:45Z] INFO  23:45:43,151 MuTect - [MUTECT] Processed 288015666 reads in 621 ms
[2015-09-30T22:45Z] INFO  23:45:43,302 MuTect - [MUTECT] Processed 146007544 reads in 678 ms
[2015-09-30T22:45Z] INFO  23:45:43,632 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:43,790 MuTect - [MUTECT] Processed 193012791 reads in 786 ms
[2015-09-30T22:45Z] INFO  23:45:43,808 MuTect - [MUTECT] Processed 289015682 reads in 657 ms
[2015-09-30T22:45Z] INFO  23:45:43,973 MuTect - [MUTECT] Processed 147007614 reads in 670 ms
[2015-09-30T22:45Z] INFO  23:45:44,455 MuTect - [MUTECT] Processed 290015732 reads in 647 ms
[2015-09-30T22:45Z] INFO  23:45:44,486 MuTect - [MUTECT] Processed 194012807 reads in 697 ms
[2015-09-30T22:45Z] INFO  23:45:44,588 MuTect - [MUTECT] Inspected 85000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:44,652 MuTect - [MUTECT] Processed 148007623 reads in 680 ms
[2015-09-30T22:45Z] INFO  23:45:45,076 MuTect - [MUTECT] Processed 291015860 reads in 621 ms
[2015-09-30T22:45Z] INFO  23:45:45,181 MuTect - [MUTECT] Processed 195012818 reads in 695 ms
[2015-09-30T22:45Z] INFO  23:45:45,193 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:45,320 MuTect - [MUTECT] Processed 149007740 reads in 668 ms
[2015-09-30T22:45Z] INFO  23:45:45,691 MuTect - [MUTECT] Processed 292015946 reads in 615 ms
[2015-09-30T22:45Z] INFO  23:45:45,927 MuTect - [MUTECT] Processed 196012880 reads in 746 ms
[2015-09-30T22:45Z] INFO  23:45:46,021 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:46,025 MuTect - [MUTECT] Processed 150007821 reads in 705 ms
[2015-09-30T22:45Z] INFO  23:45:46,332 MuTect - [MUTECT] Processed 293015960 reads in 641 ms
[2015-09-30T22:45Z] INFO  23:45:46,668 MuTect - [MUTECT] Processed 197012965 reads in 741 ms
[2015-09-30T22:45Z] INFO  23:45:46,759 MuTect - [MUTECT] Processed 151007902 reads in 734 ms
[2015-09-30T22:45Z] INFO  23:45:46,994 MuTect - [MUTECT] Processed 294015982 reads in 662 ms
[2015-09-30T22:45Z] INFO  23:45:47,016 MuTect - [MUTECT] Inspected 86000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:47,364 MuTect - [MUTECT] Processed 198013001 reads in 696 ms
[2015-09-30T22:45Z] INFO  23:45:47,510 MuTect - [MUTECT] Processed 152008016 reads in 751 ms
[2015-09-30T22:45Z] INFO  23:45:47,660 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:47,676 MuTect - [MUTECT] Processed 295016087 reads in 682 ms
[2015-09-30T22:45Z] INFO  23:45:48,065 MuTect - [MUTECT] Processed 199013053 reads in 700 ms
[2015-09-30T22:45Z] INFO  23:45:48,272 MuTect - [MUTECT] Processed 153008017 reads in 762 ms
[2015-09-30T22:45Z] INFO  23:45:48,327 MuTect - [MUTECT] Processed 296016117 reads in 651 ms
[2015-09-30T22:45Z] INFO  23:45:48,477 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:48,740 MuTect - [MUTECT] Processed 200013145 reads in 676 ms
[2015-09-30T22:45Z] INFO  23:45:48,982 MuTect - [MUTECT] Processed 297016203 reads in 655 ms
[2015-09-30T22:45Z] INFO  23:45:49,011 MuTect - [MUTECT] Processed 154008076 reads in 739 ms
[2015-09-30T22:45Z] INFO  23:45:49,393 MuTect - [MUTECT] Inspected 87000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:49,420 MuTect - [MUTECT] Processed 201013265 reads in 680 ms
[2015-09-30T22:45Z] INFO  23:45:49,615 MuTect - [MUTECT] Processed 298016263 reads in 633 ms
[2015-09-30T22:45Z] INFO  23:45:49,705 MuTect - [MUTECT] Processed 155008119 reads in 694 ms
[2015-09-30T22:45Z] INFO  23:45:50,007 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:50,082 MuTect - [MUTECT] Processed 202013342 reads in 662 ms
[2015-09-30T22:45Z] INFO  23:45:50,227 MuTect - [MUTECT] Processed 299016324 reads in 612 ms
[2015-09-30T22:45Z] INFO  23:45:50,402 MuTect - [MUTECT] Processed 156008183 reads in 697 ms
[2015-09-30T22:45Z] INFO  23:45:50,610 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:50,746 MuTect - [MUTECT] Processed 203013345 reads in 664 ms
[2015-09-30T22:45Z] INFO  23:45:50,882 MuTect - [MUTECT] Processed 300016333 reads in 655 ms
[2015-09-30T22:45Z] INFO  23:45:51,078 MuTect - [MUTECT] Processed 157008327 reads in 676 ms
[2015-09-30T22:45Z] INFO  23:45:51,416 MuTect - [MUTECT] Processed 204013504 reads in 670 ms
[2015-09-30T22:45Z] INFO  23:45:51,526 MuTect - [MUTECT] Processed 301016347 reads in 644 ms
[2015-09-30T22:45Z] INFO  23:45:51,804 MuTect - [MUTECT] Inspected 88000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:51,806 MuTect - [MUTECT] Processed 158008419 reads in 728 ms
[2015-09-30T22:45Z] INFO  23:45:52,095 MuTect - [MUTECT] Processed 205013522 reads in 679 ms
[2015-09-30T22:45Z] INFO  23:45:52,176 MuTect - [MUTECT] Processed 302016376 reads in 650 ms
[2015-09-30T22:45Z] INFO  23:45:52,282 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:52,524 MuTect - [MUTECT] Processed 159008494 reads in 718 ms
[2015-09-30T22:45Z] INFO  23:45:52,743 MuTect - [MUTECT] Processed 206013544 reads in 647 ms
[2015-09-30T22:45Z] INFO  23:45:52,824 MuTect - [MUTECT] Processed 303016483 reads in 648 ms
[2015-09-30T22:45Z] INFO  23:45:52,877 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:53,220 MuTect - [MUTECT] Processed 160008620 reads in 696 ms
[2015-09-30T22:45Z] INFO  23:45:53,420 MuTect - [MUTECT] Processed 207013572 reads in 678 ms
[2015-09-30T22:45Z] INFO  23:45:53,484 MuTect - [MUTECT] Processed 304016498 reads in 660 ms
[2015-09-30T22:45Z] INFO  23:45:53,906 MuTect - [MUTECT] Processed 161008635 reads in 686 ms
[2015-09-30T22:45Z] INFO  23:45:54,108 MuTect - [MUTECT] Processed 208013614 reads in 688 ms
[2015-09-30T22:45Z] INFO  23:45:54,126 MuTect - [MUTECT] Inspected 89000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:54,137 MuTect - [MUTECT] Processed 305016573 reads in 653 ms
[2015-09-30T22:45Z] INFO  23:45:54,563 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:54,628 MuTect - [MUTECT] Processed 162008736 reads in 722 ms
[2015-09-30T22:45Z] INFO  23:45:54,792 MuTect - [MUTECT] Processed 209013640 reads in 684 ms
[2015-09-30T22:45Z] INFO  23:45:54,812 MuTect - [MUTECT] Processed 306016583 reads in 675 ms
[2015-09-30T22:45Z] INFO  23:45:55,073 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:55,319 ProgressMeter -     17:30357914        9.05e+06    3.5 m       23.0 s     97.8%         3.6 m     4.0 s
[2015-09-30T22:45Z] INFO  23:45:55,394 MuTect - [MUTECT] Processed 163008835 reads in 766 ms
[2015-09-30T22:45Z] INFO  23:45:55,465 MuTect - [MUTECT] Processed 307016602 reads in 653 ms
[2015-09-30T22:45Z] INFO  23:45:55,470 MuTect - [MUTECT] Processed 210013715 reads in 677 ms
[2015-09-30T22:45Z] INFO  23:45:56,078 MuTect - [MUTECT] Processed 164008866 reads in 683 ms
[2015-09-30T22:45Z] INFO  23:45:56,124 MuTect - [MUTECT] Processed 308016642 reads in 659 ms
[2015-09-30T22:45Z] INFO  23:45:56,163 MuTect - [MUTECT] Processed 211013803 reads in 694 ms
[2015-09-30T22:45Z] INFO  23:45:56,557 MuTect - [MUTECT] Inspected 90000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:56,766 MuTect - [MUTECT] Processed 165009003 reads in 689 ms
[2015-09-30T22:45Z] INFO  23:45:56,770 MuTect - [MUTECT] Processed 309016685 reads in 646 ms
[2015-09-30T22:45Z] INFO  23:45:56,836 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:56,847 MuTect - [MUTECT] Processed 212013886 reads in 683 ms
[2015-09-30T22:45Z] INFO  23:45:57,221 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:57,389 MuTect - [MUTECT] Processed 310016689 reads in 619 ms
[2015-09-30T22:45Z] INFO  23:45:57,546 MuTect - [MUTECT] Processed 213013908 reads in 700 ms
[2015-09-30T22:45Z] INFO  23:45:58,003 MuTect - [MUTECT] Processed 166009093 reads in 1237 ms
[2015-09-30T22:45Z] INFO  23:45:58,008 MuTect - [MUTECT] Processed 311016740 reads in 619 ms
[2015-09-30T22:45Z] INFO  23:45:58,250 MuTect - [MUTECT] Processed 214013951 reads in 704 ms
[2015-09-30T22:45Z] INFO  23:45:58,617 MuTect - [MUTECT] Processed 312016775 reads in 609 ms
[2015-09-30T22:45Z] INFO  23:45:58,717 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:45Z] INFO  23:45:58,721 ProgressMeter -            done        9.24e+06    3.6 m       23.0 s    100.0%         3.6 m     0.0 s
[2015-09-30T22:45Z] INFO  23:45:58,721 MuTect - [MUTECT] Processed 167009098 reads in 718 ms
[2015-09-30T22:45Z] INFO  23:45:58,722 ProgressMeter - Total runtime 213.41 secs, 3.56 min, 0.06 hours
[2015-09-30T22:45Z] INFO  23:45:58,783 MicroScheduler - 247732 reads were filtered out during the traversal out of approximately 3693670 total reads (6.71%)
[2015-09-30T22:45Z] INFO  23:45:58,783 MicroScheduler -   -> 186700 reads (5.05% of total) failing DuplicateReadFilter
[2015-09-30T22:45Z] INFO  23:45:58,783 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:45Z] INFO  23:45:58,784 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:45Z] INFO  23:45:58,784 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:45Z] INFO  23:45:58,784 MicroScheduler -   -> 61032 reads (1.65% of total) failing UnmappedReadFilter
[2015-09-30T22:45Z] INFO  23:45:58,987 MuTect - [MUTECT] Processed 215013976 reads in 737 ms
[2015-09-30T22:45Z] INFO  23:45:59,408 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:59,454 MuTect - [MUTECT] Processed 168009154 reads in 733 ms
[2015-09-30T22:45Z] INFO  23:45:59,617 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:45Z] INFO  23:45:59,697 MuTect - [MUTECT] Processed 216014003 reads in 710 ms
[2015-09-30T22:45Z] INFO  23:45:59,980 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:46Z] bgzip syn3-17_0_31039439-raw-mutect.vcf
[2015-09-30T22:46Z] tabix index syn3-17_0_31039439-raw-mutect.vcf.gz
[2015-09-30T22:46Z] INFO  23:46:00,207 MuTect - [MUTECT] Processed 169009283 reads in 753 ms
[2015-09-30T22:46Z] INFO  23:46:00,402 MuTect - [MUTECT] Processed 217014031 reads in 705 ms
[2015-09-30T22:46Z] INFO  23:46:00,875 MuTect - [MUTECT] Processed 170009341 reads in 668 ms
[2015-09-30T22:46Z] INFO  23:46:01,085 MuTect - [MUTECT] Processed 218014062 reads in 683 ms
[2015-09-30T22:46Z] INFO  23:46:01,556 MuTect - [MUTECT] Processed 171009403 reads in 681 ms
[2015-09-30T22:46Z] INFO  23:46:01,728 ProgressMeter -     17:47590182        6.76e+06    2.5 m       22.0 s     66.3%         3.8 m    76.0 s
[2015-09-30T22:46Z] INFO  23:46:01,768 MuTect - [MUTECT] Processed 219014072 reads in 683 ms
[2015-09-30T22:46Z] INFO  23:46:01,791 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:01,900 ProgressMeter -     17:79681701        5.24e+06  120.0 s       22.0 s     87.5%         2.3 m    17.0 s
[2015-09-30T22:46Z] INFO  23:46:01,905 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:02,231 MuTect - [MUTECT] Processed 172009431 reads in 675 ms
[2015-09-30T22:46Z] MuTect: MuTect
[2015-09-30T22:46Z] INFO  23:46:02,450 MuTect - [MUTECT] Processed 220014115 reads in 682 ms
[2015-09-30T22:46Z] INFO  23:46:02,894 MuTect - [MUTECT] Processed 173009441 reads in 663 ms
[2015-09-30T22:46Z] INFO  23:46:03,111 MuTect - [MUTECT] Processed 221014172 reads in 661 ms
[2015-09-30T22:46Z] INFO  23:46:03,580 MuTect - [MUTECT] Processed 174009506 reads in 686 ms
[2015-09-30T22:46Z] INFO  23:46:03,793 MuTect - [MUTECT] Processed 222014293 reads in 682 ms
[2015-09-30T22:46Z] INFO  23:46:03,941 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:03,988 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:04,205 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/18/syn3-18_0_31142016-raw-mutect-regions.bed to be BED
[2015-09-30T22:46Z] INFO  23:46:04,247 MuTect - [MUTECT] Processed 175009627 reads in 666 ms
[2015-09-30T22:46Z] INFO  23:46:04,259 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:46Z] INFO  23:46:04,259 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:46Z] INFO  23:46:04,259 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:46Z] INFO  23:46:04,259 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:46Z] INFO  23:46:04,262 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/18/syn3-18_0_31142016-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/18/tx/tmpVjk0Fh/syn3-18_0_31142016-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:46Z] INFO  23:46:04,263 HelpFormatter - Date/Time: 2015/09/30 23:46:04
[2015-09-30T22:46Z] INFO  23:46:04,263 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:46Z] INFO  23:46:04,263 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:46Z] INFO  23:46:04,289 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:46Z] INFO  23:46:04,293 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:46Z] INFO  23:46:04,340 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:46Z] INFO  23:46:04,386 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:46Z] INFO  23:46:04,394 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:46Z] INFO  23:46:04,416 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:46Z] INFO  23:46:04,426 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:46Z] INFO  23:46:04,472 MuTect - [MUTECT] Processed 223014398 reads in 679 ms
[2015-09-30T22:46Z] INFO  23:46:04,594 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:46Z] INFO  23:46:04,688 IntervalUtils - Processing 1147892 bp from intervals
[2015-09-30T22:46Z] INFO  23:46:04,692 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:46Z] INFO  23:46:04,692 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:46Z] INFO  23:46:04,842 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:46Z] INFO  23:46:04,917 MuTect - [MUTECT] Processed 176009682 reads in 671 ms
[2015-09-30T22:46Z] INFO  23:46:04,989 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:46Z] INFO  23:46:04,989 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:46Z] INFO  23:46:04,990 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:46Z] INFO  23:46:04,990 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:46Z] INFO  23:46:05,136 MuTect - [MUTECT] Processed 224014461 reads in 664 ms
[2015-09-30T22:46Z] INFO  23:46:05,594 MuTect - [MUTECT] Processed 177009723 reads in 677 ms
[2015-09-30T22:46Z] INFO  23:46:05,808 MuTect - [MUTECT] Processed 225014583 reads in 672 ms
[2015-09-30T22:46Z] INFO  23:46:06,135 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:06,174 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:06,312 MuTect - [MUTECT] Processed 178009811 reads in 718 ms
[2015-09-30T22:46Z] INFO  23:46:06,491 MuTect - [MUTECT] Processed 226014650 reads in 683 ms
[2015-09-30T22:46Z] INFO  23:46:07,044 MuTect - [MUTECT] Processed 179009842 reads in 732 ms
[2015-09-30T22:46Z] INFO  23:46:07,162 MuTect - [MUTECT] Processed 227014724 reads in 671 ms
[2015-09-30T22:46Z] INFO  23:46:07,710 MuTect - [MUTECT] Processed 1000062 reads in 2673 ms
[2015-09-30T22:46Z] INFO  23:46:07,728 MuTect - [MUTECT] Processed 180009944 reads in 684 ms
[2015-09-30T22:46Z] INFO  23:46:07,857 MuTect - [MUTECT] Processed 228014761 reads in 695 ms
[2015-09-30T22:46Z] INFO  23:46:08,393 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:08,410 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:08,426 MuTect - [MUTECT] Processed 181010019 reads in 698 ms
[2015-09-30T22:46Z] INFO  23:46:08,456 MuTect - [MUTECT] Processed 2000142 reads in 747 ms
[2015-09-30T22:46Z] INFO  23:46:08,535 MuTect - [MUTECT] Processed 229014866 reads in 678 ms
[2015-09-30T22:46Z] INFO  23:46:09,090 MuTect - [MUTECT] Processed 182010110 reads in 664 ms
[2015-09-30T22:46Z] INFO  23:46:09,199 MuTect - [MUTECT] Processed 3000177 reads in 742 ms
[2015-09-30T22:46Z] INFO  23:46:09,214 MuTect - [MUTECT] Processed 230014972 reads in 679 ms
[2015-09-30T22:46Z] INFO  23:46:09,456 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:09,778 MuTect - [MUTECT] Processed 183010140 reads in 687 ms
[2015-09-30T22:46Z] INFO  23:46:09,878 MuTect - [MUTECT] Processed 4000265 reads in 680 ms
[2015-09-30T22:46Z] INFO  23:46:09,914 MuTect - [MUTECT] Processed 231015048 reads in 700 ms
[2015-09-30T22:46Z] INFO  23:46:10,450 MuTect - [MUTECT] Processed 184010180 reads in 673 ms
[2015-09-30T22:46Z] INFO  23:46:10,582 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:10,604 MuTect - [MUTECT] Processed 5000294 reads in 726 ms
[2015-09-30T22:46Z] INFO  23:46:10,621 MuTect - [MUTECT] Processed 232015098 reads in 707 ms
[2015-09-30T22:46Z] INFO  23:46:10,818 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:11,145 MuTect - [MUTECT] Processed 185010274 reads in 695 ms
[2015-09-30T22:46Z] INFO  23:46:11,318 MuTect - [MUTECT] Processed 233015105 reads in 697 ms
[2015-09-30T22:46Z] INFO  23:46:11,330 MuTect - [MUTECT] Processed 6000303 reads in 726 ms
[2015-09-30T22:46Z] INFO  23:46:11,955 MuTect - [MUTECT] Processed 186010336 reads in 809 ms
[2015-09-30T22:46Z] INFO  23:46:12,021 MuTect - [MUTECT] Processed 234015196 reads in 703 ms
[2015-09-30T22:46Z] INFO  23:46:12,043 MuTect - [MUTECT] Processed 7000380 reads in 713 ms
[2015-09-30T22:46Z] INFO  23:46:12,082 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:12,683 MuTect - [MUTECT] Processed 187010385 reads in 729 ms
[2015-09-30T22:46Z] INFO  23:46:12,718 MuTect - [MUTECT] Processed 235015213 reads in 697 ms
[2015-09-30T22:46Z] INFO  23:46:12,747 MuTect - [MUTECT] Processed 8000400 reads in 704 ms
[2015-09-30T22:46Z] INFO  23:46:12,903 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:13,053 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:13,425 MuTect - [MUTECT] Processed 188010431 reads in 742 ms
[2015-09-30T22:46Z] INFO  23:46:13,433 MuTect - [MUTECT] Processed 236015303 reads in 715 ms
[2015-09-30T22:46Z] INFO  23:46:13,490 MuTect - [MUTECT] Processed 9000432 reads in 743 ms
[2015-09-30T22:46Z] INFO  23:46:14,138 MuTect - [MUTECT] Processed 237015317 reads in 705 ms
[2015-09-30T22:46Z] INFO  23:46:14,153 MuTect - [MUTECT] Processed 189010544 reads in 728 ms
[2015-09-30T22:46Z] INFO  23:46:14,194 MuTect - [MUTECT] Processed 10000509 reads in 704 ms
[2015-09-30T22:46Z] INFO  23:46:14,713 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:14,828 MuTect - [MUTECT] Processed 238015430 reads in 690 ms
[2015-09-30T22:46Z] INFO  23:46:14,860 MuTect - [MUTECT] Processed 190010617 reads in 707 ms
[2015-09-30T22:46Z] INFO  23:46:14,877 MuTect - [MUTECT] Processed 11000545 reads in 683 ms
[2015-09-30T22:46Z] INFO  23:46:15,177 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:15,321 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:15,518 MuTect - [MUTECT] Processed 239015585 reads in 690 ms
[2015-09-30T22:46Z] INFO  23:46:15,562 MuTect - [MUTECT] Processed 191010715 reads in 702 ms
[2015-09-30T22:46Z] INFO  23:46:15,610 MuTect - [MUTECT] Processed 12000663 reads in 733 ms
[2015-09-30T22:46Z] INFO  23:46:16,181 MuTect - [MUTECT] Processed 240015711 reads in 663 ms
[2015-09-30T22:46Z] INFO  23:46:16,274 MuTect - [MUTECT] Processed 192010845 reads in 712 ms
[2015-09-30T22:46Z] INFO  23:46:16,303 MuTect - [MUTECT] Processed 13000749 reads in 693 ms
[2015-09-30T22:46Z] INFO  23:46:16,863 MuTect - [MUTECT] Processed 241015721 reads in 682 ms
[2015-09-30T22:46Z] INFO  23:46:17,027 MuTect - [MUTECT] Processed 14000760 reads in 724 ms
[2015-09-30T22:46Z] INFO  23:46:17,032 MuTect - [MUTECT] Processed 193010945 reads in 758 ms
[2015-09-30T22:46Z] INFO  23:46:17,085 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:17,538 MuTect - [MUTECT] Processed 242015734 reads in 675 ms
[2015-09-30T22:46Z] INFO  23:46:17,708 MuTect - [MUTECT] Inspected 69000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:18,070 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:18,210 MuTect - [MUTECT] Processed 194010971 reads in 1178 ms
[2015-09-30T22:46Z] INFO  23:46:18,474 MuTect - [MUTECT] Processed 15000794 reads in 1447 ms
[2015-09-30T22:46Z] INFO  23:46:18,909 MuTect - [MUTECT] Processed 243015774 reads in 1371 ms
[2015-09-30T22:46Z] INFO  23:46:18,937 MuTect - [MUTECT] Processed 195010994 reads in 727 ms
[2015-09-30T22:46Z] INFO  23:46:19,600 MuTect - [MUTECT] Processed 16000821 reads in 1126 ms
[2015-09-30T22:46Z] INFO  23:46:19,623 MuTect - [MUTECT] Processed 244015800 reads in 714 ms
[2015-09-30T22:46Z] INFO  23:46:19,650 MuTect - [MUTECT] Processed 196011071 reads in 713 ms
[2015-09-30T22:46Z] INFO  23:46:20,276 MuTect - [MUTECT] Processed 17000883 reads in 676 ms
[2015-09-30T22:46Z] INFO  23:46:20,323 MuTect - [MUTECT] Processed 245015807 reads in 700 ms
[2015-09-30T22:46Z] INFO  23:46:20,344 MuTect - [MUTECT] Processed 197011231 reads in 694 ms
[2015-09-30T22:46Z] INFO  23:46:20,403 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:20,847 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:20,984 MuTect - [MUTECT] Processed 18000932 reads in 708 ms
[2015-09-30T22:46Z] INFO  23:46:21,008 MuTect - [MUTECT] Processed 246015852 reads in 685 ms
[2015-09-30T22:46Z] INFO  23:46:21,052 MuTect - [MUTECT] Inspected 70000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:21,069 MuTect - [MUTECT] Processed 198011349 reads in 725 ms
[2015-09-30T22:46Z] INFO  23:46:21,636 MuTect - [MUTECT] Processed 19000965 reads in 651 ms
[2015-09-30T22:46Z] INFO  23:46:21,708 MuTect - [MUTECT] Processed 247015901 reads in 700 ms
[2015-09-30T22:46Z] INFO  23:46:21,794 MuTect - [MUTECT] Processed 199011400 reads in 725 ms
[2015-09-30T22:46Z] INFO  23:46:22,332 MuTect - [MUTECT] Processed 20001051 reads in 697 ms
[2015-09-30T22:46Z] INFO  23:46:22,415 MuTect - [MUTECT] Processed 248015902 reads in 707 ms
[2015-09-30T22:46Z] INFO  23:46:22,502 MuTect - [MUTECT] Processed 200011514 reads in 708 ms
[2015-09-30T22:46Z] INFO  23:46:22,585 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:46Z] INFO  23:46:22,588 ProgressMeter -            done        5.93e+06    2.3 m       23.0 s    100.0%         2.3 m     0.0 s
[2015-09-30T22:46Z] INFO  23:46:22,588 ProgressMeter - Total runtime 140.69 secs, 2.34 min, 0.04 hours
[2015-09-30T22:46Z] INFO  23:46:22,651 MicroScheduler - 166117 reads were filtered out during the traversal out of approximately 2385616 total reads (6.96%)
[2015-09-30T22:46Z] INFO  23:46:22,651 MicroScheduler -   -> 126128 reads (5.29% of total) failing DuplicateReadFilter
[2015-09-30T22:46Z] INFO  23:46:22,652 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:46Z] INFO  23:46:22,652 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:46Z] INFO  23:46:22,652 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:46Z] INFO  23:46:22,652 MicroScheduler -   -> 39989 reads (1.68% of total) failing UnmappedReadFilter
[2015-09-30T22:46Z] INFO  23:46:23,044 MuTect - [MUTECT] Processed 21001064 reads in 712 ms
[2015-09-30T22:46Z] INFO  23:46:23,126 MuTect - [MUTECT] Processed 249015931 reads in 711 ms
[2015-09-30T22:46Z] INFO  23:46:23,283 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:23,521 MuTect - [MUTECT] Inspected 71000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:23,653 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:46Z] bgzip syn3-17_62078196_81195210-raw-mutect.vcf
[2015-09-30T22:46Z] INFO  23:46:23,720 MuTect - [MUTECT] Processed 22001109 reads in 676 ms
[2015-09-30T22:46Z] tabix index syn3-17_62078196_81195210-raw-mutect.vcf.gz
[2015-09-30T22:46Z] INFO  23:46:23,849 MuTect - [MUTECT] Processed 250016038 reads in 723 ms
[2015-09-30T22:46Z] INFO  23:46:24,424 MuTect - [MUTECT] Processed 23001129 reads in 704 ms
[2015-09-30T22:46Z] INFO  23:46:24,553 MuTect - [MUTECT] Processed 251016115 reads in 704 ms
[2015-09-30T22:46Z] INFO  23:46:25,109 MuTect - [MUTECT] Processed 24001252 reads in 685 ms
[2015-09-30T22:46Z] INFO  23:46:25,266 MuTect - [MUTECT] Processed 252016133 reads in 713 ms
[2015-09-30T22:46Z] INFO  23:46:25,801 MuTect - [MUTECT] Processed 25001329 reads in 692 ms
[2015-09-30T22:46Z] INFO  23:46:25,896 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:25,931 MuTect - [MUTECT] Processed 253016161 reads in 665 ms
[2015-09-30T22:46Z] INFO  23:46:26,069 MuTect - [MUTECT] Inspected 72000 potential candidates
[2015-09-30T22:46Z] MuTect: MuTect
[2015-09-30T22:46Z] INFO  23:46:26,486 MuTect - [MUTECT] Processed 26001350 reads in 685 ms
[2015-09-30T22:46Z] INFO  23:46:26,629 MuTect - [MUTECT] Processed 254016268 reads in 698 ms
[2015-09-30T22:46Z] INFO  23:46:27,166 MuTect - [MUTECT] Processed 27001356 reads in 680 ms
[2015-09-30T22:46Z] INFO  23:46:27,308 MuTect - [MUTECT] Processed 255016276 reads in 679 ms
[2015-09-30T22:46Z] INFO  23:46:27,834 MuTect - [MUTECT] Processed 28001374 reads in 668 ms
[2015-09-30T22:46Z] INFO  23:46:27,981 MuTect - [MUTECT] Processed 256016412 reads in 673 ms
[2015-09-30T22:46Z] INFO  23:46:28,221 MuTect - [MUTECT] Inspected 73000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:28,262 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/18/syn3-18_31158315_63430522-raw-mutect-regions.bed to be BED
[2015-09-30T22:46Z] INFO  23:46:28,316 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:46Z] INFO  23:46:28,317 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:46Z] INFO  23:46:28,317 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:46Z] INFO  23:46:28,317 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:46Z] INFO  23:46:28,320 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/18/syn3-18_31158315_63430522-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/18/tx/tmpMWPFir/syn3-18_31158315_63430522-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:46Z] INFO  23:46:28,320 HelpFormatter - Date/Time: 2015/09/30 23:46:28
[2015-09-30T22:46Z] INFO  23:46:28,320 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:46Z] INFO  23:46:28,321 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:46Z] INFO  23:46:28,347 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:46Z] INFO  23:46:28,352 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:46Z] INFO  23:46:28,406 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:46Z] INFO  23:46:28,499 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:46Z] INFO  23:46:28,506 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:46Z] INFO  23:46:28,529 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:46Z] INFO  23:46:28,539 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:46Z] INFO  23:46:28,565 MuTect - [MUTECT] Processed 29001459 reads in 731 ms
[2015-09-30T22:46Z] INFO  23:46:28,609 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:28,674 MuTect - [MUTECT] Processed 257016456 reads in 693 ms
[2015-09-30T22:46Z] INFO  23:46:28,712 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:46Z] INFO  23:46:28,802 IntervalUtils - Processing 955835 bp from intervals
[2015-09-30T22:46Z] INFO  23:46:28,806 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:46Z] INFO  23:46:28,806 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:46Z] INFO  23:46:28,985 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:46Z] INFO  23:46:29,128 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:46Z] INFO  23:46:29,128 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:46Z] INFO  23:46:29,129 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:46Z] INFO  23:46:29,130 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:46Z] INFO  23:46:29,258 MuTect - [MUTECT] Processed 30001465 reads in 693 ms
[2015-09-30T22:46Z] INFO  23:46:29,366 MuTect - [MUTECT] Processed 258016574 reads in 692 ms
[2015-09-30T22:46Z] INFO  23:46:29,965 MuTect - [MUTECT] Processed 31001526 reads in 707 ms
[2015-09-30T22:46Z] INFO  23:46:30,052 MuTect - [MUTECT] Processed 259016634 reads in 686 ms
[2015-09-30T22:46Z] INFO  23:46:30,638 MuTect - [MUTECT] Inspected 74000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:30,662 MuTect - [MUTECT] Processed 32001581 reads in 697 ms
[2015-09-30T22:46Z] INFO  23:46:30,751 MuTect - [MUTECT] Processed 260016673 reads in 699 ms
[2015-09-30T22:46Z] INFO  23:46:31,303 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:31,427 MuTect - [MUTECT] Processed 33001619 reads in 765 ms
[2015-09-30T22:46Z] INFO  23:46:31,430 MuTect - [MUTECT] Processed 261016701 reads in 679 ms
[2015-09-30T22:46Z] INFO  23:46:31,729 ProgressMeter -     17:56290459        8.04e+06    3.0 m       22.0 s     79.7%         3.8 m    45.0 s
[2015-09-30T22:46Z] INFO  23:46:31,853 MuTect - [MUTECT] Processed 1000014 reads in 2676 ms
[2015-09-30T22:46Z] INFO  23:46:32,094 MuTect - [MUTECT] Processed 262016769 reads in 664 ms
[2015-09-30T22:46Z] INFO  23:46:32,211 MuTect - [MUTECT] Processed 34001621 reads in 784 ms
[2015-09-30T22:46Z] INFO  23:46:32,750 MuTect - [MUTECT] Processed 263016816 reads in 656 ms
[2015-09-30T22:46Z] INFO  23:46:32,832 MuTect - [MUTECT] Processed 2000053 reads in 979 ms
[2015-09-30T22:46Z] INFO  23:46:32,882 MuTect - [MUTECT] Inspected 75000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:32,890 MuTect - [MUTECT] Processed 35001656 reads in 679 ms
[2015-09-30T22:46Z] INFO  23:46:33,376 MuTect - [MUTECT] Processed 264016881 reads in 626 ms
[2015-09-30T22:46Z] INFO  23:46:33,564 MuTect - [MUTECT] Processed 36001656 reads in 674 ms
[2015-09-30T22:46Z] INFO  23:46:33,570 MuTect - [MUTECT] Processed 3000130 reads in 738 ms
[2015-09-30T22:46Z] INFO  23:46:33,732 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:33,999 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:34,040 MuTect - [MUTECT] Processed 265016887 reads in 664 ms
[2015-09-30T22:46Z] INFO  23:46:34,255 MuTect - [MUTECT] Processed 4000161 reads in 685 ms
[2015-09-30T22:46Z] INFO  23:46:34,309 MuTect - [MUTECT] Processed 37001673 reads in 745 ms
[2015-09-30T22:46Z] INFO  23:46:34,696 MuTect - [MUTECT] Processed 266016953 reads in 656 ms
[2015-09-30T22:46Z] INFO  23:46:34,939 MuTect - [MUTECT] Processed 5000191 reads in 684 ms
[2015-09-30T22:46Z] INFO  23:46:34,992 ProgressMeter -     18:12329874        1.27e+06   30.0 s       23.0 s     42.0%        71.0 s    41.0 s
[2015-09-30T22:46Z] INFO  23:46:35,006 MuTect - [MUTECT] Processed 38001754 reads in 697 ms
[2015-09-30T22:46Z] INFO  23:46:35,099 MuTect - [MUTECT] Inspected 76000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:35,358 MuTect - [MUTECT] Processed 267016984 reads in 662 ms
[2015-09-30T22:46Z] INFO  23:46:35,670 MuTect - [MUTECT] Processed 39001813 reads in 664 ms
[2015-09-30T22:46Z] INFO  23:46:35,672 MuTect - [MUTECT] Processed 6000240 reads in 733 ms
[2015-09-30T22:46Z] INFO  23:46:35,987 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:36,034 MuTect - [MUTECT] Processed 268017021 reads in 676 ms
[2015-09-30T22:46Z] INFO  23:46:36,333 MuTect - [MUTECT] Processed 40001814 reads in 663 ms
[2015-09-30T22:46Z] INFO  23:46:36,395 MuTect - [MUTECT] Processed 7000265 reads in 723 ms
[2015-09-30T22:46Z] INFO  23:46:36,489 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:36,705 MuTect - [MUTECT] Processed 269017042 reads in 671 ms
[2015-09-30T22:46Z] INFO  23:46:37,014 MuTect - [MUTECT] Processed 41001815 reads in 681 ms
[2015-09-30T22:46Z] INFO  23:46:37,088 MuTect - [MUTECT] Processed 8000314 reads in 693 ms
[2015-09-30T22:46Z] INFO  23:46:37,386 MuTect - [MUTECT] Processed 270017079 reads in 681 ms
[2015-09-30T22:46Z] INFO  23:46:37,631 MuTect - [MUTECT] Inspected 77000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:37,682 MuTect - [MUTECT] Processed 42001833 reads in 668 ms
[2015-09-30T22:46Z] INFO  23:46:37,811 MuTect - [MUTECT] Processed 9000357 reads in 723 ms
[2015-09-30T22:46Z] INFO  23:46:38,084 MuTect - [MUTECT] Processed 271017084 reads in 698 ms
[2015-09-30T22:46Z] INFO  23:46:38,328 MuTect - [MUTECT] Processed 43001853 reads in 646 ms
[2015-09-30T22:46Z] INFO  23:46:38,452 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:38,508 MuTect - [MUTECT] Processed 10000403 reads in 697 ms
[2015-09-30T22:46Z] INFO  23:46:38,778 MuTect - [MUTECT] Processed 272017146 reads in 694 ms
[2015-09-30T22:46Z] INFO  23:46:38,964 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:39,002 MuTect - [MUTECT] Processed 44001860 reads in 674 ms
[2015-09-30T22:46Z] INFO  23:46:39,197 MuTect - [MUTECT] Processed 11000506 reads in 689 ms
[2015-09-30T22:46Z] INFO  23:46:39,479 MuTect - [MUTECT] Processed 273017146 reads in 701 ms
[2015-09-30T22:46Z] INFO  23:46:39,636 MuTect - [MUTECT] Processed 45001869 reads in 634 ms
[2015-09-30T22:46Z] INFO  23:46:39,878 MuTect - [MUTECT] Processed 12000562 reads in 681 ms
[2015-09-30T22:46Z] INFO  23:46:40,010 MuTect - [MUTECT] Inspected 78000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:40,185 MuTect - [MUTECT] Processed 274017148 reads in 706 ms
[2015-09-30T22:46Z] INFO  23:46:40,329 MuTect - [MUTECT] Processed 46001916 reads in 693 ms
[2015-09-30T22:46Z] INFO  23:46:40,566 MuTect - [MUTECT] Processed 13000614 reads in 688 ms
[2015-09-30T22:46Z] INFO  23:46:40,813 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:40,898 MuTect - [MUTECT] Processed 275017183 reads in 713 ms
[2015-09-30T22:46Z] INFO  23:46:41,049 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:41,298 MuTect - [MUTECT] Processed 14000667 reads in 732 ms
[2015-09-30T22:46Z] INFO  23:46:41,302 MuTect - [MUTECT] Processed 47002099 reads in 973 ms
[2015-09-30T22:46Z] INFO  23:46:41,600 MuTect - [MUTECT] Processed 276017277 reads in 702 ms
[2015-09-30T22:46Z] INFO  23:46:42,005 MuTect - [MUTECT] Processed 15000704 reads in 707 ms
[2015-09-30T22:46Z] INFO  23:46:42,300 MuTect - [MUTECT] Processed 277017342 reads in 700 ms
[2015-09-30T22:46Z] INFO  23:46:42,394 MuTect - [MUTECT] Processed 48002135 reads in 1092 ms
[2015-09-30T22:46Z] INFO  23:46:42,683 MuTect - [MUTECT] Processed 16000720 reads in 678 ms
[2015-09-30T22:46Z] INFO  23:46:42,707 MuTect - [MUTECT] Inspected 79000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:43,002 MuTect - [MUTECT] Processed 278017387 reads in 702 ms
[2015-09-30T22:46Z] INFO  23:46:43,189 MuTect - [MUTECT] Processed 49002196 reads in 795 ms
[2015-09-30T22:46Z] INFO  23:46:43,354 MuTect - [MUTECT] Processed 17000723 reads in 671 ms
[2015-09-30T22:46Z] INFO  23:46:43,371 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:43,652 MuTect - [MUTECT] Processed 279017440 reads in 650 ms
[2015-09-30T22:46Z] INFO  23:46:43,749 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:44,078 MuTect - [MUTECT] Processed 18000803 reads in 724 ms
[2015-09-30T22:46Z] INFO  23:46:44,090 MuTect - [MUTECT] Processed 50002257 reads in 901 ms
[2015-09-30T22:46Z] INFO  23:46:44,311 MuTect - [MUTECT] Processed 280017454 reads in 659 ms
[2015-09-30T22:46Z] INFO  23:46:44,828 MuTect - [MUTECT] Processed 19000862 reads in 750 ms
[2015-09-30T22:46Z] INFO  23:46:44,975 MuTect - [MUTECT] Processed 281017496 reads in 664 ms
[2015-09-30T22:46Z] INFO  23:46:45,037 MuTect - [MUTECT] Processed 51002294 reads in 947 ms
[2015-09-30T22:46Z] INFO  23:46:45,321 MuTect - [MUTECT] Inspected 80000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:45,577 MuTect - [MUTECT] Processed 20000870 reads in 749 ms
[2015-09-30T22:46Z] INFO  23:46:45,642 MuTect - [MUTECT] Processed 282017571 reads in 667 ms
[2015-09-30T22:46Z] INFO  23:46:45,755 MuTect - [MUTECT] Processed 52002425 reads in 718 ms
[2015-09-30T22:46Z] INFO  23:46:46,041 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:46,252 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:46,274 MuTect - [MUTECT] Processed 21000903 reads in 697 ms
[2015-09-30T22:46Z] INFO  23:46:46,435 MuTect - [MUTECT] Processed 283017654 reads in 793 ms
[2015-09-30T22:46Z] INFO  23:46:46,437 MuTect - [MUTECT] Processed 53002474 reads in 682 ms
[2015-09-30T22:46Z] INFO  23:46:46,950 MuTect - [MUTECT] Processed 22000991 reads in 676 ms
[2015-09-30T22:46Z] INFO  23:46:47,124 MuTect - [MUTECT] Processed 284017714 reads in 689 ms
[2015-09-30T22:46Z] INFO  23:46:47,130 MuTect - [MUTECT] Processed 54002547 reads in 693 ms
[2015-09-30T22:46Z] INFO  23:46:47,774 MuTect - [MUTECT] Processed 285017817 reads in 650 ms
[2015-09-30T22:46Z] INFO  23:46:47,834 MuTect - [MUTECT] Processed 23001017 reads in 884 ms
[2015-09-30T22:46Z] INFO  23:46:48,008 MuTect - [MUTECT] Inspected 81000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:48,036 MuTect - [MUTECT] Processed 55002560 reads in 906 ms
[2015-09-30T22:46Z] INFO  23:46:48,439 MuTect - [MUTECT] Processed 286017834 reads in 665 ms
[2015-09-30T22:46Z] INFO  23:46:48,626 MuTect - [MUTECT] Processed 24001045 reads in 792 ms
[2015-09-30T22:46Z] INFO  23:46:48,776 MuTect - [MUTECT] Processed 56002579 reads in 740 ms
[2015-09-30T22:46Z] INFO  23:46:48,958 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:49,000 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:49,087 MuTect - [MUTECT] Processed 287017847 reads in 648 ms
[2015-09-30T22:46Z] INFO  23:46:49,328 MuTect - [MUTECT] Processed 25001138 reads in 702 ms
[2015-09-30T22:46Z] INFO  23:46:49,460 MuTect - [MUTECT] Processed 57002681 reads in 684 ms
[2015-09-30T22:46Z] INFO  23:46:49,775 MuTect - [MUTECT] Processed 288017913 reads in 688 ms
[2015-09-30T22:46Z] INFO  23:46:50,025 MuTect - [MUTECT] Processed 26001184 reads in 697 ms
[2015-09-30T22:46Z] INFO  23:46:50,189 MuTect - [MUTECT] Processed 58002778 reads in 729 ms
[2015-09-30T22:46Z] INFO  23:46:50,407 MuTect - [MUTECT] Processed 289017921 reads in 632 ms
[2015-09-30T22:46Z] INFO  23:46:50,463 MuTect - [MUTECT] Inspected 82000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:50,733 MuTect - [MUTECT] Processed 27001245 reads in 708 ms
[2015-09-30T22:46Z] INFO  23:46:50,890 MuTect - [MUTECT] Processed 59002839 reads in 701 ms
[2015-09-30T22:46Z] INFO  23:46:51,021 MuTect - [MUTECT] Processed 290017936 reads in 614 ms
[2015-09-30T22:46Z] INFO  23:46:51,341 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:51,395 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:51,441 MuTect - [MUTECT] Processed 28001254 reads in 708 ms
[2015-09-30T22:46Z] INFO  23:46:51,590 MuTect - [MUTECT] Processed 60002853 reads in 700 ms
[2015-09-30T22:46Z] INFO  23:46:51,682 MuTect - [MUTECT] Processed 291018040 reads in 661 ms
[2015-09-30T22:46Z] INFO  23:46:52,129 MuTect - [MUTECT] Processed 29001264 reads in 688 ms
[2015-09-30T22:46Z] INFO  23:46:52,275 MuTect - [MUTECT] Processed 61002872 reads in 685 ms
[2015-09-30T22:46Z] INFO  23:46:52,326 MuTect - [MUTECT] Processed 292018070 reads in 644 ms
[2015-09-30T22:46Z] INFO  23:46:52,655 MuTect - [MUTECT] Inspected 83000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:52,829 MuTect - [MUTECT] Processed 30001928 reads in 700 ms
[2015-09-30T22:46Z] INFO  23:46:52,973 MuTect - [MUTECT] Processed 62002910 reads in 698 ms
[2015-09-30T22:46Z] INFO  23:46:52,983 MuTect - [MUTECT] Processed 293018131 reads in 657 ms
[2015-09-30T22:46Z] INFO  23:46:53,406 MuTect - [MUTECT] Processed 31002566 reads in 577 ms
[2015-09-30T22:46Z] INFO  23:46:53,629 MuTect - [MUTECT] Processed 294018185 reads in 646 ms
[2015-09-30T22:46Z] INFO  23:46:53,669 MuTect - [MUTECT] Processed 63002913 reads in 696 ms
[2015-09-30T22:46Z] INFO  23:46:53,843 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:54,043 MuTect - [MUTECT] Processed 32003370 reads in 637 ms
[2015-09-30T22:46Z] INFO  23:46:54,298 MuTect - [MUTECT] Processed 295018283 reads in 669 ms
[2015-09-30T22:46Z] INFO  23:46:54,374 MuTect - [MUTECT] Processed 64002969 reads in 705 ms
[2015-09-30T22:46Z] INFO  23:46:54,617 MuTect - [MUTECT] Processed 33003472 reads in 574 ms
[2015-09-30T22:46Z] INFO  23:46:55,019 MuTect - [MUTECT] Processed 296018346 reads in 721 ms
[2015-09-30T22:46Z] INFO  23:46:55,063 MuTect - [MUTECT] Processed 65003026 reads in 689 ms
[2015-09-30T22:46Z] INFO  23:46:55,105 MuTect - [MUTECT] Inspected 84000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:55,208 MuTect - [MUTECT] Processed 34003528 reads in 591 ms
[2015-09-30T22:46Z] INFO  23:46:55,726 MuTect - [MUTECT] Processed 297018397 reads in 707 ms
[2015-09-30T22:46Z] INFO  23:46:55,744 MuTect - [MUTECT] Processed 66003096 reads in 681 ms
[2015-09-30T22:46Z] INFO  23:46:55,912 MuTect - [MUTECT] Processed 35003624 reads in 704 ms
[2015-09-30T22:46Z] INFO  23:46:56,083 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:56,256 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:56,382 MuTect - [MUTECT] Processed 298018412 reads in 656 ms
[2015-09-30T22:46Z] INFO  23:46:56,437 MuTect - [MUTECT] Processed 67003141 reads in 693 ms
[2015-09-30T22:46Z] INFO  23:46:56,611 MuTect - [MUTECT] Processed 36003685 reads in 699 ms
[2015-09-30T22:46Z] INFO  23:46:57,063 MuTect - [MUTECT] Processed 299018457 reads in 681 ms
[2015-09-30T22:46Z] INFO  23:46:57,160 MuTect - [MUTECT] Processed 68003163 reads in 723 ms
[2015-09-30T22:46Z] INFO  23:46:57,293 MuTect - [MUTECT] Processed 37003697 reads in 682 ms
[2015-09-30T22:46Z] INFO  23:46:57,487 MuTect - [MUTECT] Inspected 85000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:57,695 MuTect - [MUTECT] Processed 300018508 reads in 632 ms
[2015-09-30T22:46Z] INFO  23:46:57,846 MuTect - [MUTECT] Processed 69003203 reads in 686 ms
[2015-09-30T22:46Z] INFO  23:46:58,002 MuTect - [MUTECT] Processed 38003715 reads in 709 ms
[2015-09-30T22:46Z] INFO  23:46:58,337 MuTect - [MUTECT] Processed 301018516 reads in 642 ms
[2015-09-30T22:46Z] INFO  23:46:58,549 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:58,585 MuTect - [MUTECT] Processed 70003245 reads in 739 ms
[2015-09-30T22:46Z] INFO  23:46:58,663 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:58,697 MuTect - [MUTECT] Processed 39003777 reads in 695 ms
[2015-09-30T22:46Z] INFO  23:46:58,974 MuTect - [MUTECT] Processed 302018546 reads in 637 ms
[2015-09-30T22:46Z] INFO  23:46:59,133 ProgressMeter -     18:46956545        1.03e+06   30.0 s       29.0 s     45.3%        66.0 s    36.0 s
[2015-09-30T22:46Z] INFO  23:46:59,288 MuTect - [MUTECT] Processed 71003270 reads in 703 ms
[2015-09-30T22:46Z] INFO  23:46:59,394 MuTect - [MUTECT] Processed 40003778 reads in 697 ms
[2015-09-30T22:46Z] INFO  23:46:59,642 MuTect - [MUTECT] Processed 303018558 reads in 668 ms
[2015-09-30T22:46Z] INFO  23:46:59,795 MuTect - [MUTECT] Inspected 86000 potential candidates
[2015-09-30T22:46Z] INFO  23:46:59,987 MuTect - [MUTECT] Processed 72003288 reads in 699 ms
[2015-09-30T22:47Z] INFO  23:47:00,083 MuTect - [MUTECT] Processed 41003825 reads in 689 ms
[2015-09-30T22:47Z] INFO  23:47:00,262 MuTect - [MUTECT] Processed 304018650 reads in 620 ms
[2015-09-30T22:47Z] INFO  23:47:00,722 MuTect - [MUTECT] Processed 73003291 reads in 735 ms
[2015-09-30T22:47Z] INFO  23:47:00,771 MuTect - [MUTECT] Processed 42003879 reads in 688 ms
[2015-09-30T22:47Z] INFO  23:47:00,890 MuTect - [MUTECT] Processed 305018779 reads in 628 ms
[2015-09-30T22:47Z] INFO  23:47:00,936 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:01,096 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:01,391 MuTect - [MUTECT] Processed 74003329 reads in 669 ms
[2015-09-30T22:47Z] INFO  23:47:01,469 MuTect - [MUTECT] Processed 43003916 reads in 698 ms
[2015-09-30T22:47Z] INFO  23:47:01,536 MuTect - [MUTECT] Processed 306018871 reads in 646 ms
[2015-09-30T22:47Z] INFO  23:47:01,731 ProgressMeter -     17:61586933        9.57e+06    3.5 m       21.0 s     96.3%         3.6 m     8.0 s
[2015-09-30T22:47Z] INFO  23:47:01,914 MuTect - [MUTECT] Inspected 87000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:02,107 MuTect - [MUTECT] Processed 75003342 reads in 716 ms
[2015-09-30T22:47Z] INFO  23:47:02,161 MuTect - [MUTECT] Processed 44003995 reads in 692 ms
[2015-09-30T22:47Z] INFO  23:47:02,199 MuTect - [MUTECT] Processed 307018920 reads in 663 ms
[2015-09-30T22:47Z] INFO  23:47:02,828 MuTect - [MUTECT] Processed 308018995 reads in 629 ms
[2015-09-30T22:47Z] INFO  23:47:02,835 MuTect - [MUTECT] Processed 45003995 reads in 674 ms
[2015-09-30T22:47Z] INFO  23:47:03,159 MuTect - [MUTECT] Processed 76003366 reads in 1052 ms
[2015-09-30T22:47Z] INFO  23:47:03,249 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:03,447 MuTect - [MUTECT] Processed 309019063 reads in 619 ms
[2015-09-30T22:47Z] INFO  23:47:03,477 MuTect - [MUTECT] Processed 46004017 reads in 642 ms
[2015-09-30T22:47Z] INFO  23:47:03,882 MuTect - [MUTECT] Processed 77003401 reads in 723 ms
[2015-09-30T22:47Z] INFO  23:47:03,912 MuTect - [MUTECT] Inspected 88000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:04,046 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:04,076 MuTect - [MUTECT] Processed 310019072 reads in 629 ms
[2015-09-30T22:47Z] INFO  23:47:04,139 MuTect - [MUTECT] Processed 47004140 reads in 662 ms
[2015-09-30T22:47Z] INFO  23:47:04,615 MuTect - [MUTECT] Processed 78003437 reads in 733 ms
[2015-09-30T22:47Z] INFO  23:47:04,713 MuTect - [MUTECT] Processed 311019158 reads in 637 ms
[2015-09-30T22:47Z] INFO  23:47:04,836 MuTect - [MUTECT] Processed 48004184 reads in 697 ms
[2015-09-30T22:47Z] INFO  23:47:04,993 ProgressMeter -     18:28989713        2.71e+06   60.0 s       22.0 s     90.3%        66.0 s     6.0 s
[2015-09-30T22:47Z] INFO  23:47:05,349 MuTect - [MUTECT] Processed 79003448 reads in 734 ms
[2015-09-30T22:47Z] INFO  23:47:05,351 MuTect - [MUTECT] Processed 312019214 reads in 638 ms
[2015-09-30T22:47Z] INFO  23:47:05,497 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:05,569 MuTect - [MUTECT] Processed 49004206 reads in 733 ms
[2015-09-30T22:47Z] INFO  23:47:05,965 MuTect - [MUTECT] Processed 313019237 reads in 614 ms
[2015-09-30T22:47Z] INFO  23:47:05,975 MuTect - [MUTECT] Inspected 89000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:06,051 MuTect - [MUTECT] Processed 80003459 reads in 702 ms
[2015-09-30T22:47Z] INFO  23:47:06,352 MuTect - [MUTECT] Processed 50004271 reads in 783 ms
[2015-09-30T22:47Z] INFO  23:47:06,574 MuTect - [MUTECT] Processed 314019262 reads in 609 ms
[2015-09-30T22:47Z] INFO  23:47:06,737 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:06,777 MuTect - [MUTECT] Processed 81003488 reads in 726 ms
[2015-09-30T22:47Z] INFO  23:47:07,062 MuTect - [MUTECT] Processed 51004392 reads in 710 ms
[2015-09-30T22:47Z] INFO  23:47:07,209 MuTect - [MUTECT] Processed 315019290 reads in 635 ms
[2015-09-30T22:47Z] INFO  23:47:07,521 MuTect - [MUTECT] Processed 82003584 reads in 744 ms
[2015-09-30T22:47Z] INFO  23:47:07,770 MuTect - [MUTECT] Processed 52004427 reads in 708 ms
[2015-09-30T22:47Z] INFO  23:47:07,861 MuTect - [MUTECT] Processed 316019333 reads in 652 ms
[2015-09-30T22:47Z] INFO  23:47:08,057 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:08,206 MuTect - [MUTECT] Inspected 90000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:08,234 MuTect - [MUTECT] Processed 83003637 reads in 713 ms
[2015-09-30T22:47Z] INFO  23:47:08,452 MuTect - [MUTECT] Processed 53004445 reads in 682 ms
[2015-09-30T22:47Z] INFO  23:47:08,533 MuTect - [MUTECT] Processed 317019432 reads in 672 ms
[2015-09-30T22:47Z] INFO  23:47:08,955 MuTect - [MUTECT] Processed 84003723 reads in 721 ms
[2015-09-30T22:47Z] INFO  23:47:09,137 MuTect - [MUTECT] Processed 54004483 reads in 685 ms
[2015-09-30T22:47Z] INFO  23:47:09,174 MuTect - [MUTECT] Processed 318019467 reads in 641 ms
[2015-09-30T22:47Z] INFO  23:47:09,273 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:09,636 MuTect - [MUTECT] Processed 85003792 reads in 681 ms
[2015-09-30T22:47Z] INFO  23:47:09,838 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:47Z] INFO  23:47:09,844 ProgressMeter -            done        9.98e+06    3.6 m       21.0 s    100.0%         3.6 m     0.0 s
[2015-09-30T22:47Z] INFO  23:47:09,845 ProgressMeter - Total runtime 218.12 secs, 3.64 min, 0.06 hours
[2015-09-30T22:47Z] INFO  23:47:09,853 MuTect - [MUTECT] Processed 55004537 reads in 716 ms
[2015-09-30T22:47Z] INFO  23:47:09,910 MicroScheduler - 249973 reads were filtered out during the traversal out of approximately 3777604 total reads (6.62%)
[2015-09-30T22:47Z] INFO  23:47:09,911 MicroScheduler -   -> 186004 reads (4.92% of total) failing DuplicateReadFilter
[2015-09-30T22:47Z] INFO  23:47:09,911 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:47Z] INFO  23:47:09,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:47Z] INFO  23:47:09,911 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:47Z] INFO  23:47:09,911 MicroScheduler -   -> 63969 reads (1.69% of total) failing UnmappedReadFilter
[2015-09-30T22:47Z] INFO  23:47:10,200 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:47Z] INFO  23:47:10,203 ProgressMeter -            done        2.99e+06   65.0 s       21.0 s    100.0%        65.0 s     0.0 s
[2015-09-30T22:47Z] INFO  23:47:10,203 ProgressMeter - Total runtime 65.21 secs, 1.09 min, 0.02 hours
[2015-09-30T22:47Z] INFO  23:47:10,269 MicroScheduler - 59951 reads were filtered out during the traversal out of approximately 1027494 total reads (5.83%)
[2015-09-30T22:47Z] INFO  23:47:10,270 MicroScheduler -   -> 43920 reads (4.27% of total) failing DuplicateReadFilter
[2015-09-30T22:47Z] INFO  23:47:10,270 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:47Z] INFO  23:47:10,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:47Z] INFO  23:47:10,270 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:47Z] INFO  23:47:10,270 MicroScheduler -   -> 16031 reads (1.56% of total) failing UnmappedReadFilter
[2015-09-30T22:47Z] INFO  23:47:10,570 MuTect - [MUTECT] Processed 56004619 reads in 717 ms
[2015-09-30T22:47Z] INFO  23:47:10,712 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:10,914 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:47Z] bgzip syn3-17_31047756_62076645-raw-mutect.vcf
[2015-09-30T22:47Z] tabix index syn3-17_31047756_62076645-raw-mutect.vcf.gz
[2015-09-30T22:47Z] INFO  23:47:11,266 MuTect - [MUTECT] Processed 57004674 reads in 696 ms
[2015-09-30T22:47Z] INFO  23:47:11,281 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:47Z] bgzip syn3-18_0_31142016-raw-mutect.vcf
[2015-09-30T22:47Z] tabix index syn3-18_0_31142016-raw-mutect.vcf.gz
[2015-09-30T22:47Z] INFO  23:47:12,031 MuTect - [MUTECT] Processed 58004705 reads in 765 ms
[2015-09-30T22:47Z] INFO  23:47:12,762 MuTect - [MUTECT] Processed 59004765 reads in 731 ms
[2015-09-30T22:47Z] MuTect: MuTect
[2015-09-30T22:47Z] INFO  23:47:13,217 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:13,514 MuTect - [MUTECT] Processed 60004839 reads in 752 ms
[2015-09-30T22:47Z] MuTect: MuTect
[2015-09-30T22:47Z] INFO  23:47:14,255 MuTect - [MUTECT] Processed 61004886 reads in 741 ms
[2015-09-30T22:47Z] INFO  23:47:14,947 MuTect - [MUTECT] Processed 62004940 reads in 692 ms
[2015-09-30T22:47Z] INFO  23:47:15,373 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/18/syn3-18_63476668_78077248-raw-mutect-regions.bed to be BED
[2015-09-30T22:47Z] INFO  23:47:15,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:15,431 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:47Z] INFO  23:47:15,431 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:47Z] INFO  23:47:15,431 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:47Z] INFO  23:47:15,435 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/18/syn3-18_63476668_78077248-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/18/tx/tmpqBUeuk/syn3-18_63476668_78077248-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:47Z] INFO  23:47:15,435 HelpFormatter - Date/Time: 2015/09/30 23:47:15
[2015-09-30T22:47Z] INFO  23:47:15,435 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:15,435 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:15,462 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:47Z] INFO  23:47:15,467 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:47Z] INFO  23:47:15,521 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:47Z] INFO  23:47:15,570 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:47Z] INFO  23:47:15,578 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:47Z] INFO  23:47:15,601 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:47Z] INFO  23:47:15,612 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:15,613 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:47Z] INFO  23:47:15,665 MuTect - [MUTECT] Processed 63005032 reads in 718 ms
[2015-09-30T22:47Z] INFO  23:47:15,787 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:47Z] INFO  23:47:15,848 IntervalUtils - Processing 280150 bp from intervals
[2015-09-30T22:47Z] INFO  23:47:15,852 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:47Z] INFO  23:47:15,852 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:47Z] INFO  23:47:15,907 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:47Z] INFO  23:47:16,262 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:47Z] INFO  23:47:16,262 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:47Z] INFO  23:47:16,262 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:47Z] INFO  23:47:16,263 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:47Z] INFO  23:47:16,269 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/19/syn3-19_0_31026185-raw-mutect-regions.bed to be BED
[2015-09-30T22:47Z] INFO  23:47:16,325 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:16,326 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:47Z] INFO  23:47:16,326 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:47Z] INFO  23:47:16,326 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:47Z] INFO  23:47:16,329 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/19/syn3-19_0_31026185-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/19/tx/tmpWMHVPx/syn3-19_0_31026185-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:47Z] INFO  23:47:16,329 HelpFormatter - Date/Time: 2015/09/30 23:47:16
[2015-09-30T22:47Z] INFO  23:47:16,330 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:16,330 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:16,358 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:47Z] INFO  23:47:16,362 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:47Z] INFO  23:47:16,418 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:47Z] INFO  23:47:16,467 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:47Z] INFO  23:47:16,475 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:47Z] INFO  23:47:16,498 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:47Z] INFO  23:47:16,509 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:47Z] INFO  23:47:16,556 MuTect - [MUTECT] Processed 64005045 reads in 891 ms
[2015-09-30T22:47Z] INFO  23:47:16,736 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:47Z] INFO  23:47:17,173 IntervalUtils - Processing 3555807 bp from intervals
[2015-09-30T22:47Z] INFO  23:47:17,177 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:47Z] INFO  23:47:17,178 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:47Z] INFO  23:47:17,234 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:47Z] INFO  23:47:17,274 MuTect - [MUTECT] Processed 65005092 reads in 718 ms
[2015-09-30T22:47Z] INFO  23:47:17,885 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:47Z] INFO  23:47:17,885 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:47Z] INFO  23:47:17,886 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:47Z] INFO  23:47:17,887 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:47Z] INFO  23:47:18,017 MuTect - [MUTECT] Processed 66005181 reads in 743 ms
[2015-09-30T22:47Z] INFO  23:47:18,336 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:18,740 MuTect - [MUTECT] Processed 67005275 reads in 723 ms
[2015-09-30T22:47Z] INFO  23:47:18,866 MuTect - [MUTECT] Processed 1000047 reads in 2507 ms
[2015-09-30T22:47Z] INFO  23:47:19,467 MuTect - [MUTECT] Processed 68005330 reads in 727 ms
[2015-09-30T22:47Z] INFO  23:47:19,662 MuTect - [MUTECT] Processed 2000082 reads in 796 ms
[2015-09-30T22:47Z] INFO  23:47:20,204 MuTect - [MUTECT] Processed 69005354 reads in 737 ms
[2015-09-30T22:47Z] INFO  23:47:20,226 MuTect - [MUTECT] Processed 1000021 reads in 2249 ms
[2015-09-30T22:47Z] INFO  23:47:21,553 MuTect - [MUTECT] Processed 70005371 reads in 1349 ms
[2015-09-30T22:47Z] INFO  23:47:21,634 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:21,828 MuTect - [MUTECT] Processed 3000158 reads in 2167 ms
[2015-09-30T22:47Z] INFO  23:47:22,121 MuTect - [MUTECT] Processed 2000059 reads in 1894 ms
[2015-09-30T22:47Z] INFO  23:47:22,291 MuTect - [MUTECT] Processed 71005406 reads in 738 ms
[2015-09-30T22:47Z] INFO  23:47:22,322 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:22,574 MuTect - [MUTECT] Processed 4000193 reads in 746 ms
[2015-09-30T22:47Z] INFO  23:47:23,014 MuTect - [MUTECT] Processed 3000151 reads in 894 ms
[2015-09-30T22:47Z] INFO  23:47:23,022 MuTect - [MUTECT] Processed 72005425 reads in 731 ms
[2015-09-30T22:47Z] INFO  23:47:23,257 MuTect - [MUTECT] Processed 5000227 reads in 683 ms
[2015-09-30T22:47Z] INFO  23:47:23,724 MuTect - [MUTECT] Processed 73005464 reads in 702 ms
[2015-09-30T22:47Z] INFO  23:47:23,780 MuTect - [MUTECT] Processed 4000172 reads in 766 ms
[2015-09-30T22:47Z] INFO  23:47:23,879 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:24,063 MuTect - [MUTECT] Processed 6000244 reads in 806 ms
[2015-09-30T22:47Z] INFO  23:47:24,200 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:24,428 MuTect - [MUTECT] Processed 74005508 reads in 704 ms
[2015-09-30T22:47Z] INFO  23:47:24,746 MuTect - [MUTECT] Processed 7000250 reads in 683 ms
[2015-09-30T22:47Z] INFO  23:47:24,981 MuTect - [MUTECT] Processed 5000274 reads in 1201 ms
[2015-09-30T22:47Z] INFO  23:47:24,986 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:25,124 MuTect - [MUTECT] Processed 75005534 reads in 696 ms
[2015-09-30T22:47Z] INFO  23:47:25,482 MuTect - [MUTECT] Processed 8000251 reads in 736 ms
[2015-09-30T22:47Z] INFO  23:47:25,667 MuTect - [MUTECT] Processed 6000333 reads in 686 ms
[2015-09-30T22:47Z] INFO  23:47:25,881 MuTect - [MUTECT] Processed 76005597 reads in 757 ms
[2015-09-30T22:47Z] INFO  23:47:26,209 MuTect - [MUTECT] Processed 9000259 reads in 727 ms
[2015-09-30T22:47Z] INFO  23:47:26,421 MuTect - [MUTECT] Processed 7000456 reads in 754 ms
[2015-09-30T22:47Z] INFO  23:47:26,547 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:26,591 MuTect - [MUTECT] Processed 77005671 reads in 710 ms
[2015-09-30T22:47Z] INFO  23:47:26,749 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:26,921 MuTect - [MUTECT] Processed 10000320 reads in 712 ms
[2015-09-30T22:47Z] INFO  23:47:27,312 MuTect - [MUTECT] Processed 78005706 reads in 721 ms
[2015-09-30T22:47Z] INFO  23:47:27,432 MuTect - [MUTECT] Processed 8000552 reads in 1011 ms
[2015-09-30T22:47Z] INFO  23:47:27,587 MuTect - [MUTECT] Processed 11000362 reads in 666 ms
[2015-09-30T22:47Z] INFO  23:47:27,702 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:28,057 MuTect - [MUTECT] Processed 79005733 reads in 745 ms
[2015-09-30T22:47Z] INFO  23:47:28,134 MuTect - [MUTECT] Processed 9000640 reads in 702 ms
[2015-09-30T22:47Z] INFO  23:47:28,250 MuTect - [MUTECT] Processed 12000470 reads in 663 ms
[2015-09-30T22:47Z] INFO  23:47:28,695 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:47Z] INFO  23:47:28,699 ProgressMeter -            done        2.27e+06   59.0 s       26.0 s    100.0%        59.0 s     0.0 s
[2015-09-30T22:47Z] INFO  23:47:28,699 ProgressMeter - Total runtime 59.57 secs, 0.99 min, 0.02 hours
[2015-09-30T22:47Z] INFO  23:47:28,766 MicroScheduler - 57872 reads were filtered out during the traversal out of approximately 956310 total reads (6.05%)
[2015-09-30T22:47Z] INFO  23:47:28,766 MicroScheduler -   -> 42587 reads (4.45% of total) failing DuplicateReadFilter
[2015-09-30T22:47Z] INFO  23:47:28,766 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:47Z] INFO  23:47:28,766 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:47Z] INFO  23:47:28,766 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:47Z] INFO  23:47:28,766 MicroScheduler -   -> 15285 reads (1.60% of total) failing UnmappedReadFilter
[2015-09-30T22:47Z] INFO  23:47:28,823 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:28,829 MuTect - [MUTECT] Processed 10000660 reads in 695 ms
[2015-09-30T22:47Z] INFO  23:47:28,908 MuTect - [MUTECT] Processed 13000598 reads in 658 ms
[2015-09-30T22:47Z] INFO  23:47:29,496 MuTect - [MUTECT] Processed 11000736 reads in 667 ms
[2015-09-30T22:47Z] INFO  23:47:29,624 MuTect - [MUTECT] Processed 14000685 reads in 716 ms
[2015-09-30T22:47Z] INFO  23:47:29,745 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:47Z] bgzip syn3-18_31158315_63430522-raw-mutect.vcf
[2015-09-30T22:47Z] tabix index syn3-18_31158315_63430522-raw-mutect.vcf.gz
[2015-09-30T22:47Z] INFO  23:47:30,200 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:30,200 MuTect - [MUTECT] Processed 12000847 reads in 704 ms
[2015-09-30T22:47Z] INFO  23:47:30,271 MuTect - [MUTECT] Processed 15000762 reads in 647 ms
[2015-09-30T22:47Z] INFO  23:47:30,852 MuTect - [MUTECT] Processed 13000881 reads in 652 ms
[2015-09-30T22:47Z] INFO  23:47:30,920 MuTect - [MUTECT] Processed 16000776 reads in 649 ms
[2015-09-30T22:47Z] INFO  23:47:31,037 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:31,519 MuTect - [MUTECT] Processed 14000957 reads in 667 ms
[2015-09-30T22:47Z] INFO  23:47:31,569 MuTect - [MUTECT] Processed 17000864 reads in 649 ms
[2015-09-30T22:47Z] MuTect: MuTect
[2015-09-30T22:47Z] INFO  23:47:32,200 MuTect - [MUTECT] Processed 15000991 reads in 681 ms
[2015-09-30T22:47Z] INFO  23:47:32,220 MuTect - [MUTECT] Processed 18000937 reads in 651 ms
[2015-09-30T22:47Z] INFO  23:47:32,473 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:33,026 MuTect - [MUTECT] Processed 16001105 reads in 826 ms
[2015-09-30T22:47Z] INFO  23:47:33,080 MuTect - [MUTECT] Processed 19001013 reads in 860 ms
[2015-09-30T22:47Z] INFO  23:47:33,246 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:33,706 MuTect - [MUTECT] Processed 17001131 reads in 680 ms
[2015-09-30T22:47Z] INFO  23:47:33,745 MuTect - [MUTECT] Processed 20001043 reads in 665 ms
[2015-09-30T22:47Z] INFO  23:47:34,330 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/19/syn3-19_31038548_59128983-raw-mutect-regions.bed to be BED
[2015-09-30T22:47Z] INFO  23:47:34,385 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:34,385 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:47Z] INFO  23:47:34,385 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:47Z] INFO  23:47:34,386 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:47Z] INFO  23:47:34,389 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/19/syn3-19_31038548_59128983-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/19/tx/tmpbyqymK/syn3-19_31038548_59128983-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:47Z] INFO  23:47:34,389 HelpFormatter - Date/Time: 2015/09/30 23:47:34
[2015-09-30T22:47Z] INFO  23:47:34,389 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:34,389 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:34,395 MuTect - [MUTECT] Processed 18001164 reads in 689 ms
[2015-09-30T22:47Z] INFO  23:47:34,416 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:47Z] INFO  23:47:34,421 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:47Z] INFO  23:47:34,453 MuTect - [MUTECT] Processed 21001109 reads in 708 ms
[2015-09-30T22:47Z] INFO  23:47:34,476 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:47Z] INFO  23:47:34,523 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:47Z] INFO  23:47:34,530 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:47Z] INFO  23:47:34,604 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2015-09-30T22:47Z] INFO  23:47:34,730 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:47Z] INFO  23:47:34,831 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:34,909 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:47Z] INFO  23:47:35,095 MuTect - [MUTECT] Processed 22001221 reads in 642 ms
[2015-09-30T22:47Z] INFO  23:47:35,164 MuTect - [MUTECT] Processed 19001250 reads in 769 ms
[2015-09-30T22:47Z] INFO  23:47:35,171 IntervalUtils - Processing 4122500 bp from intervals
[2015-09-30T22:47Z] INFO  23:47:35,176 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:47Z] INFO  23:47:35,176 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:47Z] INFO  23:47:35,230 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:47Z] INFO  23:47:35,437 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:47Z] INFO  23:47:35,437 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:47Z] INFO  23:47:35,437 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:47Z] INFO  23:47:35,438 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:47Z] INFO  23:47:35,439 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:35,672 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:47Z] INFO  23:47:35,676 ProgressMeter -            done        5.77e+05   19.0 s       33.0 s    100.0%        19.0 s     0.0 s
[2015-09-30T22:47Z] INFO  23:47:35,677 ProgressMeter - Total runtime 19.41 secs, 0.32 min, 0.01 hours
[2015-09-30T22:47Z] INFO  23:47:35,738 MicroScheduler - 17248 reads were filtered out during the traversal out of approximately 272916 total reads (6.32%)
[2015-09-30T22:47Z] INFO  23:47:35,739 MicroScheduler -   -> 12777 reads (4.68% of total) failing DuplicateReadFilter
[2015-09-30T22:47Z] INFO  23:47:35,739 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:47Z] INFO  23:47:35,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:47Z] INFO  23:47:35,739 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:47Z] INFO  23:47:35,739 MicroScheduler -   -> 4471 reads (1.64% of total) failing UnmappedReadFilter
[2015-09-30T22:47Z] INFO  23:47:35,868 MuTect - [MUTECT] Processed 20001292 reads in 704 ms
[2015-09-30T22:47Z] INFO  23:47:36,664 MuTect - [MUTECT] Processed 21001327 reads in 796 ms
[2015-09-30T22:47Z] INFO  23:47:36,745 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:47Z] bgzip syn3-18_63476668_78077248-raw-mutect.vcf
[2015-09-30T22:47Z] tabix index syn3-18_63476668_78077248-raw-mutect.vcf.gz
[2015-09-30T22:47Z] INFO  23:47:37,355 MuTect - [MUTECT] Processed 22001379 reads in 691 ms
[2015-09-30T22:47Z] INFO  23:47:37,537 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:37,742 MuTect - [MUTECT] Processed 1000000 reads in 2258 ms
[2015-09-30T22:47Z] INFO  23:47:38,064 MuTect - [MUTECT] Processed 23001509 reads in 709 ms
[2015-09-30T22:47Z] INFO  23:47:38,426 MuTect - [MUTECT] Processed 2000060 reads in 684 ms
[2015-09-30T22:47Z] INFO  23:47:38,737 MuTect - [MUTECT] Processed 24001550 reads in 673 ms
[2015-09-30T22:47Z] MuTect: MuTect
[2015-09-30T22:47Z] INFO  23:47:39,184 MuTect - [MUTECT] Processed 3000152 reads in 758 ms
[2015-09-30T22:47Z] INFO  23:47:39,420 MuTect - [MUTECT] Processed 25001619 reads in 683 ms
[2015-09-30T22:47Z] INFO  23:47:39,548 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:39,759 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:39,932 MuTect - [MUTECT] Processed 4000165 reads in 748 ms
[2015-09-30T22:47Z] INFO  23:47:40,082 MuTect - [MUTECT] Processed 26001723 reads in 662 ms
[2015-09-30T22:47Z] INFO  23:47:40,600 MuTect - [MUTECT] Processed 5000172 reads in 668 ms
[2015-09-30T22:47Z] INFO  23:47:40,770 MuTect - [MUTECT] Processed 27001743 reads in 688 ms
[2015-09-30T22:47Z] INFO  23:47:41,240 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/20/syn3-20_0_31018105-raw-mutect-regions.bed to be BED
[2015-09-30T22:47Z] INFO  23:47:41,298 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:41,298 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:47Z] INFO  23:47:41,298 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:47Z] INFO  23:47:41,298 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:47Z] INFO  23:47:41,302 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/20/syn3-20_0_31018105-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/20/tx/tmpvTsq6P/syn3-20_0_31018105-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:47Z] INFO  23:47:41,302 HelpFormatter - Date/Time: 2015/09/30 23:47:41
[2015-09-30T22:47Z] INFO  23:47:41,302 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:41,302 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:47Z] INFO  23:47:41,304 MuTect - [MUTECT] Processed 6000216 reads in 703 ms
[2015-09-30T22:47Z] INFO  23:47:41,330 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:47Z] INFO  23:47:41,335 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:47Z] INFO  23:47:41,385 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:47Z] INFO  23:47:41,424 MuTect - [MUTECT] Processed 28001764 reads in 654 ms
[2015-09-30T22:47Z] INFO  23:47:41,435 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:47Z] INFO  23:47:41,443 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:47Z] INFO  23:47:41,467 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:47Z] INFO  23:47:41,478 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:47Z] INFO  23:47:41,648 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:47Z] INFO  23:47:41,747 IntervalUtils - Processing 1298771 bp from intervals
[2015-09-30T22:47Z] INFO  23:47:41,751 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:47Z] INFO  23:47:41,751 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:47Z] INFO  23:47:41,853 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:41,903 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:41,905 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:47Z] INFO  23:47:41,987 MuTect - [MUTECT] Processed 7000221 reads in 684 ms
[2015-09-30T22:47Z] INFO  23:47:42,048 MuTect - [MUTECT] Processed 29001835 reads in 624 ms
[2015-09-30T22:47Z] INFO  23:47:42,081 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:47Z] INFO  23:47:42,081 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:47Z] INFO  23:47:42,081 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:47Z] INFO  23:47:42,082 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:47Z] INFO  23:47:42,710 MuTect - [MUTECT] Processed 30001920 reads in 662 ms
[2015-09-30T22:47Z] INFO  23:47:42,812 MuTect - [MUTECT] Processed 8000327 reads in 825 ms
[2015-09-30T22:47Z] INFO  23:47:43,355 MuTect - [MUTECT] Processed 31001933 reads in 645 ms
[2015-09-30T22:47Z] INFO  23:47:43,590 MuTect - [MUTECT] Processed 9000327 reads in 777 ms
[2015-09-30T22:47Z] INFO  23:47:44,011 MuTect - [MUTECT] Processed 32001940 reads in 656 ms
[2015-09-30T22:47Z] INFO  23:47:44,065 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:44,255 MuTect - [MUTECT] Processed 10000374 reads in 666 ms
[2015-09-30T22:47Z] INFO  23:47:44,326 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:44,646 MuTect - [MUTECT] Processed 33001958 reads in 635 ms
[2015-09-30T22:47Z] INFO  23:47:44,684 MuTect - [MUTECT] Processed 1000135 reads in 2554 ms
[2015-09-30T22:47Z] INFO  23:47:44,963 MuTect - [MUTECT] Processed 11000410 reads in 708 ms
[2015-09-30T22:47Z] INFO  23:47:45,268 MuTect - [MUTECT] Processed 34002033 reads in 622 ms
[2015-09-30T22:47Z] INFO  23:47:45,503 MuTect - [MUTECT] Processed 2000225 reads in 819 ms
[2015-09-30T22:47Z] INFO  23:47:45,641 MuTect - [MUTECT] Processed 12000491 reads in 678 ms
[2015-09-30T22:47Z] INFO  23:47:45,863 MuTect - [MUTECT] Processed 35002079 reads in 595 ms
[2015-09-30T22:47Z] INFO  23:47:46,157 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:46,221 MuTect - [MUTECT] Processed 3000245 reads in 718 ms
[2015-09-30T22:47Z] INFO  23:47:46,251 MuTect - [MUTECT] Processed 13000620 reads in 610 ms
[2015-09-30T22:47Z] INFO  23:47:46,362 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:46,476 MuTect - [MUTECT] Processed 36002196 reads in 613 ms
[2015-09-30T22:47Z] INFO  23:47:46,623 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:46,882 MuTect - [MUTECT] Processed 14000699 reads in 631 ms
[2015-09-30T22:47Z] INFO  23:47:46,937 MuTect - [MUTECT] Processed 4000323 reads in 716 ms
[2015-09-30T22:47Z] INFO  23:47:47,159 MuTect - [MUTECT] Processed 37002247 reads in 683 ms
[2015-09-30T22:47Z] INFO  23:47:47,514 MuTect - [MUTECT] Processed 15000793 reads in 632 ms
[2015-09-30T22:47Z] INFO  23:47:47,738 MuTect - [MUTECT] Processed 5000351 reads in 801 ms
[2015-09-30T22:47Z] INFO  23:47:47,888 ProgressMeter -      19:1578581        1.04e+06   30.0 s       28.0 s      9.1%         5.5 m     5.0 m
[2015-09-30T22:47Z] INFO  23:47:47,900 MuTect - [MUTECT] Processed 38002320 reads in 741 ms
[2015-09-30T22:47Z] INFO  23:47:48,205 MuTect - [MUTECT] Processed 16000829 reads in 690 ms
[2015-09-30T22:47Z] INFO  23:47:48,270 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:48,485 MuTect - [MUTECT] Processed 6000400 reads in 747 ms
[2015-09-30T22:47Z] INFO  23:47:48,567 MuTect - [MUTECT] Processed 39002353 reads in 667 ms
[2015-09-30T22:47Z] INFO  23:47:48,864 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:48,865 MuTect - [MUTECT] Processed 17000951 reads in 661 ms
[2015-09-30T22:47Z] INFO  23:47:48,869 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:49,183 MuTect - [MUTECT] Processed 7000486 reads in 698 ms
[2015-09-30T22:47Z] INFO  23:47:49,262 MuTect - [MUTECT] Processed 40002413 reads in 695 ms
[2015-09-30T22:47Z] INFO  23:47:49,508 MuTect - [MUTECT] Processed 18000964 reads in 643 ms
[2015-09-30T22:47Z] INFO  23:47:49,917 MuTect - [MUTECT] Processed 8000502 reads in 734 ms
[2015-09-30T22:47Z] INFO  23:47:50,018 MuTect - [MUTECT] Processed 41002577 reads in 756 ms
[2015-09-30T22:47Z] INFO  23:47:50,181 MuTect - [MUTECT] Processed 19001029 reads in 673 ms
[2015-09-30T22:47Z] INFO  23:47:50,541 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:50,582 MuTect - [MUTECT] Processed 9000537 reads in 665 ms
[2015-09-30T22:47Z] INFO  23:47:50,759 MuTect - [MUTECT] Processed 42002638 reads in 741 ms
[2015-09-30T22:47Z] INFO  23:47:50,859 MuTect - [MUTECT] Processed 20001091 reads in 678 ms
[2015-09-30T22:47Z] INFO  23:47:51,164 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:51,241 MuTect - [MUTECT] Processed 10000542 reads in 659 ms
[2015-09-30T22:47Z] INFO  23:47:51,281 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:51,474 MuTect - [MUTECT] Processed 43002670 reads in 715 ms
[2015-09-30T22:47Z] INFO  23:47:51,506 MuTect - [MUTECT] Processed 21001106 reads in 647 ms
[2015-09-30T22:47Z] INFO  23:47:51,934 MuTect - [MUTECT] Processed 11000629 reads in 693 ms
[2015-09-30T22:47Z] INFO  23:47:52,192 MuTect - [MUTECT] Processed 22001193 reads in 686 ms
[2015-09-30T22:47Z] INFO  23:47:52,194 MuTect - [MUTECT] Processed 44002769 reads in 720 ms
[2015-09-30T22:47Z] INFO  23:47:52,580 MuTect - [MUTECT] Processed 12000651 reads in 646 ms
[2015-09-30T22:47Z] INFO  23:47:52,866 MuTect - [MUTECT] Processed 23001255 reads in 674 ms
[2015-09-30T22:47Z] INFO  23:47:52,881 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:52,890 MuTect - [MUTECT] Processed 45002815 reads in 696 ms
[2015-09-30T22:47Z] INFO  23:47:53,310 MuTect - [MUTECT] Processed 13000747 reads in 730 ms
[2015-09-30T22:47Z] INFO  23:47:53,453 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:53,515 MuTect - [MUTECT] Processed 24001261 reads in 648 ms
[2015-09-30T22:47Z] INFO  23:47:53,569 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:53,569 MuTect - [MUTECT] Processed 46002932 reads in 679 ms
[2015-09-30T22:47Z] INFO  23:47:54,071 MuTect - [MUTECT] Processed 14000788 reads in 761 ms
[2015-09-30T22:47Z] INFO  23:47:54,156 MuTect - [MUTECT] Processed 25001334 reads in 642 ms
[2015-09-30T22:47Z] INFO  23:47:54,224 MuTect - [MUTECT] Processed 47003056 reads in 655 ms
[2015-09-30T22:47Z] INFO  23:47:54,745 MuTect - [MUTECT] Processed 15000845 reads in 674 ms
[2015-09-30T22:47Z] INFO  23:47:54,863 MuTect - [MUTECT] Processed 26001426 reads in 707 ms
[2015-09-30T22:47Z] INFO  23:47:55,094 MuTect - [MUTECT] Processed 48003090 reads in 870 ms
[2015-09-30T22:47Z] INFO  23:47:55,311 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:55,429 MuTect - [MUTECT] Processed 16000887 reads in 683 ms
[2015-09-30T22:47Z] INFO  23:47:55,472 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:55,503 MuTect - [MUTECT] Processed 27001426 reads in 640 ms
[2015-09-30T22:47Z] INFO  23:47:55,752 MuTect - [MUTECT] Processed 49003174 reads in 658 ms
[2015-09-30T22:47Z] INFO  23:47:55,881 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:56,115 MuTect - [MUTECT] Processed 17000986 reads in 687 ms
[2015-09-30T22:47Z] INFO  23:47:56,166 MuTect - [MUTECT] Processed 28001458 reads in 663 ms
[2015-09-30T22:47Z] INFO  23:47:56,421 MuTect - [MUTECT] Processed 50003315 reads in 669 ms
[2015-09-30T22:47Z] INFO  23:47:56,797 MuTect - [MUTECT] Processed 18001011 reads in 682 ms
[2015-09-30T22:47Z] INFO  23:47:56,801 MuTect - [MUTECT] Processed 29001552 reads in 634 ms
[2015-09-30T22:47Z] INFO  23:47:57,085 MuTect - [MUTECT] Processed 51003367 reads in 664 ms
[2015-09-30T22:47Z] INFO  23:47:57,426 MuTect - [MUTECT] Processed 30001604 reads in 625 ms
[2015-09-30T22:47Z] INFO  23:47:57,523 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:57,532 MuTect - [MUTECT] Processed 19001017 reads in 735 ms
[2015-09-30T22:47Z] INFO  23:47:57,539 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:57,729 MuTect - [MUTECT] Processed 52003461 reads in 643 ms
[2015-09-30T22:47Z] INFO  23:47:58,062 MuTect - [MUTECT] Processed 31001730 reads in 637 ms
[2015-09-30T22:47Z] INFO  23:47:58,120 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:58,169 MuTect - [MUTECT] Processed 20001058 reads in 637 ms
[2015-09-30T22:47Z] INFO  23:47:58,360 MuTect - [MUTECT] Processed 53003530 reads in 632 ms
[2015-09-30T22:47Z] INFO  23:47:58,728 MuTect - [MUTECT] Processed 32001827 reads in 666 ms
[2015-09-30T22:47Z] INFO  23:47:58,850 MuTect - [MUTECT] Processed 21001190 reads in 681 ms
[2015-09-30T22:47Z] INFO  23:47:59,025 MuTect - [MUTECT] Processed 54003536 reads in 665 ms
[2015-09-30T22:47Z] INFO  23:47:59,409 MuTect - [MUTECT] Processed 33001864 reads in 681 ms
[2015-09-30T22:47Z] INFO  23:47:59,513 MuTect - [MUTECT] Processed 22001340 reads in 663 ms
[2015-09-30T22:47Z] INFO  23:47:59,674 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:47Z] INFO  23:47:59,681 MuTect - [MUTECT] Processed 55003630 reads in 656 ms
[2015-09-30T22:47Z] INFO  23:47:59,717 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:00,092 MuTect - [MUTECT] Processed 34001962 reads in 683 ms
[2015-09-30T22:48Z] INFO  23:48:00,159 MuTect - [MUTECT] Processed 23001340 reads in 646 ms
[2015-09-30T22:48Z] INFO  23:48:00,177 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:00,365 MuTect - [MUTECT] Processed 56003745 reads in 684 ms
[2015-09-30T22:48Z] INFO  23:48:00,711 MuTect - [MUTECT] Processed 35001990 reads in 619 ms
[2015-09-30T22:48Z] INFO  23:48:00,838 MuTect - [MUTECT] Processed 24001368 reads in 679 ms
[2015-09-30T22:48Z] INFO  23:48:01,119 MuTect - [MUTECT] Processed 57003826 reads in 754 ms
[2015-09-30T22:48Z] INFO  23:48:01,338 MuTect - [MUTECT] Processed 36002064 reads in 627 ms
[2015-09-30T22:48Z] INFO  23:48:01,507 MuTect - [MUTECT] Processed 25001385 reads in 669 ms
[2015-09-30T22:48Z] INFO  23:48:01,645 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:01,838 MuTect - [MUTECT] Processed 58003843 reads in 719 ms
[2015-09-30T22:48Z] INFO  23:48:01,929 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:01,949 MuTect - [MUTECT] Processed 37002143 reads in 611 ms
[2015-09-30T22:48Z] INFO  23:48:02,177 MuTect - [MUTECT] Processed 26001480 reads in 669 ms
[2015-09-30T22:48Z] INFO  23:48:02,488 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:02,506 MuTect - [MUTECT] Processed 59003930 reads in 668 ms
[2015-09-30T22:48Z] INFO  23:48:02,554 MuTect - [MUTECT] Processed 38002156 reads in 605 ms
[2015-09-30T22:48Z] INFO  23:48:02,863 MuTect - [MUTECT] Processed 27001566 reads in 687 ms
[2015-09-30T22:48Z] INFO  23:48:03,146 MuTect - [MUTECT] Processed 39002170 reads in 592 ms
[2015-09-30T22:48Z] INFO  23:48:03,195 MuTect - [MUTECT] Processed 60004021 reads in 689 ms
[2015-09-30T22:48Z] INFO  23:48:03,527 MuTect - [MUTECT] Processed 28001610 reads in 664 ms
[2015-09-30T22:48Z] INFO  23:48:03,758 MuTect - [MUTECT] Processed 40002190 reads in 612 ms
[2015-09-30T22:48Z] INFO  23:48:03,762 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:03,847 MuTect - [MUTECT] Processed 61004088 reads in 652 ms
[2015-09-30T22:48Z] INFO  23:48:04,072 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:04,210 MuTect - [MUTECT] Processed 29001688 reads in 683 ms
[2015-09-30T22:48Z] INFO  23:48:04,362 MuTect - [MUTECT] Processed 41002224 reads in 604 ms
[2015-09-30T22:48Z] INFO  23:48:04,538 MuTect - [MUTECT] Processed 62004111 reads in 691 ms
[2015-09-30T22:48Z] INFO  23:48:04,711 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:04,860 MuTect - [MUTECT] Processed 30001726 reads in 650 ms
[2015-09-30T22:48Z] INFO  23:48:04,976 MuTect - [MUTECT] Processed 42002259 reads in 614 ms
[2015-09-30T22:48Z] INFO  23:48:05,235 MuTect - [MUTECT] Processed 63004179 reads in 697 ms
[2015-09-30T22:48Z] INFO  23:48:05,440 ProgressMeter -     19:36269919        1.16e+06   30.0 s       25.0 s     10.2%         4.9 m     4.4 m
[2015-09-30T22:48Z] INFO  23:48:05,564 MuTect - [MUTECT] Processed 43002277 reads in 588 ms
[2015-09-30T22:48Z] INFO  23:48:05,569 MuTect - [MUTECT] Processed 31001741 reads in 709 ms
[2015-09-30T22:48Z] INFO  23:48:05,653 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:06,010 MuTect - [MUTECT] Processed 64004254 reads in 775 ms
[2015-09-30T22:48Z] INFO  23:48:06,162 MuTect - [MUTECT] Processed 44002319 reads in 598 ms
[2015-09-30T22:48Z] INFO  23:48:06,288 MuTect - [MUTECT] Processed 32001748 reads in 719 ms
[2015-09-30T22:48Z] INFO  23:48:06,445 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:06,744 MuTect - [MUTECT] Processed 45002408 reads in 582 ms
[2015-09-30T22:48Z] INFO  23:48:06,804 MuTect - [MUTECT] Processed 65004333 reads in 794 ms
[2015-09-30T22:48Z] INFO  23:48:06,959 MuTect - [MUTECT] Processed 33001810 reads in 671 ms
[2015-09-30T22:48Z] INFO  23:48:07,325 MuTect - [MUTECT] Processed 46002458 reads in 581 ms
[2015-09-30T22:48Z] INFO  23:48:07,383 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:07,539 MuTect - [MUTECT] Processed 66004402 reads in 735 ms
[2015-09-30T22:48Z] INFO  23:48:07,619 MuTect - [MUTECT] Processed 34001826 reads in 660 ms
[2015-09-30T22:48Z] INFO  23:48:07,654 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:07,909 MuTect - [MUTECT] Processed 47002563 reads in 584 ms
[2015-09-30T22:48Z] INFO  23:48:08,252 MuTect - [MUTECT] Processed 67004462 reads in 713 ms
[2015-09-30T22:48Z] INFO  23:48:08,268 MuTect - [MUTECT] Processed 35001929 reads in 649 ms
[2015-09-30T22:48Z] INFO  23:48:08,486 MuTect - [MUTECT] Processed 48002665 reads in 577 ms
[2015-09-30T22:48Z] INFO  23:48:08,690 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:08,964 MuTect - [MUTECT] Processed 36001948 reads in 696 ms
[2015-09-30T22:48Z] INFO  23:48:08,969 MuTect - [MUTECT] Processed 68004536 reads in 717 ms
[2015-09-30T22:48Z] INFO  23:48:09,070 MuTect - [MUTECT] Processed 49002669 reads in 584 ms
[2015-09-30T22:48Z] INFO  23:48:09,519 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:09,624 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:09,634 MuTect - [MUTECT] Processed 37002054 reads in 670 ms
[2015-09-30T22:48Z] INFO  23:48:09,667 MuTect - [MUTECT] Processed 50002750 reads in 597 ms
[2015-09-30T22:48Z] INFO  23:48:09,681 MuTect - [MUTECT] Processed 69004633 reads in 712 ms
[2015-09-30T22:48Z] INFO  23:48:10,287 MuTect - [MUTECT] Processed 51002782 reads in 620 ms
[2015-09-30T22:48Z] INFO  23:48:10,323 MuTect - [MUTECT] Processed 38002128 reads in 688 ms
[2015-09-30T22:48Z] INFO  23:48:10,346 MuTect - [MUTECT] Processed 70004691 reads in 665 ms
[2015-09-30T22:48Z] INFO  23:48:10,796 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:10,907 MuTect - [MUTECT] Processed 52002839 reads in 620 ms
[2015-09-30T22:48Z] INFO  23:48:10,956 MuTect - [MUTECT] Processed 39002217 reads in 634 ms
[2015-09-30T22:48Z] INFO  23:48:10,985 MuTect - [MUTECT] Processed 71004757 reads in 639 ms
[2015-09-30T22:48Z] INFO  23:48:11,528 MuTect - [MUTECT] Processed 53002902 reads in 621 ms
[2015-09-30T22:48Z] INFO  23:48:11,605 MuTect - [MUTECT] Processed 40002286 reads in 649 ms
[2015-09-30T22:48Z] INFO  23:48:11,634 MuTect - [MUTECT] Processed 72004872 reads in 649 ms
[2015-09-30T22:48Z] INFO  23:48:11,639 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:11,734 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:12,084 ProgressMeter -      20:3899253        1.03e+06   30.0 s       29.0 s     30.5%        98.0 s    68.0 s
[2015-09-30T22:48Z] INFO  23:48:12,120 MuTect - [MUTECT] Processed 54002929 reads in 592 ms
[2015-09-30T22:48Z] INFO  23:48:12,259 MuTect - [MUTECT] Processed 73004988 reads in 625 ms
[2015-09-30T22:48Z] INFO  23:48:12,266 MuTect - [MUTECT] Processed 41002311 reads in 661 ms
[2015-09-30T22:48Z] INFO  23:48:12,718 MuTect - [MUTECT] Processed 55002971 reads in 598 ms
[2015-09-30T22:48Z] INFO  23:48:12,884 MuTect - [MUTECT] Processed 74005090 reads in 625 ms
[2015-09-30T22:48Z] INFO  23:48:12,886 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:12,942 MuTect - [MUTECT] Processed 42002373 reads in 676 ms
[2015-09-30T22:48Z] INFO  23:48:13,350 MuTect - [MUTECT] Processed 56003028 reads in 632 ms
[2015-09-30T22:48Z] INFO  23:48:13,575 MuTect - [MUTECT] Processed 75005112 reads in 691 ms
[2015-09-30T22:48Z] INFO  23:48:13,607 MuTect - [MUTECT] Processed 43002380 reads in 665 ms
[2015-09-30T22:48Z] INFO  23:48:13,750 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:13,979 MuTect - [MUTECT] Processed 57003046 reads in 629 ms
[2015-09-30T22:48Z] INFO  23:48:14,204 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:14,222 MuTect - [MUTECT] Processed 76005198 reads in 647 ms
[2015-09-30T22:48Z] INFO  23:48:14,320 MuTect - [MUTECT] Processed 44002436 reads in 713 ms
[2015-09-30T22:48Z] INFO  23:48:14,627 MuTect - [MUTECT] Processed 58003058 reads in 648 ms
[2015-09-30T22:48Z] INFO  23:48:14,910 MuTect - [MUTECT] Processed 77005209 reads in 688 ms
[2015-09-30T22:48Z] INFO  23:48:14,941 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:14,986 MuTect - [MUTECT] Processed 45002497 reads in 666 ms
[2015-09-30T22:48Z] INFO  23:48:15,257 MuTect - [MUTECT] Processed 59003102 reads in 630 ms
[2015-09-30T22:48Z] INFO  23:48:15,589 MuTect - [MUTECT] Processed 78005264 reads in 679 ms
[2015-09-30T22:48Z] INFO  23:48:15,635 MuTect - [MUTECT] Processed 46002511 reads in 649 ms
[2015-09-30T22:48Z] INFO  23:48:15,875 MuTect - [MUTECT] Processed 60003104 reads in 618 ms
[2015-09-30T22:48Z] INFO  23:48:16,076 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:16,247 MuTect - [MUTECT] Processed 79005360 reads in 658 ms
[2015-09-30T22:48Z] INFO  23:48:16,309 MuTect - [MUTECT] Processed 47002627 reads in 674 ms
[2015-09-30T22:48Z] INFO  23:48:16,429 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:16,569 MuTect - [MUTECT] Processed 61003122 reads in 694 ms
[2015-09-30T22:48Z] INFO  23:48:16,902 MuTect - [MUTECT] Processed 80005372 reads in 655 ms
[2015-09-30T22:48Z] INFO  23:48:17,000 MuTect - [MUTECT] Processed 48002668 reads in 691 ms
[2015-09-30T22:48Z] INFO  23:48:17,197 MuTect - [MUTECT] Processed 62003131 reads in 628 ms
[2015-09-30T22:48Z] INFO  23:48:17,240 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:17,720 MuTect - [MUTECT] Processed 49002741 reads in 720 ms
[2015-09-30T22:48Z] INFO  23:48:17,783 MuTect - [MUTECT] Processed 81005437 reads in 880 ms
[2015-09-30T22:48Z] INFO  23:48:17,826 MuTect - [MUTECT] Processed 63003168 reads in 629 ms
[2015-09-30T22:48Z] INFO  23:48:17,889 ProgressMeter -      19:3834827        2.24e+06   60.0 s       26.0 s     19.3%         5.2 m     4.2 m
[2015-09-30T22:48Z] INFO  23:48:18,426 MuTect - [MUTECT] Processed 50002752 reads in 706 ms
[2015-09-30T22:48Z] INFO  23:48:18,447 MuTect - [MUTECT] Processed 64003171 reads in 620 ms
[2015-09-30T22:48Z] INFO  23:48:18,474 MuTect - [MUTECT] Processed 82005498 reads in 692 ms
[2015-09-30T22:48Z] INFO  23:48:18,685 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:19,030 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:19,085 MuTect - [MUTECT] Processed 65003203 reads in 639 ms
[2015-09-30T22:48Z] INFO  23:48:19,145 MuTect - [MUTECT] Processed 51002852 reads in 719 ms
[2015-09-30T22:48Z] INFO  23:48:19,176 MuTect - [MUTECT] Processed 83005520 reads in 702 ms
[2015-09-30T22:48Z] INFO  23:48:19,392 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:19,722 MuTect - [MUTECT] Processed 66003203 reads in 637 ms
[2015-09-30T22:48Z] INFO  23:48:19,816 MuTect - [MUTECT] Processed 84005546 reads in 640 ms
[2015-09-30T22:48Z] INFO  23:48:19,853 MuTect - [MUTECT] Processed 52002913 reads in 708 ms
[2015-09-30T22:48Z] INFO  23:48:20,362 MuTect - [MUTECT] Processed 67003302 reads in 640 ms
[2015-09-30T22:48Z] INFO  23:48:20,698 MuTect - [MUTECT] Processed 85005599 reads in 882 ms
[2015-09-30T22:48Z] INFO  23:48:20,960 MuTect - [MUTECT] Processed 68003318 reads in 598 ms
[2015-09-30T22:48Z] INFO  23:48:20,961 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:21,199 MuTect - [MUTECT] Processed 53003033 reads in 1346 ms
[2015-09-30T22:48Z] INFO  23:48:21,392 MuTect - [MUTECT] Processed 86005706 reads in 694 ms
[2015-09-30T22:48Z] INFO  23:48:21,565 MuTect - [MUTECT] Processed 69003419 reads in 605 ms
[2015-09-30T22:48Z] INFO  23:48:21,714 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:22,052 MuTect - [MUTECT] Processed 54003033 reads in 853 ms
[2015-09-30T22:48Z] INFO  23:48:22,066 MuTect - [MUTECT] Processed 87005784 reads in 674 ms
[2015-09-30T22:48Z] INFO  23:48:22,188 MuTect - [MUTECT] Processed 70003537 reads in 623 ms
[2015-09-30T22:48Z] INFO  23:48:22,343 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:22,736 MuTect - [MUTECT] Processed 88005837 reads in 670 ms
[2015-09-30T22:48Z] INFO  23:48:22,830 MuTect - [MUTECT] Processed 55003062 reads in 778 ms
[2015-09-30T22:48Z] INFO  23:48:22,834 MuTect - [MUTECT] Processed 71003573 reads in 646 ms
[2015-09-30T22:48Z] INFO  23:48:23,012 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:23,413 MuTect - [MUTECT] Processed 89005900 reads in 677 ms
[2015-09-30T22:48Z] INFO  23:48:23,457 MuTect - [MUTECT] Processed 72003657 reads in 623 ms
[2015-09-30T22:48Z] INFO  23:48:23,490 MuTect - [MUTECT] Processed 56003100 reads in 660 ms
[2015-09-30T22:48Z] INFO  23:48:23,878 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:24,076 MuTect - [MUTECT] Processed 73003748 reads in 619 ms
[2015-09-30T22:48Z] INFO  23:48:24,108 MuTect - [MUTECT] Processed 90005948 reads in 695 ms
[2015-09-30T22:48Z] INFO  23:48:24,165 MuTect - [MUTECT] Processed 57003128 reads in 675 ms
[2015-09-30T22:48Z] INFO  23:48:24,709 MuTect - [MUTECT] Processed 74003842 reads in 633 ms
[2015-09-30T22:48Z] INFO  23:48:24,782 MuTect - [MUTECT] Processed 91005973 reads in 674 ms
[2015-09-30T22:48Z] INFO  23:48:24,856 MuTect - [MUTECT] Processed 58003131 reads in 691 ms
[2015-09-30T22:48Z] INFO  23:48:24,967 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:25,065 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:25,313 MuTect - [MUTECT] Processed 75003990 reads in 604 ms
[2015-09-30T22:48Z] INFO  23:48:25,508 MuTect - [MUTECT] Processed 92005995 reads in 726 ms
[2015-09-30T22:48Z] INFO  23:48:25,553 MuTect - [MUTECT] Processed 59003143 reads in 697 ms
[2015-09-30T22:48Z] INFO  23:48:25,899 MuTect - [MUTECT] Processed 76004018 reads in 586 ms
[2015-09-30T22:48Z] INFO  23:48:25,943 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:26,182 MuTect - [MUTECT] Processed 93006102 reads in 674 ms
[2015-09-30T22:48Z] INFO  23:48:26,224 MuTect - [MUTECT] Processed 60003226 reads in 671 ms
[2015-09-30T22:48Z] INFO  23:48:26,491 MuTect - [MUTECT] Processed 77004053 reads in 592 ms
[2015-09-30T22:48Z] INFO  23:48:26,863 MuTect - [MUTECT] Processed 94006212 reads in 681 ms
[2015-09-30T22:48Z] INFO  23:48:26,885 MuTect - [MUTECT] Processed 61003269 reads in 661 ms
[2015-09-30T22:48Z] INFO  23:48:26,972 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:27,125 MuTect - [MUTECT] Processed 78004103 reads in 634 ms
[2015-09-30T22:48Z] INFO  23:48:27,390 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:27,557 MuTect - [MUTECT] Processed 95006235 reads in 694 ms
[2015-09-30T22:48Z] INFO  23:48:27,568 MuTect - [MUTECT] Processed 62003327 reads in 683 ms
[2015-09-30T22:48Z] INFO  23:48:27,750 MuTect - [MUTECT] Processed 79004123 reads in 625 ms
[2015-09-30T22:48Z] INFO  23:48:28,142 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:28,216 MuTect - [MUTECT] Processed 96006303 reads in 659 ms
[2015-09-30T22:48Z] INFO  23:48:28,233 MuTect - [MUTECT] Processed 63003355 reads in 665 ms
[2015-09-30T22:48Z] INFO  23:48:28,388 MuTect - [MUTECT] Processed 80004156 reads in 638 ms
[2015-09-30T22:48Z] INFO  23:48:28,955 MuTect - [MUTECT] Processed 64003374 reads in 722 ms
[2015-09-30T22:48Z] INFO  23:48:28,966 MuTect - [MUTECT] Processed 97006340 reads in 749 ms
[2015-09-30T22:48Z] INFO  23:48:29,033 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:29,041 MuTect - [MUTECT] Processed 81004170 reads in 653 ms
[2015-09-30T22:48Z] INFO  23:48:29,635 MuTect - [MUTECT] Processed 82004270 reads in 594 ms
[2015-09-30T22:48Z] INFO  23:48:29,647 MuTect - [MUTECT] Processed 98006431 reads in 682 ms
[2015-09-30T22:48Z] INFO  23:48:29,661 MuTect - [MUTECT] Processed 65003400 reads in 706 ms
[2015-09-30T22:48Z] INFO  23:48:29,939 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:30,229 MuTect - [MUTECT] Processed 83004312 reads in 594 ms
[2015-09-30T22:48Z] INFO  23:48:30,318 MuTect - [MUTECT] Processed 99006500 reads in 671 ms
[2015-09-30T22:48Z] INFO  23:48:30,359 MuTect - [MUTECT] Processed 66003400 reads in 698 ms
[2015-09-30T22:48Z] INFO  23:48:30,425 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:30,830 MuTect - [MUTECT] Processed 84004367 reads in 601 ms
[2015-09-30T22:48Z] INFO  23:48:30,972 MuTect - [MUTECT] Processed 100006512 reads in 654 ms
[2015-09-30T22:48Z] INFO  23:48:30,973 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:31,102 MuTect - [MUTECT] Processed 67003436 reads in 743 ms
[2015-09-30T22:48Z] INFO  23:48:31,470 MuTect - [MUTECT] Processed 85004474 reads in 640 ms
[2015-09-30T22:48Z] INFO  23:48:31,603 MuTect - [MUTECT] Processed 101006634 reads in 631 ms
[2015-09-30T22:48Z] INFO  23:48:31,751 MuTect - [MUTECT] Processed 68003477 reads in 649 ms
[2015-09-30T22:48Z] INFO  23:48:32,109 MuTect - [MUTECT] Processed 86004542 reads in 639 ms
[2015-09-30T22:48Z] INFO  23:48:32,237 MuTect - [MUTECT] Processed 102006671 reads in 634 ms
[2015-09-30T22:48Z] INFO  23:48:32,314 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:32,428 MuTect - [MUTECT] Processed 69003517 reads in 677 ms
[2015-09-30T22:48Z] INFO  23:48:32,541 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:32,733 MuTect - [MUTECT] Processed 87004643 reads in 624 ms
[2015-09-30T22:48Z] INFO  23:48:32,919 MuTect - [MUTECT] Processed 103006780 reads in 682 ms
[2015-09-30T22:48Z] INFO  23:48:33,046 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:33,119 MuTect - [MUTECT] Processed 70003555 reads in 691 ms
[2015-09-30T22:48Z] INFO  23:48:33,336 MuTect - [MUTECT] Processed 88004662 reads in 603 ms
[2015-09-30T22:48Z] INFO  23:48:33,615 MuTect - [MUTECT] Processed 104006877 reads in 696 ms
[2015-09-30T22:48Z] INFO  23:48:33,788 MuTect - [MUTECT] Processed 71003665 reads in 669 ms
[2015-09-30T22:48Z] INFO  23:48:33,962 MuTect - [MUTECT] Processed 89004673 reads in 626 ms
[2015-09-30T22:48Z] INFO  23:48:34,289 MuTect - [MUTECT] Processed 105006996 reads in 674 ms
[2015-09-30T22:48Z] INFO  23:48:34,456 MuTect - [MUTECT] Processed 72003775 reads in 668 ms
[2015-09-30T22:48Z] INFO  23:48:34,610 MuTect - [MUTECT] Processed 90004675 reads in 648 ms
[2015-09-30T22:48Z] INFO  23:48:34,635 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:34,812 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:34,929 MuTect - [MUTECT] Processed 106007026 reads in 640 ms
[2015-09-30T22:48Z] INFO  23:48:35,077 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:35,227 MuTect - [MUTECT] Processed 91004785 reads in 617 ms
[2015-09-30T22:48Z] INFO  23:48:35,285 MuTect - [MUTECT] Processed 73003813 reads in 829 ms
[2015-09-30T22:48Z] INFO  23:48:35,441 ProgressMeter -     19:39389913        2.56e+06   60.0 s       23.0 s     21.4%         4.7 m     3.7 m
[2015-09-30T22:48Z] INFO  23:48:35,596 MuTect - [MUTECT] Processed 107007046 reads in 666 ms
[2015-09-30T22:48Z] INFO  23:48:35,823 MuTect - [MUTECT] Processed 92004865 reads in 596 ms
[2015-09-30T22:48Z] INFO  23:48:35,969 MuTect - [MUTECT] Processed 74003904 reads in 684 ms
[2015-09-30T22:48Z] INFO  23:48:36,244 MuTect - [MUTECT] Processed 108007133 reads in 649 ms
[2015-09-30T22:48Z] INFO  23:48:36,427 MuTect - [MUTECT] Processed 93004923 reads in 604 ms
[2015-09-30T22:48Z] INFO  23:48:36,656 MuTect - [MUTECT] Processed 75003962 reads in 687 ms
[2015-09-30T22:48Z] INFO  23:48:36,836 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:36,924 MuTect - [MUTECT] Processed 109007187 reads in 680 ms
[2015-09-30T22:48Z] INFO  23:48:37,026 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:37,079 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:37,111 MuTect - [MUTECT] Processed 94005022 reads in 684 ms
[2015-09-30T22:48Z] INFO  23:48:37,319 MuTect - [MUTECT] Processed 76003988 reads in 663 ms
[2015-09-30T22:48Z] INFO  23:48:37,601 MuTect - [MUTECT] Processed 110007198 reads in 677 ms
[2015-09-30T22:48Z] INFO  23:48:37,748 MuTect - [MUTECT] Processed 95005058 reads in 637 ms
[2015-09-30T22:48Z] INFO  23:48:38,023 MuTect - [MUTECT] Processed 77004006 reads in 704 ms
[2015-09-30T22:48Z] INFO  23:48:38,307 MuTect - [MUTECT] Processed 111007252 reads in 706 ms
[2015-09-30T22:48Z] INFO  23:48:38,409 MuTect - [MUTECT] Processed 96005133 reads in 661 ms
[2015-09-30T22:48Z] INFO  23:48:38,747 MuTect - [MUTECT] Processed 78004067 reads in 724 ms
[2015-09-30T22:48Z] INFO  23:48:38,945 MuTect - [MUTECT] Processed 112007293 reads in 638 ms
[2015-09-30T22:48Z] INFO  23:48:39,006 MuTect - [MUTECT] Processed 97005136 reads in 597 ms
[2015-09-30T22:48Z] INFO  23:48:39,191 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:39,211 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:39,439 MuTect - [MUTECT] Processed 79004168 reads in 692 ms
[2015-09-30T22:48Z] INFO  23:48:39,443 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:39,578 MuTect - [MUTECT] Processed 113007344 reads in 633 ms
[2015-09-30T22:48Z] INFO  23:48:39,614 MuTect - [MUTECT] Processed 98005169 reads in 608 ms
[2015-09-30T22:48Z] INFO  23:48:40,119 MuTect - [MUTECT] Processed 80004226 reads in 680 ms
[2015-09-30T22:48Z] INFO  23:48:40,221 MuTect - [MUTECT] Processed 99005284 reads in 607 ms
[2015-09-30T22:48Z] INFO  23:48:40,237 MuTect - [MUTECT] Processed 114007371 reads in 659 ms
[2015-09-30T22:48Z] INFO  23:48:40,781 MuTect - [MUTECT] Processed 81004272 reads in 662 ms
[2015-09-30T22:48Z] INFO  23:48:40,827 MuTect - [MUTECT] Processed 100005336 reads in 606 ms
[2015-09-30T22:48Z] INFO  23:48:40,933 MuTect - [MUTECT] Processed 115007415 reads in 696 ms
[2015-09-30T22:48Z] INFO  23:48:41,365 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:41,429 MuTect - [MUTECT] Processed 82004291 reads in 648 ms
[2015-09-30T22:48Z] INFO  23:48:41,443 MuTect - [MUTECT] Processed 101005462 reads in 616 ms
[2015-09-30T22:48Z] INFO  23:48:41,547 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:41,683 MuTect - [MUTECT] Processed 116007419 reads in 750 ms
[2015-09-30T22:48Z] INFO  23:48:41,683 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:42,053 MuTect - [MUTECT] Processed 102005524 reads in 610 ms
[2015-09-30T22:48Z] INFO  23:48:42,085 ProgressMeter -     20:20123635        2.33e+06   60.0 s       25.0 s     70.5%        85.0 s    25.0 s
[2015-09-30T22:48Z] INFO  23:48:42,114 MuTect - [MUTECT] Processed 83004364 reads in 685 ms
[2015-09-30T22:48Z] INFO  23:48:42,341 MuTect - [MUTECT] Processed 117007468 reads in 658 ms
[2015-09-30T22:48Z] INFO  23:48:42,721 MuTect - [MUTECT] Processed 103005643 reads in 668 ms
[2015-09-30T22:48Z] INFO  23:48:42,837 MuTect - [MUTECT] Processed 84004392 reads in 723 ms
[2015-09-30T22:48Z] INFO  23:48:42,991 MuTect - [MUTECT] Processed 118007551 reads in 650 ms
[2015-09-30T22:48Z] INFO  23:48:43,343 MuTect - [MUTECT] Processed 104005646 reads in 622 ms
[2015-09-30T22:48Z] INFO  23:48:43,501 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:43,504 MuTect - [MUTECT] Processed 85004461 reads in 667 ms
[2015-09-30T22:48Z] INFO  23:48:43,608 MuTect - [MUTECT] Processed 119007624 reads in 617 ms
[2015-09-30T22:48Z] INFO  23:48:43,770 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:44,007 MuTect - [MUTECT] Processed 105005725 reads in 664 ms
[2015-09-30T22:48Z] INFO  23:48:44,041 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:44,183 MuTect - [MUTECT] Processed 86004477 reads in 679 ms
[2015-09-30T22:48Z] INFO  23:48:44,254 MuTect - [MUTECT] Processed 120007706 reads in 646 ms
[2015-09-30T22:48Z] INFO  23:48:44,675 MuTect - [MUTECT] Processed 106005749 reads in 668 ms
[2015-09-30T22:48Z] INFO  23:48:44,860 MuTect - [MUTECT] Processed 87004506 reads in 677 ms
[2015-09-30T22:48Z] INFO  23:48:44,916 MuTect - [MUTECT] Processed 121007746 reads in 662 ms
[2015-09-30T22:48Z] INFO  23:48:45,292 MuTect - [MUTECT] Processed 107005869 reads in 617 ms
[2015-09-30T22:48Z] INFO  23:48:45,526 MuTect - [MUTECT] Processed 88004538 reads in 666 ms
[2015-09-30T22:48Z] INFO  23:48:45,551 MuTect - [MUTECT] Processed 122007775 reads in 635 ms
[2015-09-30T22:48Z] INFO  23:48:45,589 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:45,858 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:46,017 MuTect - [MUTECT] Processed 108005937 reads in 725 ms
[2015-09-30T22:48Z] INFO  23:48:46,166 MuTect - [MUTECT] Processed 123007864 reads in 615 ms
[2015-09-30T22:48Z] INFO  23:48:46,198 MuTect - [MUTECT] Processed 89004638 reads in 672 ms
[2015-09-30T22:48Z] INFO  23:48:46,530 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:46,703 MuTect - [MUTECT] Processed 109006009 reads in 686 ms
[2015-09-30T22:48Z] INFO  23:48:46,768 MuTect - [MUTECT] Processed 124007882 reads in 602 ms
[2015-09-30T22:48Z] INFO  23:48:46,854 MuTect - [MUTECT] Processed 90004677 reads in 655 ms
[2015-09-30T22:48Z] INFO  23:48:47,412 MuTect - [MUTECT] Processed 110006009 reads in 709 ms
[2015-09-30T22:48Z] INFO  23:48:47,426 MuTect - [MUTECT] Processed 125007953 reads in 658 ms
[2015-09-30T22:48Z] INFO  23:48:47,533 MuTect - [MUTECT] Processed 91004753 reads in 680 ms
[2015-09-30T22:48Z] INFO  23:48:47,890 ProgressMeter -      19:6427259        3.48e+06   90.0 s       25.0 s     30.4%         4.9 m     3.4 m
[2015-09-30T22:48Z] INFO  23:48:47,917 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:48,046 MuTect - [MUTECT] Processed 111006071 reads in 634 ms
[2015-09-30T22:48Z] INFO  23:48:48,088 MuTect - [MUTECT] Processed 126008014 reads in 662 ms
[2015-09-30T22:48Z] INFO  23:48:48,234 MuTect - [MUTECT] Processed 92004844 reads in 701 ms
[2015-09-30T22:48Z] INFO  23:48:48,446 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:48,671 MuTect - [MUTECT] Processed 112006115 reads in 625 ms
[2015-09-30T22:48Z] INFO  23:48:48,781 MuTect - [MUTECT] Processed 127008077 reads in 693 ms
[2015-09-30T22:48Z] INFO  23:48:48,965 MuTect - [MUTECT] Processed 93004906 reads in 731 ms
[2015-09-30T22:48Z] INFO  23:48:49,035 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:49,308 MuTect - [MUTECT] Processed 113006220 reads in 637 ms
[2015-09-30T22:48Z] INFO  23:48:49,429 MuTect - [MUTECT] Processed 128008166 reads in 648 ms
[2015-09-30T22:48Z] INFO  23:48:49,749 MuTect - [MUTECT] Processed 94004927 reads in 784 ms
[2015-09-30T22:48Z] INFO  23:48:49,941 MuTect - [MUTECT] Processed 114006283 reads in 633 ms
[2015-09-30T22:48Z] INFO  23:48:50,044 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:50,056 MuTect - [MUTECT] Processed 129008244 reads in 627 ms
[2015-09-30T22:48Z] INFO  23:48:50,460 MuTect - [MUTECT] Processed 95005029 reads in 711 ms
[2015-09-30T22:48Z] INFO  23:48:50,590 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:50,592 MuTect - [MUTECT] Processed 115006414 reads in 651 ms
[2015-09-30T22:48Z] INFO  23:48:50,696 MuTect - [MUTECT] Processed 130008345 reads in 640 ms
[2015-09-30T22:48Z] INFO  23:48:51,151 MuTect - [MUTECT] Processed 96005120 reads in 691 ms
[2015-09-30T22:48Z] INFO  23:48:51,245 MuTect - [MUTECT] Processed 116006479 reads in 653 ms
[2015-09-30T22:48Z] INFO  23:48:51,350 MuTect - [MUTECT] Processed 131008439 reads in 654 ms
[2015-09-30T22:48Z] INFO  23:48:51,383 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:51,857 MuTect - [MUTECT] Processed 97005224 reads in 706 ms
[2015-09-30T22:48Z] INFO  23:48:51,934 MuTect - [MUTECT] Processed 117006514 reads in 689 ms
[2015-09-30T22:48Z] INFO  23:48:51,961 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:51,980 MuTect - [MUTECT] Processed 132008581 reads in 630 ms
[2015-09-30T22:48Z] INFO  23:48:52,572 MuTect - [MUTECT] Processed 98005310 reads in 715 ms
[2015-09-30T22:48Z] INFO  23:48:52,586 MuTect - [MUTECT] Processed 118006575 reads in 652 ms
[2015-09-30T22:48Z] INFO  23:48:52,603 MuTect - [MUTECT] Processed 133008616 reads in 623 ms
[2015-09-30T22:48Z] INFO  23:48:52,742 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:53,224 MuTect - [MUTECT] Processed 119006633 reads in 638 ms
[2015-09-30T22:48Z] INFO  23:48:53,254 MuTect - [MUTECT] Processed 99005361 reads in 682 ms
[2015-09-30T22:48Z] INFO  23:48:53,279 MuTect - [MUTECT] Processed 134008648 reads in 676 ms
[2015-09-30T22:48Z] INFO  23:48:53,707 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:53,847 MuTect - [MUTECT] Processed 120006756 reads in 623 ms
[2015-09-30T22:48Z] INFO  23:48:53,950 MuTect - [MUTECT] Processed 100005391 reads in 696 ms
[2015-09-30T22:48Z] INFO  23:48:53,973 MuTect - [MUTECT] Processed 135008673 reads in 694 ms
[2015-09-30T22:48Z] INFO  23:48:54,069 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:54,457 MuTect - [MUTECT] Processed 121006851 reads in 610 ms
[2015-09-30T22:48Z] INFO  23:48:54,654 MuTect - [MUTECT] Processed 101005394 reads in 704 ms
[2015-09-30T22:48Z] INFO  23:48:54,675 MuTect - [MUTECT] Processed 136008676 reads in 702 ms
[2015-09-30T22:48Z] INFO  23:48:54,792 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:55,068 MuTect - [MUTECT] Processed 122006913 reads in 611 ms
[2015-09-30T22:48Z] INFO  23:48:55,346 MuTect - [MUTECT] Processed 102005453 reads in 692 ms
[2015-09-30T22:48Z] INFO  23:48:55,378 MuTect - [MUTECT] Processed 137008751 reads in 703 ms
[2015-09-30T22:48Z] INFO  23:48:55,656 MuTect - [MUTECT] Processed 123007038 reads in 588 ms
[2015-09-30T22:48Z] INFO  23:48:56,009 MuTect - [MUTECT] Processed 103005485 reads in 662 ms
[2015-09-30T22:48Z] INFO  23:48:56,057 MuTect - [MUTECT] Processed 138008810 reads in 679 ms
[2015-09-30T22:48Z] INFO  23:48:56,132 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:56,260 MuTect - [MUTECT] Processed 124007119 reads in 604 ms
[2015-09-30T22:48Z] INFO  23:48:56,674 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:56,731 MuTect - [MUTECT] Processed 104005645 reads in 723 ms
[2015-09-30T22:48Z] INFO  23:48:56,808 MuTect - [MUTECT] Processed 139008886 reads in 751 ms
[2015-09-30T22:48Z] INFO  23:48:56,812 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:56,877 MuTect - [MUTECT] Processed 125007167 reads in 617 ms
[2015-09-30T22:48Z] INFO  23:48:57,466 MuTect - [MUTECT] Processed 126007185 reads in 589 ms
[2015-09-30T22:48Z] INFO  23:48:57,487 MuTect - [MUTECT] Processed 140008998 reads in 679 ms
[2015-09-30T22:48Z] INFO  23:48:58,060 MuTect - [MUTECT] Processed 127007188 reads in 594 ms
[2015-09-30T22:48Z] INFO  23:48:58,372 MuTect - [MUTECT] Processed 105005770 reads in 1641 ms
[2015-09-30T22:48Z] INFO  23:48:58,603 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:58,642 MuTect - [MUTECT] Processed 128007298 reads in 582 ms
[2015-09-30T22:48Z] INFO  23:48:59,246 MuTect - [MUTECT] Processed 129007313 reads in 604 ms
[2015-09-30T22:48Z] INFO  23:48:59,253 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:48Z] INFO  23:48:59,855 MuTect - [MUTECT] Processed 130007364 reads in 608 ms
[2015-09-30T22:48Z] INFO  23:48:59,967 MuTect - [MUTECT] Processed 106005866 reads in 1595 ms
[2015-09-30T22:49Z] INFO  23:49:00,533 MuTect - [MUTECT] Processed 131007396 reads in 679 ms
[2015-09-30T22:49Z] INFO  23:49:00,553 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:01,254 MuTect - [MUTECT] Processed 132007438 reads in 721 ms
[2015-09-30T22:49Z] INFO  23:49:01,877 MuTect - [MUTECT] Processed 133007512 reads in 623 ms
[2015-09-30T22:49Z] INFO  23:49:02,488 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:02,490 MuTect - [MUTECT] Processed 107005887 reads in 2523 ms
[2015-09-30T22:49Z] INFO  23:49:02,594 MuTect - [MUTECT] Processed 134007514 reads in 717 ms
[2015-09-30T22:49Z] INFO  23:49:03,247 MuTect - [MUTECT] Processed 135007526 reads in 653 ms
[2015-09-30T22:49Z] INFO  23:49:03,346 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:03,920 MuTect - [MUTECT] Processed 136007558 reads in 673 ms
[2015-09-30T22:49Z] INFO  23:49:04,467 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:04,527 MuTect - [MUTECT] Processed 137007630 reads in 607 ms
[2015-09-30T22:49Z] INFO  23:49:05,080 MuTect - [MUTECT] Processed 108005973 reads in 2590 ms
[2015-09-30T22:49Z] INFO  23:49:05,114 MuTect - [MUTECT] Processed 138007638 reads in 587 ms
[2015-09-30T22:49Z] INFO  23:49:05,442 ProgressMeter -     19:41825409        3.87e+06   90.0 s       23.0 s     31.6%         4.7 m     3.2 m
[2015-09-30T22:49Z] INFO  23:49:05,709 MuTect - [MUTECT] Processed 139007723 reads in 595 ms
[2015-09-30T22:49Z] INFO  23:49:06,284 MuTect - [MUTECT] Processed 141011017 reads in 8797 ms
[2015-09-30T22:49Z] INFO  23:49:06,338 MuTect - [MUTECT] Processed 140007748 reads in 629 ms
[2015-09-30T22:49Z] INFO  23:49:06,505 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:06,962 MuTect - [MUTECT] Processed 141007818 reads in 624 ms
[2015-09-30T22:49Z] INFO  23:49:07,606 MuTect - [MUTECT] Processed 142007921 reads in 644 ms
[2015-09-30T22:49Z] INFO  23:49:07,879 MuTect - [MUTECT] Processed 109006022 reads in 2799 ms
[2015-09-30T22:49Z] INFO  23:49:08,265 MuTect - [MUTECT] Processed 143007947 reads in 658 ms
[2015-09-30T22:49Z] INFO  23:49:08,423 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:08,448 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:08,539 MuTect - [MUTECT] Processed 110006158 reads in 660 ms
[2015-09-30T22:49Z] INFO  23:49:08,867 MuTect - [MUTECT] Processed 144008000 reads in 603 ms
[2015-09-30T22:49Z] INFO  23:49:09,006 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:09,155 MuTect - [MUTECT] Processed 111006256 reads in 616 ms
[2015-09-30T22:49Z] INFO  23:49:09,189 MuTect - [MUTECT] Processed 142011077 reads in 2905 ms
[2015-09-30T22:49Z] INFO  23:49:09,489 MuTect - [MUTECT] Processed 145008079 reads in 622 ms
[2015-09-30T22:49Z] INFO  23:49:09,764 MuTect - [MUTECT] Processed 112006266 reads in 609 ms
[2015-09-30T22:49Z] INFO  23:49:09,863 MuTect - [MUTECT] Processed 143011122 reads in 674 ms
[2015-09-30T22:49Z] INFO  23:49:10,131 MuTect - [MUTECT] Processed 146008177 reads in 642 ms
[2015-09-30T22:49Z] INFO  23:49:10,436 MuTect - [MUTECT] Processed 113006304 reads in 672 ms
[2015-09-30T22:49Z] INFO  23:49:10,475 MuTect - [MUTECT] Processed 144011252 reads in 612 ms
[2015-09-30T22:49Z] INFO  23:49:10,494 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:10,577 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:10,785 MuTect - [MUTECT] Processed 147008223 reads in 654 ms
[2015-09-30T22:49Z] INFO  23:49:11,080 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:11,081 MuTect - [MUTECT] Processed 114006355 reads in 644 ms
[2015-09-30T22:49Z] INFO  23:49:11,096 MuTect - [MUTECT] Processed 145011273 reads in 621 ms
[2015-09-30T22:49Z] INFO  23:49:11,396 MuTect - [MUTECT] Processed 148008263 reads in 611 ms
[2015-09-30T22:49Z] INFO  23:49:11,743 MuTect - [MUTECT] Processed 115006372 reads in 663 ms
[2015-09-30T22:49Z] INFO  23:49:11,748 MuTect - [MUTECT] Processed 146011294 reads in 652 ms
[2015-09-30T22:49Z] INFO  23:49:12,030 MuTect - [MUTECT] Processed 149008343 reads in 634 ms
[2015-09-30T22:49Z] INFO  23:49:12,086 ProgressMeter -     20:30486424        3.12e+06   90.0 s       28.0 s     94.4%        95.0 s     5.0 s
[2015-09-30T22:49Z] INFO  23:49:12,339 MuTect - [MUTECT] Processed 147011403 reads in 591 ms
[2015-09-30T22:49Z] INFO  23:49:12,416 MuTect - [MUTECT] Processed 116006416 reads in 673 ms
[2015-09-30T22:49Z] INFO  23:49:12,473 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:12,648 MuTect - [MUTECT] Processed 150008376 reads in 618 ms
[2015-09-30T22:49Z] INFO  23:49:12,945 MuTect - [MUTECT] Processed 148011410 reads in 606 ms
[2015-09-30T22:49Z] INFO  23:49:13,050 MuTect - [MUTECT] Processed 117006594 reads in 634 ms
[2015-09-30T22:49Z] INFO  23:49:13,057 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:13,249 MuTect - [MUTECT] Processed 151008458 reads in 601 ms
[2015-09-30T22:49Z] INFO  23:49:13,294 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:13,600 MuTect - [MUTECT] Processed 149011428 reads in 654 ms
[2015-09-30T22:49Z] INFO  23:49:13,666 MuTect - [MUTECT] Processed 118006598 reads in 616 ms
[2015-09-30T22:49Z] INFO  23:49:13,833 MuTect - [MUTECT] Processed 152008470 reads in 584 ms
[2015-09-30T22:49Z] INFO  23:49:14,237 MuTect - [MUTECT] Processed 150011528 reads in 638 ms
[2015-09-30T22:49Z] INFO  23:49:14,326 MuTect - [MUTECT] Processed 119006617 reads in 660 ms
[2015-09-30T22:49Z] INFO  23:49:14,401 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:14,449 MuTect - [MUTECT] Processed 153008518 reads in 616 ms
[2015-09-30T22:49Z] INFO  23:49:14,931 MuTect - [MUTECT] Processed 151011582 reads in 694 ms
[2015-09-30T22:49Z] INFO  23:49:15,005 MuTect - [MUTECT] Processed 120006704 reads in 679 ms
[2015-09-30T22:49Z] INFO  23:49:15,056 MuTect - [MUTECT] Processed 154008607 reads in 607 ms
[2015-09-30T22:49Z] INFO  23:49:15,229 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:15,592 MuTect - [MUTECT] Processed 152011683 reads in 661 ms
[2015-09-30T22:49Z] INFO  23:49:15,650 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:15,650 MuTect - [MUTECT] Processed 155008617 reads in 594 ms
[2015-09-30T22:49Z] INFO  23:49:15,694 MuTect - [MUTECT] Processed 121006723 reads in 689 ms
[2015-09-30T22:49Z] INFO  23:49:16,216 MuTect - [MUTECT] Processed 156008637 reads in 566 ms
[2015-09-30T22:49Z] INFO  23:49:16,260 MuTect - [MUTECT] Processed 153011718 reads in 668 ms
[2015-09-30T22:49Z] INFO  23:49:16,314 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:16,368 MuTect - [MUTECT] Processed 122006859 reads in 674 ms
[2015-09-30T22:49Z] INFO  23:49:16,794 MuTect - [MUTECT] Processed 157008666 reads in 578 ms
[2015-09-30T22:49Z] INFO  23:49:16,888 MuTect - [MUTECT] Processed 154011799 reads in 628 ms
[2015-09-30T22:49Z] INFO  23:49:17,011 MuTect - [MUTECT] Processed 123006965 reads in 643 ms
[2015-09-30T22:49Z] INFO  23:49:17,178 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:17,317 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:49Z] INFO  23:49:17,403 MuTect - [MUTECT] Processed 158008786 reads in 609 ms
[2015-09-30T22:49Z] INFO  23:49:17,498 MuTect - [MUTECT] Processed 155011800 reads in 610 ms
[2015-09-30T22:49Z] INFO  23:49:17,891 ProgressMeter -      19:7982158        4.38e+06  120.0 s       27.0 s     37.8%         5.3 m     3.3 m
[2015-09-30T22:49Z] INFO  23:49:17,900 ProgressMeter -            done        3.33e+06   95.0 s       28.0 s    100.0%        95.0 s     0.0 s
[2015-09-30T22:49Z] INFO  23:49:17,901 ProgressMeter - Total runtime 95.82 secs, 1.60 min, 0.03 hours
[2015-09-30T22:49Z] INFO  23:49:18,010 MicroScheduler - 96186 reads were filtered out during the traversal out of approximately 1482912 total reads (6.49%)
[2015-09-30T22:49Z] INFO  23:49:18,010 MicroScheduler -   -> 72114 reads (4.86% of total) failing DuplicateReadFilter
[2015-09-30T22:49Z] INFO  23:49:18,010 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:49Z] INFO  23:49:18,010 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:49Z] INFO  23:49:18,011 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:49Z] INFO  23:49:18,011 MicroScheduler -   -> 24072 reads (1.62% of total) failing UnmappedReadFilter
[2015-09-30T22:49Z] INFO  23:49:18,109 MuTect - [MUTECT] Processed 159008806 reads in 706 ms
[2015-09-30T22:49Z] INFO  23:49:18,129 MuTect - [MUTECT] Processed 156011873 reads in 631 ms
[2015-09-30T22:49Z] INFO  23:49:18,386 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:18,726 MuTect - [MUTECT] Processed 160008935 reads in 617 ms
[2015-09-30T22:49Z] INFO  23:49:18,754 MuTect - [MUTECT] Processed 157011886 reads in 625 ms
[2015-09-30T22:49Z] INFO  23:49:19,271 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:19,378 MuTect - [MUTECT] Processed 161008939 reads in 652 ms
[2015-09-30T22:49Z] INFO  23:49:19,429 MuTect - [MUTECT] Processed 158011899 reads in 675 ms
[2015-09-30T22:49Z] INFO  23:49:19,694 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:49Z] INFO  23:49:20,007 MuTect - [MUTECT] Processed 162008960 reads in 629 ms
[2015-09-30T22:49Z] INFO  23:49:20,080 MuTect - [MUTECT] Processed 159011927 reads in 651 ms
[2015-09-30T22:49Z] INFO  23:49:20,546 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:20,628 MuTect - [MUTECT] Processed 163008984 reads in 621 ms
[2015-09-30T22:49Z] INFO  23:49:20,758 MuTect - [MUTECT] Processed 160011929 reads in 678 ms
[2015-09-30T22:49Z] bgzip syn3-20_0_31018105-raw-mutect.vcf
[2015-09-30T22:49Z] INFO  23:49:21,248 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:21,294 MuTect - [MUTECT] Processed 164008984 reads in 666 ms
[2015-09-30T22:49Z] INFO  23:49:21,410 MuTect - [MUTECT] Processed 161011983 reads in 652 ms
[2015-09-30T22:49Z] tabix index syn3-20_0_31018105-raw-mutect.vcf.gz
[2015-09-30T22:49Z] INFO  23:49:22,020 MuTect - [MUTECT] Processed 165009040 reads in 726 ms
[2015-09-30T22:49Z] INFO  23:49:22,105 MuTect - [MUTECT] Processed 162011998 reads in 695 ms
[2015-09-30T22:49Z] INFO  23:49:22,730 MuTect - [MUTECT] Processed 166009043 reads in 710 ms
[2015-09-30T22:49Z] INFO  23:49:22,748 MuTect - [MUTECT] Processed 163012027 reads in 643 ms
[2015-09-30T22:49Z] INFO  23:49:22,786 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:23,322 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:23,357 MuTect - [MUTECT] Processed 164012131 reads in 609 ms
[2015-09-30T22:49Z] INFO  23:49:23,454 MuTect - [MUTECT] Processed 167009140 reads in 724 ms
[2015-09-30T22:49Z] MuTect: MuTect
[2015-09-30T22:49Z] INFO  23:49:24,020 MuTect - [MUTECT] Processed 165012142 reads in 663 ms
[2015-09-30T22:49Z] INFO  23:49:24,227 MuTect - [MUTECT] Processed 168009222 reads in 773 ms
[2015-09-30T22:49Z] INFO  23:49:24,685 MuTect - [MUTECT] Processed 166012249 reads in 665 ms
[2015-09-30T22:49Z] INFO  23:49:24,937 MuTect - [MUTECT] Processed 169009242 reads in 710 ms
[2015-09-30T22:49Z] INFO  23:49:25,015 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:25,319 MuTect - [MUTECT] Processed 167012378 reads in 634 ms
[2015-09-30T22:49Z] INFO  23:49:25,467 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:25,647 MuTect - [MUTECT] Processed 170009309 reads in 710 ms
[2015-09-30T22:49Z] INFO  23:49:25,991 MuTect - [MUTECT] Processed 168012416 reads in 672 ms
[2015-09-30T22:49Z] INFO  23:49:26,043 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/20/syn3-20_31018873_62038916-raw-mutect-regions.bed to be BED
[2015-09-30T22:49Z] INFO  23:49:26,097 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:49Z] INFO  23:49:26,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:49Z] INFO  23:49:26,098 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:49Z] INFO  23:49:26,098 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:49Z] INFO  23:49:26,102 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/20/syn3-20_31018873_62038916-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/20/tx/tmpo0utRM/syn3-20_31018873_62038916-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:49Z] INFO  23:49:26,102 HelpFormatter - Date/Time: 2015/09/30 23:49:26
[2015-09-30T22:49Z] INFO  23:49:26,102 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:49Z] INFO  23:49:26,102 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:49Z] INFO  23:49:26,129 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:49Z] INFO  23:49:26,134 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:49Z] INFO  23:49:26,181 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:49Z] INFO  23:49:26,229 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:49Z] INFO  23:49:26,237 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:49Z] INFO  23:49:26,260 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:49Z] INFO  23:49:26,270 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:49Z] INFO  23:49:26,300 MuTect - [MUTECT] Processed 171009380 reads in 653 ms
[2015-09-30T22:49Z] INFO  23:49:26,444 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:49Z] INFO  23:49:26,567 IntervalUtils - Processing 2222004 bp from intervals
[2015-09-30T22:49Z] INFO  23:49:26,572 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:49Z] INFO  23:49:26,572 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:49Z] INFO  23:49:26,644 MuTect - [MUTECT] Processed 169012441 reads in 653 ms
[2015-09-30T22:49Z] INFO  23:49:26,750 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:49Z] INFO  23:49:26,933 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:49Z] INFO  23:49:26,934 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:49Z] INFO  23:49:26,934 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:49Z] INFO  23:49:26,935 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:49Z] INFO  23:49:26,956 MuTect - [MUTECT] Processed 172009469 reads in 656 ms
[2015-09-30T22:49Z] INFO  23:49:27,248 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:27,321 MuTect - [MUTECT] Processed 170012454 reads in 677 ms
[2015-09-30T22:49Z] INFO  23:49:27,614 MuTect - [MUTECT] Processed 173009589 reads in 658 ms
[2015-09-30T22:49Z] INFO  23:49:27,636 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:28,004 MuTect - [MUTECT] Processed 171012537 reads in 683 ms
[2015-09-30T22:49Z] INFO  23:49:28,227 MuTect - [MUTECT] Processed 174009633 reads in 613 ms
[2015-09-30T22:49Z] INFO  23:49:28,846 MuTect - [MUTECT] Processed 175009685 reads in 619 ms
[2015-09-30T22:49Z] INFO  23:49:29,171 MuTect - [MUTECT] Processed 1000108 reads in 2189 ms
[2015-09-30T22:49Z] INFO  23:49:29,354 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:29,470 MuTect - [MUTECT] Processed 172012565 reads in 1466 ms
[2015-09-30T22:49Z] INFO  23:49:29,508 MuTect - [MUTECT] Processed 176009774 reads in 662 ms
[2015-09-30T22:49Z] INFO  23:49:29,912 MuTect - [MUTECT] Processed 2000200 reads in 741 ms
[2015-09-30T22:49Z] INFO  23:49:29,938 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:30,248 MuTect - [MUTECT] Processed 177009774 reads in 740 ms
[2015-09-30T22:49Z] INFO  23:49:30,608 MuTect - [MUTECT] Processed 3000268 reads in 697 ms
[2015-09-30T22:49Z] INFO  23:49:30,850 MuTect - [MUTECT] Processed 173012673 reads in 1380 ms
[2015-09-30T22:49Z] INFO  23:49:30,893 MuTect - [MUTECT] Processed 178009796 reads in 645 ms
[2015-09-30T22:49Z] INFO  23:49:30,949 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:31,325 MuTect - [MUTECT] Processed 4000318 reads in 717 ms
[2015-09-30T22:49Z] INFO  23:49:31,566 MuTect - [MUTECT] Processed 179009800 reads in 673 ms
[2015-09-30T22:49Z] INFO  23:49:31,596 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:31,836 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:31,914 MuTect - [MUTECT] Processed 174012739 reads in 1064 ms
[2015-09-30T22:49Z] INFO  23:49:32,007 MuTect - [MUTECT] Processed 5000325 reads in 682 ms
[2015-09-30T22:49Z] INFO  23:49:32,235 MuTect - [MUTECT] Processed 180009865 reads in 669 ms
[2015-09-30T22:49Z] INFO  23:49:32,648 MuTect - [MUTECT] Processed 175012826 reads in 734 ms
[2015-09-30T22:49Z] INFO  23:49:32,726 MuTect - [MUTECT] Processed 6000433 reads in 719 ms
[2015-09-30T22:49Z] INFO  23:49:32,871 MuTect - [MUTECT] Processed 181009912 reads in 636 ms
[2015-09-30T22:49Z] INFO  23:49:33,308 MuTect - [MUTECT] Processed 176012907 reads in 660 ms
[2015-09-30T22:49Z] INFO  23:49:33,418 MuTect - [MUTECT] Processed 7000499 reads in 692 ms
[2015-09-30T22:49Z] INFO  23:49:33,447 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:33,511 MuTect - [MUTECT] Processed 182009959 reads in 640 ms
[2015-09-30T22:49Z] INFO  23:49:33,816 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:33,858 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:33,933 MuTect - [MUTECT] Processed 177012982 reads in 625 ms
[2015-09-30T22:49Z] INFO  23:49:34,145 MuTect - [MUTECT] Processed 183010028 reads in 634 ms
[2015-09-30T22:49Z] INFO  23:49:34,149 MuTect - [MUTECT] Processed 8000620 reads in 731 ms
[2015-09-30T22:49Z] INFO  23:49:34,577 MuTect - [MUTECT] Processed 178013008 reads in 644 ms
[2015-09-30T22:49Z] INFO  23:49:34,837 MuTect - [MUTECT] Processed 9000712 reads in 688 ms
[2015-09-30T22:49Z] INFO  23:49:34,838 MuTect - [MUTECT] Processed 184010036 reads in 693 ms
[2015-09-30T22:49Z] INFO  23:49:35,250 MuTect - [MUTECT] Processed 179013023 reads in 673 ms
[2015-09-30T22:49Z] INFO  23:49:35,443 ProgressMeter -     19:44983895        5.02e+06  120.0 s       23.0 s     42.2%         4.7 m     2.7 m
[2015-09-30T22:49Z] INFO  23:49:35,464 MuTect - [MUTECT] Processed 185010048 reads in 626 ms
[2015-09-30T22:49Z] INFO  23:49:35,540 MuTect - [MUTECT] Processed 10000767 reads in 703 ms
[2015-09-30T22:49Z] INFO  23:49:35,743 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:35,895 MuTect - [MUTECT] Processed 180013104 reads in 645 ms
[2015-09-30T22:49Z] INFO  23:49:35,906 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:35,969 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:36,105 MuTect - [MUTECT] Processed 186010110 reads in 641 ms
[2015-09-30T22:49Z] INFO  23:49:36,213 MuTect - [MUTECT] Processed 11000876 reads in 673 ms
[2015-09-30T22:49Z] INFO  23:49:36,582 MuTect - [MUTECT] Processed 181013108 reads in 687 ms
[2015-09-30T22:49Z] INFO  23:49:36,754 MuTect - [MUTECT] Processed 187010152 reads in 649 ms
[2015-09-30T22:49Z] INFO  23:49:36,888 MuTect - [MUTECT] Processed 12000935 reads in 675 ms
[2015-09-30T22:49Z] INFO  23:49:37,222 MuTect - [MUTECT] Processed 182013183 reads in 640 ms
[2015-09-30T22:49Z] INFO  23:49:37,380 MuTect - [MUTECT] Processed 188010267 reads in 626 ms
[2015-09-30T22:49Z] INFO  23:49:37,601 MuTect - [MUTECT] Processed 13001044 reads in 713 ms
[2015-09-30T22:49Z] INFO  23:49:37,897 MuTect - [MUTECT] Processed 183013212 reads in 675 ms
[2015-09-30T22:49Z] INFO  23:49:37,934 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:37,977 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:37,998 MuTect - [MUTECT] Processed 189010286 reads in 618 ms
[2015-09-30T22:49Z] INFO  23:49:38,273 MuTect - [MUTECT] Processed 14001096 reads in 672 ms
[2015-09-30T22:49Z] INFO  23:49:38,283 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:38,538 MuTect - [MUTECT] Processed 184013272 reads in 641 ms
[2015-09-30T22:49Z] INFO  23:49:38,640 MuTect - [MUTECT] Processed 190010305 reads in 642 ms
[2015-09-30T22:49Z] INFO  23:49:38,957 MuTect - [MUTECT] Processed 15001167 reads in 684 ms
[2015-09-30T22:49Z] INFO  23:49:39,155 MuTect - [MUTECT] Processed 185013311 reads in 617 ms
[2015-09-30T22:49Z] INFO  23:49:39,299 MuTect - [MUTECT] Processed 191010382 reads in 659 ms
[2015-09-30T22:49Z] INFO  23:49:39,637 MuTect - [MUTECT] Processed 16001201 reads in 680 ms
[2015-09-30T22:49Z] INFO  23:49:39,810 MuTect - [MUTECT] Processed 186013322 reads in 655 ms
[2015-09-30T22:49Z] INFO  23:49:39,936 MuTect - [MUTECT] Processed 192010448 reads in 637 ms
[2015-09-30T22:49Z] INFO  23:49:40,036 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:40,135 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:40,297 MuTect - [MUTECT] Processed 17001209 reads in 660 ms
[2015-09-30T22:49Z] INFO  23:49:40,346 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:40,542 MuTect - [MUTECT] Processed 187013447 reads in 731 ms
[2015-09-30T22:49Z] INFO  23:49:40,552 MuTect - [MUTECT] Processed 193010520 reads in 616 ms
[2015-09-30T22:49Z] INFO  23:49:40,963 MuTect - [MUTECT] Processed 18001259 reads in 666 ms
[2015-09-30T22:49Z] INFO  23:49:41,163 MuTect - [MUTECT] Processed 194010583 reads in 611 ms
[2015-09-30T22:49Z] INFO  23:49:41,222 MuTect - [MUTECT] Processed 188013551 reads in 681 ms
[2015-09-30T22:49Z] INFO  23:49:41,611 MuTect - [MUTECT] Processed 19001306 reads in 648 ms
[2015-09-30T22:49Z] INFO  23:49:41,778 MuTect - [MUTECT] Processed 195010690 reads in 615 ms
[2015-09-30T22:49Z] INFO  23:49:41,876 MuTect - [MUTECT] Processed 189013666 reads in 654 ms
[2015-09-30T22:49Z] INFO  23:49:42,048 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:42,239 MuTect - [MUTECT] Processed 20001380 reads in 628 ms
[2015-09-30T22:49Z] INFO  23:49:42,277 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:42,320 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:42,364 MuTect - [MUTECT] Processed 196010788 reads in 586 ms
[2015-09-30T22:49Z] INFO  23:49:42,514 MuTect - [MUTECT] Processed 190013762 reads in 638 ms
[2015-09-30T22:49Z] INFO  23:49:42,868 MuTect - [MUTECT] Processed 21001471 reads in 629 ms
[2015-09-30T22:49Z] INFO  23:49:43,002 MuTect - [MUTECT] Processed 197010875 reads in 638 ms
[2015-09-30T22:49Z] INFO  23:49:43,211 MuTect - [MUTECT] Processed 191013804 reads in 697 ms
[2015-09-30T22:49Z] INFO  23:49:43,506 MuTect - [MUTECT] Processed 22001511 reads in 638 ms
[2015-09-30T22:49Z] INFO  23:49:43,598 MuTect - [MUTECT] Processed 198010900 reads in 596 ms
[2015-09-30T22:49Z] INFO  23:49:43,846 MuTect - [MUTECT] Processed 192013905 reads in 635 ms
[2015-09-30T22:49Z] INFO  23:49:44,061 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:44,166 MuTect - [MUTECT] Processed 23001594 reads in 660 ms
[2015-09-30T22:49Z] INFO  23:49:44,208 MuTect - [MUTECT] Processed 199010980 reads in 610 ms
[2015-09-30T22:49Z] INFO  23:49:44,422 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:44,491 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:44,503 MuTect - [MUTECT] Processed 193013936 reads in 657 ms
[2015-09-30T22:49Z] INFO  23:49:44,813 MuTect - [MUTECT] Processed 24001619 reads in 647 ms
[2015-09-30T22:49Z] INFO  23:49:44,838 MuTect - [MUTECT] Processed 200011031 reads in 630 ms
[2015-09-30T22:49Z] INFO  23:49:45,137 MuTect - [MUTECT] Processed 194014053 reads in 634 ms
[2015-09-30T22:49Z] INFO  23:49:45,461 MuTect - [MUTECT] Processed 25001658 reads in 648 ms
[2015-09-30T22:49Z] INFO  23:49:45,483 MuTect - [MUTECT] Processed 201011130 reads in 645 ms
[2015-09-30T22:49Z] INFO  23:49:45,806 MuTect - [MUTECT] Processed 195014071 reads in 669 ms
[2015-09-30T22:49Z] INFO  23:49:46,040 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:46,103 MuTect - [MUTECT] Processed 26001658 reads in 642 ms
[2015-09-30T22:49Z] INFO  23:49:46,109 MuTect - [MUTECT] Processed 202011223 reads in 626 ms
[2015-09-30T22:49Z] INFO  23:49:46,468 MuTect - [MUTECT] Processed 196014154 reads in 662 ms
[2015-09-30T22:49Z] INFO  23:49:46,679 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:46,706 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:46,729 MuTect - [MUTECT] Processed 203011319 reads in 620 ms
[2015-09-30T22:49Z] INFO  23:49:46,785 MuTect - [MUTECT] Processed 27001707 reads in 682 ms
[2015-09-30T22:49Z] INFO  23:49:47,114 MuTect - [MUTECT] Processed 197014224 reads in 646 ms
[2015-09-30T22:49Z] INFO  23:49:47,321 MuTect - [MUTECT] Processed 204011347 reads in 592 ms
[2015-09-30T22:49Z] INFO  23:49:47,424 MuTect - [MUTECT] Processed 28001774 reads in 639 ms
[2015-09-30T22:49Z] INFO  23:49:47,817 MuTect - [MUTECT] Processed 198014324 reads in 703 ms
[2015-09-30T22:49Z] INFO  23:49:47,892 ProgressMeter -     19:10426617        5.61e+06    2.5 m       26.0 s     49.0%         5.1 m     2.6 m
[2015-09-30T22:49Z] INFO  23:49:47,941 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:47,972 MuTect - [MUTECT] Processed 205011377 reads in 651 ms
[2015-09-30T22:49Z] INFO  23:49:48,091 MuTect - [MUTECT] Processed 29001788 reads in 667 ms
[2015-09-30T22:49Z] INFO  23:49:48,500 MuTect - [MUTECT] Processed 199014368 reads in 683 ms
[2015-09-30T22:49Z] INFO  23:49:48,609 MuTect - [MUTECT] Processed 206011447 reads in 637 ms
[2015-09-30T22:49Z] INFO  23:49:48,764 MuTect - [MUTECT] Processed 30001871 reads in 673 ms
[2015-09-30T22:49Z] INFO  23:49:48,985 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:49,015 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:49,170 MuTect - [MUTECT] Processed 200014369 reads in 670 ms
[2015-09-30T22:49Z] INFO  23:49:49,260 MuTect - [MUTECT] Processed 207011579 reads in 651 ms
[2015-09-30T22:49Z] INFO  23:49:49,456 MuTect - [MUTECT] Processed 31001916 reads in 692 ms
[2015-09-30T22:49Z] INFO  23:49:49,850 MuTect - [MUTECT] Processed 201014481 reads in 680 ms
[2015-09-30T22:49Z] INFO  23:49:49,925 MuTect - [MUTECT] Processed 208011622 reads in 665 ms
[2015-09-30T22:49Z] INFO  23:49:50,023 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:50,124 MuTect - [MUTECT] Processed 32002016 reads in 668 ms
[2015-09-30T22:49Z] INFO  23:49:50,467 MuTect - [MUTECT] Processed 202014481 reads in 617 ms
[2015-09-30T22:49Z] INFO  23:49:50,586 MuTect - [MUTECT] Processed 209011686 reads in 661 ms
[2015-09-30T22:49Z] INFO  23:49:50,790 MuTect - [MUTECT] Processed 33002089 reads in 666 ms
[2015-09-30T22:49Z] INFO  23:49:50,966 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:51,086 MuTect - [MUTECT] Processed 203014568 reads in 619 ms
[2015-09-30T22:49Z] INFO  23:49:51,232 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:51,235 MuTect - [MUTECT] Processed 210011760 reads in 648 ms
[2015-09-30T22:49Z] INFO  23:49:51,468 MuTect - [MUTECT] Processed 34002178 reads in 678 ms
[2015-09-30T22:49Z] INFO  23:49:51,711 MuTect - [MUTECT] Processed 204014626 reads in 625 ms
[2015-09-30T22:49Z] INFO  23:49:51,859 MuTect - [MUTECT] Processed 211011850 reads in 625 ms
[2015-09-30T22:49Z] INFO  23:49:52,097 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:52,135 MuTect - [MUTECT] Processed 35002260 reads in 667 ms
[2015-09-30T22:49Z] INFO  23:49:52,367 MuTect - [MUTECT] Processed 205014655 reads in 656 ms
[2015-09-30T22:49Z] INFO  23:49:52,455 MuTect - [MUTECT] Processed 212011903 reads in 596 ms
[2015-09-30T22:49Z] INFO  23:49:52,810 MuTect - [MUTECT] Processed 36002301 reads in 675 ms
[2015-09-30T22:49Z] INFO  23:49:52,998 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:53,048 MuTect - [MUTECT] Processed 206014673 reads in 681 ms
[2015-09-30T22:49Z] INFO  23:49:53,064 MuTect - [MUTECT] Processed 213011976 reads in 608 ms
[2015-09-30T22:49Z] INFO  23:49:53,351 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:53,465 MuTect - [MUTECT] Processed 37002323 reads in 655 ms
[2015-09-30T22:49Z] INFO  23:49:53,685 MuTect - [MUTECT] Processed 214011997 reads in 622 ms
[2015-09-30T22:49Z] INFO  23:49:53,719 MuTect - [MUTECT] Processed 207014700 reads in 671 ms
[2015-09-30T22:49Z] INFO  23:49:54,068 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:54,158 MuTect - [MUTECT] Processed 38002355 reads in 693 ms
[2015-09-30T22:49Z] INFO  23:49:54,355 MuTect - [MUTECT] Processed 215012015 reads in 670 ms
[2015-09-30T22:49Z] INFO  23:49:54,361 MuTect - [MUTECT] Processed 208014709 reads in 642 ms
[2015-09-30T22:49Z] INFO  23:49:54,838 MuTect - [MUTECT] Processed 39002358 reads in 679 ms
[2015-09-30T22:49Z] INFO  23:49:54,984 MuTect - [MUTECT] Processed 216012067 reads in 629 ms
[2015-09-30T22:49Z] INFO  23:49:54,996 MuTect - [MUTECT] Processed 209014809 reads in 635 ms
[2015-09-30T22:49Z] INFO  23:49:55,290 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:55,524 MuTect - [MUTECT] Processed 40002466 reads in 686 ms
[2015-09-30T22:49Z] INFO  23:49:55,594 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:55,606 MuTect - [MUTECT] Processed 217012089 reads in 622 ms
[2015-09-30T22:49Z] INFO  23:49:55,625 MuTect - [MUTECT] Processed 210014901 reads in 629 ms
[2015-09-30T22:49Z] INFO  23:49:56,099 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:56,204 MuTect - [MUTECT] Processed 41002532 reads in 681 ms
[2015-09-30T22:49Z] INFO  23:49:56,220 MuTect - [MUTECT] Processed 218012147 reads in 614 ms
[2015-09-30T22:49Z] INFO  23:49:56,251 MuTect - [MUTECT] Processed 211014981 reads in 626 ms
[2015-09-30T22:49Z] INFO  23:49:56,832 MuTect - [MUTECT] Processed 219012197 reads in 612 ms
[2015-09-30T22:49Z] INFO  23:49:56,870 MuTect - [MUTECT] Processed 212015029 reads in 618 ms
[2015-09-30T22:49Z] INFO  23:49:56,899 MuTect - [MUTECT] Processed 42002626 reads in 695 ms
[2015-09-30T22:49Z] INFO  23:49:56,936 ProgressMeter -     20:33999833        1.35e+06   30.0 s       22.0 s     18.2%         2.7 m     2.2 m
[2015-09-30T22:49Z] INFO  23:49:57,349 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:57,454 MuTect - [MUTECT] Processed 220012209 reads in 622 ms
[2015-09-30T22:49Z] INFO  23:49:57,491 MuTect - [MUTECT] Processed 213015067 reads in 622 ms
[2015-09-30T22:49Z] INFO  23:49:57,556 MuTect - [MUTECT] Processed 43002707 reads in 657 ms
[2015-09-30T22:49Z] INFO  23:49:57,958 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:58,039 MuTect - [MUTECT] Inspected 67000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:58,059 MuTect - [MUTECT] Processed 221012225 reads in 605 ms
[2015-09-30T22:49Z] INFO  23:49:58,096 MuTect - [MUTECT] Processed 214015117 reads in 605 ms
[2015-09-30T22:49Z] INFO  23:49:58,220 MuTect - [MUTECT] Processed 44002741 reads in 664 ms
[2015-09-30T22:49Z] INFO  23:49:58,672 MuTect - [MUTECT] Processed 222012312 reads in 613 ms
[2015-09-30T22:49Z] INFO  23:49:58,753 MuTect - [MUTECT] Processed 215015180 reads in 657 ms
[2015-09-30T22:49Z] INFO  23:49:58,855 MuTect - [MUTECT] Processed 45002754 reads in 635 ms
[2015-09-30T22:49Z] INFO  23:49:59,274 MuTect - [MUTECT] Processed 223012396 reads in 602 ms
[2015-09-30T22:49Z] INFO  23:49:59,391 MuTect - [MUTECT] Processed 216015184 reads in 638 ms
[2015-09-30T22:49Z] INFO  23:49:59,510 MuTect - [MUTECT] Processed 46002758 reads in 655 ms
[2015-09-30T22:49Z] INFO  23:49:59,650 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:49Z] INFO  23:49:59,875 MuTect - [MUTECT] Processed 224012470 reads in 601 ms
[2015-09-30T22:50Z] INFO  23:50:00,022 MuTect - [MUTECT] Inspected 68000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:00,043 MuTect - [MUTECT] Processed 217015212 reads in 652 ms
[2015-09-30T22:50Z] INFO  23:50:00,143 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:00,164 MuTect - [MUTECT] Processed 47002837 reads in 654 ms
[2015-09-30T22:50Z] INFO  23:50:00,476 MuTect - [MUTECT] Processed 225012533 reads in 601 ms
[2015-09-30T22:50Z] INFO  23:50:00,713 MuTect - [MUTECT] Processed 218015259 reads in 670 ms
[2015-09-30T22:50Z] INFO  23:50:00,836 MuTect - [MUTECT] Processed 48002849 reads in 672 ms
[2015-09-30T22:50Z] INFO  23:50:01,092 MuTect - [MUTECT] Processed 226012611 reads in 616 ms
[2015-09-30T22:50Z] INFO  23:50:01,348 MuTect - [MUTECT] Processed 219015365 reads in 635 ms
[2015-09-30T22:50Z] INFO  23:50:01,481 MuTect - [MUTECT] Processed 49002918 reads in 645 ms
[2015-09-30T22:50Z] INFO  23:50:01,680 MuTect - [MUTECT] Processed 227012611 reads in 588 ms
[2015-09-30T22:50Z] INFO  23:50:01,757 MuTect - [MUTECT] Inspected 69000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:01,989 MuTect - [MUTECT] Inspected 69000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:01,997 MuTect - [MUTECT] Processed 220015375 reads in 649 ms
[2015-09-30T22:50Z] INFO  23:50:02,130 MuTect - [MUTECT] Processed 50002935 reads in 649 ms
[2015-09-30T22:50Z] INFO  23:50:02,219 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:02,272 MuTect - [MUTECT] Processed 228012712 reads in 592 ms
[2015-09-30T22:50Z] INFO  23:50:02,607 MuTect - [MUTECT] Processed 221015453 reads in 610 ms
[2015-09-30T22:50Z] INFO  23:50:02,781 MuTect - [MUTECT] Processed 51002963 reads in 651 ms
[2015-09-30T22:50Z] INFO  23:50:02,886 MuTect - [MUTECT] Processed 229012717 reads in 614 ms
[2015-09-30T22:50Z] INFO  23:50:03,234 MuTect - [MUTECT] Processed 222015481 reads in 627 ms
[2015-09-30T22:50Z] INFO  23:50:03,483 MuTect - [MUTECT] Processed 230012754 reads in 597 ms
[2015-09-30T22:50Z] INFO  23:50:03,484 MuTect - [MUTECT] Processed 52003015 reads in 703 ms
[2015-09-30T22:50Z] INFO  23:50:03,749 MuTect - [MUTECT] Inspected 70000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:03,842 MuTect - [MUTECT] Processed 223015603 reads in 608 ms
[2015-09-30T22:50Z] INFO  23:50:04,008 MuTect - [MUTECT] Inspected 70000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:04,097 MuTect - [MUTECT] Processed 231012817 reads in 614 ms
[2015-09-30T22:50Z] INFO  23:50:04,148 MuTect - [MUTECT] Processed 53003051 reads in 664 ms
[2015-09-30T22:50Z] INFO  23:50:04,344 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:04,458 MuTect - [MUTECT] Processed 224015697 reads in 616 ms
[2015-09-30T22:50Z] INFO  23:50:04,713 MuTect - [MUTECT] Processed 232012893 reads in 616 ms
[2015-09-30T22:50Z] INFO  23:50:04,794 MuTect - [MUTECT] Processed 54003161 reads in 646 ms
[2015-09-30T22:50Z] INFO  23:50:05,058 MuTect - [MUTECT] Processed 225015745 reads in 600 ms
[2015-09-30T22:50Z] INFO  23:50:05,328 MuTect - [MUTECT] Processed 233012928 reads in 615 ms
[2015-09-30T22:50Z] INFO  23:50:05,444 ProgressMeter -     19:47865455        6.27e+06    2.5 m       23.0 s     52.6%         4.8 m     2.3 m
[2015-09-30T22:50Z] INFO  23:50:05,453 MuTect - [MUTECT] Processed 55003246 reads in 659 ms
[2015-09-30T22:50Z] INFO  23:50:05,668 MuTect - [MUTECT] Processed 226015843 reads in 610 ms
[2015-09-30T22:50Z] INFO  23:50:05,761 MuTect - [MUTECT] Inspected 71000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:05,928 MuTect - [MUTECT] Processed 234013063 reads in 600 ms
[2015-09-30T22:50Z] INFO  23:50:05,976 MuTect - [MUTECT] Inspected 71000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:06,114 MuTect - [MUTECT] Processed 56003261 reads in 661 ms
[2015-09-30T22:50Z] INFO  23:50:06,294 MuTect - [MUTECT] Processed 227016005 reads in 626 ms
[2015-09-30T22:50Z] INFO  23:50:06,393 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:06,531 MuTect - [MUTECT] Processed 235013128 reads in 603 ms
[2015-09-30T22:50Z] INFO  23:50:06,742 MuTect - [MUTECT] Processed 57003310 reads in 628 ms
[2015-09-30T22:50Z] INFO  23:50:06,906 MuTect - [MUTECT] Processed 228016086 reads in 612 ms
[2015-09-30T22:50Z] INFO  23:50:07,133 MuTect - [MUTECT] Processed 236013189 reads in 602 ms
[2015-09-30T22:50Z] INFO  23:50:07,414 MuTect - [MUTECT] Processed 58003364 reads in 672 ms
[2015-09-30T22:50Z] INFO  23:50:07,516 MuTect - [MUTECT] Processed 229016144 reads in 610 ms
[2015-09-30T22:50Z] INFO  23:50:07,727 MuTect - [MUTECT] Processed 237013298 reads in 594 ms
[2015-09-30T22:50Z] INFO  23:50:07,799 MuTect - [MUTECT] Inspected 72000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:07,826 MuTect - [MUTECT] Inspected 72000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:08,053 MuTect - [MUTECT] Processed 59003437 reads in 639 ms
[2015-09-30T22:50Z] INFO  23:50:08,143 MuTect - [MUTECT] Processed 230016184 reads in 627 ms
[2015-09-30T22:50Z] INFO  23:50:08,309 MuTect - [MUTECT] Processed 238013416 reads in 582 ms
[2015-09-30T22:50Z] INFO  23:50:08,448 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:08,766 MuTect - [MUTECT] Processed 60003545 reads in 713 ms
[2015-09-30T22:50Z] INFO  23:50:08,769 MuTect - [MUTECT] Processed 231016215 reads in 626 ms
[2015-09-30T22:50Z] INFO  23:50:08,919 MuTect - [MUTECT] Processed 239013418 reads in 610 ms
[2015-09-30T22:50Z] INFO  23:50:09,419 MuTect - [MUTECT] Processed 232016243 reads in 650 ms
[2015-09-30T22:50Z] INFO  23:50:09,420 MuTect - [MUTECT] Processed 61003551 reads in 654 ms
[2015-09-30T22:50Z] INFO  23:50:09,537 MuTect - [MUTECT] Processed 240013473 reads in 618 ms
[2015-09-30T22:50Z] INFO  23:50:09,804 MuTect - [MUTECT] Inspected 73000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:10,049 MuTect - [MUTECT] Processed 233016330 reads in 629 ms
[2015-09-30T22:50Z] INFO  23:50:10,079 MuTect - [MUTECT] Processed 62003565 reads in 659 ms
[2015-09-30T22:50Z] INFO  23:50:10,125 MuTect - [MUTECT] Inspected 73000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:10,210 MuTect - [MUTECT] Processed 241013553 reads in 673 ms
[2015-09-30T22:50Z] INFO  23:50:10,673 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:10,715 MuTect - [MUTECT] Processed 63003600 reads in 636 ms
[2015-09-30T22:50Z] INFO  23:50:10,718 MuTect - [MUTECT] Processed 234016358 reads in 670 ms
[2015-09-30T22:50Z] INFO  23:50:10,862 MuTect - [MUTECT] Processed 242013640 reads in 652 ms
[2015-09-30T22:50Z] INFO  23:50:11,354 MuTect - [MUTECT] Processed 235016438 reads in 636 ms
[2015-09-30T22:50Z] INFO  23:50:11,399 MuTect - [MUTECT] Processed 64003700 reads in 684 ms
[2015-09-30T22:50Z] INFO  23:50:11,520 MuTect - [MUTECT] Processed 243013645 reads in 658 ms
[2015-09-30T22:50Z] INFO  23:50:11,782 MuTect - [MUTECT] Inspected 74000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:12,005 MuTect - [MUTECT] Processed 236016442 reads in 651 ms
[2015-09-30T22:50Z] INFO  23:50:12,074 MuTect - [MUTECT] Processed 65003746 reads in 675 ms
[2015-09-30T22:50Z] INFO  23:50:12,227 MuTect - [MUTECT] Processed 244013737 reads in 707 ms
[2015-09-30T22:50Z] INFO  23:50:12,422 MuTect - [MUTECT] Inspected 74000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:12,666 MuTect - [MUTECT] Processed 237016494 reads in 661 ms
[2015-09-30T22:50Z] INFO  23:50:12,732 MuTect - [MUTECT] Processed 66003764 reads in 658 ms
[2015-09-30T22:50Z] INFO  23:50:12,935 MuTect - [MUTECT] Processed 245013812 reads in 708 ms
[2015-09-30T22:50Z] INFO  23:50:13,062 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:13,314 MuTect - [MUTECT] Processed 238016535 reads in 648 ms
[2015-09-30T22:50Z] INFO  23:50:13,382 MuTect - [MUTECT] Processed 67003780 reads in 650 ms
[2015-09-30T22:50Z] INFO  23:50:13,594 MuTect - [MUTECT] Processed 246013909 reads in 659 ms
[2015-09-30T22:50Z] INFO  23:50:13,822 MuTect - [MUTECT] Inspected 75000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:14,017 MuTect - [MUTECT] Processed 239016586 reads in 703 ms
[2015-09-30T22:50Z] INFO  23:50:14,029 MuTect - [MUTECT] Processed 68003782 reads in 647 ms
[2015-09-30T22:50Z] INFO  23:50:14,227 MuTect - [MUTECT] Processed 247013963 reads in 633 ms
[2015-09-30T22:50Z] INFO  23:50:14,600 MuTect - [MUTECT] Inspected 75000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:14,648 MuTect - [MUTECT] Processed 69003853 reads in 619 ms
[2015-09-30T22:50Z] INFO  23:50:14,661 MuTect - [MUTECT] Processed 240016590 reads in 644 ms
[2015-09-30T22:50Z] INFO  23:50:14,894 MuTect - [MUTECT] Processed 248014048 reads in 667 ms
[2015-09-30T22:50Z] INFO  23:50:15,264 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:15,267 MuTect - [MUTECT] Processed 70003899 reads in 619 ms
[2015-09-30T22:50Z] INFO  23:50:15,291 MuTect - [MUTECT] Processed 241016687 reads in 630 ms
[2015-09-30T22:50Z] INFO  23:50:15,526 MuTect - [MUTECT] Processed 249014109 reads in 632 ms
[2015-09-30T22:50Z] INFO  23:50:15,903 MuTect - [MUTECT] Processed 71003927 reads in 636 ms
[2015-09-30T22:50Z] INFO  23:50:15,909 MuTect - [MUTECT] Processed 242016721 reads in 618 ms
[2015-09-30T22:50Z] INFO  23:50:15,924 MuTect - [MUTECT] Inspected 76000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:16,138 MuTect - [MUTECT] Processed 250014118 reads in 612 ms
[2015-09-30T22:50Z] INFO  23:50:16,542 MuTect - [MUTECT] Processed 243016752 reads in 633 ms
[2015-09-30T22:50Z] INFO  23:50:16,551 MuTect - [MUTECT] Processed 72003984 reads in 648 ms
[2015-09-30T22:50Z] INFO  23:50:16,734 MuTect - [MUTECT] Inspected 76000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:16,758 MuTect - [MUTECT] Processed 251014140 reads in 620 ms
[2015-09-30T22:50Z] INFO  23:50:17,158 MuTect - [MUTECT] Processed 244016781 reads in 616 ms
[2015-09-30T22:50Z] INFO  23:50:17,188 MuTect - [MUTECT] Processed 73003984 reads in 637 ms
[2015-09-30T22:50Z] INFO  23:50:17,378 MuTect - [MUTECT] Processed 252014177 reads in 620 ms
[2015-09-30T22:50Z] INFO  23:50:17,500 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:17,773 MuTect - [MUTECT] Processed 245016812 reads in 615 ms
[2015-09-30T22:50Z] INFO  23:50:17,832 MuTect - [MUTECT] Processed 74004061 reads in 644 ms
[2015-09-30T22:50Z] INFO  23:50:17,893 ProgressMeter -     19:12868386        6.90e+06    3.0 m       26.0 s     61.3%         4.9 m   113.0 s
[2015-09-30T22:50Z] INFO  23:50:17,909 MuTect - [MUTECT] Inspected 77000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:18,002 MuTect - [MUTECT] Processed 253014295 reads in 624 ms
[2015-09-30T22:50Z] INFO  23:50:18,377 MuTect - [MUTECT] Processed 246016881 reads in 604 ms
[2015-09-30T22:50Z] INFO  23:50:18,462 MuTect - [MUTECT] Processed 75004155 reads in 630 ms
[2015-09-30T22:50Z] INFO  23:50:18,678 MuTect - [MUTECT] Processed 254014316 reads in 676 ms
[2015-09-30T22:50Z] INFO  23:50:18,797 MuTect - [MUTECT] Inspected 77000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:19,031 MuTect - [MUTECT] Processed 247016906 reads in 654 ms
[2015-09-30T22:50Z] INFO  23:50:19,109 MuTect - [MUTECT] Processed 76004227 reads in 647 ms
[2015-09-30T22:50Z] INFO  23:50:19,332 MuTect - [MUTECT] Processed 255014330 reads in 654 ms
[2015-09-30T22:50Z] INFO  23:50:19,631 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:19,725 MuTect - [MUTECT] Processed 248017008 reads in 694 ms
[2015-09-30T22:50Z] INFO  23:50:19,805 MuTect - [MUTECT] Processed 77004294 reads in 696 ms
[2015-09-30T22:50Z] INFO  23:50:19,943 MuTect - [MUTECT] Processed 256014345 reads in 611 ms
[2015-09-30T22:50Z] INFO  23:50:20,023 MuTect - [MUTECT] Inspected 78000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:20,362 MuTect - [MUTECT] Processed 249017105 reads in 637 ms
[2015-09-30T22:50Z] INFO  23:50:20,475 MuTect - [MUTECT] Processed 78004296 reads in 670 ms
[2015-09-30T22:50Z] INFO  23:50:20,577 MuTect - [MUTECT] Processed 257014467 reads in 634 ms
[2015-09-30T22:50Z] INFO  23:50:21,009 MuTect - [MUTECT] Processed 250017132 reads in 647 ms
[2015-09-30T22:50Z] INFO  23:50:21,105 MuTect - [MUTECT] Processed 79004346 reads in 630 ms
[2015-09-30T22:50Z] INFO  23:50:21,159 MuTect - [MUTECT] Inspected 78000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:21,267 MuTect - [MUTECT] Processed 258014506 reads in 690 ms
[2015-09-30T22:50Z] INFO  23:50:21,658 MuTect - [MUTECT] Processed 251017183 reads in 648 ms
[2015-09-30T22:50Z] INFO  23:50:21,737 MuTect - [MUTECT] Processed 80004397 reads in 632 ms
[2015-09-30T22:50Z] INFO  23:50:21,846 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:21,911 MuTect - [MUTECT] Processed 259014508 reads in 644 ms
[2015-09-30T22:50Z] INFO  23:50:22,128 MuTect - [MUTECT] Inspected 79000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:22,331 MuTect - [MUTECT] Processed 252017198 reads in 674 ms
[2015-09-30T22:50Z] INFO  23:50:22,358 MuTect - [MUTECT] Processed 81004448 reads in 621 ms
[2015-09-30T22:50Z] INFO  23:50:22,576 MuTect - [MUTECT] Processed 260014549 reads in 665 ms
[2015-09-30T22:50Z] INFO  23:50:22,972 MuTect - [MUTECT] Processed 82004482 reads in 614 ms
[2015-09-30T22:50Z] INFO  23:50:22,978 MuTect - [MUTECT] Processed 253017274 reads in 647 ms
[2015-09-30T22:50Z] INFO  23:50:23,213 MuTect - [MUTECT] Processed 261014597 reads in 637 ms
[2015-09-30T22:50Z] INFO  23:50:23,376 MuTect - [MUTECT] Inspected 79000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:23,602 MuTect - [MUTECT] Processed 83004514 reads in 630 ms
[2015-09-30T22:50Z] INFO  23:50:23,638 MuTect - [MUTECT] Processed 254017294 reads in 660 ms
[2015-09-30T22:50Z] INFO  23:50:23,849 MuTect - [MUTECT] Processed 262014641 reads in 636 ms
[2015-09-30T22:50Z] INFO  23:50:24,019 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:24,196 MuTect - [MUTECT] Inspected 80000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:24,257 MuTect - [MUTECT] Processed 84004576 reads in 654 ms
[2015-09-30T22:50Z] INFO  23:50:24,274 MuTect - [MUTECT] Processed 255017365 reads in 636 ms
[2015-09-30T22:50Z] INFO  23:50:24,521 MuTect - [MUTECT] Processed 263014706 reads in 672 ms
[2015-09-30T22:50Z] INFO  23:50:24,925 MuTect - [MUTECT] Processed 256017400 reads in 651 ms
[2015-09-30T22:50Z] INFO  23:50:24,931 MuTect - [MUTECT] Processed 85004615 reads in 675 ms
[2015-09-30T22:50Z] INFO  23:50:25,206 MuTect - [MUTECT] Processed 264014780 reads in 685 ms
[2015-09-30T22:50Z] INFO  23:50:25,500 MuTect - [MUTECT] Inspected 80000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:25,552 MuTect - [MUTECT] Processed 86004637 reads in 621 ms
[2015-09-30T22:50Z] INFO  23:50:25,585 MuTect - [MUTECT] Processed 257017502 reads in 660 ms
[2015-09-30T22:50Z] INFO  23:50:25,879 MuTect - [MUTECT] Processed 265014884 reads in 673 ms
[2015-09-30T22:50Z] INFO  23:50:26,189 MuTect - [MUTECT] Processed 87004661 reads in 637 ms
[2015-09-30T22:50Z] INFO  23:50:26,233 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:26,274 MuTect - [MUTECT] Inspected 81000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:26,343 MuTect - [MUTECT] Processed 258017528 reads in 758 ms
[2015-09-30T22:50Z] INFO  23:50:26,506 MuTect - [MUTECT] Processed 266014944 reads in 627 ms
[2015-09-30T22:50Z] INFO  23:50:26,806 MuTect - [MUTECT] Processed 88004776 reads in 617 ms
[2015-09-30T22:50Z] INFO  23:50:26,937 ProgressMeter -     20:39797672        2.59e+06   60.0 s       23.0 s     39.0%         2.6 m    93.0 s
[2015-09-30T22:50Z] INFO  23:50:27,007 MuTect - [MUTECT] Processed 259017601 reads in 664 ms
[2015-09-30T22:50Z] INFO  23:50:27,161 MuTect - [MUTECT] Processed 267015023 reads in 655 ms
[2015-09-30T22:50Z] INFO  23:50:27,418 MuTect - [MUTECT] Processed 89004840 reads in 612 ms
[2015-09-30T22:50Z] INFO  23:50:27,687 MuTect - [MUTECT] Processed 260017609 reads in 680 ms
[2015-09-30T22:50Z] INFO  23:50:27,723 MuTect - [MUTECT] Inspected 81000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:27,896 MuTect - [MUTECT] Processed 268015055 reads in 735 ms
[2015-09-30T22:50Z] INFO  23:50:28,021 MuTect - [MUTECT] Processed 90004905 reads in 603 ms
[2015-09-30T22:50Z] INFO  23:50:28,259 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:28,361 MuTect - [MUTECT] Processed 261017632 reads in 674 ms
[2015-09-30T22:50Z] INFO  23:50:28,622 MuTect - [MUTECT] Processed 91004989 reads in 601 ms
[2015-09-30T22:50Z] INFO  23:50:28,640 MuTect - [MUTECT] Processed 269015164 reads in 744 ms
[2015-09-30T22:50Z] INFO  23:50:28,647 MuTect - [MUTECT] Inspected 82000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:28,995 MuTect - [MUTECT] Processed 262017676 reads in 634 ms
[2015-09-30T22:50Z] INFO  23:50:29,227 MuTect - [MUTECT] Processed 92005015 reads in 605 ms
[2015-09-30T22:50Z] INFO  23:50:29,291 MuTect - [MUTECT] Processed 270015166 reads in 651 ms
[2015-09-30T22:50Z] INFO  23:50:29,647 MuTect - [MUTECT] Processed 263017712 reads in 652 ms
[2015-09-30T22:50Z] INFO  23:50:29,849 MuTect - [MUTECT] Processed 93005033 reads in 622 ms
[2015-09-30T22:50Z] INFO  23:50:29,903 MuTect - [MUTECT] Inspected 82000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:29,957 MuTect - [MUTECT] Processed 271015219 reads in 666 ms
[2015-09-30T22:50Z] INFO  23:50:30,278 MuTect - [MUTECT] Processed 264017757 reads in 631 ms
[2015-09-30T22:50Z] INFO  23:50:30,464 MuTect - [MUTECT] Processed 94005084 reads in 615 ms
[2015-09-30T22:50Z] INFO  23:50:30,481 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:30,658 MuTect - [MUTECT] Processed 272015330 reads in 701 ms
[2015-09-30T22:50Z] INFO  23:50:30,868 MuTect - [MUTECT] Inspected 83000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:30,897 MuTect - [MUTECT] Processed 265017847 reads in 619 ms
[2015-09-30T22:50Z] INFO  23:50:31,101 MuTect - [MUTECT] Processed 95005105 reads in 637 ms
[2015-09-30T22:50Z] INFO  23:50:31,308 MuTect - [MUTECT] Processed 273015463 reads in 650 ms
[2015-09-30T22:50Z] INFO  23:50:31,514 MuTect - [MUTECT] Processed 266017847 reads in 617 ms
[2015-09-30T22:50Z] INFO  23:50:31,771 MuTect - [MUTECT] Processed 96005109 reads in 670 ms
[2015-09-30T22:50Z] INFO  23:50:31,874 MuTect - [MUTECT] Inspected 83000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:32,006 MuTect - [MUTECT] Processed 274015540 reads in 698 ms
[2015-09-30T22:50Z] INFO  23:50:32,125 MuTect - [MUTECT] Processed 267017967 reads in 611 ms
[2015-09-30T22:50Z] INFO  23:50:32,383 MuTect - [MUTECT] Processed 97005118 reads in 612 ms
[2015-09-30T22:50Z] INFO  23:50:32,602 MuTect - [MUTECT] Processed 275015546 reads in 596 ms
[2015-09-30T22:50Z] INFO  23:50:32,750 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:32,768 MuTect - [MUTECT] Processed 268018052 reads in 643 ms
[2015-09-30T22:50Z] INFO  23:50:32,976 MuTect - [MUTECT] Inspected 84000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:32,986 MuTect - [MUTECT] Processed 98005175 reads in 603 ms
[2015-09-30T22:50Z] INFO  23:50:33,228 MuTect - [MUTECT] Processed 276015637 reads in 626 ms
[2015-09-30T22:50Z] INFO  23:50:33,372 MuTect - [MUTECT] Processed 269018160 reads in 604 ms
[2015-09-30T22:50Z] INFO  23:50:33,616 MuTect - [MUTECT] Processed 99005215 reads in 630 ms
[2015-09-30T22:50Z] INFO  23:50:33,800 MuTect - [MUTECT] Inspected 84000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:33,839 MuTect - [MUTECT] Processed 277015702 reads in 611 ms
[2015-09-30T22:50Z] INFO  23:50:33,985 MuTect - [MUTECT] Processed 270018186 reads in 613 ms
[2015-09-30T22:50Z] INFO  23:50:34,286 MuTect - [MUTECT] Processed 100005278 reads in 670 ms
[2015-09-30T22:50Z] INFO  23:50:34,477 MuTect - [MUTECT] Processed 278015740 reads in 638 ms
[2015-09-30T22:50Z] INFO  23:50:34,583 MuTect - [MUTECT] Processed 271018325 reads in 598 ms
[2015-09-30T22:50Z] INFO  23:50:34,897 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:34,906 MuTect - [MUTECT] Processed 101005345 reads in 620 ms
[2015-09-30T22:50Z] INFO  23:50:34,935 MuTect - [MUTECT] Inspected 85000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:35,114 MuTect - [MUTECT] Processed 279015778 reads in 637 ms
[2015-09-30T22:50Z] INFO  23:50:35,181 MuTect - [MUTECT] Processed 272018344 reads in 598 ms
[2015-09-30T22:50Z] INFO  23:50:35,445 ProgressMeter -     19:49962486        7.58e+06    3.0 m       23.0 s     62.8%         4.8 m   106.0 s
[2015-09-30T22:50Z] INFO  23:50:35,530 MuTect - [MUTECT] Processed 102005389 reads in 624 ms
[2015-09-30T22:50Z] INFO  23:50:35,718 MuTect - [MUTECT] Inspected 85000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:35,856 MuTect - [MUTECT] Processed 273018459 reads in 675 ms
[2015-09-30T22:50Z] INFO  23:50:35,980 MuTect - [MUTECT] Processed 280015848 reads in 866 ms
[2015-09-30T22:50Z] INFO  23:50:36,165 MuTect - [MUTECT] Processed 103005424 reads in 635 ms
[2015-09-30T22:50Z] INFO  23:50:36,457 MuTect - [MUTECT] Processed 274018518 reads in 601 ms
[2015-09-30T22:50Z] INFO  23:50:36,597 MuTect - [MUTECT] Processed 281015954 reads in 617 ms
[2015-09-30T22:50Z] INFO  23:50:36,788 MuTect - [MUTECT] Processed 104005528 reads in 623 ms
[2015-09-30T22:50Z] INFO  23:50:37,088 MuTect - [MUTECT] Processed 275018617 reads in 631 ms
[2015-09-30T22:50Z] INFO  23:50:37,161 MuTect - [MUTECT] Inspected 86000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:37,223 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:37,290 MuTect - [MUTECT] Processed 282016078 reads in 693 ms
[2015-09-30T22:50Z] INFO  23:50:37,428 MuTect - [MUTECT] Processed 105005531 reads in 640 ms
[2015-09-30T22:50Z] INFO  23:50:37,734 MuTect - [MUTECT] Processed 276018717 reads in 646 ms
[2015-09-30T22:50Z] INFO  23:50:37,914 MuTect - [MUTECT] Processed 283016128 reads in 624 ms
[2015-09-30T22:50Z] INFO  23:50:38,007 MuTect - [MUTECT] Inspected 86000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:38,063 MuTect - [MUTECT] Processed 106005656 reads in 635 ms
[2015-09-30T22:50Z] INFO  23:50:38,449 MuTect - [MUTECT] Processed 277018813 reads in 715 ms
[2015-09-30T22:50Z] INFO  23:50:38,580 MuTect - [MUTECT] Processed 284016253 reads in 666 ms
[2015-09-30T22:50Z] INFO  23:50:38,704 MuTect - [MUTECT] Processed 107005656 reads in 641 ms
[2015-09-30T22:50Z] INFO  23:50:39,113 MuTect - [MUTECT] Processed 278018834 reads in 664 ms
[2015-09-30T22:50Z] INFO  23:50:39,141 MuTect - [MUTECT] Inspected 87000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:39,241 MuTect - [MUTECT] Processed 285016258 reads in 661 ms
[2015-09-30T22:50Z] INFO  23:50:39,309 MuTect - [MUTECT] Processed 108005675 reads in 605 ms
[2015-09-30T22:50Z] INFO  23:50:39,488 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:39,783 MuTect - [MUTECT] Processed 279018945 reads in 670 ms
[2015-09-30T22:50Z] INFO  23:50:39,865 MuTect - [MUTECT] Processed 286016286 reads in 624 ms
[2015-09-30T22:50Z] INFO  23:50:39,976 MuTect - [MUTECT] Processed 109005735 reads in 667 ms
[2015-09-30T22:50Z] INFO  23:50:40,133 MuTect - [MUTECT] Inspected 87000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:40,449 MuTect - [MUTECT] Processed 280018961 reads in 666 ms
[2015-09-30T22:50Z] INFO  23:50:40,510 MuTect - [MUTECT] Processed 287016321 reads in 645 ms
[2015-09-30T22:50Z] INFO  23:50:40,592 MuTect - [MUTECT] Processed 110005790 reads in 616 ms
[2015-09-30T22:50Z] INFO  23:50:41,132 MuTect - [MUTECT] Inspected 88000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:41,134 MuTect - [MUTECT] Processed 288016371 reads in 623 ms
[2015-09-30T22:50Z] INFO  23:50:41,184 MuTect - [MUTECT] Processed 281018994 reads in 735 ms
[2015-09-30T22:50Z] INFO  23:50:41,234 MuTect - [MUTECT] Processed 111005827 reads in 642 ms
[2015-09-30T22:50Z] INFO  23:50:41,667 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:41,790 MuTect - [MUTECT] Processed 289016441 reads in 657 ms
[2015-09-30T22:50Z] INFO  23:50:41,846 MuTect - [MUTECT] Processed 112005863 reads in 612 ms
[2015-09-30T22:50Z] INFO  23:50:41,872 MuTect - [MUTECT] Processed 282019087 reads in 688 ms
[2015-09-30T22:50Z] INFO  23:50:42,222 MuTect - [MUTECT] Inspected 88000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:42,427 MuTect - [MUTECT] Processed 290016559 reads in 637 ms
[2015-09-30T22:50Z] INFO  23:50:42,455 MuTect - [MUTECT] Processed 113005884 reads in 609 ms
[2015-09-30T22:50Z] INFO  23:50:42,554 MuTect - [MUTECT] Processed 283019136 reads in 682 ms
[2015-09-30T22:50Z] INFO  23:50:43,070 MuTect - [MUTECT] Processed 291016654 reads in 643 ms
[2015-09-30T22:50Z] INFO  23:50:43,080 MuTect - [MUTECT] Processed 114005996 reads in 625 ms
[2015-09-30T22:50Z] INFO  23:50:43,180 MuTect - [MUTECT] Inspected 89000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:43,214 MuTect - [MUTECT] Processed 284019186 reads in 660 ms
[2015-09-30T22:50Z] INFO  23:50:43,728 MuTect - [MUTECT] Processed 115006040 reads in 648 ms
[2015-09-30T22:50Z] INFO  23:50:43,731 MuTect - [MUTECT] Processed 292016778 reads in 661 ms
[2015-09-30T22:50Z] INFO  23:50:43,879 MuTect - [MUTECT] Processed 285019207 reads in 665 ms
[2015-09-30T22:50Z] INFO  23:50:43,917 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:44,354 MuTect - [MUTECT] Inspected 89000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:44,360 MuTect - [MUTECT] Processed 293016820 reads in 629 ms
[2015-09-30T22:50Z] INFO  23:50:44,363 MuTect - [MUTECT] Processed 116006046 reads in 635 ms
[2015-09-30T22:50Z] INFO  23:50:44,570 MuTect - [MUTECT] Processed 286019307 reads in 691 ms
[2015-09-30T22:50Z] INFO  23:50:44,977 MuTect - [MUTECT] Processed 294016888 reads in 617 ms
[2015-09-30T22:50Z] INFO  23:50:45,008 MuTect - [MUTECT] Processed 117006139 reads in 645 ms
[2015-09-30T22:50Z] INFO  23:50:45,189 MuTect - [MUTECT] Inspected 90000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:45,223 MuTect - [MUTECT] Processed 287019381 reads in 653 ms
[2015-09-30T22:50Z] INFO  23:50:45,607 MuTect - [MUTECT] Processed 295016895 reads in 630 ms
[2015-09-30T22:50Z] INFO  23:50:45,676 MuTect - [MUTECT] Processed 118006183 reads in 668 ms
[2015-09-30T22:50Z] INFO  23:50:45,868 MuTect - [MUTECT] Processed 288019521 reads in 645 ms
[2015-09-30T22:50Z] INFO  23:50:46,260 MuTect - [MUTECT] Processed 296016972 reads in 653 ms
[2015-09-30T22:50Z] INFO  23:50:46,350 MuTect - [MUTECT] Processed 119006235 reads in 674 ms
[2015-09-30T22:50Z] INFO  23:50:46,457 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:46,467 MuTect - [MUTECT] Inspected 90000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:46,485 MuTect - [MUTECT] Processed 289019621 reads in 617 ms
[2015-09-30T22:50Z] INFO  23:50:46,897 MuTect - [MUTECT] Processed 297016989 reads in 637 ms
[2015-09-30T22:50Z] INFO  23:50:46,972 MuTect - [MUTECT] Processed 120006350 reads in 622 ms
[2015-09-30T22:50Z] INFO  23:50:47,101 MuTect - [MUTECT] Processed 290019630 reads in 616 ms
[2015-09-30T22:50Z] INFO  23:50:47,242 MuTect - [MUTECT] Inspected 91000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:47,533 MuTect - [MUTECT] Processed 298017125 reads in 636 ms
[2015-09-30T22:50Z] INFO  23:50:47,586 MuTect - [MUTECT] Processed 121006458 reads in 614 ms
[2015-09-30T22:50Z] INFO  23:50:47,713 MuTect - [MUTECT] Processed 291019633 reads in 612 ms
[2015-09-30T22:50Z] INFO  23:50:47,894 ProgressMeter -     19:15538792        8.17e+06    3.5 m       25.0 s     72.9%         4.8 m    77.0 s
[2015-09-30T22:50Z] INFO  23:50:48,160 MuTect - [MUTECT] Processed 299017220 reads in 627 ms
[2015-09-30T22:50Z] INFO  23:50:48,213 MuTect - [MUTECT] Processed 122006498 reads in 627 ms
[2015-09-30T22:50Z] INFO  23:50:48,342 MuTect - [MUTECT] Processed 292019690 reads in 629 ms
[2015-09-30T22:50Z] INFO  23:50:48,548 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:48,587 MuTect - [MUTECT] Inspected 91000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:48,786 MuTect - [MUTECT] Processed 300017249 reads in 626 ms
[2015-09-30T22:50Z] INFO  23:50:48,885 MuTect - [MUTECT] Processed 123006621 reads in 672 ms
[2015-09-30T22:50Z] INFO  23:50:49,001 MuTect - [MUTECT] Processed 293019758 reads in 659 ms
[2015-09-30T22:50Z] INFO  23:50:49,383 MuTect - [MUTECT] Inspected 92000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:49,462 MuTect - [MUTECT] Processed 301017298 reads in 676 ms
[2015-09-30T22:50Z] INFO  23:50:49,536 MuTect - [MUTECT] Processed 124006624 reads in 651 ms
[2015-09-30T22:50Z] INFO  23:50:49,696 MuTect - [MUTECT] Processed 294019883 reads in 695 ms
[2015-09-30T22:50Z] INFO  23:50:50,097 MuTect - [MUTECT] Processed 302017314 reads in 635 ms
[2015-09-30T22:50Z] INFO  23:50:50,171 MuTect - [MUTECT] Processed 125006661 reads in 635 ms
[2015-09-30T22:50Z] INFO  23:50:50,424 MuTect - [MUTECT] Processed 295019953 reads in 728 ms
[2015-09-30T22:50Z] INFO  23:50:50,703 MuTect - [MUTECT] Processed 303017444 reads in 606 ms
[2015-09-30T22:50Z] INFO  23:50:50,725 MuTect - [MUTECT] Inspected 92000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:50,808 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:50,841 MuTect - [MUTECT] Processed 126006689 reads in 670 ms
[2015-09-30T22:50Z] INFO  23:50:51,236 MuTect - [MUTECT] Processed 296019992 reads in 812 ms
[2015-09-30T22:50Z] INFO  23:50:51,264 MuTect - [MUTECT] Inspected 93000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:51,289 MuTect - [MUTECT] Processed 304017534 reads in 586 ms
[2015-09-30T22:50Z] INFO  23:50:51,483 MuTect - [MUTECT] Processed 127006808 reads in 642 ms
[2015-09-30T22:50Z] INFO  23:50:51,861 MuTect - [MUTECT] Processed 305017621 reads in 572 ms
[2015-09-30T22:50Z] INFO  23:50:52,013 MuTect - [MUTECT] Processed 297020067 reads in 777 ms
[2015-09-30T22:50Z] INFO  23:50:52,125 MuTect - [MUTECT] Processed 128006864 reads in 642 ms
[2015-09-30T22:50Z] INFO  23:50:52,437 MuTect - [MUTECT] Processed 306017709 reads in 576 ms
[2015-09-30T22:50Z] INFO  23:50:52,773 MuTect - [MUTECT] Processed 129006932 reads in 648 ms
[2015-09-30T22:50Z] INFO  23:50:52,786 MuTect - [MUTECT] Processed 298020075 reads in 773 ms
[2015-09-30T22:50Z] INFO  23:50:52,898 MuTect - [MUTECT] Inspected 93000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:52,938 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:53,055 MuTect - [MUTECT] Processed 307017768 reads in 618 ms
[2015-09-30T22:50Z] INFO  23:50:53,091 MuTect - [MUTECT] Inspected 94000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:53,435 MuTect - [MUTECT] Processed 130006938 reads in 662 ms
[2015-09-30T22:50Z] INFO  23:50:53,568 MuTect - [MUTECT] Processed 299020106 reads in 782 ms
[2015-09-30T22:50Z] INFO  23:50:53,663 MuTect - [MUTECT] Processed 308017778 reads in 608 ms
[2015-09-30T22:50Z] INFO  23:50:54,103 MuTect - [MUTECT] Processed 131007040 reads in 668 ms
[2015-09-30T22:50Z] INFO  23:50:54,253 MuTect - [MUTECT] Processed 309017841 reads in 590 ms
[2015-09-30T22:50Z] INFO  23:50:54,730 MuTect - [MUTECT] Processed 300020116 reads in 1162 ms
[2015-09-30T22:50Z] INFO  23:50:54,767 MuTect - [MUTECT] Processed 132007082 reads in 664 ms
[2015-09-30T22:50Z] INFO  23:50:54,842 MuTect - [MUTECT] Processed 310017925 reads in 589 ms
[2015-09-30T22:50Z] INFO  23:50:54,913 MuTect - [MUTECT] Inspected 95000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:55,185 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:55,419 MuTect - [MUTECT] Processed 301020182 reads in 689 ms
[2015-09-30T22:50Z] INFO  23:50:55,426 MuTect - [MUTECT] Processed 133007094 reads in 659 ms
[2015-09-30T22:50Z] INFO  23:50:55,462 MuTect - [MUTECT] Processed 311018001 reads in 620 ms
[2015-09-30T22:50Z] INFO  23:50:55,541 MuTect - [MUTECT] Inspected 94000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:56,035 MuTect - [MUTECT] Processed 312018060 reads in 573 ms
[2015-09-30T22:50Z] INFO  23:50:56,062 MuTect - [MUTECT] Processed 134007140 reads in 636 ms
[2015-09-30T22:50Z] INFO  23:50:56,109 MuTect - [MUTECT] Processed 302020236 reads in 690 ms
[2015-09-30T22:50Z] INFO  23:50:56,627 MuTect - [MUTECT] Processed 313018143 reads in 592 ms
[2015-09-30T22:50Z] INFO  23:50:56,732 MuTect - [MUTECT] Processed 135007214 reads in 670 ms
[2015-09-30T22:50Z] INFO  23:50:56,794 MuTect - [MUTECT] Processed 303020266 reads in 685 ms
[2015-09-30T22:50Z] INFO  23:50:56,906 MuTect - [MUTECT] Inspected 96000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:56,938 ProgressMeter -     20:45212433        3.98e+06   90.0 s       22.0 s     59.3%         2.5 m    61.0 s
[2015-09-30T22:50Z] INFO  23:50:57,236 MuTect - [MUTECT] Processed 314018223 reads in 609 ms
[2015-09-30T22:50Z] INFO  23:50:57,400 MuTect - [MUTECT] Processed 136007300 reads in 668 ms
[2015-09-30T22:50Z] INFO  23:50:57,480 MuTect - [MUTECT] Processed 304020334 reads in 686 ms
[2015-09-30T22:50Z] INFO  23:50:57,494 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:57,728 MuTect - [MUTECT] Inspected 95000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:57,834 MuTect - [MUTECT] Processed 315018338 reads in 598 ms
[2015-09-30T22:50Z] INFO  23:50:58,049 MuTect - [MUTECT] Processed 137007300 reads in 649 ms
[2015-09-30T22:50Z] INFO  23:50:58,123 MuTect - [MUTECT] Processed 305020421 reads in 643 ms
[2015-09-30T22:50Z] INFO  23:50:58,499 MuTect - [MUTECT] Processed 316018341 reads in 665 ms
[2015-09-30T22:50Z] INFO  23:50:58,718 MuTect - [MUTECT] Processed 138007376 reads in 669 ms
[2015-09-30T22:50Z] INFO  23:50:58,779 MuTect - [MUTECT] Processed 306020433 reads in 656 ms
[2015-09-30T22:50Z] INFO  23:50:59,108 MuTect - [MUTECT] Inspected 97000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:59,165 MuTect - [MUTECT] Processed 317018376 reads in 666 ms
[2015-09-30T22:50Z] INFO  23:50:59,392 MuTect - [MUTECT] Processed 139007430 reads in 674 ms
[2015-09-30T22:50Z] INFO  23:50:59,406 MuTect - [MUTECT] Processed 307020533 reads in 627 ms
[2015-09-30T22:50Z] INFO  23:50:59,803 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:50Z] INFO  23:50:59,828 MuTect - [MUTECT] Processed 318018471 reads in 663 ms
[2015-09-30T22:50Z] INFO  23:50:59,877 MuTect - [MUTECT] Inspected 96000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:00,014 MuTect - [MUTECT] Processed 308020590 reads in 608 ms
[2015-09-30T22:51Z] INFO  23:51:00,082 MuTect - [MUTECT] Processed 140007470 reads in 690 ms
[2015-09-30T22:51Z] INFO  23:51:00,507 MuTect - [MUTECT] Processed 319018576 reads in 679 ms
[2015-09-30T22:51Z] INFO  23:51:00,629 MuTect - [MUTECT] Processed 309020706 reads in 615 ms
[2015-09-30T22:51Z] INFO  23:51:00,780 MuTect - [MUTECT] Processed 141007548 reads in 698 ms
[2015-09-30T22:51Z] INFO  23:51:01,140 MuTect - [MUTECT] Processed 320018631 reads in 633 ms
[2015-09-30T22:51Z] INFO  23:51:01,243 MuTect - [MUTECT] Inspected 98000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:01,246 MuTect - [MUTECT] Processed 310020789 reads in 617 ms
[2015-09-30T22:51Z] INFO  23:51:01,457 MuTect - [MUTECT] Processed 142007651 reads in 676 ms
[2015-09-30T22:51Z] INFO  23:51:01,814 MuTect - [MUTECT] Processed 321018753 reads in 674 ms
[2015-09-30T22:51Z] INFO  23:51:01,877 MuTect - [MUTECT] Processed 311020838 reads in 631 ms
[2015-09-30T22:51Z] INFO  23:51:01,984 MuTect - [MUTECT] Inspected 97000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:02,146 MuTect - [MUTECT] Processed 143007688 reads in 690 ms
[2015-09-30T22:51Z] INFO  23:51:02,169 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:02,439 MuTect - [MUTECT] Processed 322018894 reads in 625 ms
[2015-09-30T22:51Z] INFO  23:51:02,502 MuTect - [MUTECT] Processed 312020925 reads in 625 ms
[2015-09-30T22:51Z] INFO  23:51:02,853 MuTect - [MUTECT] Processed 144007749 reads in 707 ms
[2015-09-30T22:51Z] INFO  23:51:03,062 MuTect - [MUTECT] Processed 323018970 reads in 623 ms
[2015-09-30T22:51Z] INFO  23:51:03,131 MuTect - [MUTECT] Processed 313021029 reads in 629 ms
[2015-09-30T22:51Z] INFO  23:51:03,500 MuTect - [MUTECT] Processed 145007802 reads in 647 ms
[2015-09-30T22:51Z] INFO  23:51:03,684 MuTect - [MUTECT] Processed 324019035 reads in 622 ms
[2015-09-30T22:51Z] INFO  23:51:03,728 MuTect - [MUTECT] Inspected 99000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:03,786 MuTect - [MUTECT] Processed 314021031 reads in 655 ms
[2015-09-30T22:51Z] INFO  23:51:03,944 MuTect - [MUTECT] Inspected 98000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:04,147 MuTect - [MUTECT] Processed 146007853 reads in 647 ms
[2015-09-30T22:51Z] INFO  23:51:04,193 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:04,295 MuTect - [MUTECT] Processed 325019136 reads in 611 ms
[2015-09-30T22:51Z] INFO  23:51:04,424 MuTect - [MUTECT] Processed 315021122 reads in 638 ms
[2015-09-30T22:51Z] INFO  23:51:04,805 MuTect - [MUTECT] Processed 147007938 reads in 658 ms
[2015-09-30T22:51Z] INFO  23:51:04,938 MuTect - [MUTECT] Processed 326019239 reads in 643 ms
[2015-09-30T22:51Z] INFO  23:51:05,078 MuTect - [MUTECT] Processed 316021154 reads in 654 ms
[2015-09-30T22:51Z] INFO  23:51:05,420 MuTect - [MUTECT] Processed 148007980 reads in 615 ms
[2015-09-30T22:51Z] INFO  23:51:05,446 ProgressMeter -     19:51920516        8.95e+06    3.5 m       23.0 s     73.0%         4.8 m    77.0 s
[2015-09-30T22:51Z] INFO  23:51:05,546 MuTect - [MUTECT] Processed 327019303 reads in 608 ms
[2015-09-30T22:51Z] INFO  23:51:05,692 MuTect - [MUTECT] Inspected 100000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:05,747 MuTect - [MUTECT] Processed 317021196 reads in 669 ms
[2015-09-30T22:51Z] INFO  23:51:06,060 MuTect - [MUTECT] Processed 149008004 reads in 640 ms
[2015-09-30T22:51Z] INFO  23:51:06,068 MuTect - [MUTECT] Inspected 99000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:06,167 MuTect - [MUTECT] Processed 328019372 reads in 621 ms
[2015-09-30T22:51Z] INFO  23:51:06,428 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:06,429 MuTect - [MUTECT] Processed 318021228 reads in 682 ms
[2015-09-30T22:51Z] INFO  23:51:06,684 MuTect - [MUTECT] Processed 150008089 reads in 624 ms
[2015-09-30T22:51Z] INFO  23:51:06,832 MuTect - [MUTECT] Processed 329019423 reads in 665 ms
[2015-09-30T22:51Z] INFO  23:51:07,085 MuTect - [MUTECT] Processed 319021272 reads in 656 ms
[2015-09-30T22:51Z] INFO  23:51:07,334 MuTect - [MUTECT] Processed 151008183 reads in 650 ms
[2015-09-30T22:51Z] INFO  23:51:07,454 MuTect - [MUTECT] Processed 330019432 reads in 622 ms
[2015-09-30T22:51Z] INFO  23:51:07,706 MuTect - [MUTECT] Processed 320021287 reads in 621 ms
[2015-09-30T22:51Z] INFO  23:51:07,818 MuTect - [MUTECT] Inspected 101000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:07,963 MuTect - [MUTECT] Processed 152008256 reads in 629 ms
[2015-09-30T22:51Z] INFO  23:51:08,113 MuTect - [MUTECT] Processed 331019509 reads in 659 ms
[2015-09-30T22:51Z] INFO  23:51:08,137 MuTect - [MUTECT] Inspected 100000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:08,353 MuTect - [MUTECT] Processed 321021372 reads in 647 ms
[2015-09-30T22:51Z] INFO  23:51:08,540 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:08,613 MuTect - [MUTECT] Processed 153008306 reads in 650 ms
[2015-09-30T22:51Z] INFO  23:51:08,765 MuTect - [MUTECT] Processed 332019604 reads in 652 ms
[2015-09-30T22:51Z] INFO  23:51:08,956 MuTect - [MUTECT] Processed 322021445 reads in 603 ms
[2015-09-30T22:51Z] INFO  23:51:09,218 MuTect - [MUTECT] Processed 154008406 reads in 605 ms
[2015-09-30T22:51Z] INFO  23:51:09,376 MuTect - [MUTECT] Processed 333019696 reads in 611 ms
[2015-09-30T22:51Z] INFO  23:51:09,548 MuTect - [MUTECT] Processed 323021454 reads in 592 ms
[2015-09-30T22:51Z] INFO  23:51:09,865 MuTect - [MUTECT] Processed 155008525 reads in 647 ms
[2015-09-30T22:51Z] INFO  23:51:09,993 MuTect - [MUTECT] Processed 334019720 reads in 617 ms
[2015-09-30T22:51Z] INFO  23:51:10,032 MuTect - [MUTECT] Inspected 102000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:10,115 MuTect - [MUTECT] Inspected 101000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:10,138 MuTect - [MUTECT] Processed 324021551 reads in 590 ms
[2015-09-30T22:51Z] INFO  23:51:10,503 MuTect - [MUTECT] Processed 156008545 reads in 638 ms
[2015-09-30T22:51Z] INFO  23:51:10,577 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:10,619 MuTect - [MUTECT] Processed 335019799 reads in 626 ms
[2015-09-30T22:51Z] INFO  23:51:10,743 MuTect - [MUTECT] Processed 325021594 reads in 605 ms
[2015-09-30T22:51Z] INFO  23:51:11,116 MuTect - [MUTECT] Processed 157008623 reads in 613 ms
[2015-09-30T22:51Z] INFO  23:51:11,255 MuTect - [MUTECT] Processed 336019867 reads in 636 ms
[2015-09-30T22:51Z] INFO  23:51:11,444 MuTect - [MUTECT] Processed 326021648 reads in 701 ms
[2015-09-30T22:51Z] INFO  23:51:11,772 MuTect - [MUTECT] Processed 158008635 reads in 656 ms
[2015-09-30T22:51Z] INFO  23:51:11,877 MuTect - [MUTECT] Processed 337019897 reads in 622 ms
[2015-09-30T22:51Z] INFO  23:51:12,072 MuTect - [MUTECT] Processed 327021728 reads in 628 ms
[2015-09-30T22:51Z] INFO  23:51:12,171 MuTect - [MUTECT] Inspected 102000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:12,226 MuTect - [MUTECT] Inspected 103000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:12,379 MuTect - [MUTECT] Processed 159008679 reads in 607 ms
[2015-09-30T22:51Z] INFO  23:51:12,527 MuTect - [MUTECT] Processed 338019925 reads in 650 ms
[2015-09-30T22:51Z] INFO  23:51:12,640 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:12,690 MuTect - [MUTECT] Processed 328021755 reads in 618 ms
[2015-09-30T22:51Z] INFO  23:51:13,007 MuTect - [MUTECT] Processed 160008764 reads in 628 ms
[2015-09-30T22:51Z] INFO  23:51:13,203 MuTect - [MUTECT] Processed 339019972 reads in 676 ms
[2015-09-30T22:51Z] INFO  23:51:13,313 MuTect - [MUTECT] Processed 329021785 reads in 623 ms
[2015-09-30T22:51Z] INFO  23:51:13,596 MuTect - [MUTECT] Processed 161008873 reads in 589 ms
[2015-09-30T22:51Z] INFO  23:51:13,910 MuTect - [MUTECT] Processed 340019986 reads in 707 ms
[2015-09-30T22:51Z] INFO  23:51:13,917 MuTect - [MUTECT] Processed 330021834 reads in 604 ms
[2015-09-30T22:51Z] INFO  23:51:14,119 MuTect - [MUTECT] Inspected 103000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:14,198 MuTect - [MUTECT] Processed 162008926 reads in 602 ms
[2015-09-30T22:51Z] INFO  23:51:14,527 MuTect - [MUTECT] Inspected 104000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:14,534 MuTect - [MUTECT] Processed 331021866 reads in 617 ms
[2015-09-30T22:51Z] INFO  23:51:14,670 MuTect - [MUTECT] Processed 341020052 reads in 760 ms
[2015-09-30T22:51Z] INFO  23:51:14,833 MuTect - [MUTECT] Processed 163008982 reads in 635 ms
[2015-09-30T22:51Z] INFO  23:51:14,860 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:15,190 MuTect - [MUTECT] Processed 332021955 reads in 656 ms
[2015-09-30T22:51Z] INFO  23:51:15,319 MuTect - [MUTECT] Processed 342020092 reads in 648 ms
[2015-09-30T22:51Z] INFO  23:51:15,451 MuTect - [MUTECT] Processed 164009034 reads in 618 ms
[2015-09-30T22:51Z] INFO  23:51:15,820 MuTect - [MUTECT] Processed 333022042 reads in 630 ms
[2015-09-30T22:51Z] INFO  23:51:16,001 MuTect - [MUTECT] Processed 343020195 reads in 683 ms
[2015-09-30T22:51Z] INFO  23:51:16,088 MuTect - [MUTECT] Processed 165009087 reads in 637 ms
[2015-09-30T22:51Z] INFO  23:51:16,118 MuTect - [MUTECT] Inspected 104000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:16,462 MuTect - [MUTECT] Processed 334022120 reads in 642 ms
[2015-09-30T22:51Z] INFO  23:51:16,665 MuTect - [MUTECT] Processed 344020266 reads in 664 ms
[2015-09-30T22:51Z] INFO  23:51:16,726 MuTect - [MUTECT] Inspected 105000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:16,734 MuTect - [MUTECT] Processed 166009133 reads in 646 ms
[2015-09-30T22:51Z] INFO  23:51:17,062 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:17,098 MuTect - [MUTECT] Processed 335022229 reads in 636 ms
[2015-09-30T22:51Z] INFO  23:51:17,267 MuTect - [MUTECT] Processed 345020319 reads in 602 ms
[2015-09-30T22:51Z] INFO  23:51:17,419 MuTect - [MUTECT] Processed 167009223 reads in 685 ms
[2015-09-30T22:51Z] INFO  23:51:17,745 MuTect - [MUTECT] Processed 336022232 reads in 647 ms
[2015-09-30T22:51Z] INFO  23:51:17,896 ProgressMeter -     19:17953510        9.46e+06    4.0 m       25.0 s     84.1%         4.8 m    45.0 s
[2015-09-30T22:51Z] INFO  23:51:17,902 MuTect - [MUTECT] Processed 346020365 reads in 635 ms
[2015-09-30T22:51Z] INFO  23:51:18,067 MuTect - [MUTECT] Inspected 105000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:18,080 MuTect - [MUTECT] Processed 168009245 reads in 661 ms
[2015-09-30T22:51Z] INFO  23:51:18,413 MuTect - [MUTECT] Processed 337022248 reads in 668 ms
[2015-09-30T22:51Z] INFO  23:51:18,588 MuTect - [MUTECT] Processed 347020374 reads in 685 ms
[2015-09-30T22:51Z] INFO  23:51:18,749 MuTect - [MUTECT] Processed 169009254 reads in 669 ms
[2015-09-30T22:51Z] INFO  23:51:19,090 MuTect - [MUTECT] Processed 338022381 reads in 677 ms
[2015-09-30T22:51Z] INFO  23:51:19,225 MuTect - [MUTECT] Inspected 106000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:19,299 MuTect - [MUTECT] Processed 348020424 reads in 712 ms
[2015-09-30T22:51Z] INFO  23:51:19,396 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:19,408 MuTect - [MUTECT] Processed 170009299 reads in 659 ms
[2015-09-30T22:51Z] INFO  23:51:19,712 MuTect - [MUTECT] Processed 339022456 reads in 622 ms
[2015-09-30T22:51Z] INFO  23:51:19,965 MuTect - [MUTECT] Processed 349020434 reads in 666 ms
[2015-09-30T22:51Z] INFO  23:51:20,043 MuTect - [MUTECT] Processed 171009359 reads in 635 ms
[2015-09-30T22:51Z] INFO  23:51:20,687 MuTect - [MUTECT] Processed 350020497 reads in 722 ms
[2015-09-30T22:51Z] INFO  23:51:20,736 MuTect - [MUTECT] Processed 172009412 reads in 693 ms
[2015-09-30T22:51Z] INFO  23:51:20,848 MuTect - [MUTECT] Inspected 106000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:20,952 MuTect - [MUTECT] Processed 340022491 reads in 1240 ms
[2015-09-30T22:51Z] INFO  23:51:21,371 MuTect - [MUTECT] Processed 351020541 reads in 684 ms
[2015-09-30T22:51Z] INFO  23:51:21,426 MuTect - [MUTECT] Processed 173009431 reads in 690 ms
[2015-09-30T22:51Z] INFO  23:51:21,585 MuTect - [MUTECT] Processed 341022607 reads in 633 ms
[2015-09-30T22:51Z] INFO  23:51:21,654 MuTect - [MUTECT] Inspected 107000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:21,693 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:22,053 MuTect - [MUTECT] Processed 174009456 reads in 627 ms
[2015-09-30T22:51Z] INFO  23:51:22,066 MuTect - [MUTECT] Processed 352020568 reads in 695 ms
[2015-09-30T22:51Z] INFO  23:51:22,221 MuTect - [MUTECT] Processed 342022632 reads in 636 ms
[2015-09-30T22:51Z] INFO  23:51:22,659 MuTect - [MUTECT] Processed 175009555 reads in 605 ms
[2015-09-30T22:51Z] INFO  23:51:22,744 MuTect - [MUTECT] Processed 353020598 reads in 678 ms
[2015-09-30T22:51Z] INFO  23:51:22,823 MuTect - [MUTECT] Processed 343022732 reads in 602 ms
[2015-09-30T22:51Z] INFO  23:51:22,858 MuTect - [MUTECT] Inspected 107000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:23,285 MuTect - [MUTECT] Processed 176009590 reads in 627 ms
[2015-09-30T22:51Z] INFO  23:51:23,426 MuTect - [MUTECT] Processed 354020638 reads in 682 ms
[2015-09-30T22:51Z] INFO  23:51:23,445 MuTect - [MUTECT] Processed 344022827 reads in 622 ms
[2015-09-30T22:51Z] INFO  23:51:23,871 MuTect - [MUTECT] Inspected 108000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:23,909 MuTect - [MUTECT] Processed 177009601 reads in 624 ms
[2015-09-30T22:51Z] INFO  23:51:23,923 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:24,062 MuTect - [MUTECT] Processed 345022896 reads in 617 ms
[2015-09-30T22:51Z] INFO  23:51:24,092 MuTect - [MUTECT] Processed 355020643 reads in 666 ms
[2015-09-30T22:51Z] INFO  23:51:24,523 MuTect - [MUTECT] Processed 178009633 reads in 614 ms
[2015-09-30T22:51Z] INFO  23:51:24,680 MuTect - [MUTECT] Processed 346022985 reads in 618 ms
[2015-09-30T22:51Z] INFO  23:51:24,717 MuTect - [MUTECT] Processed 356020742 reads in 625 ms
[2015-09-30T22:51Z] INFO  23:51:24,761 MuTect - [MUTECT] Inspected 108000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:25,148 MuTect - [MUTECT] Processed 179009748 reads in 625 ms
[2015-09-30T22:51Z] INFO  23:51:25,264 MuTect - [MUTECT] Processed 347023035 reads in 584 ms
[2015-09-30T22:51Z] INFO  23:51:25,356 MuTect - [MUTECT] Processed 357020758 reads in 639 ms
[2015-09-30T22:51Z] INFO  23:51:25,780 MuTect - [MUTECT] Processed 180009855 reads in 631 ms
[2015-09-30T22:51Z] INFO  23:51:25,902 MuTect - [MUTECT] Processed 348023042 reads in 638 ms
[2015-09-30T22:51Z] INFO  23:51:25,953 MuTect - [MUTECT] Inspected 109000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:26,017 MuTect - [MUTECT] Processed 358020769 reads in 661 ms
[2015-09-30T22:51Z] INFO  23:51:26,132 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:26,430 MuTect - [MUTECT] Processed 181009955 reads in 651 ms
[2015-09-30T22:51Z] INFO  23:51:26,526 MuTect - [MUTECT] Processed 349023120 reads in 624 ms
[2015-09-30T22:51Z] INFO  23:51:26,641 MuTect - [MUTECT] Processed 359020890 reads in 624 ms
[2015-09-30T22:51Z] INFO  23:51:26,758 MuTect - [MUTECT] Inspected 109000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:26,940 ProgressMeter -     20:56236945        5.31e+06  120.0 s       22.0 s     80.9%         2.5 m    28.0 s
[2015-09-30T22:51Z] INFO  23:51:27,080 MuTect - [MUTECT] Processed 182009981 reads in 650 ms
[2015-09-30T22:51Z] INFO  23:51:27,153 MuTect - [MUTECT] Processed 350023163 reads in 627 ms
[2015-09-30T22:51Z] INFO  23:51:27,262 MuTect - [MUTECT] Processed 360020922 reads in 621 ms
[2015-09-30T22:51Z] INFO  23:51:27,735 MuTect - [MUTECT] Processed 183010029 reads in 655 ms
[2015-09-30T22:51Z] INFO  23:51:27,779 MuTect - [MUTECT] Processed 351023218 reads in 626 ms
[2015-09-30T22:51Z] INFO  23:51:27,871 MuTect - [MUTECT] Processed 361020989 reads in 609 ms
[2015-09-30T22:51Z] INFO  23:51:27,912 MuTect - [MUTECT] Inspected 110000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:28,389 MuTect - [MUTECT] Processed 184010071 reads in 654 ms
[2015-09-30T22:51Z] INFO  23:51:28,401 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:28,433 MuTect - [MUTECT] Processed 352023232 reads in 654 ms
[2015-09-30T22:51Z] INFO  23:51:28,511 MuTect - [MUTECT] Processed 362021055 reads in 640 ms
[2015-09-30T22:51Z] INFO  23:51:28,852 MuTect - [MUTECT] Inspected 110000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:29,013 MuTect - [MUTECT] Processed 185010123 reads in 624 ms
[2015-09-30T22:51Z] INFO  23:51:29,121 MuTect - [MUTECT] Processed 353023234 reads in 688 ms
[2015-09-30T22:51Z] INFO  23:51:29,164 MuTect - [MUTECT] Processed 363021169 reads in 653 ms
[2015-09-30T22:51Z] INFO  23:51:29,663 MuTect - [MUTECT] Processed 186010160 reads in 650 ms
[2015-09-30T22:51Z] INFO  23:51:29,790 MuTect - [MUTECT] Processed 354023259 reads in 669 ms
[2015-09-30T22:51Z] INFO  23:51:29,933 MuTect - [MUTECT] Processed 364021292 reads in 769 ms
[2015-09-30T22:51Z] INFO  23:51:29,998 MuTect - [MUTECT] Inspected 111000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:30,315 MuTect - [MUTECT] Processed 187010193 reads in 652 ms
[2015-09-30T22:51Z] INFO  23:51:30,458 MuTect - [MUTECT] Processed 355023309 reads in 668 ms
[2015-09-30T22:51Z] INFO  23:51:30,548 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:30,732 MuTect - [MUTECT] Processed 365021299 reads in 799 ms
[2015-09-30T22:51Z] INFO  23:51:30,934 MuTect - [MUTECT] Inspected 111000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:30,949 MuTect - [MUTECT] Processed 188010255 reads in 634 ms
[2015-09-30T22:51Z] INFO  23:51:31,090 MuTect - [MUTECT] Processed 356023312 reads in 632 ms
[2015-09-30T22:51Z] INFO  23:51:31,437 MuTect - [MUTECT] Processed 366021311 reads in 705 ms
[2015-09-30T22:51Z] INFO  23:51:31,592 MuTect - [MUTECT] Processed 189010304 reads in 643 ms
[2015-09-30T22:51Z] INFO  23:51:31,718 MuTect - [MUTECT] Processed 357023327 reads in 628 ms
[2015-09-30T22:51Z] INFO  23:51:32,127 MuTect - [MUTECT] Inspected 112000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:32,141 MuTect - [MUTECT] Processed 367021357 reads in 704 ms
[2015-09-30T22:51Z] INFO  23:51:32,253 MuTect - [MUTECT] Processed 190010336 reads in 661 ms
[2015-09-30T22:51Z] INFO  23:51:32,381 MuTect - [MUTECT] Processed 358023405 reads in 663 ms
[2015-09-30T22:51Z] INFO  23:51:32,836 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:32,939 MuTect - [MUTECT] Processed 191010373 reads in 686 ms
[2015-09-30T22:51Z] INFO  23:51:33,052 MuTect - [MUTECT] Processed 359023482 reads in 671 ms
[2015-09-30T22:51Z] INFO  23:51:33,240 MuTect - [MUTECT] Inspected 112000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:33,342 MuTect - [MUTECT] Processed 368021473 reads in 1201 ms
[2015-09-30T22:51Z] INFO  23:51:33,609 MuTect - [MUTECT] Processed 192010378 reads in 670 ms
[2015-09-30T22:51Z] INFO  23:51:33,730 MuTect - [MUTECT] Processed 360023576 reads in 678 ms
[2015-09-30T22:51Z] INFO  23:51:33,938 MuTect - [MUTECT] Processed 369021478 reads in 596 ms
[2015-09-30T22:51Z] INFO  23:51:34,300 MuTect - [MUTECT] Processed 193010444 reads in 691 ms
[2015-09-30T22:51Z] INFO  23:51:34,355 MuTect - [MUTECT] Inspected 113000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:34,384 MuTect - [MUTECT] Processed 361023658 reads in 654 ms
[2015-09-30T22:51Z] INFO  23:51:34,551 MuTect - [MUTECT] Processed 370021568 reads in 613 ms
[2015-09-30T22:51Z] INFO  23:51:35,062 MuTect - [MUTECT] Processed 362023732 reads in 678 ms
[2015-09-30T22:51Z] INFO  23:51:35,107 MuTect - [MUTECT] Processed 194010464 reads in 807 ms
[2015-09-30T22:51Z] INFO  23:51:35,201 MuTect - [MUTECT] Processed 371021632 reads in 650 ms
[2015-09-30T22:51Z] INFO  23:51:35,410 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:35,448 ProgressMeter -     19:55048328        1.01e+07    4.0 m       23.0 s     83.9%         4.8 m    46.0 s
[2015-09-30T22:51Z] INFO  23:51:35,497 MuTect - [MUTECT] Inspected 113000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:35,739 MuTect - [MUTECT] Processed 363023774 reads in 677 ms
[2015-09-30T22:51Z] INFO  23:51:35,762 MuTect - [MUTECT] Processed 195010487 reads in 655 ms
[2015-09-30T22:51Z] INFO  23:51:35,897 MuTect - [MUTECT] Processed 372021755 reads in 696 ms
[2015-09-30T22:51Z] INFO  23:51:36,366 MuTect - [MUTECT] Inspected 114000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:36,414 MuTect - [MUTECT] Processed 364023865 reads in 675 ms
[2015-09-30T22:51Z] INFO  23:51:36,419 MuTect - [MUTECT] Processed 196010574 reads in 657 ms
[2015-09-30T22:51Z] INFO  23:51:36,631 MuTect - [MUTECT] Processed 373021792 reads in 734 ms
[2015-09-30T22:51Z] INFO  23:51:37,066 MuTect - [MUTECT] Processed 365023990 reads in 652 ms
[2015-09-30T22:51Z] INFO  23:51:37,163 MuTect - [MUTECT] Processed 197010669 reads in 744 ms
[2015-09-30T22:51Z] INFO  23:51:37,349 MuTect - [MUTECT] Processed 374021938 reads in 718 ms
[2015-09-30T22:51Z] INFO  23:51:37,653 MuTect - [MUTECT] Inspected 114000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:37,684 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:37,719 MuTect - [MUTECT] Processed 366024058 reads in 653 ms
[2015-09-30T22:51Z] INFO  23:51:37,883 MuTect - [MUTECT] Processed 198010715 reads in 720 ms
[2015-09-30T22:51Z] INFO  23:51:38,003 MuTect - [MUTECT] Processed 375021957 reads in 654 ms
[2015-09-30T22:51Z] INFO  23:51:38,378 MuTect - [MUTECT] Processed 367024142 reads in 659 ms
[2015-09-30T22:51Z] INFO  23:51:38,536 MuTect - [MUTECT] Inspected 115000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:38,562 MuTect - [MUTECT] Processed 199010794 reads in 679 ms
[2015-09-30T22:51Z] INFO  23:51:38,677 MuTect - [MUTECT] Processed 376021971 reads in 674 ms
[2015-09-30T22:51Z] INFO  23:51:39,048 MuTect - [MUTECT] Processed 368024212 reads in 670 ms
[2015-09-30T22:51Z] INFO  23:51:39,224 MuTect - [MUTECT] Processed 200010903 reads in 662 ms
[2015-09-30T22:51Z] INFO  23:51:39,334 MuTect - [MUTECT] Processed 377022036 reads in 657 ms
[2015-09-30T22:51Z] INFO  23:51:39,737 MuTect - [MUTECT] Processed 369024320 reads in 688 ms
[2015-09-30T22:51Z] INFO  23:51:39,875 MuTect - [MUTECT] Inspected 115000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:39,878 MuTect - [MUTECT] Processed 201010910 reads in 654 ms
[2015-09-30T22:51Z] INFO  23:51:39,943 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:39,958 MuTect - [MUTECT] Processed 378022061 reads in 624 ms
[2015-09-30T22:51Z] INFO  23:51:40,397 MuTect - [MUTECT] Processed 370024443 reads in 660 ms
[2015-09-30T22:51Z] INFO  23:51:40,568 MuTect - [MUTECT] Processed 202010987 reads in 690 ms
[2015-09-30T22:51Z] INFO  23:51:40,622 MuTect - [MUTECT] Processed 379022098 reads in 664 ms
[2015-09-30T22:51Z] INFO  23:51:40,778 MuTect - [MUTECT] Inspected 116000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:41,062 MuTect - [MUTECT] Processed 371024444 reads in 665 ms
[2015-09-30T22:51Z] INFO  23:51:41,226 MuTect - [MUTECT] Processed 203011059 reads in 658 ms
[2015-09-30T22:51Z] INFO  23:51:41,309 MuTect - [MUTECT] Processed 380022185 reads in 687 ms
[2015-09-30T22:51Z] INFO  23:51:41,687 MuTect - [MUTECT] Processed 372024565 reads in 626 ms
[2015-09-30T22:51Z] INFO  23:51:41,875 MuTect - [MUTECT] Processed 204011085 reads in 649 ms
[2015-09-30T22:51Z] INFO  23:51:41,953 MuTect - [MUTECT] Processed 381022212 reads in 644 ms
[2015-09-30T22:51Z] INFO  23:51:42,094 MuTect - [MUTECT] Inspected 116000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:42,263 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:42,308 MuTect - [MUTECT] Processed 373024630 reads in 621 ms
[2015-09-30T22:51Z] INFO  23:51:42,507 MuTect - [MUTECT] Processed 205011243 reads in 631 ms
[2015-09-30T22:51Z] INFO  23:51:42,562 MuTect - [MUTECT] Processed 382022292 reads in 609 ms
[2015-09-30T22:51Z] INFO  23:51:42,805 MuTect - [MUTECT] Inspected 117000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:42,934 MuTect - [MUTECT] Processed 374024732 reads in 626 ms
[2015-09-30T22:51Z] INFO  23:51:43,139 MuTect - [MUTECT] Processed 206011375 reads in 632 ms
[2015-09-30T22:51Z] INFO  23:51:43,202 MuTect - [MUTECT] Processed 383022371 reads in 640 ms
[2015-09-30T22:51Z] INFO  23:51:43,557 MuTect - [MUTECT] Processed 375024792 reads in 623 ms
[2015-09-30T22:51Z] INFO  23:51:43,787 MuTect - [MUTECT] Processed 207011464 reads in 649 ms
[2015-09-30T22:51Z] INFO  23:51:43,823 MuTect - [MUTECT] Processed 384022439 reads in 621 ms
[2015-09-30T22:51Z] INFO  23:51:44,156 MuTect - [MUTECT] Inspected 117000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:44,174 MuTect - [MUTECT] Processed 376024909 reads in 617 ms
[2015-09-30T22:51Z] INFO  23:51:44,375 MuTect - [MUTECT] Inspected 61000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:44,448 MuTect - [MUTECT] Processed 208011528 reads in 661 ms
[2015-09-30T22:51Z] INFO  23:51:44,492 MuTect - [MUTECT] Processed 385022547 reads in 669 ms
[2015-09-30T22:51Z] INFO  23:51:44,786 MuTect - [MUTECT] Inspected 118000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:44,838 MuTect - [MUTECT] Processed 377024962 reads in 664 ms
[2015-09-30T22:51Z] INFO  23:51:45,094 MuTect - [MUTECT] Processed 209011658 reads in 646 ms
[2015-09-30T22:51Z] INFO  23:51:45,121 MuTect - [MUTECT] Processed 386022653 reads in 629 ms
[2015-09-30T22:51Z] INFO  23:51:45,533 MuTect - [MUTECT] Processed 378025008 reads in 695 ms
[2015-09-30T22:51Z] INFO  23:51:45,731 MuTect - [MUTECT] Processed 387022765 reads in 610 ms
[2015-09-30T22:51Z] INFO  23:51:45,750 MuTect - [MUTECT] Processed 210011683 reads in 656 ms
[2015-09-30T22:51Z] INFO  23:51:46,242 MuTect - [MUTECT] Processed 379025058 reads in 709 ms
[2015-09-30T22:51Z] INFO  23:51:46,383 MuTect - [MUTECT] Processed 388022781 reads in 652 ms
[2015-09-30T22:51Z] INFO  23:51:46,392 MuTect - [MUTECT] Processed 211011706 reads in 642 ms
[2015-09-30T22:51Z] INFO  23:51:46,509 MuTect - [MUTECT] Inspected 62000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:46,632 MuTect - [MUTECT] Inspected 118000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:46,791 MuTect - [MUTECT] Inspected 119000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:47,008 MuTect - [MUTECT] Processed 389022829 reads in 625 ms
[2015-09-30T22:51Z] INFO  23:51:47,023 MuTect - [MUTECT] Processed 380025139 reads in 781 ms
[2015-09-30T22:51Z] INFO  23:51:47,068 MuTect - [MUTECT] Processed 212011727 reads in 676 ms
[2015-09-30T22:51Z] INFO  23:51:47,639 MuTect - [MUTECT] Processed 390022850 reads in 631 ms
[2015-09-30T22:51Z] INFO  23:51:47,706 MuTect - [MUTECT] Processed 213011761 reads in 638 ms
[2015-09-30T22:51Z] INFO  23:51:47,728 MuTect - [MUTECT] Processed 381025147 reads in 705 ms
[2015-09-30T22:51Z] INFO  23:51:47,897 ProgressMeter -     19:21366065        1.07e+07    4.5 m       25.0 s     95.7%         4.7 m    12.0 s
[2015-09-30T22:51Z] INFO  23:51:48,301 MuTect - [MUTECT] Processed 391022908 reads in 662 ms
[2015-09-30T22:51Z] INFO  23:51:48,393 MuTect - [MUTECT] Processed 214011807 reads in 687 ms
[2015-09-30T22:51Z] INFO  23:51:48,538 MuTect - [MUTECT] Processed 382025148 reads in 810 ms
[2015-09-30T22:51Z] INFO  23:51:48,736 MuTect - [MUTECT] Inspected 120000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:48,744 MuTect - [MUTECT] Inspected 63000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:48,877 MuTect - [MUTECT] Inspected 119000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:48,955 MuTect - [MUTECT] Processed 392022937 reads in 654 ms
[2015-09-30T22:51Z] INFO  23:51:49,062 MuTect - [MUTECT] Processed 215011909 reads in 669 ms
[2015-09-30T22:51Z] INFO  23:51:49,265 MuTect - [MUTECT] Processed 383025160 reads in 727 ms
[2015-09-30T22:51Z] INFO  23:51:49,598 MuTect - [MUTECT] Processed 393022991 reads in 643 ms
[2015-09-30T22:51Z] INFO  23:51:49,755 MuTect - [MUTECT] Processed 216011945 reads in 693 ms
[2015-09-30T22:51Z] INFO  23:51:49,976 MuTect - [MUTECT] Processed 384025224 reads in 711 ms
[2015-09-30T22:51Z] INFO  23:51:50,255 MuTect - [MUTECT] Processed 394023016 reads in 656 ms
[2015-09-30T22:51Z] INFO  23:51:50,419 MuTect - [MUTECT] Processed 217011975 reads in 664 ms
[2015-09-30T22:51Z] INFO  23:51:50,701 MuTect - [MUTECT] Inspected 121000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:50,720 MuTect - [MUTECT] Processed 385025231 reads in 744 ms
[2015-09-30T22:51Z] INFO  23:51:50,844 MuTect - [MUTECT] Inspected 64000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:50,873 MuTect - [MUTECT] Processed 395023022 reads in 619 ms
[2015-09-30T22:51Z] INFO  23:51:51,035 MuTect - [MUTECT] Processed 218012034 reads in 616 ms
[2015-09-30T22:51Z] INFO  23:51:51,275 MuTect - [MUTECT] Inspected 120000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:51,381 MuTect - [MUTECT] Processed 386025290 reads in 661 ms
[2015-09-30T22:51Z] INFO  23:51:51,466 MuTect - [MUTECT] Processed 396023128 reads in 593 ms
[2015-09-30T22:51Z] INFO  23:51:51,667 MuTect - [MUTECT] Processed 219012114 reads in 632 ms
[2015-09-30T22:51Z] INFO  23:51:52,045 MuTect - [MUTECT] Processed 387025303 reads in 664 ms
[2015-09-30T22:51Z] INFO  23:51:52,077 MuTect - [MUTECT] Processed 397023203 reads in 611 ms
[2015-09-30T22:51Z] INFO  23:51:52,316 MuTect - [MUTECT] Processed 220012170 reads in 649 ms
[2015-09-30T22:51Z] INFO  23:51:52,604 MuTect - [MUTECT] Inspected 122000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:52,698 MuTect - [MUTECT] Processed 398023212 reads in 621 ms
[2015-09-30T22:51Z] INFO  23:51:52,722 MuTect - [MUTECT] Processed 388025378 reads in 677 ms
[2015-09-30T22:51Z] INFO  23:51:52,963 MuTect - [MUTECT] Processed 221012206 reads in 647 ms
[2015-09-30T22:51Z] INFO  23:51:53,132 MuTect - [MUTECT] Inspected 65000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:53,298 MuTect - [MUTECT] Processed 399023309 reads in 600 ms
[2015-09-30T22:51Z] INFO  23:51:53,440 MuTect - [MUTECT] Processed 389025420 reads in 718 ms
[2015-09-30T22:51Z] INFO  23:51:53,456 MuTect - [MUTECT] Inspected 121000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:53,641 MuTect - [MUTECT] Processed 222012252 reads in 678 ms
[2015-09-30T22:51Z] INFO  23:51:53,933 MuTect - [MUTECT] Processed 400023350 reads in 635 ms
[2015-09-30T22:51Z] INFO  23:51:54,135 MuTect - [MUTECT] Processed 390025469 reads in 695 ms
[2015-09-30T22:51Z] INFO  23:51:54,268 MuTect - [MUTECT] Processed 223012296 reads in 626 ms
[2015-09-30T22:51Z] INFO  23:51:54,579 MuTect - [MUTECT] Processed 401023376 reads in 646 ms
[2015-09-30T22:51Z] INFO  23:51:54,803 MuTect - [MUTECT] Inspected 123000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:54,812 MuTect - [MUTECT] Processed 391025565 reads in 677 ms
[2015-09-30T22:51Z] INFO  23:51:54,886 MuTect - [MUTECT] Processed 224012408 reads in 619 ms
[2015-09-30T22:51Z] INFO  23:51:55,253 MuTect - [MUTECT] Processed 402023395 reads in 674 ms
[2015-09-30T22:51Z] INFO  23:51:55,409 MuTect - [MUTECT] Inspected 66000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:55,468 MuTect - [MUTECT] Processed 392025628 reads in 656 ms
[2015-09-30T22:51Z] INFO  23:51:55,604 MuTect - [MUTECT] Processed 225012499 reads in 718 ms
[2015-09-30T22:51Z] INFO  23:51:55,859 MuTect - [MUTECT] Inspected 122000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:55,911 MuTect - [MUTECT] Processed 403023411 reads in 658 ms
[2015-09-30T22:51Z] INFO  23:51:56,136 MuTect - [MUTECT] Processed 393025642 reads in 668 ms
[2015-09-30T22:51Z] INFO  23:51:56,245 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:51Z] INFO  23:51:56,248 ProgressMeter -            done        1.09e+07    4.6 m       25.0 s    100.0%         4.6 m     0.0 s
[2015-09-30T22:51Z] INFO  23:51:56,249 ProgressMeter - Total runtime 278.36 secs, 4.64 min, 0.08 hours
[2015-09-30T22:51Z] INFO  23:51:56,292 MuTect - [MUTECT] Processed 226012532 reads in 688 ms
[2015-09-30T22:51Z] INFO  23:51:56,314 MicroScheduler - 337333 reads were filtered out during the traversal out of approximately 4683946 total reads (7.20%)
[2015-09-30T22:51Z] INFO  23:51:56,314 MicroScheduler -   -> 255339 reads (5.45% of total) failing DuplicateReadFilter
[2015-09-30T22:51Z] INFO  23:51:56,315 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:51Z] INFO  23:51:56,315 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:51Z] INFO  23:51:56,315 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:51Z] INFO  23:51:56,315 MicroScheduler -   -> 81994 reads (1.75% of total) failing UnmappedReadFilter
[2015-09-30T22:51Z] INFO  23:51:56,582 MuTect - [MUTECT] Processed 404023438 reads in 671 ms
[2015-09-30T22:51Z] INFO  23:51:56,684 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:51Z] INFO  23:51:56,687 ProgressMeter -            done        6.70e+06    2.5 m       22.0 s    100.0%         2.5 m     0.0 s
[2015-09-30T22:51Z] INFO  23:51:56,687 ProgressMeter - Total runtime 149.75 secs, 2.50 min, 0.04 hours
[2015-09-30T22:51Z] INFO  23:51:56,749 MicroScheduler - 181774 reads were filtered out during the traversal out of approximately 2713197 total reads (6.70%)
[2015-09-30T22:51Z] INFO  23:51:56,749 MicroScheduler -   -> 137392 reads (5.06% of total) failing DuplicateReadFilter
[2015-09-30T22:51Z] INFO  23:51:56,749 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:51Z] INFO  23:51:56,749 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:51Z] INFO  23:51:56,750 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:51Z] INFO  23:51:56,750 MicroScheduler -   -> 44382 reads (1.64% of total) failing UnmappedReadFilter
[2015-09-30T22:51Z] INFO  23:51:57,023 MuTect - [MUTECT] Inspected 124000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:57,260 MuTect - [MUTECT] Processed 405023530 reads in 678 ms
[2015-09-30T22:51Z] INFO  23:51:57,405 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:51Z] bgzip syn3-19_0_31026185-raw-mutect.vcf
[2015-09-30T22:51Z] tabix index syn3-19_0_31026185-raw-mutect.vcf.gz
[2015-09-30T22:51Z] INFO  23:51:57,742 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:51Z] bgzip syn3-20_31018873_62038916-raw-mutect.vcf
[2015-09-30T22:51Z] tabix index syn3-20_31018873_62038916-raw-mutect.vcf.gz
[2015-09-30T22:51Z] INFO  23:51:57,963 MuTect - [MUTECT] Processed 406023563 reads in 703 ms
[2015-09-30T22:51Z] INFO  23:51:58,587 MuTect - [MUTECT] Processed 407023645 reads in 624 ms
[2015-09-30T22:51Z] INFO  23:51:59,088 MuTect - [MUTECT] Inspected 125000 potential candidates
[2015-09-30T22:51Z] INFO  23:51:59,198 MuTect - [MUTECT] Processed 408023678 reads in 611 ms
[2015-09-30T22:51Z] MuTect: MuTect
[2015-09-30T22:51Z] INFO  23:51:59,860 MuTect - [MUTECT] Processed 409023694 reads in 662 ms
[2015-09-30T22:52Z] MuTect: MuTect
[2015-09-30T22:52Z] INFO  23:52:00,508 MuTect - [MUTECT] Processed 410023708 reads in 648 ms
[2015-09-30T22:52Z] INFO  23:52:01,136 MuTect - [MUTECT] Processed 411023782 reads in 628 ms
[2015-09-30T22:52Z] INFO  23:52:01,309 MuTect - [MUTECT] Inspected 126000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:01,815 MuTect - [MUTECT] Processed 412023864 reads in 679 ms
[2015-09-30T22:52Z] INFO  23:52:02,467 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/21/syn3-21_0_31023863-raw-mutect-regions.bed to be BED
[2015-09-30T22:52Z] INFO  23:52:02,468 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/20/syn3-20_62039427_63025520-raw-mutect-regions.bed to be BED
[2015-09-30T22:52Z] INFO  23:52:02,477 MuTect - [MUTECT] Processed 413023935 reads in 662 ms
[2015-09-30T22:52Z] INFO  23:52:02,523 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:02,523 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:52Z] INFO  23:52:02,523 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:02,523 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:52Z] INFO  23:52:02,524 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:52Z] INFO  23:52:02,524 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:52Z] INFO  23:52:02,523 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:52Z] INFO  23:52:02,524 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:52Z] INFO  23:52:02,527 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/21/syn3-21_0_31023863-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/21/tx/tmpPfMF8_/syn3-21_0_31023863-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:52Z] INFO  23:52:02,527 HelpFormatter - Date/Time: 2015/09/30 23:52:02
[2015-09-30T22:52Z] INFO  23:52:02,527 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/20/syn3-20_62039427_63025520-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/20/tx/tmpje1jAw/syn3-20_62039427_63025520-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:52Z] INFO  23:52:02,527 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:02,528 HelpFormatter - Date/Time: 2015/09/30 23:52:02
[2015-09-30T22:52Z] INFO  23:52:02,527 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:02,528 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:02,528 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:02,555 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:02,555 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:02,560 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:02,560 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:02,618 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:52Z] INFO  23:52:02,668 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:52Z] INFO  23:52:02,675 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:52Z] INFO  23:52:02,680 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:52Z] INFO  23:52:02,699 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:52Z] INFO  23:52:02,711 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] INFO  23:52:02,730 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:52Z] INFO  23:52:02,738 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:52Z] INFO  23:52:02,761 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:52Z] INFO  23:52:02,773 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] INFO  23:52:02,890 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] INFO  23:52:02,951 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] INFO  23:52:02,957 IntervalUtils - Processing 352675 bp from intervals
[2015-09-30T22:52Z] INFO  23:52:02,961 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:02,962 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:03,006 IntervalUtils - Processing 181131 bp from intervals
[2015-09-30T22:52Z] INFO  23:52:03,010 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:03,011 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:03,018 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:52Z] INFO  23:52:03,064 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:52Z] INFO  23:52:03,132 MuTect - [MUTECT] Processed 414023994 reads in 655 ms
[2015-09-30T22:52Z] INFO  23:52:03,238 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:52Z] INFO  23:52:03,238 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:52Z] INFO  23:52:03,238 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:52Z] INFO  23:52:03,239 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:52Z] INFO  23:52:03,258 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:52Z] INFO  23:52:03,258 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:52Z] INFO  23:52:03,259 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:52Z] INFO  23:52:03,260 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:52Z] INFO  23:52:03,545 MuTect - [MUTECT] Inspected 127000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:03,810 MuTect - [MUTECT] Processed 415024036 reads in 678 ms
[2015-09-30T22:52Z] INFO  23:52:04,458 MuTect - [MUTECT] Processed 416024049 reads in 648 ms
[2015-09-30T22:52Z] INFO  23:52:05,101 MuTect - [MUTECT] Processed 417024158 reads in 643 ms
[2015-09-30T22:52Z] INFO  23:52:05,448 ProgressMeter -     19:57985769        1.14e+07    4.5 m       23.0 s     95.2%         4.7 m    13.0 s
[2015-09-30T22:52Z] INFO  23:52:05,670 MuTect - [MUTECT] Processed 1000070 reads in 2364 ms
[2015-09-30T22:52Z] INFO  23:52:05,788 MuTect - [MUTECT] Processed 418024190 reads in 687 ms
[2015-09-30T22:52Z] INFO  23:52:05,794 MuTect - [MUTECT] Inspected 128000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:06,072 MuTect - [MUTECT] Processed 1002852 reads in 2786 ms
[2015-09-30T22:52Z] INFO  23:52:06,508 MuTect - [MUTECT] Processed 419024277 reads in 720 ms
[2015-09-30T22:52Z] INFO  23:52:06,689 MuTect - [MUTECT] Processed 2000108 reads in 1019 ms
[2015-09-30T22:52Z] INFO  23:52:07,114 MuTect - [MUTECT] Processed 420024301 reads in 605 ms
[2015-09-30T22:52Z] INFO  23:52:07,151 MuTect - [MUTECT] Processed 2002861 reads in 1079 ms
[2015-09-30T22:52Z] INFO  23:52:07,294 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:07,409 MuTect - [MUTECT] Processed 3000149 reads in 720 ms
[2015-09-30T22:52Z] INFO  23:52:07,743 MuTect - [MUTECT] Processed 421024362 reads in 630 ms
[2015-09-30T22:52Z] INFO  23:52:07,958 MuTect - [MUTECT] Inspected 129000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:08,061 MuTect - [MUTECT] Processed 3003098 reads in 910 ms
[2015-09-30T22:52Z] INFO  23:52:08,090 MuTect - [MUTECT] Processed 4000165 reads in 681 ms
[2015-09-30T22:52Z] INFO  23:52:08,408 MuTect - [MUTECT] Processed 422024457 reads in 665 ms
[2015-09-30T22:52Z] INFO  23:52:08,810 MuTect - [MUTECT] Processed 5000219 reads in 720 ms
[2015-09-30T22:52Z] INFO  23:52:08,897 MuTect - [MUTECT] Processed 4003210 reads in 836 ms
[2015-09-30T22:52Z] INFO  23:52:09,043 MuTect - [MUTECT] Processed 423024552 reads in 635 ms
[2015-09-30T22:52Z] INFO  23:52:09,565 MuTect - [MUTECT] Processed 6000238 reads in 755 ms
[2015-09-30T22:52Z] INFO  23:52:09,595 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:09,690 MuTect - [MUTECT] Processed 424024626 reads in 647 ms
[2015-09-30T22:52Z] INFO  23:52:10,075 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:10,260 MuTect - [MUTECT] Processed 7000349 reads in 695 ms
[2015-09-30T22:52Z] INFO  23:52:10,289 MuTect - [MUTECT] Inspected 130000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:10,305 MuTect - [MUTECT] Processed 425024655 reads in 615 ms
[2015-09-30T22:52Z] INFO  23:52:10,650 MuTect - [MUTECT] Processed 5003298 reads in 1753 ms
[2015-09-30T22:52Z] INFO  23:52:10,908 MuTect - [MUTECT] Processed 426024717 reads in 603 ms
[2015-09-30T22:52Z] INFO  23:52:10,985 MuTect - [MUTECT] Processed 8000451 reads in 725 ms
[2015-09-30T22:52Z] INFO  23:52:11,515 MuTect - [MUTECT] Processed 427024789 reads in 607 ms
[2015-09-30T22:52Z] INFO  23:52:11,708 MuTect - [MUTECT] Processed 9000516 reads in 723 ms
[2015-09-30T22:52Z] INFO  23:52:11,815 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:11,847 MuTect - [MUTECT] Processed 6003449 reads in 1197 ms
[2015-09-30T22:52Z] INFO  23:52:12,143 MuTect - [MUTECT] Processed 428024888 reads in 628 ms
[2015-09-30T22:52Z] INFO  23:52:12,316 MuTect - [MUTECT] Inspected 131000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:12,390 MuTect - [MUTECT] Processed 10000606 reads in 682 ms
[2015-09-30T22:52Z] INFO  23:52:12,768 MuTect - [MUTECT] Processed 429024979 reads in 625 ms
[2015-09-30T22:52Z] INFO  23:52:13,080 MuTect - [MUTECT] Processed 11000613 reads in 689 ms
[2015-09-30T22:52Z] INFO  23:52:13,343 MuTect - [MUTECT] Processed 7003460 reads in 1496 ms
[2015-09-30T22:52Z] INFO  23:52:13,400 MuTect - [MUTECT] Processed 430025064 reads in 632 ms
[2015-09-30T22:52Z] INFO  23:52:13,789 MuTect - [MUTECT] Processed 12000730 reads in 710 ms
[2015-09-30T22:52Z] INFO  23:52:14,001 MuTect - [MUTECT] Processed 431025105 reads in 601 ms
[2015-09-30T22:52Z] INFO  23:52:14,134 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:14,253 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:14,258 MuTect - [MUTECT] Processed 8003517 reads in 915 ms
[2015-09-30T22:52Z] INFO  23:52:14,375 MuTect - [MUTECT] Inspected 132000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:14,542 MuTect - [MUTECT] Processed 13000764 reads in 753 ms
[2015-09-30T22:52Z] INFO  23:52:14,610 MuTect - [MUTECT] Processed 432025178 reads in 609 ms
[2015-09-30T22:52Z] INFO  23:52:15,153 MuTect - [MUTECT] Processed 9003537 reads in 894 ms
[2015-09-30T22:52Z] INFO  23:52:15,219 MuTect - [MUTECT] Processed 433025260 reads in 609 ms
[2015-09-30T22:52Z] INFO  23:52:15,230 MuTect - [MUTECT] Processed 14000779 reads in 688 ms
[2015-09-30T22:52Z] INFO  23:52:15,820 MuTect - [MUTECT] Processed 434025369 reads in 601 ms
[2015-09-30T22:52Z] INFO  23:52:15,891 MuTect - [MUTECT] Processed 15000843 reads in 661 ms
[2015-09-30T22:52Z] INFO  23:52:15,958 MuTect - [MUTECT] Processed 10003545 reads in 806 ms
[2015-09-30T22:52Z] INFO  23:52:16,403 MuTect - [MUTECT] Processed 435025459 reads in 583 ms
[2015-09-30T22:52Z] INFO  23:52:16,445 MuTect - [MUTECT] Inspected 133000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:16,527 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:16,596 MuTect - [MUTECT] Processed 16000936 reads in 705 ms
[2015-09-30T22:52Z] INFO  23:52:16,726 MuTect - [MUTECT] Processed 11003556 reads in 768 ms
[2015-09-30T22:52Z] INFO  23:52:16,991 MuTect - [MUTECT] Processed 436025564 reads in 588 ms
[2015-09-30T22:52Z] INFO  23:52:17,026 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:17,287 MuTect - [MUTECT] Processed 17000950 reads in 691 ms
[2015-09-30T22:52Z] INFO  23:52:17,468 MuTect - [MUTECT] Processed 12003590 reads in 742 ms
[2015-09-30T22:52Z] INFO  23:52:17,585 MuTect - [MUTECT] Processed 437025580 reads in 594 ms
[2015-09-30T22:52Z] INFO  23:52:17,958 MuTect - [MUTECT] Processed 18001016 reads in 671 ms
[2015-09-30T22:52Z] INFO  23:52:18,179 MuTect - [MUTECT] Processed 438025662 reads in 594 ms
[2015-09-30T22:52Z] INFO  23:52:18,227 MuTect - [MUTECT] Processed 13003609 reads in 759 ms
[2015-09-30T22:52Z] INFO  23:52:18,396 MuTect - [MUTECT] Inspected 134000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:18,625 MuTect - [MUTECT] Processed 19001138 reads in 667 ms
[2015-09-30T22:52Z] INFO  23:52:18,813 MuTect - [MUTECT] Processed 439025671 reads in 634 ms
[2015-09-30T22:52Z] INFO  23:52:18,917 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:18,981 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:52Z] INFO  23:52:18,996 MuTect - [MUTECT] Processed 14003649 reads in 768 ms
[2015-09-30T22:52Z] INFO  23:52:19,132 ProgressMeter -            done        1.18e+07    4.7 m       23.0 s    100.0%         4.7 m     0.0 s
[2015-09-30T22:52Z] INFO  23:52:19,132 ProgressMeter - Total runtime 283.69 secs, 4.73 min, 0.08 hours
[2015-09-30T22:52Z] INFO  23:52:19,198 MicroScheduler - 357718 reads were filtered out during the traversal out of approximately 5186646 total reads (6.90%)
[2015-09-30T22:52Z] INFO  23:52:19,198 MicroScheduler -   -> 268706 reads (5.18% of total) failing DuplicateReadFilter
[2015-09-30T22:52Z] INFO  23:52:19,198 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:52Z] INFO  23:52:19,198 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:52Z] INFO  23:52:19,198 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:52Z] INFO  23:52:19,198 MicroScheduler -   -> 89012 reads (1.72% of total) failing UnmappedReadFilter
[2015-09-30T22:52Z] INFO  23:52:19,297 MuTect - [MUTECT] Processed 20001189 reads in 672 ms
[2015-09-30T22:52Z] INFO  23:52:19,746 MuTect - [MUTECT] Processed 15003664 reads in 751 ms
[2015-09-30T22:52Z] INFO  23:52:19,851 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:19,971 MuTect - [MUTECT] Processed 21001251 reads in 674 ms
[2015-09-30T22:52Z] INFO  23:52:20,272 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:52Z] bgzip syn3-19_31038548_59128983-raw-mutect.vcf
[2015-09-30T22:52Z] INFO  23:52:20,500 MuTect - [MUTECT] Processed 16003698 reads in 754 ms
[2015-09-30T22:52Z] tabix index syn3-19_31038548_59128983-raw-mutect.vcf.gz
[2015-09-30T22:52Z] INFO  23:52:20,648 MuTect - [MUTECT] Processed 22001280 reads in 677 ms
[2015-09-30T22:52Z] INFO  23:52:20,948 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:52Z] INFO  23:52:20,952 ProgressMeter -            done        5.85e+05   17.0 s       30.0 s    100.0%        17.0 s     0.0 s
[2015-09-30T22:52Z] INFO  23:52:20,953 ProgressMeter - Total runtime 17.69 secs, 0.29 min, 0.00 hours
[2015-09-30T22:52Z] INFO  23:52:21,017 MicroScheduler - 19757 reads were filtered out during the traversal out of approximately 267179 total reads (7.39%)
[2015-09-30T22:52Z] INFO  23:52:21,017 MicroScheduler -   -> 15235 reads (5.70% of total) failing DuplicateReadFilter
[2015-09-30T22:52Z] INFO  23:52:21,018 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:52Z] INFO  23:52:21,018 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:52Z] INFO  23:52:21,018 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:52Z] INFO  23:52:21,018 MicroScheduler -   -> 4522 reads (1.69% of total) failing UnmappedReadFilter
[2015-09-30T22:52Z] INFO  23:52:21,280 MuTect - [MUTECT] Processed 17003713 reads in 780 ms
[2015-09-30T22:52Z] INFO  23:52:21,994 MuTect - [MUTECT] Processed 18003759 reads in 714 ms
[2015-09-30T22:52Z] INFO  23:52:22,029 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:52Z] INFO  23:52:22,367 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:22,668 MuTect - [MUTECT] Processed 19003785 reads in 674 ms
[2015-09-30T22:52Z] INFO  23:52:23,317 MuTect - [MUTECT] Processed 20003839 reads in 649 ms
[2015-09-30T22:52Z] bgzip syn3-20_62039427_63025520-raw-mutect.vcf
[2015-09-30T22:52Z] tabix index syn3-20_62039427_63025520-raw-mutect.vcf.gz
[2015-09-30T22:52Z] INFO  23:52:23,979 MuTect - [MUTECT] Processed 21003839 reads in 662 ms
[2015-09-30T22:52Z] MuTect: MuTect
[2015-09-30T22:52Z] INFO  23:52:24,740 MuTect - [MUTECT] Processed 22003869 reads in 761 ms
[2015-09-30T22:52Z] INFO  23:52:24,809 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:25,471 MuTect - [MUTECT] Processed 23003946 reads in 731 ms
[2015-09-30T22:52Z] INFO  23:52:26,183 MuTect - [MUTECT] Processed 24003974 reads in 712 ms
[2015-09-30T22:52Z] INFO  23:52:26,260 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/21/syn3-21_31026814_48129895-raw-mutect-regions.bed to be BED
[2015-09-30T22:52Z] INFO  23:52:26,319 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:26,319 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:52Z] INFO  23:52:26,319 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:52Z] INFO  23:52:26,319 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:52Z] INFO  23:52:26,323 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/21/syn3-21_31026814_48129895-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/21/tx/tmpbFvSxa/syn3-21_31026814_48129895-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:52Z] INFO  23:52:26,323 HelpFormatter - Date/Time: 2015/09/30 23:52:26
[2015-09-30T22:52Z] INFO  23:52:26,323 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:26,323 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:26,350 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:26,355 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:26,404 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:52Z] MuTect: MuTect
[2015-09-30T22:52Z] INFO  23:52:26,455 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:52Z] INFO  23:52:26,463 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:52Z] INFO  23:52:26,486 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:52Z] INFO  23:52:26,498 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] INFO  23:52:26,674 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] INFO  23:52:26,776 IntervalUtils - Processing 1326168 bp from intervals
[2015-09-30T22:52Z] INFO  23:52:26,780 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:26,780 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:26,901 MuTect - [MUTECT] Processed 25004009 reads in 718 ms
[2015-09-30T22:52Z] INFO  23:52:26,959 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:52Z] INFO  23:52:27,119 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:52Z] INFO  23:52:27,119 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:52Z] INFO  23:52:27,119 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:52Z] INFO  23:52:27,120 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:52Z] INFO  23:52:27,580 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:27,610 MuTect - [MUTECT] Processed 26004011 reads in 709 ms
[2015-09-30T22:52Z] INFO  23:52:27,963 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:52Z] INFO  23:52:27,967 ProgressMeter -            done        8.08e+05   24.0 s       30.0 s    100.0%        24.0 s     0.0 s
[2015-09-30T22:52Z] INFO  23:52:27,967 ProgressMeter - Total runtime 24.73 secs, 0.41 min, 0.01 hours
[2015-09-30T22:52Z] INFO  23:52:28,034 MicroScheduler - 20382 reads were filtered out during the traversal out of approximately 319641 total reads (6.38%)
[2015-09-30T22:52Z] INFO  23:52:28,034 MicroScheduler -   -> 15441 reads (4.83% of total) failing DuplicateReadFilter
[2015-09-30T22:52Z] INFO  23:52:28,034 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:52Z] INFO  23:52:28,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:52Z] INFO  23:52:28,034 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:52Z] INFO  23:52:28,035 MicroScheduler -   -> 4941 reads (1.55% of total) failing UnmappedReadFilter
[2015-09-30T22:52Z] INFO  23:52:28,754 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/22/syn3-22_0_31019358-raw-mutect-regions.bed to be BED
[2015-09-30T22:52Z] INFO  23:52:28,809 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:28,810 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:52Z] INFO  23:52:28,810 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:52Z] INFO  23:52:28,810 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:52Z] INFO  23:52:28,813 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/22/syn3-22_0_31019358-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/22/tx/tmp7VTltF/syn3-22_0_31019358-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:52Z] INFO  23:52:28,814 HelpFormatter - Date/Time: 2015/09/30 23:52:28
[2015-09-30T22:52Z] INFO  23:52:28,814 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:28,814 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:28,841 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:28,845 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:28,981 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:52Z] INFO  23:52:29,029 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:52Z] INFO  23:52:29,036 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:52Z] INFO  23:52:29,057 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:52Z] INFO  23:52:29,059 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:52Z] INFO  23:52:29,071 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] bgzip syn3-21_0_31023863-raw-mutect.vcf
[2015-09-30T22:52Z] INFO  23:52:29,247 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] INFO  23:52:29,351 IntervalUtils - Processing 1534650 bp from intervals
[2015-09-30T22:52Z] INFO  23:52:29,355 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:29,355 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:29,525 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:52Z] INFO  23:52:29,692 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:52Z] INFO  23:52:29,692 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:52Z] INFO  23:52:29,693 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:52Z] INFO  23:52:29,694 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:52Z] INFO  23:52:29,721 MuTect - [MUTECT] Processed 1000028 reads in 2551 ms
[2015-09-30T22:52Z] tabix index syn3-21_0_31023863-raw-mutect.vcf.gz
[2015-09-30T22:52Z] INFO  23:52:30,648 MuTect - [MUTECT] Processed 2000041 reads in 928 ms
[2015-09-30T22:52Z] INFO  23:52:31,439 MuTect - [MUTECT] Processed 3000109 reads in 791 ms
[2015-09-30T22:52Z] INFO  23:52:32,023 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:52Z] MuTect: MuTect
[2015-09-30T22:52Z] INFO  23:52:32,188 MuTect - [MUTECT] Processed 4000139 reads in 749 ms
[2015-09-30T22:52Z] INFO  23:52:32,327 MuTect - [MUTECT] Processed 1000137 reads in 2401 ms
[2015-09-30T22:52Z] INFO  23:52:32,934 MuTect - [MUTECT] Processed 5000139 reads in 745 ms
[2015-09-30T22:52Z] INFO  23:52:33,267 MuTect - [MUTECT] Processed 2000291 reads in 940 ms
[2015-09-30T22:52Z] INFO  23:52:33,641 MuTect - [MUTECT] Processed 6000159 reads in 708 ms
[2015-09-30T22:52Z] INFO  23:52:34,278 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/22/syn3-22_31022170_51304566-raw-mutect-regions.bed to be BED
[2015-09-30T22:52Z] INFO  23:52:34,336 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:34,336 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:52Z] INFO  23:52:34,337 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:52Z] INFO  23:52:34,337 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:52Z] INFO  23:52:34,340 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/22/syn3-22_31022170_51304566-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/22/tx/tmp5t_1bD/syn3-22_31022170_51304566-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:52Z] INFO  23:52:34,340 HelpFormatter - Date/Time: 2015/09/30 23:52:34
[2015-09-30T22:52Z] INFO  23:52:34,340 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:34,341 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:52Z] INFO  23:52:34,369 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:34,373 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:52Z] INFO  23:52:34,384 MuTect - [MUTECT] Processed 7000276 reads in 743 ms
[2015-09-30T22:52Z] INFO  23:52:34,424 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:52Z] INFO  23:52:34,473 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:52Z] INFO  23:52:34,481 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:52Z] INFO  23:52:34,505 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:52Z] INFO  23:52:34,516 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] INFO  23:52:34,518 MuTect - [MUTECT] Processed 3000359 reads in 1251 ms
[2015-09-30T22:52Z] INFO  23:52:34,602 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:34,692 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:52Z] INFO  23:52:34,805 IntervalUtils - Processing 1855729 bp from intervals
[2015-09-30T22:52Z] INFO  23:52:34,810 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:34,810 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:52Z] INFO  23:52:35,107 MuTect - [MUTECT] Processed 8000341 reads in 723 ms
[2015-09-30T22:52Z] INFO  23:52:35,211 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:52Z] INFO  23:52:35,249 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:35,283 MuTect - [MUTECT] Processed 4000368 reads in 765 ms
[2015-09-30T22:52Z] INFO  23:52:35,390 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:52Z] INFO  23:52:35,390 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:52Z] INFO  23:52:35,390 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:52Z] INFO  23:52:35,391 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:52Z] INFO  23:52:35,796 MuTect - [MUTECT] Processed 9000406 reads in 688 ms
[2015-09-30T22:52Z] INFO  23:52:36,094 MuTect - [MUTECT] Processed 5000380 reads in 811 ms
[2015-09-30T22:52Z] INFO  23:52:36,493 MuTect - [MUTECT] Processed 10000408 reads in 698 ms
[2015-09-30T22:52Z] INFO  23:52:36,871 MuTect - [MUTECT] Processed 6000415 reads in 777 ms
[2015-09-30T22:52Z] INFO  23:52:37,088 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:37,183 MuTect - [MUTECT] Processed 11000502 reads in 690 ms
[2015-09-30T22:52Z] INFO  23:52:37,564 MuTect - [MUTECT] Processed 7000421 reads in 693 ms
[2015-09-30T22:52Z] INFO  23:52:37,574 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:37,793 MuTect - [MUTECT] Processed 1000067 reads in 2354 ms
[2015-09-30T22:52Z] INFO  23:52:37,923 MuTect - [MUTECT] Processed 12000556 reads in 740 ms
[2015-09-30T22:52Z] INFO  23:52:38,258 MuTect - [MUTECT] Processed 8000443 reads in 693 ms
[2015-09-30T22:52Z] INFO  23:52:38,534 MuTect - [MUTECT] Processed 2000143 reads in 741 ms
[2015-09-30T22:52Z] INFO  23:52:38,642 MuTect - [MUTECT] Processed 13000604 reads in 719 ms
[2015-09-30T22:52Z] INFO  23:52:38,957 MuTect - [MUTECT] Processed 9000467 reads in 700 ms
[2015-09-30T22:52Z] INFO  23:52:39,252 MuTect - [MUTECT] Processed 3000168 reads in 718 ms
[2015-09-30T22:52Z] INFO  23:52:39,346 MuTect - [MUTECT] Processed 14000659 reads in 703 ms
[2015-09-30T22:52Z] INFO  23:52:39,548 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:39,598 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:39,640 MuTect - [MUTECT] Processed 10000511 reads in 683 ms
[2015-09-30T22:52Z] INFO  23:52:39,906 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:39,956 MuTect - [MUTECT] Processed 4000203 reads in 704 ms
[2015-09-30T22:52Z] INFO  23:52:40,082 MuTect - [MUTECT] Processed 15000695 reads in 737 ms
[2015-09-30T22:52Z] INFO  23:52:40,310 MuTect - [MUTECT] Processed 11000525 reads in 669 ms
[2015-09-30T22:52Z] INFO  23:52:40,651 MuTect - [MUTECT] Processed 5000273 reads in 694 ms
[2015-09-30T22:52Z] INFO  23:52:40,847 MuTect - [MUTECT] Processed 16000725 reads in 765 ms
[2015-09-30T22:52Z] INFO  23:52:41,011 MuTect - [MUTECT] Processed 12000534 reads in 702 ms
[2015-09-30T22:52Z] INFO  23:52:41,365 MuTect - [MUTECT] Processed 6000299 reads in 715 ms
[2015-09-30T22:52Z] INFO  23:52:41,530 MuTect - [MUTECT] Processed 17000814 reads in 683 ms
[2015-09-30T22:52Z] INFO  23:52:41,621 MuTect - [MUTECT] Processed 13000545 reads in 609 ms
[2015-09-30T22:52Z] INFO  23:52:41,796 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:42,086 MuTect - [MUTECT] Processed 7000408 reads in 721 ms
[2015-09-30T22:52Z] INFO  23:52:42,104 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:42,143 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:42,244 MuTect - [MUTECT] Processed 18000876 reads in 714 ms
[2015-09-30T22:52Z] INFO  23:52:42,256 MuTect - [MUTECT] Processed 14000629 reads in 636 ms
[2015-09-30T22:52Z] INFO  23:52:42,815 MuTect - [MUTECT] Processed 8000469 reads in 729 ms
[2015-09-30T22:52Z] INFO  23:52:42,875 MuTect - [MUTECT] Processed 15000692 reads in 619 ms
[2015-09-30T22:52Z] INFO  23:52:42,970 MuTect - [MUTECT] Processed 19000953 reads in 726 ms
[2015-09-30T22:52Z] INFO  23:52:43,509 MuTect - [MUTECT] Processed 9000547 reads in 694 ms
[2015-09-30T22:52Z] INFO  23:52:43,523 MuTect - [MUTECT] Processed 16000695 reads in 648 ms
[2015-09-30T22:52Z] INFO  23:52:43,651 MuTect - [MUTECT] Processed 20000976 reads in 681 ms
[2015-09-30T22:52Z] INFO  23:52:43,943 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:44,234 MuTect - [MUTECT] Processed 10000620 reads in 725 ms
[2015-09-30T22:52Z] INFO  23:52:44,243 MuTect - [MUTECT] Processed 17000867 reads in 720 ms
[2015-09-30T22:52Z] INFO  23:52:44,321 MuTect - [MUTECT] Processed 21001032 reads in 670 ms
[2015-09-30T22:52Z] INFO  23:52:44,519 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:44,836 MuTect - [MUTECT] Processed 18000990 reads in 593 ms
[2015-09-30T22:52Z] INFO  23:52:44,947 MuTect - [MUTECT] Processed 11000635 reads in 713 ms
[2015-09-30T22:52Z] INFO  23:52:44,953 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:44,975 MuTect - [MUTECT] Processed 22001051 reads in 654 ms
[2015-09-30T22:52Z] INFO  23:52:45,472 MuTect - [MUTECT] Processed 19001171 reads in 636 ms
[2015-09-30T22:52Z] INFO  23:52:45,642 MuTect - [MUTECT] Processed 23001143 reads in 667 ms
[2015-09-30T22:52Z] INFO  23:52:45,664 MuTect - [MUTECT] Processed 12000671 reads in 717 ms
[2015-09-30T22:52Z] INFO  23:52:46,296 MuTect - [MUTECT] Processed 20001545 reads in 824 ms
[2015-09-30T22:52Z] INFO  23:52:46,320 MuTect - [MUTECT] Processed 24001186 reads in 678 ms
[2015-09-30T22:52Z] INFO  23:52:46,367 MuTect - [MUTECT] Processed 13000678 reads in 703 ms
[2015-09-30T22:52Z] INFO  23:52:46,456 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:46,937 MuTect - [MUTECT] Processed 21001876 reads in 641 ms
[2015-09-30T22:52Z] INFO  23:52:46,968 MuTect - [MUTECT] Processed 25001247 reads in 648 ms
[2015-09-30T22:52Z] INFO  23:52:46,999 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:47,046 MuTect - [MUTECT] Processed 14000732 reads in 679 ms
[2015-09-30T22:52Z] INFO  23:52:47,667 MuTect - [MUTECT] Processed 26001285 reads in 698 ms
[2015-09-30T22:52Z] INFO  23:52:47,734 MuTect - [MUTECT] Processed 15000765 reads in 688 ms
[2015-09-30T22:52Z] INFO  23:52:47,860 MuTect - [MUTECT] Processed 22002077 reads in 923 ms
[2015-09-30T22:52Z] INFO  23:52:48,335 MuTect - [MUTECT] Processed 27001322 reads in 669 ms
[2015-09-30T22:52Z] INFO  23:52:48,405 MuTect - [MUTECT] Processed 16000837 reads in 671 ms
[2015-09-30T22:52Z] INFO  23:52:48,785 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:48,831 MuTect - [MUTECT] Processed 23002177 reads in 971 ms
[2015-09-30T22:52Z] INFO  23:52:49,010 MuTect - [MUTECT] Processed 28001377 reads in 675 ms
[2015-09-30T22:52Z] INFO  23:52:49,105 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:49,144 MuTect - [MUTECT] Processed 17000841 reads in 739 ms
[2015-09-30T22:52Z] INFO  23:52:49,527 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:49,536 MuTect - [MUTECT] Processed 24002205 reads in 705 ms
[2015-09-30T22:52Z] INFO  23:52:49,733 MuTect - [MUTECT] Processed 29001444 reads in 723 ms
[2015-09-30T22:52Z] INFO  23:52:49,834 MuTect - [MUTECT] Processed 18000899 reads in 690 ms
[2015-09-30T22:52Z] INFO  23:52:50,254 MuTect - [MUTECT] Processed 25002220 reads in 717 ms
[2015-09-30T22:52Z] INFO  23:52:50,426 MuTect - [MUTECT] Processed 30001508 reads in 692 ms
[2015-09-30T22:52Z] INFO  23:52:50,520 MuTect - [MUTECT] Processed 19000992 reads in 686 ms
[2015-09-30T22:52Z] INFO  23:52:50,922 MuTect - [MUTECT] Processed 26002235 reads in 668 ms
[2015-09-30T22:52Z] INFO  23:52:51,140 MuTect - [MUTECT] Processed 31001542 reads in 715 ms
[2015-09-30T22:52Z] INFO  23:52:51,222 MuTect - [MUTECT] Processed 20001009 reads in 702 ms
[2015-09-30T22:52Z] INFO  23:52:51,232 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:51,436 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:51,566 MuTect - [MUTECT] Processed 27002294 reads in 645 ms
[2015-09-30T22:52Z] INFO  23:52:51,858 MuTect - [MUTECT] Processed 32001600 reads in 718 ms
[2015-09-30T22:52Z] INFO  23:52:52,023 MuTect - [MUTECT] Processed 21001029 reads in 801 ms
[2015-09-30T22:52Z] INFO  23:52:52,084 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:52,176 MuTect - [MUTECT] Processed 28002330 reads in 610 ms
[2015-09-30T22:52Z] INFO  23:52:52,541 MuTect - [MUTECT] Processed 33001662 reads in 683 ms
[2015-09-30T22:52Z] INFO  23:52:52,718 MuTect - [MUTECT] Processed 22001046 reads in 695 ms
[2015-09-30T22:52Z] INFO  23:52:52,795 MuTect - [MUTECT] Processed 29002356 reads in 619 ms
[2015-09-30T22:52Z] INFO  23:52:53,226 MuTect - [MUTECT] Processed 34001664 reads in 685 ms
[2015-09-30T22:52Z] INFO  23:52:53,404 MuTect - [MUTECT] Processed 23001093 reads in 686 ms
[2015-09-30T22:52Z] INFO  23:52:53,413 MuTect - [MUTECT] Processed 30002422 reads in 618 ms
[2015-09-30T22:52Z] INFO  23:52:53,652 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:53,848 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:53,935 MuTect - [MUTECT] Processed 35001676 reads in 709 ms
[2015-09-30T22:52Z] INFO  23:52:54,028 MuTect - [MUTECT] Processed 31002483 reads in 615 ms
[2015-09-30T22:52Z] INFO  23:52:54,106 MuTect - [MUTECT] Processed 24001153 reads in 702 ms
[2015-09-30T22:52Z] INFO  23:52:54,558 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:54,622 MuTect - [MUTECT] Processed 36001733 reads in 687 ms
[2015-09-30T22:52Z] INFO  23:52:54,651 MuTect - [MUTECT] Processed 32002544 reads in 623 ms
[2015-09-30T22:52Z] INFO  23:52:54,813 MuTect - [MUTECT] Processed 25001157 reads in 707 ms
[2015-09-30T22:52Z] INFO  23:52:55,285 MuTect - [MUTECT] Processed 33002574 reads in 634 ms
[2015-09-30T22:52Z] INFO  23:52:55,291 MuTect - [MUTECT] Processed 37001832 reads in 669 ms
[2015-09-30T22:52Z] INFO  23:52:55,499 MuTect - [MUTECT] Processed 26001245 reads in 685 ms
[2015-09-30T22:52Z] INFO  23:52:55,677 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:55,909 MuTect - [MUTECT] Processed 34002632 reads in 624 ms
[2015-09-30T22:52Z] INFO  23:52:55,981 MuTect - [MUTECT] Processed 38001958 reads in 690 ms
[2015-09-30T22:52Z] INFO  23:52:56,218 MuTect - [MUTECT] Processed 27001310 reads in 720 ms
[2015-09-30T22:52Z] INFO  23:52:56,253 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:56,532 MuTect - [MUTECT] Processed 35002750 reads in 623 ms
[2015-09-30T22:52Z] INFO  23:52:56,672 MuTect - [MUTECT] Processed 39001972 reads in 691 ms
[2015-09-30T22:52Z] INFO  23:52:56,923 MuTect - [MUTECT] Processed 28001364 reads in 705 ms
[2015-09-30T22:52Z] INFO  23:52:56,972 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:57,122 ProgressMeter -     21:38522269        1.34e+06   30.0 s       22.0 s     35.4%        84.0 s    54.0 s
[2015-09-30T22:52Z] INFO  23:52:57,138 MuTect - [MUTECT] Processed 36002867 reads in 606 ms
[2015-09-30T22:52Z] INFO  23:52:57,409 MuTect - [MUTECT] Processed 40002002 reads in 737 ms
[2015-09-30T22:52Z] INFO  23:52:57,583 MuTect - [MUTECT] Processed 29001499 reads in 660 ms
[2015-09-30T22:52Z] INFO  23:52:57,797 MuTect - [MUTECT] Processed 37002892 reads in 659 ms
[2015-09-30T22:52Z] INFO  23:52:57,849 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:58,263 MuTect - [MUTECT] Processed 30001624 reads in 680 ms
[2015-09-30T22:52Z] INFO  23:52:58,267 MuTect - [MUTECT] Processed 41002053 reads in 858 ms
[2015-09-30T22:52Z] INFO  23:52:58,438 MuTect - [MUTECT] Processed 38003018 reads in 641 ms
[2015-09-30T22:52Z] INFO  23:52:58,538 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:58,935 MuTect - [MUTECT] Processed 42002060 reads in 668 ms
[2015-09-30T22:52Z] INFO  23:52:58,945 MuTect - [MUTECT] Processed 31001627 reads in 682 ms
[2015-09-30T22:52Z] INFO  23:52:59,161 MuTect - [MUTECT] Processed 39003148 reads in 723 ms
[2015-09-30T22:52Z] INFO  23:52:59,523 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:52Z] INFO  23:52:59,605 MuTect - [MUTECT] Processed 43002124 reads in 670 ms
[2015-09-30T22:52Z] INFO  23:52:59,636 MuTect - [MUTECT] Processed 32001682 reads in 691 ms
[2015-09-30T22:52Z] INFO  23:52:59,695 ProgressMeter -     22:19961584        9.87e+05   30.0 s       30.0 s     23.2%         2.2 m    99.0 s
[2015-09-30T22:52Z] INFO  23:52:59,803 MuTect - [MUTECT] Processed 40003218 reads in 642 ms
[2015-09-30T22:52Z] INFO  23:52:59,985 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:00,293 MuTect - [MUTECT] Processed 44002143 reads in 687 ms
[2015-09-30T22:53Z] INFO  23:53:00,343 MuTect - [MUTECT] Processed 33001789 reads in 707 ms
[2015-09-30T22:53Z] INFO  23:53:00,421 MuTect - [MUTECT] Processed 41003321 reads in 618 ms
[2015-09-30T22:53Z] INFO  23:53:00,793 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:00,948 MuTect - [MUTECT] Processed 45002227 reads in 656 ms
[2015-09-30T22:53Z] INFO  23:53:00,995 MuTect - [MUTECT] Processed 34001845 reads in 652 ms
[2015-09-30T22:53Z] INFO  23:53:01,052 MuTect - [MUTECT] Processed 42003433 reads in 630 ms
[2015-09-30T22:53Z] INFO  23:53:01,629 MuTect - [MUTECT] Processed 46002295 reads in 681 ms
[2015-09-30T22:53Z] INFO  23:53:01,695 MuTect - [MUTECT] Processed 43003470 reads in 644 ms
[2015-09-30T22:53Z] INFO  23:53:01,713 MuTect - [MUTECT] Processed 35001846 reads in 718 ms
[2015-09-30T22:53Z] INFO  23:53:01,951 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:02,132 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:02,326 MuTect - [MUTECT] Processed 44003595 reads in 631 ms
[2015-09-30T22:53Z] INFO  23:53:02,388 MuTect - [MUTECT] Processed 47002386 reads in 759 ms
[2015-09-30T22:53Z] INFO  23:53:02,481 MuTect - [MUTECT] Processed 36001880 reads in 768 ms
[2015-09-30T22:53Z] INFO  23:53:02,992 MuTect - [MUTECT] Processed 45003622 reads in 666 ms
[2015-09-30T22:53Z] INFO  23:53:03,094 MuTect - [MUTECT] Processed 48002389 reads in 705 ms
[2015-09-30T22:53Z] INFO  23:53:03,095 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:03,148 MuTect - [MUTECT] Processed 37001896 reads in 667 ms
[2015-09-30T22:53Z] INFO  23:53:03,651 MuTect - [MUTECT] Processed 46003766 reads in 659 ms
[2015-09-30T22:53Z] INFO  23:53:03,773 MuTect - [MUTECT] Processed 49002444 reads in 680 ms
[2015-09-30T22:53Z] INFO  23:53:03,799 MuTect - [MUTECT] Processed 38001938 reads in 651 ms
[2015-09-30T22:53Z] INFO  23:53:04,228 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:04,285 MuTect - [MUTECT] Processed 47003832 reads in 634 ms
[2015-09-30T22:53Z] INFO  23:53:04,336 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:04,468 MuTect - [MUTECT] Processed 50002448 reads in 695 ms
[2015-09-30T22:53Z] INFO  23:53:04,503 MuTect - [MUTECT] Processed 39001992 reads in 704 ms
[2015-09-30T22:53Z] INFO  23:53:05,004 MuTect - [MUTECT] Processed 48003931 reads in 719 ms
[2015-09-30T22:53Z] INFO  23:53:05,160 MuTect - [MUTECT] Processed 40002044 reads in 657 ms
[2015-09-30T22:53Z] INFO  23:53:05,160 MuTect - [MUTECT] Processed 51002485 reads in 692 ms
[2015-09-30T22:53Z] INFO  23:53:05,179 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:05,393 ProgressMeter -     22:36906709        1.21e+06   30.0 s       24.0 s     21.4%         2.3 m   110.0 s
[2015-09-30T22:53Z] INFO  23:53:05,750 MuTect - [MUTECT] Processed 49003933 reads in 746 ms
[2015-09-30T22:53Z] INFO  23:53:05,799 MuTect - [MUTECT] Processed 41002053 reads in 639 ms
[2015-09-30T22:53Z] INFO  23:53:05,870 MuTect - [MUTECT] Processed 52002522 reads in 710 ms
[2015-09-30T22:53Z] INFO  23:53:06,417 MuTect - [MUTECT] Processed 50003944 reads in 667 ms
[2015-09-30T22:53Z] INFO  23:53:06,520 MuTect - [MUTECT] Processed 42002163 reads in 721 ms
[2015-09-30T22:53Z] INFO  23:53:06,776 MuTect - [MUTECT] Processed 53002550 reads in 906 ms
[2015-09-30T22:53Z] INFO  23:53:06,983 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:07,019 MuTect - [MUTECT] Processed 51003947 reads in 602 ms
[2015-09-30T22:53Z] INFO  23:53:07,189 MuTect - [MUTECT] Processed 43002262 reads in 669 ms
[2015-09-30T22:53Z] INFO  23:53:07,476 MuTect - [MUTECT] Processed 54002641 reads in 700 ms
[2015-09-30T22:53Z] INFO  23:53:07,512 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:07,799 MuTect - [MUTECT] Processed 52004008 reads in 780 ms
[2015-09-30T22:53Z] INFO  23:53:07,922 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:07,953 MuTect - [MUTECT] Processed 44002331 reads in 764 ms
[2015-09-30T22:53Z] INFO  23:53:08,154 MuTect - [MUTECT] Processed 55002677 reads in 678 ms
[2015-09-30T22:53Z] INFO  23:53:08,481 MuTect - [MUTECT] Processed 53004025 reads in 681 ms
[2015-09-30T22:53Z] INFO  23:53:08,640 MuTect - [MUTECT] Processed 45002352 reads in 686 ms
[2015-09-30T22:53Z] INFO  23:53:08,852 MuTect - [MUTECT] Processed 56002678 reads in 698 ms
[2015-09-30T22:53Z] INFO  23:53:09,190 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:09,222 MuTect - [MUTECT] Processed 54004126 reads in 742 ms
[2015-09-30T22:53Z] INFO  23:53:09,307 MuTect - [MUTECT] Processed 46002414 reads in 668 ms
[2015-09-30T22:53Z] INFO  23:53:09,511 MuTect - [MUTECT] Processed 57002808 reads in 659 ms
[2015-09-30T22:53Z] INFO  23:53:09,691 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:09,835 MuTect - [MUTECT] Processed 55004189 reads in 613 ms
[2015-09-30T22:53Z] INFO  23:53:09,977 MuTect - [MUTECT] Processed 47002501 reads in 670 ms
[2015-09-30T22:53Z] INFO  23:53:10,169 MuTect - [MUTECT] Processed 58002839 reads in 658 ms
[2015-09-30T22:53Z] INFO  23:53:10,254 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:10,421 MuTect - [MUTECT] Processed 56004219 reads in 586 ms
[2015-09-30T22:53Z] INFO  23:53:10,653 MuTect - [MUTECT] Processed 48002520 reads in 675 ms
[2015-09-30T22:53Z] INFO  23:53:10,826 MuTect - [MUTECT] Processed 59002942 reads in 657 ms
[2015-09-30T22:53Z] INFO  23:53:11,022 MuTect - [MUTECT] Processed 57004305 reads in 601 ms
[2015-09-30T22:53Z] INFO  23:53:11,177 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:11,378 MuTect - [MUTECT] Processed 49002576 reads in 726 ms
[2015-09-30T22:53Z] INFO  23:53:11,506 MuTect - [MUTECT] Processed 60003032 reads in 680 ms
[2015-09-30T22:53Z] INFO  23:53:11,616 MuTect - [MUTECT] Processed 58004321 reads in 594 ms
[2015-09-30T22:53Z] INFO  23:53:11,956 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:12,133 MuTect - [MUTECT] Processed 50002679 reads in 755 ms
[2015-09-30T22:53Z] INFO  23:53:12,207 MuTect - [MUTECT] Processed 61003063 reads in 700 ms
[2015-09-30T22:53Z] INFO  23:53:12,318 MuTect - [MUTECT] Processed 59004423 reads in 702 ms
[2015-09-30T22:53Z] INFO  23:53:12,416 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:12,797 MuTect - [MUTECT] Processed 51002721 reads in 664 ms
[2015-09-30T22:53Z] INFO  23:53:12,876 MuTect - [MUTECT] Processed 62003134 reads in 670 ms
[2015-09-30T22:53Z] INFO  23:53:13,013 MuTect - [MUTECT] Processed 60004467 reads in 695 ms
[2015-09-30T22:53Z] INFO  23:53:13,441 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:13,455 MuTect - [MUTECT] Processed 52002754 reads in 658 ms
[2015-09-30T22:53Z] INFO  23:53:13,543 MuTect - [MUTECT] Processed 63003220 reads in 667 ms
[2015-09-30T22:53Z] INFO  23:53:13,692 MuTect - [MUTECT] Processed 61004505 reads in 679 ms
[2015-09-30T22:53Z] INFO  23:53:14,095 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:14,099 MuTect - [MUTECT] Processed 53002796 reads in 644 ms
[2015-09-30T22:53Z] INFO  23:53:14,236 MuTect - [MUTECT] Processed 64003301 reads in 693 ms
[2015-09-30T22:53Z] INFO  23:53:14,318 MuTect - [MUTECT] Processed 62004532 reads in 626 ms
[2015-09-30T22:53Z] INFO  23:53:14,745 MuTect - [MUTECT] Processed 54002816 reads in 646 ms
[2015-09-30T22:53Z] INFO  23:53:14,784 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:14,888 MuTect - [MUTECT] Processed 65003329 reads in 652 ms
[2015-09-30T22:53Z] INFO  23:53:14,951 MuTect - [MUTECT] Processed 63004617 reads in 633 ms
[2015-09-30T22:53Z] INFO  23:53:15,386 MuTect - [MUTECT] Processed 55002866 reads in 641 ms
[2015-09-30T22:53Z] INFO  23:53:15,537 MuTect - [MUTECT] Processed 66003376 reads in 649 ms
[2015-09-30T22:53Z] INFO  23:53:15,607 MuTect - [MUTECT] Processed 64004664 reads in 656 ms
[2015-09-30T22:53Z] INFO  23:53:15,684 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:16,018 MuTect - [MUTECT] Processed 56002932 reads in 632 ms
[2015-09-30T22:53Z] INFO  23:53:16,231 MuTect - [MUTECT] Processed 67003489 reads in 694 ms
[2015-09-30T22:53Z] INFO  23:53:16,274 MuTect - [MUTECT] Processed 65004764 reads in 667 ms
[2015-09-30T22:53Z] INFO  23:53:16,473 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:16,722 MuTect - [MUTECT] Processed 57002983 reads in 704 ms
[2015-09-30T22:53Z] INFO  23:53:16,862 MuTect - [MUTECT] Processed 68003495 reads in 631 ms
[2015-09-30T22:53Z] INFO  23:53:16,886 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:16,916 MuTect - [MUTECT] Processed 66004837 reads in 642 ms
[2015-09-30T22:53Z] INFO  23:53:17,399 MuTect - [MUTECT] Processed 58003074 reads in 677 ms
[2015-09-30T22:53Z] INFO  23:53:17,502 MuTect - [MUTECT] Processed 69003523 reads in 640 ms
[2015-09-30T22:53Z] INFO  23:53:17,521 MuTect - [MUTECT] Processed 67004882 reads in 605 ms
[2015-09-30T22:53Z] INFO  23:53:17,882 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:18,089 MuTect - [MUTECT] Processed 59003202 reads in 690 ms
[2015-09-30T22:53Z] INFO  23:53:18,167 MuTect - [MUTECT] Processed 68004954 reads in 646 ms
[2015-09-30T22:53Z] INFO  23:53:18,208 MuTect - [MUTECT] Processed 70003554 reads in 706 ms
[2015-09-30T22:53Z] INFO  23:53:18,704 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:18,741 MuTect - [MUTECT] Processed 60003349 reads in 652 ms
[2015-09-30T22:53Z] INFO  23:53:18,780 MuTect - [MUTECT] Processed 69004997 reads in 613 ms
[2015-09-30T22:53Z] INFO  23:53:18,910 MuTect - [MUTECT] Processed 71003596 reads in 702 ms
[2015-09-30T22:53Z] INFO  23:53:18,927 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:19,396 MuTect - [MUTECT] Processed 61003468 reads in 655 ms
[2015-09-30T22:53Z] INFO  23:53:19,457 MuTect - [MUTECT] Processed 70005201 reads in 677 ms
[2015-09-30T22:53Z] INFO  23:53:19,625 MuTect - [MUTECT] Processed 72003621 reads in 715 ms
[2015-09-30T22:53Z] INFO  23:53:20,038 MuTect - [MUTECT] Processed 62003517 reads in 641 ms
[2015-09-30T22:53Z] INFO  23:53:20,103 MuTect - [MUTECT] Processed 71005415 reads in 645 ms
[2015-09-30T22:53Z] INFO  23:53:20,171 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:20,317 MuTect - [MUTECT] Processed 73003661 reads in 692 ms
[2015-09-30T22:53Z] INFO  23:53:20,684 MuTect - [MUTECT] Processed 63003539 reads in 647 ms
[2015-09-30T22:53Z] INFO  23:53:20,786 MuTect - [MUTECT] Processed 72005420 reads in 684 ms
[2015-09-30T22:53Z] INFO  23:53:20,868 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:21,331 MuTect - [MUTECT] Processed 64003568 reads in 647 ms
[2015-09-30T22:53Z] INFO  23:53:21,433 MuTect - [MUTECT] Processed 73005601 reads in 647 ms
[2015-09-30T22:53Z] INFO  23:53:21,965 MuTect - [MUTECT] Processed 74003701 reads in 1648 ms
[2015-09-30T22:53Z] INFO  23:53:21,971 MuTect - [MUTECT] Processed 65003625 reads in 640 ms
[2015-09-30T22:53Z] INFO  23:53:22,159 MuTect - [MUTECT] Processed 74005786 reads in 726 ms
[2015-09-30T22:53Z] INFO  23:53:22,620 MuTect - [MUTECT] Processed 66003766 reads in 649 ms
[2015-09-30T22:53Z] INFO  23:53:22,671 MuTect - [MUTECT] Processed 75003715 reads in 706 ms
[2015-09-30T22:53Z] INFO  23:53:23,030 MuTect - [MUTECT] Processed 75006020 reads in 871 ms
[2015-09-30T22:53Z] INFO  23:53:23,080 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:23,256 MuTect - [MUTECT] Processed 67003874 reads in 636 ms
[2015-09-30T22:53Z] INFO  23:53:23,322 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:23,350 MuTect - [MUTECT] Processed 76003739 reads in 679 ms
[2015-09-30T22:53Z] INFO  23:53:23,489 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:23,894 MuTect - [MUTECT] Processed 76006128 reads in 864 ms
[2015-09-30T22:53Z] INFO  23:53:23,924 MuTect - [MUTECT] Processed 68003898 reads in 668 ms
[2015-09-30T22:53Z] INFO  23:53:24,031 MuTect - [MUTECT] Processed 77003797 reads in 681 ms
[2015-09-30T22:53Z] INFO  23:53:24,582 MuTect - [MUTECT] Processed 77006131 reads in 688 ms
[2015-09-30T22:53Z] INFO  23:53:24,636 MuTect - [MUTECT] Processed 69003973 reads in 712 ms
[2015-09-30T22:53Z] INFO  23:53:24,665 MuTect - [MUTECT] Processed 78003821 reads in 634 ms
[2015-09-30T22:53Z] INFO  23:53:25,171 MuTect - [MUTECT] Processed 78006195 reads in 589 ms
[2015-09-30T22:53Z] INFO  23:53:25,284 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:25,301 MuTect - [MUTECT] Processed 79003896 reads in 636 ms
[2015-09-30T22:53Z] INFO  23:53:25,348 MuTect - [MUTECT] Processed 70004080 reads in 712 ms
[2015-09-30T22:53Z] INFO  23:53:25,655 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:25,773 MuTect - [MUTECT] Processed 79006272 reads in 602 ms
[2015-09-30T22:53Z] INFO  23:53:25,961 MuTect - [MUTECT] Processed 80003924 reads in 660 ms
[2015-09-30T22:53Z] INFO  23:53:26,048 MuTect - [MUTECT] Processed 71004122 reads in 700 ms
[2015-09-30T22:53Z] INFO  23:53:26,387 MuTect - [MUTECT] Processed 80006396 reads in 614 ms
[2015-09-30T22:53Z] INFO  23:53:26,520 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:26,662 MuTect - [MUTECT] Processed 81003993 reads in 701 ms
[2015-09-30T22:53Z] INFO  23:53:26,704 MuTect - [MUTECT] Processed 72004179 reads in 656 ms
[2015-09-30T22:53Z] INFO  23:53:27,051 MuTect - [MUTECT] Processed 81006492 reads in 663 ms
[2015-09-30T22:53Z] INFO  23:53:27,123 ProgressMeter -     21:45112899        2.51e+06   60.0 s       23.0 s     68.0%        88.0 s    28.0 s
[2015-09-30T22:53Z] INFO  23:53:27,342 MuTect - [MUTECT] Processed 82004073 reads in 680 ms
[2015-09-30T22:53Z] INFO  23:53:27,399 MuTect - [MUTECT] Processed 73004246 reads in 695 ms
[2015-09-30T22:53Z] INFO  23:53:27,590 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:27,692 MuTect - [MUTECT] Processed 82006593 reads in 642 ms
[2015-09-30T22:53Z] INFO  23:53:27,915 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:28,025 MuTect - [MUTECT] Processed 83004181 reads in 683 ms
[2015-09-30T22:53Z] INFO  23:53:28,038 MuTect - [MUTECT] Processed 74004257 reads in 639 ms
[2015-09-30T22:53Z] INFO  23:53:28,359 MuTect - [MUTECT] Processed 83006602 reads in 666 ms
[2015-09-30T22:53Z] INFO  23:53:28,689 MuTect - [MUTECT] Processed 75004320 reads in 651 ms
[2015-09-30T22:53Z] INFO  23:53:28,744 MuTect - [MUTECT] Processed 84004282 reads in 719 ms
[2015-09-30T22:53Z] INFO  23:53:28,750 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:29,019 MuTect - [MUTECT] Processed 84006649 reads in 661 ms
[2015-09-30T22:53Z] INFO  23:53:29,355 MuTect - [MUTECT] Processed 76004374 reads in 665 ms
[2015-09-30T22:53Z] INFO  23:53:29,422 MuTect - [MUTECT] Processed 85004372 reads in 678 ms
[2015-09-30T22:53Z] INFO  23:53:29,696 ProgressMeter -     22:22318128        2.17e+06   60.0 s       27.0 s     47.5%         2.1 m    66.0 s
[2015-09-30T22:53Z] INFO  23:53:29,703 MuTect - [MUTECT] Processed 85006652 reads in 684 ms
[2015-09-30T22:53Z] INFO  23:53:29,917 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:30,011 MuTect - [MUTECT] Processed 77004404 reads in 657 ms
[2015-09-30T22:53Z] INFO  23:53:30,097 MuTect - [MUTECT] Processed 86004394 reads in 675 ms
[2015-09-30T22:53Z] INFO  23:53:30,111 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:30,372 MuTect - [MUTECT] Processed 86006704 reads in 669 ms
[2015-09-30T22:53Z] INFO  23:53:30,674 MuTect - [MUTECT] Processed 78004503 reads in 663 ms
[2015-09-30T22:53Z] INFO  23:53:30,696 MuTect - [MUTECT] Processed 87004398 reads in 599 ms
[2015-09-30T22:53Z] INFO  23:53:31,072 MuTect - [MUTECT] Processed 87006852 reads in 700 ms
[2015-09-30T22:53Z] INFO  23:53:31,091 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:31,325 MuTect - [MUTECT] Processed 88004508 reads in 629 ms
[2015-09-30T22:53Z] INFO  23:53:31,339 MuTect - [MUTECT] Processed 79004571 reads in 665 ms
[2015-09-30T22:53Z] INFO  23:53:31,932 MuTect - [MUTECT] Processed 88006865 reads in 860 ms
[2015-09-30T22:53Z] INFO  23:53:32,004 MuTect - [MUTECT] Processed 89004579 reads in 679 ms
[2015-09-30T22:53Z] INFO  23:53:32,023 MuTect - [MUTECT] Processed 80004702 reads in 684 ms
[2015-09-30T22:53Z] INFO  23:53:32,173 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:32,303 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:32,654 MuTect - [MUTECT] Processed 90004694 reads in 650 ms
[2015-09-30T22:53Z] INFO  23:53:32,695 MuTect - [MUTECT] Processed 89006974 reads in 763 ms
[2015-09-30T22:53Z] INFO  23:53:32,777 MuTect - [MUTECT] Processed 81004728 reads in 754 ms
[2015-09-30T22:53Z] INFO  23:53:33,256 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:33,347 MuTect - [MUTECT] Processed 90007047 reads in 652 ms
[2015-09-30T22:53Z] INFO  23:53:33,373 MuTect - [MUTECT] Processed 91004797 reads in 719 ms
[2015-09-30T22:53Z] INFO  23:53:33,508 MuTect - [MUTECT] Processed 82004811 reads in 731 ms
[2015-09-30T22:53Z] INFO  23:53:34,001 MuTect - [MUTECT] Processed 91007059 reads in 654 ms
[2015-09-30T22:53Z] INFO  23:53:34,004 MuTect - [MUTECT] Processed 92004901 reads in 631 ms
[2015-09-30T22:53Z] INFO  23:53:34,229 MuTect - [MUTECT] Processed 83004890 reads in 721 ms
[2015-09-30T22:53Z] INFO  23:53:34,375 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:34,395 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:34,650 MuTect - [MUTECT] Processed 93005024 reads in 646 ms
[2015-09-30T22:53Z] INFO  23:53:34,773 MuTect - [MUTECT] Processed 92007160 reads in 772 ms
[2015-09-30T22:53Z] INFO  23:53:34,905 MuTect - [MUTECT] Processed 84004909 reads in 676 ms
[2015-09-30T22:53Z] INFO  23:53:35,282 MuTect - [MUTECT] Processed 94005126 reads in 632 ms
[2015-09-30T22:53Z] INFO  23:53:35,393 ProgressMeter -     22:39715817        2.47e+06   60.0 s       24.0 s     42.8%         2.3 m    80.0 s
[2015-09-30T22:53Z] INFO  23:53:35,489 MuTect - [MUTECT] Processed 93007259 reads in 716 ms
[2015-09-30T22:53Z] INFO  23:53:35,535 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:35,581 MuTect - [MUTECT] Processed 85004962 reads in 676 ms
[2015-09-30T22:53Z] INFO  23:53:35,942 MuTect - [MUTECT] Processed 95005151 reads in 660 ms
[2015-09-30T22:53Z] INFO  23:53:36,176 MuTect - [MUTECT] Processed 94007324 reads in 687 ms
[2015-09-30T22:53Z] INFO  23:53:36,261 MuTect - [MUTECT] Processed 86005031 reads in 680 ms
[2015-09-30T22:53Z] INFO  23:53:36,501 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:36,602 MuTect - [MUTECT] Processed 96005282 reads in 660 ms
[2015-09-30T22:53Z] INFO  23:53:36,646 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:36,911 MuTect - [MUTECT] Processed 87005057 reads in 650 ms
[2015-09-30T22:53Z] INFO  23:53:36,934 MuTect - [MUTECT] Processed 95007444 reads in 758 ms
[2015-09-30T22:53Z] INFO  23:53:37,249 MuTect - [MUTECT] Processed 97005362 reads in 647 ms
[2015-09-30T22:53Z] INFO  23:53:37,575 MuTect - [MUTECT] Processed 96007544 reads in 641 ms
[2015-09-30T22:53Z] INFO  23:53:37,578 MuTect - [MUTECT] Processed 88005117 reads in 667 ms
[2015-09-30T22:53Z] INFO  23:53:37,898 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:37,979 MuTect - [MUTECT] Processed 98005406 reads in 730 ms
[2015-09-30T22:53Z] INFO  23:53:38,210 MuTect - [MUTECT] Processed 97007585 reads in 635 ms
[2015-09-30T22:53Z] INFO  23:53:38,260 MuTect - [MUTECT] Processed 89005198 reads in 682 ms
[2015-09-30T22:53Z] INFO  23:53:38,633 MuTect - [MUTECT] Processed 99005453 reads in 654 ms
[2015-09-30T22:53Z] INFO  23:53:38,656 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:38,840 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:38,932 MuTect - [MUTECT] Processed 98007701 reads in 722 ms
[2015-09-30T22:53Z] INFO  23:53:38,970 MuTect - [MUTECT] Processed 90005312 reads in 710 ms
[2015-09-30T22:53Z] INFO  23:53:39,364 MuTect - [MUTECT] Processed 100005457 reads in 731 ms
[2015-09-30T22:53Z] INFO  23:53:39,590 MuTect - [MUTECT] Processed 99007807 reads in 658 ms
[2015-09-30T22:53Z] INFO  23:53:39,679 MuTect - [MUTECT] Processed 91005449 reads in 708 ms
[2015-09-30T22:53Z] INFO  23:53:40,205 MuTect - [MUTECT] Processed 101005476 reads in 841 ms
[2015-09-30T22:53Z] INFO  23:53:40,352 MuTect - [MUTECT] Processed 92005457 reads in 674 ms
[2015-09-30T22:53Z] INFO  23:53:40,373 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:40,404 MuTect - [MUTECT] Processed 100007830 reads in 814 ms
[2015-09-30T22:53Z] INFO  23:53:40,963 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:40,988 MuTect - [MUTECT] Processed 93005471 reads in 636 ms
[2015-09-30T22:53Z] INFO  23:53:41,015 MuTect - [MUTECT] Processed 102005499 reads in 810 ms
[2015-09-30T22:53Z] INFO  23:53:41,116 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:41,131 MuTect - [MUTECT] Processed 101007884 reads in 727 ms
[2015-09-30T22:53Z] INFO  23:53:41,626 MuTect - [MUTECT] Processed 94005489 reads in 638 ms
[2015-09-30T22:53Z] INFO  23:53:41,770 MuTect - [MUTECT] Processed 103005565 reads in 755 ms
[2015-09-30T22:53Z] INFO  23:53:41,871 MuTect - [MUTECT] Processed 102007963 reads in 740 ms
[2015-09-30T22:53Z] INFO  23:53:42,303 MuTect - [MUTECT] Processed 95005497 reads in 677 ms
[2015-09-30T22:53Z] INFO  23:53:42,435 MuTect - [MUTECT] Processed 104005691 reads in 665 ms
[2015-09-30T22:53Z] INFO  23:53:42,557 MuTect - [MUTECT] Processed 103008005 reads in 686 ms
[2015-09-30T22:53Z] INFO  23:53:42,580 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:42,959 MuTect - [MUTECT] Processed 96005530 reads in 656 ms
[2015-09-30T22:53Z] INFO  23:53:43,097 MuTect - [MUTECT] Processed 105005747 reads in 662 ms
[2015-09-30T22:53Z] INFO  23:53:43,188 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:43,244 MuTect - [MUTECT] Processed 104008016 reads in 687 ms
[2015-09-30T22:53Z] INFO  23:53:43,338 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:43,615 MuTect - [MUTECT] Processed 97005628 reads in 656 ms
[2015-09-30T22:53Z] INFO  23:53:43,739 MuTect - [MUTECT] Processed 106005803 reads in 642 ms
[2015-09-30T22:53Z] INFO  23:53:43,890 MuTect - [MUTECT] Processed 105008092 reads in 646 ms
[2015-09-30T22:53Z] INFO  23:53:44,255 MuTect - [MUTECT] Processed 98005667 reads in 640 ms
[2015-09-30T22:53Z] INFO  23:53:44,391 MuTect - [MUTECT] Processed 107005866 reads in 652 ms
[2015-09-30T22:53Z] INFO  23:53:44,560 MuTect - [MUTECT] Processed 106008118 reads in 670 ms
[2015-09-30T22:53Z] INFO  23:53:44,792 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:44,922 MuTect - [MUTECT] Processed 99005675 reads in 667 ms
[2015-09-30T22:53Z] INFO  23:53:45,049 MuTect - [MUTECT] Processed 108005886 reads in 658 ms
[2015-09-30T22:53Z] INFO  23:53:45,201 MuTect - [MUTECT] Processed 107008184 reads in 641 ms
[2015-09-30T22:53Z] INFO  23:53:45,366 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:45,538 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:45,607 MuTect - [MUTECT] Processed 100005713 reads in 685 ms
[2015-09-30T22:53Z] INFO  23:53:45,710 MuTect - [MUTECT] Processed 109005913 reads in 661 ms
[2015-09-30T22:53Z] INFO  23:53:45,944 MuTect - [MUTECT] Processed 108008298 reads in 743 ms
[2015-09-30T22:53Z] INFO  23:53:46,273 MuTect - [MUTECT] Processed 101005777 reads in 666 ms
[2015-09-30T22:53Z] INFO  23:53:46,372 MuTect - [MUTECT] Processed 110005971 reads in 662 ms
[2015-09-30T22:53Z] INFO  23:53:46,596 MuTect - [MUTECT] Processed 109008347 reads in 652 ms
[2015-09-30T22:53Z] INFO  23:53:46,862 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:46,938 MuTect - [MUTECT] Processed 102005790 reads in 665 ms
[2015-09-30T22:53Z] INFO  23:53:47,102 MuTect - [MUTECT] Processed 111006006 reads in 730 ms
[2015-09-30T22:53Z] INFO  23:53:47,272 MuTect - [MUTECT] Processed 110008374 reads in 676 ms
[2015-09-30T22:53Z] INFO  23:53:47,581 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:47,628 MuTect - [MUTECT] Processed 103005909 reads in 690 ms
[2015-09-30T22:53Z] INFO  23:53:47,884 MuTect - [MUTECT] Processed 111008492 reads in 612 ms
[2015-09-30T22:53Z] INFO  23:53:47,922 MuTect - [MUTECT] Processed 112006137 reads in 820 ms
[2015-09-30T22:53Z] INFO  23:53:47,987 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:48,304 MuTect - [MUTECT] Processed 104005943 reads in 676 ms
[2015-09-30T22:53Z] INFO  23:53:48,543 MuTect - [MUTECT] Processed 112008609 reads in 659 ms
[2015-09-30T22:53Z] INFO  23:53:48,627 MuTect - [MUTECT] Processed 113006179 reads in 705 ms
[2015-09-30T22:53Z] INFO  23:53:48,960 MuTect - [MUTECT] Processed 105006015 reads in 656 ms
[2015-09-30T22:53Z] INFO  23:53:49,229 MuTect - [MUTECT] Processed 113008660 reads in 686 ms
[2015-09-30T22:53Z] INFO  23:53:49,400 MuTect - [MUTECT] Processed 114006210 reads in 773 ms
[2015-09-30T22:53Z] INFO  23:53:49,612 MuTect - [MUTECT] Processed 106006100 reads in 652 ms
[2015-09-30T22:53Z] INFO  23:53:49,771 MuTect - [MUTECT] Inspected 31000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:49,838 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:49,900 MuTect - [MUTECT] Processed 114008783 reads in 671 ms
[2015-09-30T22:53Z] INFO  23:53:50,095 MuTect - [MUTECT] Processed 115006262 reads in 695 ms
[2015-09-30T22:53Z] INFO  23:53:50,271 MuTect - [MUTECT] Processed 107006123 reads in 659 ms
[2015-09-30T22:53Z] INFO  23:53:50,293 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:50,536 MuTect - [MUTECT] Processed 115008842 reads in 636 ms
[2015-09-30T22:53Z] INFO  23:53:50,821 MuTect - [MUTECT] Processed 116006324 reads in 726 ms
[2015-09-30T22:53Z] INFO  23:53:50,896 MuTect - [MUTECT] Processed 108006206 reads in 625 ms
[2015-09-30T22:53Z] INFO  23:53:51,128 MuTect - [MUTECT] Processed 116008922 reads in 592 ms
[2015-09-30T22:53Z] INFO  23:53:51,535 MuTect - [MUTECT] Processed 109006261 reads in 639 ms
[2015-09-30T22:53Z] INFO  23:53:51,592 MuTect - [MUTECT] Processed 117006424 reads in 771 ms
[2015-09-30T22:53Z] INFO  23:53:51,740 MuTect - [MUTECT] Processed 117009045 reads in 612 ms
[2015-09-30T22:53Z] INFO  23:53:51,846 MuTect - [MUTECT] Inspected 32000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:52,091 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:52,153 MuTect - [MUTECT] Processed 110006306 reads in 618 ms
[2015-09-30T22:53Z] INFO  23:53:52,299 MuTect - [MUTECT] Processed 118006471 reads in 707 ms
[2015-09-30T22:53Z] INFO  23:53:52,410 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:52,416 MuTect - [MUTECT] Processed 118009266 reads in 676 ms
[2015-09-30T22:53Z] INFO  23:53:52,809 MuTect - [MUTECT] Processed 111006403 reads in 656 ms
[2015-09-30T22:53Z] INFO  23:53:53,041 MuTect - [MUTECT] Processed 119006571 reads in 742 ms
[2015-09-30T22:53Z] INFO  23:53:53,081 MuTect - [MUTECT] Processed 119009266 reads in 665 ms
[2015-09-30T22:53Z] INFO  23:53:53,457 MuTect - [MUTECT] Processed 112006449 reads in 648 ms
[2015-09-30T22:53Z] INFO  23:53:53,711 MuTect - [MUTECT] Processed 120006619 reads in 670 ms
[2015-09-30T22:53Z] INFO  23:53:53,733 MuTect - [MUTECT] Processed 120009368 reads in 652 ms
[2015-09-30T22:53Z] INFO  23:53:54,095 MuTect - [MUTECT] Processed 113006516 reads in 638 ms
[2015-09-30T22:53Z] INFO  23:53:54,185 MuTect - [MUTECT] Inspected 33000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:54,360 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:54,361 MuTect - [MUTECT] Processed 121009424 reads in 628 ms
[2015-09-30T22:53Z] INFO  23:53:54,396 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:54,406 MuTect - [MUTECT] Processed 121006646 reads in 695 ms
[2015-09-30T22:53Z] INFO  23:53:54,713 MuTect - [MUTECT] Processed 114006518 reads in 618 ms
[2015-09-30T22:53Z] INFO  23:53:55,003 MuTect - [MUTECT] Processed 122009518 reads in 642 ms
[2015-09-30T22:53Z] INFO  23:53:55,102 MuTect - [MUTECT] Processed 122006731 reads in 696 ms
[2015-09-30T22:53Z] INFO  23:53:55,341 MuTect - [MUTECT] Processed 115006542 reads in 628 ms
[2015-09-30T22:53Z] INFO  23:53:55,687 MuTect - [MUTECT] Processed 123009625 reads in 684 ms
[2015-09-30T22:53Z] INFO  23:53:55,777 MuTect - [MUTECT] Processed 123006794 reads in 675 ms
[2015-09-30T22:53Z] INFO  23:53:55,993 MuTect - [MUTECT] Processed 116006640 reads in 652 ms
[2015-09-30T22:53Z] INFO  23:53:56,431 MuTect - [MUTECT] Processed 124006897 reads in 654 ms
[2015-09-30T22:53Z] INFO  23:53:56,474 MuTect - [MUTECT] Processed 124009685 reads in 787 ms
[2015-09-30T22:53Z] INFO  23:53:56,475 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:56,556 MuTect - [MUTECT] Inspected 34000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:56,655 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:56,678 MuTect - [MUTECT] Processed 117006683 reads in 685 ms
[2015-09-30T22:53Z] INFO  23:53:57,039 MuTect - [MUTECT] Processed 125006900 reads in 608 ms
[2015-09-30T22:53Z] INFO  23:53:57,124 ProgressMeter -     21:47769441        3.77e+06   90.0 s       23.0 s     95.2%        94.0 s     4.0 s
[2015-09-30T22:53Z] INFO  23:53:57,180 MuTect - [MUTECT] Processed 125009755 reads in 706 ms
[2015-09-30T22:53Z] INFO  23:53:57,338 MuTect - [MUTECT] Processed 118006756 reads in 660 ms
[2015-09-30T22:53Z] INFO  23:53:57,761 MuTect - [MUTECT] Processed 126006966 reads in 722 ms
[2015-09-30T22:53Z] INFO  23:53:57,827 MuTect - [MUTECT] Processed 126009848 reads in 647 ms
[2015-09-30T22:53Z] INFO  23:53:58,002 MuTect - [MUTECT] Processed 119006810 reads in 664 ms
[2015-09-30T22:53Z] INFO  23:53:58,431 MuTect - [MUTECT] Processed 127009875 reads in 604 ms
[2015-09-30T22:53Z] INFO  23:53:58,653 MuTect - [MUTECT] Processed 127007045 reads in 892 ms
[2015-09-30T22:53Z] INFO  23:53:58,685 MuTect - [MUTECT] Processed 120006897 reads in 683 ms
[2015-09-30T22:53Z] INFO  23:53:58,768 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:58,968 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:58,979 MuTect - [MUTECT] Inspected 35000 potential candidates
[2015-09-30T22:53Z] INFO  23:53:59,048 MuTect - [MUTECT] Processed 128009943 reads in 617 ms
[2015-09-30T22:53Z] INFO  23:53:59,323 MuTect - [MUTECT] Processed 121006919 reads in 638 ms
[2015-09-30T22:53Z] INFO  23:53:59,349 MuTect - [MUTECT] Processed 128007080 reads in 696 ms
[2015-09-30T22:53Z] INFO  23:53:59,697 ProgressMeter -     22:25602970        3.25e+06   90.0 s       27.0 s     73.1%         2.1 m    33.0 s
[2015-09-30T22:53Z] INFO  23:53:59,730 MuTect - [MUTECT] Processed 129009996 reads in 682 ms
[2015-09-30T22:53Z] INFO  23:53:59,971 MuTect - [MUTECT] Processed 122007031 reads in 648 ms
[2015-09-30T22:53Z] INFO  23:53:59,993 MuTect - [MUTECT] Processed 129007211 reads in 644 ms
[2015-09-30T22:54Z] INFO  23:54:00,443 MuTect - [MUTECT] Processed 130010122 reads in 713 ms
[2015-09-30T22:54Z] INFO  23:54:00,606 MuTect - [MUTECT] Processed 123007036 reads in 635 ms
[2015-09-30T22:54Z] INFO  23:54:00,634 MuTect - [MUTECT] Processed 130007309 reads in 641 ms
[2015-09-30T22:54Z] INFO  23:54:00,869 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:01,114 MuTect - [MUTECT] Processed 131010137 reads in 671 ms
[2015-09-30T22:54Z] INFO  23:54:01,156 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:01,244 MuTect - [MUTECT] Inspected 36000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:01,298 MuTect - [MUTECT] Processed 124007125 reads in 692 ms
[2015-09-30T22:54Z] INFO  23:54:01,319 MuTect - [MUTECT] Processed 131007367 reads in 685 ms
[2015-09-30T22:54Z] INFO  23:54:01,763 MuTect - [MUTECT] Processed 132010177 reads in 649 ms
[2015-09-30T22:54Z] INFO  23:54:01,889 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:54Z] INFO  23:54:01,892 ProgressMeter -            done        4.02e+06   94.0 s       23.0 s    100.0%        94.0 s     0.0 s
[2015-09-30T22:54Z] INFO  23:54:01,893 ProgressMeter - Total runtime 94.77 secs, 1.58 min, 0.03 hours
[2015-09-30T22:54Z] INFO  23:54:01,956 MicroScheduler - 106237 reads were filtered out during the traversal out of approximately 1586549 total reads (6.70%)
[2015-09-30T22:54Z] INFO  23:54:01,956 MicroScheduler -   -> 80244 reads (5.06% of total) failing DuplicateReadFilter
[2015-09-30T22:54Z] INFO  23:54:01,956 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:54Z] INFO  23:54:01,957 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:54Z] INFO  23:54:01,957 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:54Z] INFO  23:54:01,957 MicroScheduler -   -> 25993 reads (1.64% of total) failing UnmappedReadFilter
[2015-09-30T22:54Z] INFO  23:54:01,999 MuTect - [MUTECT] Processed 125007168 reads in 701 ms
[2015-09-30T22:54Z] INFO  23:54:02,390 MuTect - [MUTECT] Processed 133010205 reads in 627 ms
[2015-09-30T22:54Z] INFO  23:54:02,640 MuTect - [MUTECT] Processed 126007191 reads in 641 ms
[2015-09-30T22:54Z] INFO  23:54:02,960 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:54Z] bgzip syn3-21_31026814_48129895-raw-mutect.vcf
[2015-09-30T22:54Z] INFO  23:54:03,043 MuTect - [MUTECT] Processed 134010211 reads in 653 ms
[2015-09-30T22:54Z] tabix index syn3-21_31026814_48129895-raw-mutect.vcf.gz
[2015-09-30T22:54Z] INFO  23:54:03,231 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:03,316 MuTect - [MUTECT] Processed 127007248 reads in 676 ms
[2015-09-30T22:54Z] INFO  23:54:03,545 MuTect - [MUTECT] Inspected 37000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:03,699 MuTect - [MUTECT] Processed 135010274 reads in 656 ms
[2015-09-30T22:54Z] INFO  23:54:04,051 MuTect - [MUTECT] Processed 128007333 reads in 735 ms
[2015-09-30T22:54Z] INFO  23:54:04,332 MuTect - [MUTECT] Processed 136010361 reads in 633 ms
[2015-09-30T22:54Z] INFO  23:54:04,746 MuTect - [MUTECT] Processed 129007344 reads in 695 ms
[2015-09-30T22:54Z] INFO  23:54:04,989 MuTect - [MUTECT] Processed 137010390 reads in 657 ms
[2015-09-30T22:54Z] MuTect: MuTect
[2015-09-30T22:54Z] INFO  23:54:05,394 ProgressMeter -     22:42972568        3.75e+06   90.0 s       24.0 s     65.2%         2.3 m    48.0 s
[2015-09-30T22:54Z] INFO  23:54:05,490 MuTect - [MUTECT] Processed 130007349 reads in 744 ms
[2015-09-30T22:54Z] INFO  23:54:05,652 MuTect - [MUTECT] Processed 138010505 reads in 663 ms
[2015-09-30T22:54Z] INFO  23:54:05,757 MuTect - [MUTECT] Inspected 38000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:06,036 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:06,161 MuTect - [MUTECT] Processed 131007406 reads in 671 ms
[2015-09-30T22:54Z] INFO  23:54:06,299 MuTect - [MUTECT] Processed 139010568 reads in 647 ms
[2015-09-30T22:54Z] INFO  23:54:06,860 MuTect - [MUTECT] Processed 132007423 reads in 699 ms
[2015-09-30T22:54Z] INFO  23:54:06,955 MuTect - [MUTECT] Processed 140010587 reads in 656 ms
[2015-09-30T22:54Z] INFO  23:54:07,376 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/X/syn3-X_0_31090302-raw-mutect-regions.bed to be BED
[2015-09-30T22:54Z] INFO  23:54:07,431 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:54Z] INFO  23:54:07,431 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:54Z] INFO  23:54:07,431 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:54Z] INFO  23:54:07,431 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:54Z] INFO  23:54:07,435 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/X/syn3-X_0_31090302-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/X/tx/tmpvliVNg/syn3-X_0_31090302-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:54Z] INFO  23:54:07,435 HelpFormatter - Date/Time: 2015/09/30 23:54:07
[2015-09-30T22:54Z] INFO  23:54:07,435 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:54Z] INFO  23:54:07,435 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:54Z] INFO  23:54:07,463 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:54Z] INFO  23:54:07,467 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:54Z] INFO  23:54:07,517 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:54Z] INFO  23:54:07,553 MuTect - [MUTECT] Processed 133007501 reads in 693 ms
[2015-09-30T22:54Z] INFO  23:54:07,565 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:54Z] INFO  23:54:07,573 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:54Z] INFO  23:54:07,595 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:54Z] INFO  23:54:07,606 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:54Z] INFO  23:54:07,612 MuTect - [MUTECT] Processed 141010680 reads in 657 ms
[2015-09-30T22:54Z] INFO  23:54:07,778 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:54Z] INFO  23:54:07,868 IntervalUtils - Processing 993323 bp from intervals
[2015-09-30T22:54Z] INFO  23:54:07,872 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:54Z] INFO  23:54:07,872 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:54Z] INFO  23:54:07,912 MuTect - [MUTECT] Inspected 39000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:08,026 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:54Z] INFO  23:54:08,163 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:54Z] INFO  23:54:08,163 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:54Z] INFO  23:54:08,163 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:54Z] INFO  23:54:08,164 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:54Z] INFO  23:54:08,236 MuTect - [MUTECT] Processed 134007521 reads in 683 ms
[2015-09-30T22:54Z] INFO  23:54:08,248 MuTect - [MUTECT] Processed 142010694 reads in 636 ms
[2015-09-30T22:54Z] INFO  23:54:08,317 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:08,896 MuTect - [MUTECT] Processed 143010753 reads in 648 ms
[2015-09-30T22:54Z] INFO  23:54:08,937 MuTect - [MUTECT] Processed 135007547 reads in 701 ms
[2015-09-30T22:54Z] INFO  23:54:09,552 MuTect - [MUTECT] Processed 144010844 reads in 656 ms
[2015-09-30T22:54Z] INFO  23:54:09,659 MuTect - [MUTECT] Processed 136007657 reads in 722 ms
[2015-09-30T22:54Z] INFO  23:54:10,299 MuTect - [MUTECT] Processed 145010898 reads in 747 ms
[2015-09-30T22:54Z] INFO  23:54:10,442 MuTect - [MUTECT] Processed 137007706 reads in 783 ms
[2015-09-30T22:54Z] INFO  23:54:10,475 MuTect - [MUTECT] Inspected 40000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:10,692 MuTect - [MUTECT] Processed 1000122 reads in 2481 ms
[2015-09-30T22:54Z] INFO  23:54:10,740 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:10,963 MuTect - [MUTECT] Processed 146010925 reads in 664 ms
[2015-09-30T22:54Z] INFO  23:54:11,207 MuTect - [MUTECT] Processed 138007741 reads in 765 ms
[2015-09-30T22:54Z] INFO  23:54:11,563 MuTect - [MUTECT] Processed 2000130 reads in 872 ms
[2015-09-30T22:54Z] INFO  23:54:11,596 MuTect - [MUTECT] Processed 147011027 reads in 633 ms
[2015-09-30T22:54Z] INFO  23:54:11,875 MuTect - [MUTECT] Processed 139007793 reads in 668 ms
[2015-09-30T22:54Z] INFO  23:54:12,238 MuTect - [MUTECT] Processed 148011096 reads in 642 ms
[2015-09-30T22:54Z] INFO  23:54:12,294 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:12,312 MuTect - [MUTECT] Processed 3000144 reads in 749 ms
[2015-09-30T22:54Z] INFO  23:54:12,568 MuTect - [MUTECT] Processed 140007816 reads in 693 ms
[2015-09-30T22:54Z] INFO  23:54:12,708 MuTect - [MUTECT] Inspected 41000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:13,088 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:13,196 MuTect - [MUTECT] Processed 4000213 reads in 884 ms
[2015-09-30T22:54Z] INFO  23:54:13,283 MuTect - [MUTECT] Processed 141007899 reads in 715 ms
[2015-09-30T22:54Z] INFO  23:54:13,454 MuTect - [MUTECT] Processed 149011221 reads in 1216 ms
[2015-09-30T22:54Z] INFO  23:54:13,962 MuTect - [MUTECT] Processed 5000345 reads in 766 ms
[2015-09-30T22:54Z] INFO  23:54:14,041 MuTect - [MUTECT] Processed 142007911 reads in 758 ms
[2015-09-30T22:54Z] INFO  23:54:14,073 MuTect - [MUTECT] Processed 150011307 reads in 619 ms
[2015-09-30T22:54Z] INFO  23:54:14,515 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:14,672 MuTect - [MUTECT] Processed 6000372 reads in 710 ms
[2015-09-30T22:54Z] INFO  23:54:14,745 MuTect - [MUTECT] Processed 143007927 reads in 704 ms
[2015-09-30T22:54Z] INFO  23:54:14,788 MuTect - [MUTECT] Processed 151011395 reads in 715 ms
[2015-09-30T22:54Z] INFO  23:54:15,395 MuTect - [MUTECT] Processed 152011419 reads in 607 ms
[2015-09-30T22:54Z] INFO  23:54:15,454 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:15,474 MuTect - [MUTECT] Processed 144008014 reads in 729 ms
[2015-09-30T22:54Z] INFO  23:54:15,516 MuTect - [MUTECT] Processed 7000381 reads in 844 ms
[2015-09-30T22:54Z] INFO  23:54:15,602 MuTect - [MUTECT] Inspected 42000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:16,005 MuTect - [MUTECT] Processed 153011484 reads in 610 ms
[2015-09-30T22:54Z] INFO  23:54:16,184 MuTect - [MUTECT] Processed 145008066 reads in 710 ms
[2015-09-30T22:54Z] INFO  23:54:16,260 MuTect - [MUTECT] Processed 8000471 reads in 744 ms
[2015-09-30T22:54Z] INFO  23:54:16,641 MuTect - [MUTECT] Processed 154011487 reads in 635 ms
[2015-09-30T22:54Z] INFO  23:54:16,890 MuTect - [MUTECT] Processed 146008128 reads in 706 ms
[2015-09-30T22:54Z] INFO  23:54:17,024 MuTect - [MUTECT] Processed 9000480 reads in 764 ms
[2015-09-30T22:54Z] INFO  23:54:17,214 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:17,263 MuTect - [MUTECT] Processed 155011596 reads in 623 ms
[2015-09-30T22:54Z] INFO  23:54:17,579 MuTect - [MUTECT] Processed 147008239 reads in 689 ms
[2015-09-30T22:54Z] INFO  23:54:17,740 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:17,751 MuTect - [MUTECT] Inspected 43000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:17,866 MuTect - [MUTECT] Processed 10000515 reads in 842 ms
[2015-09-30T22:54Z] INFO  23:54:17,919 MuTect - [MUTECT] Processed 156011692 reads in 656 ms
[2015-09-30T22:54Z] INFO  23:54:18,263 MuTect - [MUTECT] Processed 148008287 reads in 684 ms
[2015-09-30T22:54Z] INFO  23:54:18,543 MuTect - [MUTECT] Processed 157011715 reads in 624 ms
[2015-09-30T22:54Z] INFO  23:54:18,608 MuTect - [MUTECT] Processed 11000603 reads in 742 ms
[2015-09-30T22:54Z] INFO  23:54:19,022 MuTect - [MUTECT] Processed 149008371 reads in 759 ms
[2015-09-30T22:54Z] INFO  23:54:19,174 MuTect - [MUTECT] Processed 158011812 reads in 631 ms
[2015-09-30T22:54Z] INFO  23:54:19,357 MuTect - [MUTECT] Processed 12000611 reads in 749 ms
[2015-09-30T22:54Z] INFO  23:54:19,665 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:19,725 MuTect - [MUTECT] Processed 150008450 reads in 703 ms
[2015-09-30T22:54Z] INFO  23:54:19,800 MuTect - [MUTECT] Processed 159011913 reads in 626 ms
[2015-09-30T22:54Z] INFO  23:54:19,947 MuTect - [MUTECT] Inspected 44000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:20,084 MuTect - [MUTECT] Processed 13000697 reads in 726 ms
[2015-09-30T22:54Z] INFO  23:54:20,156 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:20,415 MuTect - [MUTECT] Processed 151008520 reads in 690 ms
[2015-09-30T22:54Z] INFO  23:54:20,454 MuTect - [MUTECT] Processed 160011933 reads in 654 ms
[2015-09-30T22:54Z] INFO  23:54:20,820 MuTect - [MUTECT] Processed 14000744 reads in 737 ms
[2015-09-30T22:54Z] INFO  23:54:21,093 MuTect - [MUTECT] Processed 161011975 reads in 639 ms
[2015-09-30T22:54Z] INFO  23:54:21,123 MuTect - [MUTECT] Processed 152008534 reads in 708 ms
[2015-09-30T22:54Z] INFO  23:54:21,547 MuTect - [MUTECT] Processed 15000750 reads in 727 ms
[2015-09-30T22:54Z] INFO  23:54:21,707 MuTect - [MUTECT] Processed 162011976 reads in 614 ms
[2015-09-30T22:54Z] INFO  23:54:21,847 MuTect - [MUTECT] Processed 153008545 reads in 724 ms
[2015-09-30T22:54Z] INFO  23:54:22,129 MuTect - [MUTECT] Inspected 45000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:22,319 MuTect - [MUTECT] Processed 16000789 reads in 772 ms
[2015-09-30T22:54Z] INFO  23:54:22,325 MuTect - [MUTECT] Processed 163012029 reads in 618 ms
[2015-09-30T22:54Z] INFO  23:54:22,431 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:22,527 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:22,589 MuTect - [MUTECT] Processed 154008632 reads in 742 ms
[2015-09-30T22:54Z] INFO  23:54:22,903 MuTect - [MUTECT] Processed 164012043 reads in 578 ms
[2015-09-30T22:54Z] INFO  23:54:23,066 MuTect - [MUTECT] Processed 17000843 reads in 747 ms
[2015-09-30T22:54Z] INFO  23:54:23,317 MuTect - [MUTECT] Processed 155008703 reads in 728 ms
[2015-09-30T22:54Z] INFO  23:54:23,535 MuTect - [MUTECT] Processed 165012099 reads in 632 ms
[2015-09-30T22:54Z] INFO  23:54:23,849 MuTect - [MUTECT] Processed 18000905 reads in 783 ms
[2015-09-30T22:54Z] INFO  23:54:24,019 MuTect - [MUTECT] Processed 156008713 reads in 702 ms
[2015-09-30T22:54Z] INFO  23:54:24,166 MuTect - [MUTECT] Processed 166012169 reads in 631 ms
[2015-09-30T22:54Z] INFO  23:54:24,212 MuTect - [MUTECT] Inspected 46000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:24,550 MuTect - [MUTECT] Processed 19000930 reads in 701 ms
[2015-09-30T22:54Z] INFO  23:54:24,700 MuTect - [MUTECT] Processed 157008727 reads in 681 ms
[2015-09-30T22:54Z] INFO  23:54:24,784 MuTect - [MUTECT] Processed 167012169 reads in 618 ms
[2015-09-30T22:54Z] INFO  23:54:24,953 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:25,075 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:25,261 MuTect - [MUTECT] Processed 20001007 reads in 710 ms
[2015-09-30T22:54Z] INFO  23:54:25,382 MuTect - [MUTECT] Processed 168012211 reads in 598 ms
[2015-09-30T22:54Z] INFO  23:54:25,392 MuTect - [MUTECT] Processed 158008866 reads in 692 ms
[2015-09-30T22:54Z] INFO  23:54:25,976 MuTect - [MUTECT] Processed 21001039 reads in 716 ms
[2015-09-30T22:54Z] INFO  23:54:26,024 MuTect - [MUTECT] Processed 169012314 reads in 642 ms
[2015-09-30T22:54Z] INFO  23:54:26,067 MuTect - [MUTECT] Processed 159008930 reads in 675 ms
[2015-09-30T22:54Z] INFO  23:54:26,179 MuTect - [MUTECT] Inspected 47000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:26,624 MuTect - [MUTECT] Processed 22001069 reads in 648 ms
[2015-09-30T22:54Z] INFO  23:54:26,639 MuTect - [MUTECT] Processed 170012349 reads in 615 ms
[2015-09-30T22:54Z] INFO  23:54:26,768 MuTect - [MUTECT] Processed 160008940 reads in 701 ms
[2015-09-30T22:54Z] INFO  23:54:27,249 MuTect - [MUTECT] Processed 171012385 reads in 610 ms
[2015-09-30T22:54Z] INFO  23:54:27,279 MuTect - [MUTECT] Inspected 48000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:27,287 MuTect - [MUTECT] Processed 23001171 reads in 663 ms
[2015-09-30T22:54Z] INFO  23:54:27,311 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:27,470 MuTect - [MUTECT] Processed 161008972 reads in 702 ms
[2015-09-30T22:54Z] INFO  23:54:27,912 MuTect - [MUTECT] Processed 172012387 reads in 663 ms
[2015-09-30T22:54Z] INFO  23:54:27,965 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:54Z] INFO  23:54:27,969 ProgressMeter -            done        4.45e+06  118.0 s       26.0 s    100.0%       118.0 s     0.0 s
[2015-09-30T22:54Z] INFO  23:54:27,969 ProgressMeter - Total runtime 118.28 secs, 1.97 min, 0.03 hours
[2015-09-30T22:54Z] INFO  23:54:27,979 MuTect - [MUTECT] Processed 24001225 reads in 692 ms
[2015-09-30T22:54Z] INFO  23:54:28,033 MicroScheduler - 139142 reads were filtered out during the traversal out of approximately 2057516 total reads (6.76%)
[2015-09-30T22:54Z] INFO  23:54:28,033 MicroScheduler -   -> 105358 reads (5.12% of total) failing DuplicateReadFilter
[2015-09-30T22:54Z] INFO  23:54:28,033 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:54Z] INFO  23:54:28,033 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:54Z] INFO  23:54:28,033 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:54Z] INFO  23:54:28,033 MicroScheduler -   -> 33784 reads (1.64% of total) failing UnmappedReadFilter
[2015-09-30T22:54Z] INFO  23:54:28,152 MuTect - [MUTECT] Processed 162009066 reads in 682 ms
[2015-09-30T22:54Z] INFO  23:54:28,670 MuTect - [MUTECT] Processed 25001314 reads in 691 ms
[2015-09-30T22:54Z] INFO  23:54:28,860 MuTect - [MUTECT] Processed 163009142 reads in 708 ms
[2015-09-30T22:54Z] INFO  23:54:29,031 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:54Z] bgzip syn3-22_0_31019358-raw-mutect.vcf
[2015-09-30T22:54Z] tabix index syn3-22_0_31019358-raw-mutect.vcf.gz
[2015-09-30T22:54Z] INFO  23:54:29,345 MuTect - [MUTECT] Processed 26001341 reads in 675 ms
[2015-09-30T22:54Z] INFO  23:54:29,566 MuTect - [MUTECT] Processed 164009147 reads in 706 ms
[2015-09-30T22:54Z] INFO  23:54:29,611 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:29,616 MuTect - [MUTECT] Inspected 49000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:30,002 MuTect - [MUTECT] Processed 27001424 reads in 657 ms
[2015-09-30T22:54Z] INFO  23:54:30,317 MuTect - [MUTECT] Processed 165009249 reads in 751 ms
[2015-09-30T22:54Z] INFO  23:54:30,705 MuTect - [MUTECT] Processed 28001471 reads in 703 ms
[2015-09-30T22:54Z] INFO  23:54:31,018 MuTect - [MUTECT] Processed 166009348 reads in 701 ms
[2015-09-30T22:54Z] INFO  23:54:31,372 MuTect - [MUTECT] Processed 29001476 reads in 666 ms
[2015-09-30T22:54Z] MuTect: MuTect
[2015-09-30T22:54Z] INFO  23:54:31,707 MuTect - [MUTECT] Processed 167009363 reads in 689 ms
[2015-09-30T22:54Z] INFO  23:54:31,930 MuTect - [MUTECT] Inspected 50000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:32,032 MuTect - [MUTECT] Processed 30001553 reads in 661 ms
[2015-09-30T22:54Z] INFO  23:54:32,075 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:32,398 MuTect - [MUTECT] Processed 168009378 reads in 690 ms
[2015-09-30T22:54Z] INFO  23:54:32,689 MuTect - [MUTECT] Processed 31001608 reads in 657 ms
[2015-09-30T22:54Z] INFO  23:54:33,101 MuTect - [MUTECT] Processed 169009487 reads in 704 ms
[2015-09-30T22:54Z] INFO  23:54:33,354 MuTect - [MUTECT] Processed 32001650 reads in 665 ms
[2015-09-30T22:54Z] INFO  23:54:33,672 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/X/syn3-X_31132529_62519711-raw-mutect-regions.bed to be BED
[2015-09-30T22:54Z] INFO  23:54:33,728 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:54Z] INFO  23:54:33,728 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:54Z] INFO  23:54:33,728 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:54Z] INFO  23:54:33,728 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:54Z] INFO  23:54:33,732 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/X/syn3-X_31132529_62519711-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/X/tx/tmpKSsoCk/syn3-X_31132529_62519711-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:54Z] INFO  23:54:33,732 HelpFormatter - Date/Time: 2015/09/30 23:54:33
[2015-09-30T22:54Z] INFO  23:54:33,732 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:54Z] INFO  23:54:33,732 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:54Z] INFO  23:54:33,760 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:54Z] INFO  23:54:33,765 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:54Z] INFO  23:54:33,814 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:54Z] INFO  23:54:33,841 MuTect - [MUTECT] Processed 170009519 reads in 740 ms
[2015-09-30T22:54Z] INFO  23:54:33,862 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:54Z] INFO  23:54:33,870 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:54Z] INFO  23:54:33,893 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:54Z] INFO  23:54:33,904 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:54Z] INFO  23:54:34,021 MuTect - [MUTECT] Processed 33001657 reads in 667 ms
[2015-09-30T22:54Z] INFO  23:54:34,078 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:54Z] INFO  23:54:34,180 IntervalUtils - Processing 1301828 bp from intervals
[2015-09-30T22:54Z] INFO  23:54:34,184 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:54Z] INFO  23:54:34,184 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:54Z] INFO  23:54:34,362 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:54Z] INFO  23:54:34,401 MuTect - [MUTECT] Inspected 51000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:34,512 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:34,556 MuTect - [MUTECT] Processed 171009567 reads in 715 ms
[2015-09-30T22:54Z] INFO  23:54:34,566 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:54Z] INFO  23:54:34,566 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:54Z] INFO  23:54:34,566 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:54Z] INFO  23:54:34,567 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:54Z] INFO  23:54:34,704 MuTect - [MUTECT] Processed 34001718 reads in 683 ms
[2015-09-30T22:54Z] INFO  23:54:35,284 MuTect - [MUTECT] Processed 172009650 reads in 728 ms
[2015-09-30T22:54Z] INFO  23:54:35,386 MuTect - [MUTECT] Processed 35001757 reads in 682 ms
[2015-09-30T22:54Z] INFO  23:54:35,396 ProgressMeter -     22:49290581        4.88e+06  120.0 s       24.0 s     86.3%         2.3 m    19.0 s
[2015-09-30T22:54Z] INFO  23:54:36,045 MuTect - [MUTECT] Processed 173009731 reads in 761 ms
[2015-09-30T22:54Z] INFO  23:54:36,108 MuTect - [MUTECT] Processed 36001832 reads in 722 ms
[2015-09-30T22:54Z] INFO  23:54:36,741 MuTect - [MUTECT] Processed 174009805 reads in 696 ms
[2015-09-30T22:54Z] INFO  23:54:36,786 MuTect - [MUTECT] Inspected 52000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:36,813 MuTect - [MUTECT] Processed 37001914 reads in 705 ms
[2015-09-30T22:54Z] INFO  23:54:37,011 MuTect - [MUTECT] Processed 1000027 reads in 2396 ms
[2015-09-30T22:54Z] INFO  23:54:37,150 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:37,427 MuTect - [MUTECT] Processed 175009934 reads in 686 ms
[2015-09-30T22:54Z] INFO  23:54:37,535 MuTect - [MUTECT] Processed 38001921 reads in 722 ms
[2015-09-30T22:54Z] INFO  23:54:37,842 MuTect - [MUTECT] Processed 2000056 reads in 831 ms
[2015-09-30T22:54Z] INFO  23:54:38,166 ProgressMeter -      X:15474103        1.02e+06   30.0 s       29.0 s     43.8%        68.0 s    38.0 s
[2015-09-30T22:54Z] INFO  23:54:38,194 MuTect - [MUTECT] Processed 176010054 reads in 767 ms
[2015-09-30T22:54Z] INFO  23:54:38,251 MuTect - [MUTECT] Processed 39001992 reads in 716 ms
[2015-09-30T22:54Z] INFO  23:54:38,632 MuTect - [MUTECT] Processed 3000069 reads in 790 ms
[2015-09-30T22:54Z] INFO  23:54:38,887 MuTect - [MUTECT] Processed 177010145 reads in 693 ms
[2015-09-30T22:54Z] INFO  23:54:38,952 MuTect - [MUTECT] Processed 40002078 reads in 701 ms
[2015-09-30T22:54Z] INFO  23:54:39,177 MuTect - [MUTECT] Inspected 53000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:39,296 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:39,376 MuTect - [MUTECT] Processed 4000076 reads in 744 ms
[2015-09-30T22:54Z] INFO  23:54:39,563 MuTect - [MUTECT] Processed 178010194 reads in 676 ms
[2015-09-30T22:54Z] INFO  23:54:39,642 MuTect - [MUTECT] Processed 41002080 reads in 690 ms
[2015-09-30T22:54Z] INFO  23:54:39,896 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:40,141 MuTect - [MUTECT] Processed 5000160 reads in 765 ms
[2015-09-30T22:54Z] INFO  23:54:40,318 MuTect - [MUTECT] Processed 179010230 reads in 755 ms
[2015-09-30T22:54Z] INFO  23:54:40,370 MuTect - [MUTECT] Processed 42002147 reads in 728 ms
[2015-09-30T22:54Z] INFO  23:54:40,871 MuTect - [MUTECT] Processed 6000175 reads in 730 ms
[2015-09-30T22:54Z] INFO  23:54:41,059 MuTect - [MUTECT] Processed 180010233 reads in 741 ms
[2015-09-30T22:54Z] INFO  23:54:41,064 MuTect - [MUTECT] Processed 43002183 reads in 694 ms
[2015-09-30T22:54Z] INFO  23:54:41,411 MuTect - [MUTECT] Inspected 54000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:41,561 MuTect - [MUTECT] Processed 7000217 reads in 690 ms
[2015-09-30T22:54Z] INFO  23:54:41,753 MuTect - [MUTECT] Processed 44002252 reads in 689 ms
[2015-09-30T22:54Z] INFO  23:54:41,832 MuTect - [MUTECT] Processed 181010285 reads in 773 ms
[2015-09-30T22:54Z] INFO  23:54:41,860 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:42,233 MuTect - [MUTECT] Processed 8000320 reads in 672 ms
[2015-09-30T22:54Z] INFO  23:54:42,448 MuTect - [MUTECT] Processed 45002345 reads in 695 ms
[2015-09-30T22:54Z] INFO  23:54:42,473 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:42,517 MuTect - [MUTECT] Processed 182010359 reads in 685 ms
[2015-09-30T22:54Z] INFO  23:54:42,868 MuTect - [MUTECT] Processed 9000377 reads in 635 ms
[2015-09-30T22:54Z] INFO  23:54:43,142 MuTect - [MUTECT] Processed 46002359 reads in 694 ms
[2015-09-30T22:54Z] INFO  23:54:43,230 MuTect - [MUTECT] Processed 183010446 reads in 713 ms
[2015-09-30T22:54Z] INFO  23:54:43,499 MuTect - [MUTECT] Processed 10000384 reads in 631 ms
[2015-09-30T22:54Z] INFO  23:54:43,701 MuTect - [MUTECT] Inspected 55000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:43,837 MuTect - [MUTECT] Processed 47002441 reads in 695 ms
[2015-09-30T22:54Z] INFO  23:54:43,930 MuTect - [MUTECT] Processed 184010510 reads in 700 ms
[2015-09-30T22:54Z] INFO  23:54:44,107 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:44,165 MuTect - [MUTECT] Processed 11000428 reads in 666 ms
[2015-09-30T22:54Z] INFO  23:54:44,528 MuTect - [MUTECT] Processed 48002474 reads in 691 ms
[2015-09-30T22:54Z] INFO  23:54:44,619 MuTect - [MUTECT] Processed 185010527 reads in 689 ms
[2015-09-30T22:54Z] INFO  23:54:44,844 MuTect - [MUTECT] Processed 12000463 reads in 679 ms
[2015-09-30T22:54Z] INFO  23:54:44,959 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:45,195 MuTect - [MUTECT] Processed 49002484 reads in 667 ms
[2015-09-30T22:54Z] INFO  23:54:45,295 MuTect - [MUTECT] Processed 186010619 reads in 676 ms
[2015-09-30T22:54Z] INFO  23:54:45,527 MuTect - [MUTECT] Processed 13000549 reads in 683 ms
[2015-09-30T22:54Z] INFO  23:54:45,851 MuTect - [MUTECT] Processed 50002560 reads in 655 ms
[2015-09-30T22:54Z] INFO  23:54:45,897 MuTect - [MUTECT] Inspected 56000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:46,067 MuTect - [MUTECT] Processed 187010647 reads in 772 ms
[2015-09-30T22:54Z] INFO  23:54:46,178 MuTect - [MUTECT] Processed 14000580 reads in 651 ms
[2015-09-30T22:54Z] INFO  23:54:46,499 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:46,527 MuTect - [MUTECT] Processed 51002631 reads in 677 ms
[2015-09-30T22:54Z] INFO  23:54:46,750 MuTect - [MUTECT] Processed 188010706 reads in 683 ms
[2015-09-30T22:54Z] INFO  23:54:46,817 MuTect - [MUTECT] Processed 15000625 reads in 639 ms
[2015-09-30T22:54Z] INFO  23:54:47,183 MuTect - [MUTECT] Processed 52002645 reads in 656 ms
[2015-09-30T22:54Z] INFO  23:54:47,437 MuTect - [MUTECT] Processed 189010766 reads in 687 ms
[2015-09-30T22:54Z] INFO  23:54:47,443 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:47,487 MuTect - [MUTECT] Processed 16000720 reads in 670 ms
[2015-09-30T22:54Z] INFO  23:54:47,830 MuTect - [MUTECT] Processed 53002661 reads in 647 ms
[2015-09-30T22:54Z] INFO  23:54:48,089 MuTect - [MUTECT] Inspected 57000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:48,128 MuTect - [MUTECT] Processed 190010888 reads in 691 ms
[2015-09-30T22:54Z] INFO  23:54:48,161 MuTect - [MUTECT] Processed 17000743 reads in 674 ms
[2015-09-30T22:54Z] INFO  23:54:48,468 MuTect - [MUTECT] Processed 54002677 reads in 638 ms
[2015-09-30T22:54Z] INFO  23:54:48,829 MuTect - [MUTECT] Processed 191010936 reads in 701 ms
[2015-09-30T22:54Z] INFO  23:54:48,841 MuTect - [MUTECT] Processed 18000835 reads in 680 ms
[2015-09-30T22:54Z] INFO  23:54:49,063 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:49,104 MuTect - [MUTECT] Processed 55002680 reads in 636 ms
[2015-09-30T22:54Z] INFO  23:54:49,485 MuTect - [MUTECT] Processed 192010974 reads in 656 ms
[2015-09-30T22:54Z] INFO  23:54:49,529 MuTect - [MUTECT] Processed 19000889 reads in 688 ms
[2015-09-30T22:54Z] INFO  23:54:49,727 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:49,729 MuTect - [MUTECT] Processed 56002688 reads in 625 ms
[2015-09-30T22:54Z] INFO  23:54:50,133 MuTect - [MUTECT] Processed 193011112 reads in 648 ms
[2015-09-30T22:54Z] INFO  23:54:50,214 MuTect - [MUTECT] Processed 20000926 reads in 685 ms
[2015-09-30T22:54Z] INFO  23:54:50,394 MuTect - [MUTECT] Processed 57002753 reads in 665 ms
[2015-09-30T22:54Z] INFO  23:54:50,603 MuTect - [MUTECT] Inspected 58000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:50,796 MuTect - [MUTECT] Processed 194011208 reads in 663 ms
[2015-09-30T22:54Z] INFO  23:54:50,887 MuTect - [MUTECT] Processed 21000933 reads in 673 ms
[2015-09-30T22:54Z] INFO  23:54:51,027 MuTect - [MUTECT] Processed 58002774 reads in 633 ms
[2015-09-30T22:54Z] INFO  23:54:51,499 MuTect - [MUTECT] Processed 195011310 reads in 703 ms
[2015-09-30T22:54Z] INFO  23:54:51,601 MuTect - [MUTECT] Processed 22000980 reads in 714 ms
[2015-09-30T22:54Z] INFO  23:54:51,671 MuTect - [MUTECT] Processed 59002807 reads in 644 ms
[2015-09-30T22:54Z] INFO  23:54:51,741 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:52,017 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:52,163 MuTect - [MUTECT] Processed 196011346 reads in 664 ms
[2015-09-30T22:54Z] INFO  23:54:52,288 MuTect - [MUTECT] Processed 23001009 reads in 687 ms
[2015-09-30T22:54Z] INFO  23:54:52,297 MuTect - [MUTECT] Processed 60002878 reads in 626 ms
[2015-09-30T22:54Z] INFO  23:54:52,844 MuTect - [MUTECT] Processed 197011428 reads in 681 ms
[2015-09-30T22:54Z] INFO  23:54:52,909 MuTect - [MUTECT] Inspected 59000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:52,926 MuTect - [MUTECT] Processed 61002967 reads in 629 ms
[2015-09-30T22:54Z] INFO  23:54:53,018 MuTect - [MUTECT] Processed 24001023 reads in 730 ms
[2015-09-30T22:54Z] INFO  23:54:53,506 MuTect - [MUTECT] Processed 198011557 reads in 662 ms
[2015-09-30T22:54Z] INFO  23:54:53,558 MuTect - [MUTECT] Processed 62003032 reads in 632 ms
[2015-09-30T22:54Z] INFO  23:54:53,719 MuTect - [MUTECT] Processed 25001086 reads in 701 ms
[2015-09-30T22:54Z] INFO  23:54:54,172 MuTect - [MUTECT] Processed 199011588 reads in 666 ms
[2015-09-30T22:54Z] INFO  23:54:54,214 MuTect - [MUTECT] Processed 63003036 reads in 656 ms
[2015-09-30T22:54Z] INFO  23:54:54,380 MuTect - [MUTECT] Processed 26001147 reads in 661 ms
[2015-09-30T22:54Z] INFO  23:54:54,411 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:54,657 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:54,839 MuTect - [MUTECT] Processed 200011671 reads in 667 ms
[2015-09-30T22:54Z] INFO  23:54:54,902 MuTect - [MUTECT] Processed 64003103 reads in 688 ms
[2015-09-30T22:54Z] INFO  23:54:54,954 MuTect - [MUTECT] Inspected 60000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:55,341 MuTect - [MUTECT] Processed 27001159 reads in 961 ms
[2015-09-30T22:54Z] INFO  23:54:55,477 MuTect - [MUTECT] Processed 201011797 reads in 638 ms
[2015-09-30T22:54Z] INFO  23:54:55,608 MuTect - [MUTECT] Processed 65003154 reads in 706 ms
[2015-09-30T22:54Z] INFO  23:54:56,123 MuTect - [MUTECT] Processed 202011839 reads in 646 ms
[2015-09-30T22:54Z] INFO  23:54:56,251 MuTect - [MUTECT] Processed 66003193 reads in 643 ms
[2015-09-30T22:54Z] INFO  23:54:56,418 MuTect - [MUTECT] Processed 28001189 reads in 1077 ms
[2015-09-30T22:54Z] INFO  23:54:56,522 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:54Z] INFO  23:54:56,526 ProgressMeter -            done        5.61e+06    2.4 m       25.0 s    100.0%         2.4 m     0.0 s
[2015-09-30T22:54Z] INFO  23:54:56,526 ProgressMeter - Total runtime 141.14 secs, 2.35 min, 0.04 hours
[2015-09-30T22:54Z] INFO  23:54:56,591 MicroScheduler - 170298 reads were filtered out during the traversal out of approximately 2431498 total reads (7.00%)
[2015-09-30T22:54Z] INFO  23:54:56,592 MicroScheduler -   -> 129367 reads (5.32% of total) failing DuplicateReadFilter
[2015-09-30T22:54Z] INFO  23:54:56,592 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:54Z] INFO  23:54:56,592 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:54Z] INFO  23:54:56,592 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:54Z] INFO  23:54:56,592 MicroScheduler -   -> 40931 reads (1.68% of total) failing UnmappedReadFilter
[2015-09-30T22:54Z] INFO  23:54:56,917 MuTect - [MUTECT] Processed 67003228 reads in 666 ms
[2015-09-30T22:54Z] INFO  23:54:57,092 MuTect - [MUTECT] Processed 29001191 reads in 674 ms
[2015-09-30T22:54Z] INFO  23:54:57,174 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:57,586 MuTect - [MUTECT] Processed 68003259 reads in 669 ms
[2015-09-30T22:54Z] INFO  23:54:57,657 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:57,718 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:54Z] INFO  23:54:57,746 MuTect - [MUTECT] Processed 30001257 reads in 654 ms
[2015-09-30T22:54Z] bgzip syn3-22_31022170_51304566-raw-mutect.vcf
[2015-09-30T22:54Z] tabix index syn3-22_31022170_51304566-raw-mutect.vcf.gz
[2015-09-30T22:54Z] INFO  23:54:58,268 MuTect - [MUTECT] Processed 69003306 reads in 682 ms
[2015-09-30T22:54Z] INFO  23:54:58,433 MuTect - [MUTECT] Processed 31001303 reads in 687 ms
[2015-09-30T22:54Z] INFO  23:54:58,969 MuTect - [MUTECT] Processed 70003310 reads in 701 ms
[2015-09-30T22:54Z] INFO  23:54:59,087 MuTect - [MUTECT] Processed 32001304 reads in 654 ms
[2015-09-30T22:54Z] INFO  23:54:59,428 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:54Z] INFO  23:54:59,650 MuTect - [MUTECT] Processed 71003310 reads in 681 ms
[2015-09-30T22:54Z] INFO  23:54:59,720 MuTect - [MUTECT] Processed 33001337 reads in 633 ms
[2015-09-30T22:55Z] INFO  23:55:00,057 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:55Z] MuTect: MuTect
[2015-09-30T22:55Z] INFO  23:55:00,319 MuTect - [MUTECT] Processed 72003366 reads in 669 ms
[2015-09-30T22:55Z] INFO  23:55:00,362 MuTect - [MUTECT] Processed 34001430 reads in 642 ms
[2015-09-30T22:55Z] INFO  23:55:00,971 MuTect - [MUTECT] Processed 73003395 reads in 652 ms
[2015-09-30T22:55Z] INFO  23:55:00,990 MuTect - [MUTECT] Processed 35001505 reads in 628 ms
[2015-09-30T22:55Z] INFO  23:55:01,611 MuTect - [MUTECT] Processed 36001557 reads in 620 ms
[2015-09-30T22:55Z] INFO  23:55:01,621 MuTect - [MUTECT] Processed 74003447 reads in 650 ms
[2015-09-30T22:55Z] INFO  23:55:01,860 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:02,165 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:02,257 MuTect - [MUTECT] Processed 37001588 reads in 647 ms
[2015-09-30T22:55Z] INFO  23:55:02,282 MuTect - [MUTECT] Processed 75003448 reads in 661 ms
[2015-09-30T22:55Z] INFO  23:55:02,365 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/X/syn3-X_62568928_94148729-raw-mutect-regions.bed to be BED
[2015-09-30T22:55Z] INFO  23:55:02,421 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:02,421 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:55Z] INFO  23:55:02,421 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:55Z] INFO  23:55:02,421 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:55Z] INFO  23:55:02,425 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/X/syn3-X_62568928_94148729-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/X/tx/tmpznggiu/syn3-X_62568928_94148729-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:55Z] INFO  23:55:02,425 HelpFormatter - Date/Time: 2015/09/30 23:55:02
[2015-09-30T22:55Z] INFO  23:55:02,425 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:02,425 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:02,452 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:55Z] INFO  23:55:02,456 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:55Z] INFO  23:55:02,505 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:55Z] INFO  23:55:02,553 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:55Z] INFO  23:55:02,560 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:55Z] INFO  23:55:02,583 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:55Z] INFO  23:55:02,594 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:55Z] INFO  23:55:02,770 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:55Z] INFO  23:55:02,848 IntervalUtils - Processing 829325 bp from intervals
[2015-09-30T22:55Z] INFO  23:55:02,852 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:55Z] INFO  23:55:02,852 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:55Z] INFO  23:55:02,904 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:55Z] INFO  23:55:02,922 MuTect - [MUTECT] Processed 38001717 reads in 665 ms
[2015-09-30T22:55Z] INFO  23:55:02,944 MuTect - [MUTECT] Processed 76003480 reads in 662 ms
[2015-09-30T22:55Z] INFO  23:55:03,155 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:55Z] INFO  23:55:03,155 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:55Z] INFO  23:55:03,155 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:55Z] INFO  23:55:03,156 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:55Z] INFO  23:55:03,586 MuTect - [MUTECT] Processed 39001747 reads in 664 ms
[2015-09-30T22:55Z] INFO  23:55:03,625 MuTect - [MUTECT] Processed 77003542 reads in 681 ms
[2015-09-30T22:55Z] INFO  23:55:04,218 MuTect - [MUTECT] Processed 40001842 reads in 632 ms
[2015-09-30T22:55Z] INFO  23:55:04,294 MuTect - [MUTECT] Processed 78003570 reads in 669 ms
[2015-09-30T22:55Z] INFO  23:55:04,315 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:04,569 ProgressMeter -      X:47548884        1.20e+06   30.0 s       24.0 s     40.6%        73.0 s    43.0 s
[2015-09-30T22:55Z] INFO  23:55:04,647 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:04,839 MuTect - [MUTECT] Processed 41001937 reads in 620 ms
[2015-09-30T22:55Z] INFO  23:55:04,952 MuTect - [MUTECT] Processed 79003612 reads in 658 ms
[2015-09-30T22:55Z] INFO  23:55:05,442 MuTect - [MUTECT] Processed 1000020 reads in 2242 ms
[2015-09-30T22:55Z] INFO  23:55:05,510 MuTect - [MUTECT] Processed 42001969 reads in 672 ms
[2015-09-30T22:55Z] INFO  23:55:05,624 MuTect - [MUTECT] Processed 80003661 reads in 672 ms
[2015-09-30T22:55Z] INFO  23:55:06,143 MuTect - [MUTECT] Processed 43002028 reads in 633 ms
[2015-09-30T22:55Z] INFO  23:55:06,229 MuTect - [MUTECT] Processed 2000022 reads in 787 ms
[2015-09-30T22:55Z] INFO  23:55:06,301 MuTect - [MUTECT] Processed 81003696 reads in 677 ms
[2015-09-30T22:55Z] INFO  23:55:06,802 MuTect - [MUTECT] Processed 44002056 reads in 659 ms
[2015-09-30T22:55Z] INFO  23:55:06,897 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:06,965 MuTect - [MUTECT] Processed 82003746 reads in 664 ms
[2015-09-30T22:55Z] INFO  23:55:07,054 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:07,186 MuTect - [MUTECT] Processed 3000079 reads in 956 ms
[2015-09-30T22:55Z] INFO  23:55:07,392 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:55Z] INFO  23:55:07,396 ProgressMeter -            done        2.37e+06   59.0 s       24.0 s    100.0%        59.0 s     0.0 s
[2015-09-30T22:55Z] INFO  23:55:07,396 ProgressMeter - Total runtime 59.23 secs, 0.99 min, 0.02 hours
[2015-09-30T22:55Z] INFO  23:55:07,462 MicroScheduler - 59882 reads were filtered out during the traversal out of approximately 990937 total reads (6.04%)
[2015-09-30T22:55Z] INFO  23:55:07,463 MicroScheduler -   -> 44425 reads (4.48% of total) failing DuplicateReadFilter
[2015-09-30T22:55Z] INFO  23:55:07,463 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:55Z] INFO  23:55:07,463 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:55Z] INFO  23:55:07,463 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:55Z] INFO  23:55:07,464 MuTect - [MUTECT] Processed 45002108 reads in 662 ms
[2015-09-30T22:55Z] INFO  23:55:07,463 MicroScheduler -   -> 15457 reads (1.56% of total) failing UnmappedReadFilter
[2015-09-30T22:55Z] INFO  23:55:07,559 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:07,879 MuTect - [MUTECT] Processed 4000172 reads in 694 ms
[2015-09-30T22:55Z] INFO  23:55:08,063 MuTect - [MUTECT] Processed 46002111 reads in 599 ms
[2015-09-30T22:55Z] INFO  23:55:08,466 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:55Z] bgzip syn3-X_0_31090302-raw-mutect.vcf
[2015-09-30T22:55Z] INFO  23:55:08,564 MuTect - [MUTECT] Processed 5000254 reads in 685 ms
[2015-09-30T22:55Z] tabix index syn3-X_0_31090302-raw-mutect.vcf.gz
[2015-09-30T22:55Z] INFO  23:55:08,720 MuTect - [MUTECT] Processed 47002190 reads in 657 ms
[2015-09-30T22:55Z] INFO  23:55:09,295 MuTect - [MUTECT] Processed 6000364 reads in 731 ms
[2015-09-30T22:55Z] INFO  23:55:09,328 MuTect - [MUTECT] Processed 48002209 reads in 608 ms
[2015-09-30T22:55Z] INFO  23:55:09,435 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:09,948 MuTect - [MUTECT] Processed 49002241 reads in 620 ms
[2015-09-30T22:55Z] INFO  23:55:10,067 MuTect - [MUTECT] Processed 7000387 reads in 772 ms
[2015-09-30T22:55Z] INFO  23:55:10,102 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:10,593 MuTect - [MUTECT] Processed 50002343 reads in 645 ms
[2015-09-30T22:55Z] INFO  23:55:10,793 MuTect - [MUTECT] Processed 8000462 reads in 726 ms
[2015-09-30T22:55Z] MuTect: MuTect
[2015-09-30T22:55Z] INFO  23:55:11,202 MuTect - [MUTECT] Processed 51002347 reads in 609 ms
[2015-09-30T22:55Z] INFO  23:55:11,420 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:11,503 MuTect - [MUTECT] Processed 9000497 reads in 710 ms
[2015-09-30T22:55Z] INFO  23:55:11,833 MuTect - [MUTECT] Processed 52002440 reads in 631 ms
[2015-09-30T22:55Z] INFO  23:55:12,187 MuTect - [MUTECT] Processed 10000583 reads in 684 ms
[2015-09-30T22:55Z] INFO  23:55:12,473 MuTect - [MUTECT] Processed 53002473 reads in 639 ms
[2015-09-30T22:55Z] INFO  23:55:12,608 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:12,883 MuTect - [MUTECT] Processed 11000648 reads in 696 ms
[2015-09-30T22:55Z] INFO  23:55:12,927 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/X/syn3-X_94317773_125687021-raw-mutect-regions.bed to be BED
[2015-09-30T22:55Z] INFO  23:55:12,978 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:12,978 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:55Z] INFO  23:55:12,978 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:55Z] INFO  23:55:12,979 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:55Z] INFO  23:55:12,982 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/X/syn3-X_94317773_125687021-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/X/tx/tmpr8Kb6y/syn3-X_94317773_125687021-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:55Z] INFO  23:55:12,982 HelpFormatter - Date/Time: 2015/09/30 23:55:12
[2015-09-30T22:55Z] INFO  23:55:12,982 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:12,982 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:13,008 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:55Z] INFO  23:55:13,012 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:55Z] INFO  23:55:13,060 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:55Z] INFO  23:55:13,106 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:55Z] INFO  23:55:13,113 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:55Z] INFO  23:55:13,132 MuTect - [MUTECT] Processed 54002512 reads in 660 ms
[2015-09-30T22:55Z] INFO  23:55:13,135 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:55Z] INFO  23:55:13,145 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:55Z] INFO  23:55:13,313 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:55Z] INFO  23:55:13,465 IntervalUtils - Processing 1156902 bp from intervals
[2015-09-30T22:55Z] INFO  23:55:13,468 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:55Z] INFO  23:55:13,469 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:55Z] INFO  23:55:13,567 MuTect - [MUTECT] Processed 12000674 reads in 684 ms
[2015-09-30T22:55Z] INFO  23:55:13,601 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:13,785 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:55Z] INFO  23:55:13,806 MuTect - [MUTECT] Processed 55002579 reads in 674 ms
[2015-09-30T22:55Z] INFO  23:55:14,223 MuTect - [MUTECT] Processed 13000701 reads in 656 ms
[2015-09-30T22:55Z] INFO  23:55:14,446 MuTect - [MUTECT] Processed 56002674 reads in 640 ms
[2015-09-30T22:55Z] INFO  23:55:14,686 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:55Z] INFO  23:55:14,686 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:55Z] INFO  23:55:14,686 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:55Z] INFO  23:55:14,687 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:55Z] INFO  23:55:14,814 MuTect - [MUTECT] Processed 14000768 reads in 591 ms
[2015-09-30T22:55Z] INFO  23:55:15,080 MuTect - [MUTECT] Processed 57002696 reads in 634 ms
[2015-09-30T22:55Z] INFO  23:55:15,476 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:15,486 MuTect - [MUTECT] Processed 15000851 reads in 672 ms
[2015-09-30T22:55Z] INFO  23:55:15,649 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:15,739 MuTect - [MUTECT] Processed 58002709 reads in 659 ms
[2015-09-30T22:55Z] INFO  23:55:16,140 MuTect - [MUTECT] Processed 16000885 reads in 654 ms
[2015-09-30T22:55Z] INFO  23:55:16,381 MuTect - [MUTECT] Processed 59002807 reads in 642 ms
[2015-09-30T22:55Z] INFO  23:55:16,792 MuTect - [MUTECT] Processed 17000903 reads in 652 ms
[2015-09-30T22:55Z] INFO  23:55:17,042 MuTect - [MUTECT] Processed 60002885 reads in 661 ms
[2015-09-30T22:55Z] INFO  23:55:17,465 MuTect - [MUTECT] Processed 18001000 reads in 673 ms
[2015-09-30T22:55Z] INFO  23:55:17,501 MuTect - [MUTECT] Processed 1000042 reads in 2672 ms
[2015-09-30T22:55Z] INFO  23:55:17,574 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:17,705 MuTect - [MUTECT] Processed 61002916 reads in 663 ms
[2015-09-30T22:55Z] INFO  23:55:17,850 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:18,150 MuTect - [MUTECT] Processed 19001022 reads in 685 ms
[2015-09-30T22:55Z] INFO  23:55:18,249 MuTect - [MUTECT] Processed 2000120 reads in 749 ms
[2015-09-30T22:55Z] INFO  23:55:18,404 MuTect - [MUTECT] Processed 62003007 reads in 699 ms
[2015-09-30T22:55Z] INFO  23:55:18,788 MuTect - [MUTECT] Processed 20001073 reads in 638 ms
[2015-09-30T22:55Z] INFO  23:55:18,953 MuTect - [MUTECT] Processed 3000121 reads in 704 ms
[2015-09-30T22:55Z] INFO  23:55:19,003 MuTect - [MUTECT] Processed 63003105 reads in 599 ms
[2015-09-30T22:55Z] INFO  23:55:19,376 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:19,422 MuTect - [MUTECT] Processed 21001121 reads in 634 ms
[2015-09-30T22:55Z] INFO  23:55:19,609 MuTect - [MUTECT] Processed 64003174 reads in 606 ms
[2015-09-30T22:55Z] INFO  23:55:19,658 MuTect - [MUTECT] Processed 4000197 reads in 705 ms
[2015-09-30T22:55Z] INFO  23:55:19,934 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:19,958 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:20,055 MuTect - [MUTECT] Processed 22001193 reads in 633 ms
[2015-09-30T22:55Z] INFO  23:55:20,214 MuTect - [MUTECT] Processed 65003265 reads in 605 ms
[2015-09-30T22:55Z] INFO  23:55:20,368 MuTect - [MUTECT] Processed 5000197 reads in 710 ms
[2015-09-30T22:55Z] INFO  23:55:20,753 MuTect - [MUTECT] Processed 23001269 reads in 698 ms
[2015-09-30T22:55Z] INFO  23:55:20,828 MuTect - [MUTECT] Processed 66003332 reads in 614 ms
[2015-09-30T22:55Z] INFO  23:55:21,067 MuTect - [MUTECT] Processed 6000279 reads in 699 ms
[2015-09-30T22:55Z] INFO  23:55:21,405 MuTect - [MUTECT] Processed 24001376 reads in 652 ms
[2015-09-30T22:55Z] INFO  23:55:21,471 MuTect - [MUTECT] Processed 67003353 reads in 643 ms
[2015-09-30T22:55Z] INFO  23:55:21,746 MuTect - [MUTECT] Processed 7000291 reads in 679 ms
[2015-09-30T22:55Z] INFO  23:55:21,870 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:22,034 MuTect - [MUTECT] Processed 25001477 reads in 629 ms
[2015-09-30T22:55Z] INFO  23:55:22,105 MuTect - [MUTECT] Processed 68003613 reads in 634 ms
[2015-09-30T22:55Z] INFO  23:55:22,310 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:22,425 MuTect - [MUTECT] Processed 8000312 reads in 679 ms
[2015-09-30T22:55Z] INFO  23:55:22,648 MuTect - [MUTECT] Processed 26001514 reads in 614 ms
[2015-09-30T22:55Z] INFO  23:55:22,684 MuTect - [MUTECT] Processed 69003806 reads in 579 ms
[2015-09-30T22:55Z] INFO  23:55:23,111 MuTect - [MUTECT] Processed 9000345 reads in 686 ms
[2015-09-30T22:55Z] INFO  23:55:23,255 MuTect - [MUTECT] Processed 70004024 reads in 571 ms
[2015-09-30T22:55Z] INFO  23:55:23,301 MuTect - [MUTECT] Processed 27001566 reads in 653 ms
[2015-09-30T22:55Z] INFO  23:55:23,835 MuTect - [MUTECT] Processed 10000378 reads in 724 ms
[2015-09-30T22:55Z] INFO  23:55:23,842 MuTect - [MUTECT] Processed 71004072 reads in 587 ms
[2015-09-30T22:55Z] INFO  23:55:23,915 MuTect - [MUTECT] Processed 28001608 reads in 614 ms
[2015-09-30T22:55Z] INFO  23:55:24,289 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:24,399 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:24,440 MuTect - [MUTECT] Processed 72004118 reads in 598 ms
[2015-09-30T22:55Z] INFO  23:55:24,528 MuTect - [MUTECT] Processed 29001642 reads in 613 ms
[2015-09-30T22:55Z] INFO  23:55:24,529 MuTect - [MUTECT] Processed 11000386 reads in 694 ms
[2015-09-30T22:55Z] INFO  23:55:25,109 MuTect - [MUTECT] Processed 73004270 reads in 669 ms
[2015-09-30T22:55Z] INFO  23:55:25,167 MuTect - [MUTECT] Processed 30001684 reads in 639 ms
[2015-09-30T22:55Z] INFO  23:55:25,244 MuTect - [MUTECT] Processed 12000449 reads in 715 ms
[2015-09-30T22:55Z] INFO  23:55:25,562 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:25,753 MuTect - [MUTECT] Processed 74004361 reads in 644 ms
[2015-09-30T22:55Z] INFO  23:55:25,776 MuTect - [MUTECT] Processed 31001726 reads in 609 ms
[2015-09-30T22:55Z] INFO  23:55:25,955 MuTect - [MUTECT] Processed 13000487 reads in 711 ms
[2015-09-30T22:55Z] INFO  23:55:26,386 MuTect - [MUTECT] Processed 75004456 reads in 633 ms
[2015-09-30T22:55Z] INFO  23:55:26,389 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:26,407 MuTect - [MUTECT] Processed 32001757 reads in 630 ms
[2015-09-30T22:55Z] INFO  23:55:26,609 MuTect - [MUTECT] Processed 14000548 reads in 654 ms
[2015-09-30T22:55Z] INFO  23:55:26,712 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:26,996 MuTect - [MUTECT] Processed 76004481 reads in 610 ms
[2015-09-30T22:55Z] INFO  23:55:27,077 MuTect - [MUTECT] Processed 33001787 reads in 671 ms
[2015-09-30T22:55Z] INFO  23:55:27,311 MuTect - [MUTECT] Processed 15000574 reads in 702 ms
[2015-09-30T22:55Z] INFO  23:55:27,598 MuTect - [MUTECT] Processed 77004517 reads in 602 ms
[2015-09-30T22:55Z] INFO  23:55:27,760 MuTect - [MUTECT] Processed 34001852 reads in 683 ms
[2015-09-30T22:55Z] INFO  23:55:27,962 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:28,015 MuTect - [MUTECT] Processed 16000684 reads in 704 ms
[2015-09-30T22:55Z] INFO  23:55:28,212 MuTect - [MUTECT] Processed 78004597 reads in 614 ms
[2015-09-30T22:55Z] INFO  23:55:28,434 MuTect - [MUTECT] Processed 35001898 reads in 674 ms
[2015-09-30T22:55Z] INFO  23:55:28,666 MuTect - [MUTECT] Processed 17000724 reads in 651 ms
[2015-09-30T22:55Z] INFO  23:55:28,828 MuTect - [MUTECT] Processed 79004637 reads in 616 ms
[2015-09-30T22:55Z] INFO  23:55:29,042 MuTect - [MUTECT] Processed 36002040 reads in 608 ms
[2015-09-30T22:55Z] INFO  23:55:29,261 MuTect - [MUTECT] Processed 18000819 reads in 595 ms
[2015-09-30T22:55Z] INFO  23:55:29,456 MuTect - [MUTECT] Processed 80004734 reads in 628 ms
[2015-09-30T22:55Z] INFO  23:55:29,467 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:29,725 MuTect - [MUTECT] Processed 37002083 reads in 683 ms
[2015-09-30T22:55Z] INFO  23:55:29,882 MuTect - [MUTECT] Processed 19000863 reads in 621 ms
[2015-09-30T22:55Z] INFO  23:55:30,117 MuTect - [MUTECT] Processed 81004738 reads in 661 ms
[2015-09-30T22:55Z] INFO  23:55:30,211 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:30,418 MuTect - [MUTECT] Processed 38002141 reads in 693 ms
[2015-09-30T22:55Z] INFO  23:55:30,520 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:30,527 MuTect - [MUTECT] Processed 20000918 reads in 645 ms
[2015-09-30T22:55Z] INFO  23:55:30,740 MuTect - [MUTECT] Processed 82004743 reads in 623 ms
[2015-09-30T22:55Z] INFO  23:55:31,084 MuTect - [MUTECT] Processed 39002227 reads in 665 ms
[2015-09-30T22:55Z] INFO  23:55:31,146 MuTect - [MUTECT] Processed 21000978 reads in 619 ms
[2015-09-30T22:55Z] INFO  23:55:31,321 MuTect - [MUTECT] Processed 83004744 reads in 581 ms
[2015-09-30T22:55Z] INFO  23:55:31,758 MuTect - [MUTECT] Processed 40002246 reads in 675 ms
[2015-09-30T22:55Z] INFO  23:55:31,788 MuTect - [MUTECT] Processed 22000995 reads in 642 ms
[2015-09-30T22:55Z] INFO  23:55:31,850 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:31,912 MuTect - [MUTECT] Processed 84004749 reads in 591 ms
[2015-09-30T22:55Z] INFO  23:55:32,433 MuTect - [MUTECT] Processed 23001043 reads in 645 ms
[2015-09-30T22:55Z] INFO  23:55:32,439 MuTect - [MUTECT] Processed 41002270 reads in 681 ms
[2015-09-30T22:55Z] INFO  23:55:32,568 MuTect - [MUTECT] Processed 85004826 reads in 655 ms
[2015-09-30T22:55Z] INFO  23:55:32,786 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:33,066 MuTect - [MUTECT] Processed 24001163 reads in 632 ms
[2015-09-30T22:55Z] INFO  23:55:33,086 MuTect - [MUTECT] Processed 42002325 reads in 646 ms
[2015-09-30T22:55Z] INFO  23:55:33,158 ProgressMeter -      X:72094789        1.17e+06   30.0 s       25.0 s     54.7%        54.0 s    24.0 s
[2015-09-30T22:55Z] INFO  23:55:33,217 MuTect - [MUTECT] Processed 86004862 reads in 650 ms
[2015-09-30T22:55Z] INFO  23:55:33,711 MuTect - [MUTECT] Processed 25001175 reads in 646 ms
[2015-09-30T22:55Z] INFO  23:55:33,746 MuTect - [MUTECT] Processed 43002366 reads in 661 ms
[2015-09-30T22:55Z] INFO  23:55:33,856 MuTect - [MUTECT] Processed 87004943 reads in 639 ms
[2015-09-30T22:55Z] INFO  23:55:34,363 MuTect - [MUTECT] Processed 26001191 reads in 652 ms
[2015-09-30T22:55Z] INFO  23:55:34,431 MuTect - [MUTECT] Processed 44002396 reads in 685 ms
[2015-09-30T22:55Z] INFO  23:55:34,568 MuTect - [MUTECT] Processed 88005035 reads in 712 ms
[2015-09-30T22:55Z] INFO  23:55:34,570 ProgressMeter -      X:53106838        2.65e+06   60.0 s       22.0 s     77.0%        77.0 s    17.0 s
[2015-09-30T22:55Z] INFO  23:55:34,966 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:35,052 MuTect - [MUTECT] Processed 27001248 reads in 689 ms
[2015-09-30T22:55Z] INFO  23:55:35,064 MuTect - [MUTECT] Processed 45002429 reads in 633 ms
[2015-09-30T22:55Z] INFO  23:55:35,188 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:35,195 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:35,204 MuTect - [MUTECT] Processed 89005055 reads in 636 ms
[2015-09-30T22:55Z] INFO  23:55:35,702 MuTect - [MUTECT] Processed 28001333 reads in 650 ms
[2015-09-30T22:55Z] INFO  23:55:35,710 MuTect - [MUTECT] Processed 46002477 reads in 646 ms
[2015-09-30T22:55Z] INFO  23:55:35,826 MuTect - [MUTECT] Processed 90005146 reads in 622 ms
[2015-09-30T22:55Z] INFO  23:55:36,363 MuTect - [MUTECT] Processed 29001348 reads in 661 ms
[2015-09-30T22:55Z] INFO  23:55:36,365 MuTect - [MUTECT] Processed 47002581 reads in 655 ms
[2015-09-30T22:55Z] INFO  23:55:36,445 MuTect - [MUTECT] Processed 91005227 reads in 619 ms
[2015-09-30T22:55Z] INFO  23:55:36,913 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:37,051 MuTect - [MUTECT] Processed 30001412 reads in 688 ms
[2015-09-30T22:55Z] INFO  23:55:37,063 MuTect - [MUTECT] Processed 48002641 reads in 698 ms
[2015-09-30T22:55Z] INFO  23:55:37,087 MuTect - [MUTECT] Processed 92005349 reads in 642 ms
[2015-09-30T22:55Z] INFO  23:55:37,644 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:37,724 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:37,729 MuTect - [MUTECT] Processed 93005408 reads in 642 ms
[2015-09-30T22:55Z] INFO  23:55:37,739 MuTect - [MUTECT] Processed 31001441 reads in 688 ms
[2015-09-30T22:55Z] INFO  23:55:37,746 MuTect - [MUTECT] Processed 49002648 reads in 683 ms
[2015-09-30T22:55Z] INFO  23:55:38,356 MuTect - [MUTECT] Processed 94005423 reads in 627 ms
[2015-09-30T22:55Z] INFO  23:55:38,409 MuTect - [MUTECT] Processed 32001447 reads in 670 ms
[2015-09-30T22:55Z] INFO  23:55:38,417 MuTect - [MUTECT] Processed 50002651 reads in 671 ms
[2015-09-30T22:55Z] INFO  23:55:39,019 MuTect - [MUTECT] Processed 95005435 reads in 663 ms
[2015-09-30T22:55Z] INFO  23:55:39,047 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:39,071 MuTect - [MUTECT] Processed 51002682 reads in 654 ms
[2015-09-30T22:55Z] INFO  23:55:39,088 MuTect - [MUTECT] Processed 33001500 reads in 679 ms
[2015-09-30T22:55Z] INFO  23:55:39,669 MuTect - [MUTECT] Processed 96005435 reads in 650 ms
[2015-09-30T22:55Z] INFO  23:55:39,749 MuTect - [MUTECT] Processed 34001554 reads in 661 ms
[2015-09-30T22:55Z] INFO  23:55:39,886 MuTect - [MUTECT] Processed 52002694 reads in 815 ms
[2015-09-30T22:55Z] INFO  23:55:40,217 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:40,325 MuTect - [MUTECT] Processed 97005487 reads in 656 ms
[2015-09-30T22:55Z] INFO  23:55:40,451 MuTect - [MUTECT] Processed 35001578 reads in 702 ms
[2015-09-30T22:55Z] INFO  23:55:40,471 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:40,716 MuTect - [MUTECT] Processed 53002745 reads in 830 ms
[2015-09-30T22:55Z] INFO  23:55:40,955 MuTect - [MUTECT] Processed 98005517 reads in 630 ms
[2015-09-30T22:55Z] INFO  23:55:41,147 MuTect - [MUTECT] Processed 36001654 reads in 696 ms
[2015-09-30T22:55Z] INFO  23:55:41,390 MuTect - [MUTECT] Processed 54002746 reads in 674 ms
[2015-09-30T22:55Z] INFO  23:55:41,468 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:41,576 MuTect - [MUTECT] Processed 99005531 reads in 621 ms
[2015-09-30T22:55Z] INFO  23:55:41,766 MuTect - [MUTECT] Processed 37001673 reads in 619 ms
[2015-09-30T22:55Z] INFO  23:55:42,086 MuTect - [MUTECT] Processed 55002786 reads in 696 ms
[2015-09-30T22:55Z] INFO  23:55:42,202 MuTect - [MUTECT] Processed 100005540 reads in 625 ms
[2015-09-30T22:55Z] INFO  23:55:42,429 MuTect - [MUTECT] Processed 38001690 reads in 662 ms
[2015-09-30T22:55Z] INFO  23:55:42,509 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:42,786 MuTect - [MUTECT] Processed 56002786 reads in 700 ms
[2015-09-30T22:55Z] INFO  23:55:42,826 MuTect - [MUTECT] Processed 101005609 reads in 625 ms
[2015-09-30T22:55Z] INFO  23:55:43,074 MuTect - [MUTECT] Processed 39001700 reads in 646 ms
[2015-09-30T22:55Z] INFO  23:55:43,201 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:43,453 MuTect - [MUTECT] Processed 57002886 reads in 667 ms
[2015-09-30T22:55Z] INFO  23:55:43,457 MuTect - [MUTECT] Processed 102005662 reads in 631 ms
[2015-09-30T22:55Z] INFO  23:55:43,691 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:43,720 MuTect - [MUTECT] Processed 40001707 reads in 646 ms
[2015-09-30T22:55Z] INFO  23:55:44,101 MuTect - [MUTECT] Processed 103005682 reads in 644 ms
[2015-09-30T22:55Z] INFO  23:55:44,114 MuTect - [MUTECT] Processed 58002926 reads in 661 ms
[2015-09-30T22:55Z] INFO  23:55:44,366 MuTect - [MUTECT] Processed 41001730 reads in 646 ms
[2015-09-30T22:55Z] INFO  23:55:44,689 ProgressMeter -     X:107405207        1.21e+06   30.0 s       24.0 s     43.7%        68.0 s    38.0 s
[2015-09-30T22:55Z] INFO  23:55:44,731 MuTect - [MUTECT] Processed 104005684 reads in 630 ms
[2015-09-30T22:55Z] INFO  23:55:44,792 MuTect - [MUTECT] Processed 59002946 reads in 678 ms
[2015-09-30T22:55Z] INFO  23:55:44,802 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:45,012 MuTect - [MUTECT] Processed 42001740 reads in 645 ms
[2015-09-30T22:55Z] INFO  23:55:45,368 MuTect - [MUTECT] Processed 105005764 reads in 637 ms
[2015-09-30T22:55Z] INFO  23:55:45,478 MuTect - [MUTECT] Processed 60003040 reads in 686 ms
[2015-09-30T22:55Z] INFO  23:55:45,664 MuTect - [MUTECT] Processed 43001786 reads in 653 ms
[2015-09-30T22:55Z] INFO  23:55:45,718 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:45,855 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:46,010 MuTect - [MUTECT] Processed 106005858 reads in 642 ms
[2015-09-30T22:55Z] INFO  23:55:46,180 MuTect - [MUTECT] Processed 61003100 reads in 701 ms
[2015-09-30T22:55Z] INFO  23:55:46,334 MuTect - [MUTECT] Processed 44001859 reads in 670 ms
[2015-09-30T22:55Z] INFO  23:55:46,654 MuTect - [MUTECT] Processed 107005901 reads in 644 ms
[2015-09-30T22:55Z] INFO  23:55:46,857 MuTect - [MUTECT] Processed 62003171 reads in 678 ms
[2015-09-30T22:55Z] INFO  23:55:47,001 MuTect - [MUTECT] Processed 45001870 reads in 667 ms
[2015-09-30T22:55Z] INFO  23:55:47,271 MuTect - [MUTECT] Processed 108005965 reads in 617 ms
[2015-09-30T22:55Z] INFO  23:55:47,330 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:47,529 MuTect - [MUTECT] Processed 63003223 reads in 672 ms
[2015-09-30T22:55Z] INFO  23:55:47,664 MuTect - [MUTECT] Processed 46001910 reads in 663 ms
[2015-09-30T22:55Z] INFO  23:55:47,908 MuTect - [MUTECT] Processed 109006034 reads in 637 ms
[2015-09-30T22:55Z] INFO  23:55:48,068 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:48,228 MuTect - [MUTECT] Processed 64003259 reads in 699 ms
[2015-09-30T22:55Z] INFO  23:55:48,311 MuTect - [MUTECT] Processed 47001911 reads in 647 ms
[2015-09-30T22:55Z] INFO  23:55:48,468 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:48,542 MuTect - [MUTECT] Processed 110006056 reads in 634 ms
[2015-09-30T22:55Z] INFO  23:55:48,961 MuTect - [MUTECT] Processed 48001942 reads in 650 ms
[2015-09-30T22:55Z] INFO  23:55:48,982 MuTect - [MUTECT] Processed 65003325 reads in 754 ms
[2015-09-30T22:55Z] INFO  23:55:49,219 MuTect - [MUTECT] Processed 111006073 reads in 677 ms
[2015-09-30T22:55Z] INFO  23:55:49,618 MuTect - [MUTECT] Processed 49001974 reads in 656 ms
[2015-09-30T22:55Z] INFO  23:55:49,683 MuTect - [MUTECT] Processed 66003329 reads in 701 ms
[2015-09-30T22:55Z] INFO  23:55:49,829 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:49,864 MuTect - [MUTECT] Processed 112006087 reads in 645 ms
[2015-09-30T22:55Z] INFO  23:55:50,258 MuTect - [MUTECT] Processed 50002043 reads in 641 ms
[2015-09-30T22:55Z] INFO  23:55:50,308 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:55Z] INFO  23:55:50,312 ProgressMeter -            done        1.99e+06   47.0 s       23.0 s    100.0%        47.0 s     0.0 s
[2015-09-30T22:55Z] INFO  23:55:50,312 ProgressMeter - Total runtime 47.16 secs, 0.79 min, 0.01 hours
[2015-09-30T22:55Z] INFO  23:55:50,376 MicroScheduler - 46490 reads were filtered out during the traversal out of approximately 782084 total reads (5.94%)
[2015-09-30T22:55Z] INFO  23:55:50,376 MicroScheduler -   -> 34038 reads (4.35% of total) failing DuplicateReadFilter
[2015-09-30T22:55Z] INFO  23:55:50,376 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:55Z] INFO  23:55:50,376 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:55Z] INFO  23:55:50,376 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:55Z] INFO  23:55:50,377 MicroScheduler -   -> 12452 reads (1.59% of total) failing UnmappedReadFilter
[2015-09-30T22:55Z] INFO  23:55:50,466 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:50,519 MuTect - [MUTECT] Processed 113006100 reads in 655 ms
[2015-09-30T22:55Z] INFO  23:55:50,909 MuTect - [MUTECT] Processed 51002101 reads in 651 ms
[2015-09-30T22:55Z] INFO  23:55:51,156 MuTect - [MUTECT] Processed 114006121 reads in 637 ms
[2015-09-30T22:55Z] INFO  23:55:51,455 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:55Z] bgzip syn3-X_62568928_94148729-raw-mutect.vcf
[2015-09-30T22:55Z] tabix index syn3-X_62568928_94148729-raw-mutect.vcf.gz
[2015-09-30T22:55Z] INFO  23:55:51,587 MuTect - [MUTECT] Processed 52002114 reads in 678 ms
[2015-09-30T22:55Z] INFO  23:55:51,832 MuTect - [MUTECT] Processed 115006231 reads in 676 ms
[2015-09-30T22:55Z] INFO  23:55:52,034 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:55Z] INFO  23:55:52,037 ProgressMeter -            done        3.57e+06   77.0 s       21.0 s    100.0%        77.0 s     0.0 s
[2015-09-30T22:55Z] INFO  23:55:52,037 ProgressMeter - Total runtime 77.47 secs, 1.29 min, 0.02 hours
[2015-09-30T22:55Z] INFO  23:55:52,101 MicroScheduler - 83306 reads were filtered out during the traversal out of approximately 1357912 total reads (6.13%)
[2015-09-30T22:55Z] INFO  23:55:52,102 MicroScheduler -   -> 60898 reads (4.48% of total) failing DuplicateReadFilter
[2015-09-30T22:55Z] INFO  23:55:52,102 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:55Z] INFO  23:55:52,102 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:55Z] INFO  23:55:52,102 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:55Z] INFO  23:55:52,102 MicroScheduler -   -> 22408 reads (1.65% of total) failing UnmappedReadFilter
[2015-09-30T22:55Z] INFO  23:55:52,182 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:52,258 MuTect - [MUTECT] Processed 53002180 reads in 671 ms
[2015-09-30T22:55Z] INFO  23:55:52,918 MuTect - [MUTECT] Processed 54002202 reads in 660 ms
[2015-09-30T22:55Z] INFO  23:55:53,104 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:55Z] bgzip syn3-X_31132529_62519711-raw-mutect.vcf
[2015-09-30T22:55Z] tabix index syn3-X_31132529_62519711-raw-mutect.vcf.gz
[2015-09-30T22:55Z] INFO  23:55:53,595 MuTect - [MUTECT] Processed 55002249 reads in 677 ms
[2015-09-30T22:55Z] MuTect: MuTect
[2015-09-30T22:55Z] INFO  23:55:54,262 MuTect - [MUTECT] Processed 56002340 reads in 667 ms
[2015-09-30T22:55Z] INFO  23:55:54,586 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:54,945 MuTect - [MUTECT] Processed 57002378 reads in 683 ms
[2015-09-30T22:55Z] MuTect: MuTect
[2015-09-30T22:55Z] INFO  23:55:55,625 MuTect - [MUTECT] Processed 58002415 reads in 680 ms
[2015-09-30T22:55Z] INFO  23:55:56,053 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/X/syn3-X_125953527_155270560-raw-mutect-regions.bed to be BED
[2015-09-30T22:55Z] INFO  23:55:56,110 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:56,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:55Z] INFO  23:55:56,111 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:55Z] INFO  23:55:56,111 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:55Z] INFO  23:55:56,115 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/X/syn3-X_125953527_155270560-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/X/tx/tmpgImmi8/syn3-X_125953527_155270560-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:55Z] INFO  23:55:56,115 HelpFormatter - Date/Time: 2015/09/30 23:55:56
[2015-09-30T22:55Z] INFO  23:55:56,115 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:56,115 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:56,143 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:55Z] INFO  23:55:56,148 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:55Z] INFO  23:55:56,198 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:55Z] INFO  23:55:56,246 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:55Z] INFO  23:55:56,254 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:55Z] INFO  23:55:56,278 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:55Z] INFO  23:55:56,289 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:55Z] INFO  23:55:56,307 MuTect - [MUTECT] Processed 59002443 reads in 682 ms
[2015-09-30T22:55Z] INFO  23:55:56,464 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:55Z] INFO  23:55:56,559 IntervalUtils - Processing 1245180 bp from intervals
[2015-09-30T22:55Z] INFO  23:55:56,563 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:55Z] INFO  23:55:56,563 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:55Z] INFO  23:55:56,727 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:55Z] INFO  23:55:56,876 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:55Z] INFO  23:55:56,877 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:55Z] INFO  23:55:56,877 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:55Z] INFO  23:55:56,878 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:55Z] INFO  23:55:57,000 MuTect - [MUTECT] Processed 60002552 reads in 693 ms
[2015-09-30T22:55Z] INFO  23:55:57,158 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:57,552 ArgumentTypeDescriptor - Dynamically determined type of /home/cancer-dream-syn3/work/mutect/Y/syn3-Y_0_28716339-raw-mutect-regions.bed to be BED
[2015-09-30T22:55Z] INFO  23:55:57,608 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:57,608 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/27 11:11:54
[2015-09-30T22:55Z] INFO  23:55:57,608 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:55Z] INFO  23:55:57,608 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:55Z] INFO  23:55:57,612 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T MuTect -U ALLOW_N_CIGAR_READS --downsample_to_coverage 10000 --read_filter NotPrimaryAlignment -I:tumor /home/cancer-dream-syn3/work/bamprep/syn3-tumor/Y/2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam --tumor_sample_name syn3-tumor -I:normal /home/cancer-dream-syn3/work/bamprep/syn3-normal/Y/1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam --normal_sample_name syn3-normal --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz --cosmic /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz -L /home/cancer-dream-syn3/work/mutect/Y/syn3-Y_0_28716339-raw-mutect-regions.bed --interval_set_rule INTERSECTION --vcf /home/cancer-dream-syn3/work/mutect/Y/tx/tmpHXGB2t/syn3-Y_0_28716339-raw-mutect-orig.vcf.gz -o /dev/null
[2015-09-30T22:55Z] INFO  23:55:57,612 HelpFormatter - Date/Time: 2015/09/30 23:55:57
[2015-09-30T22:55Z] INFO  23:55:57,612 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:57,612 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:55Z] INFO  23:55:57,640 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz to be VCF
[2015-09-30T22:55Z] INFO  23:55:57,644 ArgumentTypeDescriptor - Dynamically determined type of /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz to be VCF
[2015-09-30T22:55Z] INFO  23:55:57,694 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:55Z] INFO  23:55:57,701 MuTect - [MUTECT] Processed 61002590 reads in 701 ms
[2015-09-30T22:55Z] INFO  23:55:57,742 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000
[2015-09-30T22:55Z] INFO  23:55:57,750 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:55Z] INFO  23:55:57,773 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:55Z] INFO  23:55:57,784 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz as a tabix indexed file
[2015-09-30T22:55Z] INFO  23:55:57,958 RMDTrackBuilder - Attempting to blindly load /data/genomes/Hsapiens/GRCh37/variation/cosmic-v68-GRCh37.vcf.gz as a tabix indexed file
[2015-09-30T22:55Z] INFO  23:55:58,032 IntervalUtils - Processing 568521 bp from intervals
[2015-09-30T22:55Z] INFO  23:55:58,036 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:55Z] INFO  23:55:58,036 IndexDictionaryUtils - Track cosmic doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:55Z] INFO  23:55:58,091 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:55Z] INFO  23:55:58,290 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:55Z] INFO  23:55:58,290 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:55Z] INFO  23:55:58,291 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
[2015-09-30T22:55Z] INFO  23:55:58,292 MuTect - VERSION INFO: MuTect:1.1.4-28-g8f5ae96 Gatk:2.7-1-g42d771f
[2015-09-30T22:55Z] INFO  23:55:58,390 MuTect - [MUTECT] Processed 62002608 reads in 689 ms
[2015-09-30T22:55Z] INFO  23:55:59,071 MuTect - [MUTECT] Processed 63002617 reads in 681 ms
[2015-09-30T22:55Z] INFO  23:55:59,753 MuTect - [MUTECT] Processed 64002672 reads in 682 ms
[2015-09-30T22:55Z] INFO  23:55:59,806 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:55Z] INFO  23:55:59,820 MuTect - [MUTECT] Processed 1000035 reads in 2852 ms
[2015-09-30T22:56Z] INFO  23:56:00,426 MuTect - [MUTECT] Processed 65002673 reads in 673 ms
[2015-09-30T22:56Z] INFO  23:56:00,558 MuTect - [MUTECT] Processed 2000137 reads in 738 ms
[2015-09-30T22:56Z] INFO  23:56:01,109 MuTect - [MUTECT] Processed 66002762 reads in 683 ms
[2015-09-30T22:56Z] INFO  23:56:01,242 MuTect - [MUTECT] Processed 3000140 reads in 684 ms
[2015-09-30T22:56Z] INFO  23:56:01,705 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:01,782 MuTect - [MUTECT] Processed 67002769 reads in 673 ms
[2015-09-30T22:56Z] INFO  23:56:01,979 MuTect - [MUTECT] Processed 4000248 reads in 737 ms
[2015-09-30T22:56Z] INFO  23:56:02,292 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:02,447 MuTect - [MUTECT] Processed 68002811 reads in 665 ms
[2015-09-30T22:56Z] INFO  23:56:02,637 MuTect - [MUTECT] Processed 5000261 reads in 658 ms
[2015-09-30T22:56Z] INFO  23:56:03,123 MuTect - [MUTECT] Processed 69002855 reads in 676 ms
[2015-09-30T22:56Z] INFO  23:56:03,533 MuTect - [MUTECT] Processed 6000342 reads in 896 ms
[2015-09-30T22:56Z] INFO  23:56:03,891 MuTect - [MUTECT] Processed 70002951 reads in 768 ms
[2015-09-30T22:56Z] INFO  23:56:04,145 MuTect - [MUTECT] Inspected 2000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:04,177 MuTect - [MUTECT] Processed 7000374 reads in 644 ms
[2015-09-30T22:56Z] INFO  23:56:04,647 MuTect - [MUTECT] Processed 71002970 reads in 756 ms
[2015-09-30T22:56Z] INFO  23:56:04,800 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:04,833 MuTect - [MUTECT] Processed 8000395 reads in 656 ms
[2015-09-30T22:56Z] INFO  23:56:05,304 MuTect - [MUTECT] Processed 72003013 reads in 657 ms
[2015-09-30T22:56Z] INFO  23:56:05,488 MuTect - [MUTECT] Processed 9000464 reads in 655 ms
[2015-09-30T22:56Z] INFO  23:56:05,997 MuTect - [MUTECT] Processed 73003033 reads in 693 ms
[2015-09-30T22:56Z] INFO  23:56:06,157 MuTect - [MUTECT] Processed 10000478 reads in 669 ms
[2015-09-30T22:56Z] INFO  23:56:06,445 MuTect - [MUTECT] Inspected 3000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:06,667 MuTect - [MUTECT] Inspected 1000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:06,673 MuTect - [MUTECT] Processed 74003129 reads in 676 ms
[2015-09-30T22:56Z] INFO  23:56:06,814 MuTect - [MUTECT] Processed 11000568 reads in 657 ms
[2015-09-30T22:56Z] INFO  23:56:07,212 MuTect - [MUTECT] Processed 1000080 reads in 8871 ms
[2015-09-30T22:56Z] INFO  23:56:07,341 MuTect - [MUTECT] Processed 75003147 reads in 668 ms
[2015-09-30T22:56Z] INFO  23:56:07,462 MuTect - [MUTECT] Processed 12000588 reads in 648 ms
[2015-09-30T22:56Z] INFO  23:56:07,619 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:07,920 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:56Z] INFO  23:56:07,925 ProgressMeter -            done        8.57e+06    9.0 s        1.0 s    100.0%         9.0 s     0.0 s
[2015-09-30T22:56Z] INFO  23:56:07,925 ProgressMeter - Total runtime 9.63 secs, 0.16 min, 0.00 hours
[2015-09-30T22:56Z] INFO  23:56:07,990 MicroScheduler - 2349 reads were filtered out during the traversal out of approximately 18473 total reads (12.72%)
[2015-09-30T22:56Z] INFO  23:56:07,991 MicroScheduler -   -> 1211 reads (6.56% of total) failing DuplicateReadFilter
[2015-09-30T22:56Z] INFO  23:56:07,991 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:56Z] INFO  23:56:07,991 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:56Z] INFO  23:56:07,991 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:56Z] INFO  23:56:07,991 MicroScheduler -   -> 1138 reads (6.16% of total) failing UnmappedReadFilter
[2015-09-30T22:56Z] INFO  23:56:08,000 MuTect - [MUTECT] Processed 76003165 reads in 659 ms
[2015-09-30T22:56Z] INFO  23:56:08,110 MuTect - [MUTECT] Processed 13000647 reads in 648 ms
[2015-09-30T22:56Z] INFO  23:56:08,691 MuTect - [MUTECT] Processed 77003206 reads in 691 ms
[2015-09-30T22:56Z] INFO  23:56:08,729 MuTect - [MUTECT] Processed 14000648 reads in 619 ms
[2015-09-30T22:56Z] INFO  23:56:08,786 MuTect - [MUTECT] Inspected 4000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:08,982 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:56Z] bgzip syn3-Y_0_28716339-raw-mutect.vcf
[2015-09-30T22:56Z] INFO  23:56:09,366 MuTect - [MUTECT] Processed 78003248 reads in 675 ms
[2015-09-30T22:56Z] INFO  23:56:09,492 MuTect - [MUTECT] Processed 15000696 reads in 762 ms
[2015-09-30T22:56Z] tabix index syn3-Y_0_28716339-raw-mutect.vcf.gz
[2015-09-30T22:56Z] INFO  23:56:10,025 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:10,039 MuTect - [MUTECT] Processed 79003307 reads in 673 ms
[2015-09-30T22:56Z] INFO  23:56:10,174 MuTect - [MUTECT] Processed 16000722 reads in 683 ms
[2015-09-30T22:56Z] INFO  23:56:10,645 MuTect - [MUTECT] Processed 80003328 reads in 606 ms
[2015-09-30T22:56Z] INFO  23:56:10,832 MuTect - [MUTECT] Processed 17000778 reads in 658 ms
[2015-09-30T22:56Z] INFO  23:56:11,288 MuTect - [MUTECT] Processed 81003359 reads in 643 ms
[2015-09-30T22:56Z] INFO  23:56:11,401 MuTect - [MUTECT] Inspected 5000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:11,480 MuTect - [MUTECT] Processed 18000802 reads in 648 ms
[2015-09-30T22:56Z] INFO  23:56:11,961 MuTect - [MUTECT] Processed 82003427 reads in 673 ms
[2015-09-30T22:56Z] INFO  23:56:12,161 MuTect - [MUTECT] Processed 19000807 reads in 681 ms
[2015-09-30T22:56Z] INFO  23:56:12,628 MuTect - [MUTECT] Processed 83003472 reads in 667 ms
[2015-09-30T22:56Z] INFO  23:56:12,877 MuTect - [MUTECT] Processed 20000858 reads in 716 ms
[2015-09-30T22:56Z] INFO  23:56:13,337 MuTect - [MUTECT] Processed 84003492 reads in 709 ms
[2015-09-30T22:56Z] INFO  23:56:13,485 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:13,579 MuTect - [MUTECT] Processed 21000937 reads in 702 ms
[2015-09-30T22:56Z] INFO  23:56:13,950 MuTect - [MUTECT] Inspected 6000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:14,015 MuTect - [MUTECT] Processed 85003571 reads in 678 ms
[2015-09-30T22:56Z] INFO  23:56:14,221 MuTect - [MUTECT] Processed 22001001 reads in 642 ms
[2015-09-30T22:56Z] INFO  23:56:14,690 ProgressMeter -     X:123196861        2.78e+06   60.0 s       21.0 s     95.6%        62.0 s     2.0 s
[2015-09-30T22:56Z] INFO  23:56:14,721 MuTect - [MUTECT] Processed 86003577 reads in 706 ms
[2015-09-30T22:56Z] INFO  23:56:14,874 MuTect - [MUTECT] Processed 23001075 reads in 653 ms
[2015-09-30T22:56Z] INFO  23:56:15,384 MuTect - [MUTECT] Processed 87003616 reads in 663 ms
[2015-09-30T22:56Z] INFO  23:56:15,519 MuTect - [MUTECT] Processed 24001088 reads in 645 ms
[2015-09-30T22:56Z] INFO  23:56:16,047 MuTect - [MUTECT] Processed 88003623 reads in 663 ms
[2015-09-30T22:56Z] INFO  23:56:16,113 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:16,170 MuTect - [MUTECT] Processed 25001097 reads in 651 ms
[2015-09-30T22:56Z] INFO  23:56:16,400 MuTect - [MUTECT] Inspected 7000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:16,698 MuTect - [MUTECT] Processed 89003663 reads in 651 ms
[2015-09-30T22:56Z] INFO  23:56:16,920 MuTect - [MUTECT] Processed 26001115 reads in 750 ms
[2015-09-30T22:56Z] INFO  23:56:17,184 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:56Z] INFO  23:56:17,187 ProgressMeter -            done        2.89e+06   62.0 s       21.0 s    100.0%        62.0 s     0.0 s
[2015-09-30T22:56Z] INFO  23:56:17,187 ProgressMeter - Total runtime 62.50 secs, 1.04 min, 0.02 hours
[2015-09-30T22:56Z] Genotyping paired variants with FreeBayes
[2015-09-30T22:56Z] INFO  23:56:17,254 MicroScheduler - 61446 reads were filtered out during the traversal out of approximately 1056818 total reads (5.81%)
[2015-09-30T22:56Z] INFO  23:56:17,255 MicroScheduler -   -> 44390 reads (4.20% of total) failing DuplicateReadFilter
[2015-09-30T22:56Z] INFO  23:56:17,255 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:56Z] INFO  23:56:17,255 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:56Z] INFO  23:56:17,255 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:56Z] INFO  23:56:17,255 MicroScheduler -   -> 17056 reads (1.61% of total) failing UnmappedReadFilter
[2015-09-30T22:56Z] INFO  23:56:17,571 MuTect - [MUTECT] Processed 27001175 reads in 650 ms
[2015-09-30T22:56Z] INFO  23:56:18,263 MuTect - [MUTECT] Processed 28001273 reads in 693 ms
[2015-09-30T22:56Z] INFO  23:56:18,408 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:56Z] bgzip syn3-X_94317773_125687021-raw-mutect.vcf
[2015-09-30T22:56Z] tabix index syn3-X_94317773_125687021-raw-mutect.vcf.gz
[2015-09-30T22:56Z] INFO  23:56:18,968 MuTect - [MUTECT] Processed 29001313 reads in 705 ms
[2015-09-30T22:56Z] INFO  23:56:19,615 MuTect - [MUTECT] Processed 30001351 reads in 647 ms
[2015-09-30T22:56Z] INFO  23:56:19,945 MuTect - [MUTECT] Inspected 8000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:20,288 MuTect - [MUTECT] Processed 31001357 reads in 673 ms
[2015-09-30T22:56Z] Genotyping paired variants with FreeBayes
[2015-09-30T22:56Z] INFO  23:56:20,956 MuTect - [MUTECT] Processed 32001422 reads in 667 ms
[2015-09-30T22:56Z] INFO  23:56:21,596 MuTect - [MUTECT] Processed 33001426 reads in 641 ms
[2015-09-30T22:56Z] INFO  23:56:22,245 MuTect - [MUTECT] Processed 34001427 reads in 649 ms
[2015-09-30T22:56Z] INFO  23:56:22,354 MuTect - [MUTECT] Inspected 9000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:22,914 MuTect - [MUTECT] Processed 35001479 reads in 669 ms
[2015-09-30T22:56Z] INFO  23:56:23,637 MuTect - [MUTECT] Processed 36001544 reads in 723 ms
[2015-09-30T22:56Z] INFO  23:56:24,281 MuTect - [MUTECT] Processed 37001570 reads in 644 ms
[2015-09-30T22:56Z] INFO  23:56:24,761 MuTect - [MUTECT] Inspected 10000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:24,926 MuTect - [MUTECT] Processed 38001594 reads in 645 ms
[2015-09-30T22:56Z] INFO  23:56:25,600 MuTect - [MUTECT] Processed 39001635 reads in 674 ms
[2015-09-30T22:56Z] INFO  23:56:26,268 MuTect - [MUTECT] Processed 40001678 reads in 668 ms
[2015-09-30T22:56Z] INFO  23:56:26,924 MuTect - [MUTECT] Processed 41001711 reads in 655 ms
[2015-09-30T22:56Z] INFO  23:56:27,571 MuTect - [MUTECT] Processed 42001755 reads in 648 ms
[2015-09-30T22:56Z] INFO  23:56:27,609 MuTect - [MUTECT] Inspected 11000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:28,327 MuTect - [MUTECT] Processed 43001816 reads in 756 ms
[2015-09-30T22:56Z] INFO  23:56:29,039 MuTect - [MUTECT] Processed 44001875 reads in 712 ms
[2015-09-30T22:56Z] INFO  23:56:29,723 MuTect - [MUTECT] Processed 45001992 reads in 684 ms
[2015-09-30T22:56Z] INFO  23:56:30,197 MuTect - [MUTECT] Inspected 12000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:30,398 MuTect - [MUTECT] Processed 46002074 reads in 675 ms
[2015-09-30T22:56Z] INFO  23:56:31,126 MuTect - [MUTECT] Processed 47002102 reads in 728 ms
[2015-09-30T22:56Z] INFO  23:56:31,815 MuTect - [MUTECT] Processed 48002131 reads in 689 ms
[2015-09-30T22:56Z] INFO  23:56:32,494 MuTect - [MUTECT] Processed 49002178 reads in 679 ms
[2015-09-30T22:56Z] INFO  23:56:32,874 MuTect - [MUTECT] Inspected 13000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:33,187 MuTect - [MUTECT] Processed 50002313 reads in 693 ms
[2015-09-30T22:56Z] INFO  23:56:33,868 MuTect - [MUTECT] Processed 51002360 reads in 680 ms
[2015-09-30T22:56Z] INFO  23:56:34,519 MuTect - [MUTECT] Processed 52002383 reads in 652 ms
[2015-09-30T22:56Z] INFO  23:56:35,138 MuTect - [MUTECT] Processed 53002387 reads in 619 ms
[2015-09-30T22:56Z] INFO  23:56:35,813 MuTect - [MUTECT] Processed 54002393 reads in 675 ms
[2015-09-30T22:56Z] INFO  23:56:35,974 MuTect - [MUTECT] Inspected 14000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:36,434 MuTect - [MUTECT] Processed 55002404 reads in 621 ms
[2015-09-30T22:56Z] INFO  23:56:36,879 ProgressMeter -     X:149896299        1.64e+06   40.0 s       24.0 s     54.5%        73.0 s    33.0 s
[2015-09-30T22:56Z] INFO  23:56:37,063 MuTect - [MUTECT] Processed 56002415 reads in 629 ms
[2015-09-30T22:56Z] INFO  23:56:37,692 MuTect - [MUTECT] Processed 57002486 reads in 629 ms
[2015-09-30T22:56Z] INFO  23:56:38,316 MuTect - [MUTECT] Inspected 15000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:38,327 MuTect - [MUTECT] Processed 58002522 reads in 635 ms
[2015-09-30T22:56Z] INFO  23:56:38,988 MuTect - [MUTECT] Processed 59002609 reads in 661 ms
[2015-09-30T22:56Z] INFO  23:56:39,638 MuTect - [MUTECT] Processed 60002611 reads in 650 ms
[2015-09-30T22:56Z] INFO  23:56:40,308 MuTect - [MUTECT] Processed 61002636 reads in 670 ms
[2015-09-30T22:56Z] INFO  23:56:40,612 MuTect - [MUTECT] Inspected 16000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:41,003 MuTect - [MUTECT] Processed 62002683 reads in 695 ms
[2015-09-30T22:56Z] INFO  23:56:41,649 MuTect - [MUTECT] Processed 63002686 reads in 646 ms
[2015-09-30T22:56Z] INFO  23:56:42,315 MuTect - [MUTECT] Processed 64002748 reads in 666 ms
[2015-09-30T22:56Z] INFO  23:56:42,963 MuTect - [MUTECT] Processed 65002828 reads in 648 ms
[2015-09-30T22:56Z] INFO  23:56:43,621 MuTect - [MUTECT] Inspected 17000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:43,672 MuTect - [MUTECT] Processed 66002916 reads in 709 ms
[2015-09-30T22:56Z] INFO  23:56:44,375 MuTect - [MUTECT] Processed 67002956 reads in 703 ms
[2015-09-30T22:56Z] INFO  23:56:45,049 MuTect - [MUTECT] Processed 68002982 reads in 674 ms
[2015-09-30T22:56Z] INFO  23:56:45,767 MuTect - [MUTECT] Processed 69003002 reads in 718 ms
[2015-09-30T22:56Z] INFO  23:56:46,305 MuTect - [MUTECT] Inspected 18000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:46,442 MuTect - [MUTECT] Processed 70003135 reads in 675 ms
[2015-09-30T22:56Z] INFO  23:56:47,106 MuTect - [MUTECT] Processed 71003200 reads in 664 ms
[2015-09-30T22:56Z] INFO  23:56:47,795 MuTect - [MUTECT] Processed 72003262 reads in 689 ms
[2015-09-30T22:56Z] INFO  23:56:48,509 MuTect - [MUTECT] Processed 73003347 reads in 714 ms
[2015-09-30T22:56Z] INFO  23:56:48,530 MuTect - [MUTECT] Inspected 19000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:49,248 MuTect - [MUTECT] Processed 74003420 reads in 739 ms
[2015-09-30T22:56Z] INFO  23:56:50,000 MuTect - [MUTECT] Processed 75003452 reads in 752 ms
[2015-09-30T22:56Z] INFO  23:56:50,712 MuTect - [MUTECT] Processed 76003516 reads in 712 ms
[2015-09-30T22:56Z] INFO  23:56:50,955 MuTect - [MUTECT] Inspected 20000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:51,390 MuTect - [MUTECT] Processed 77003554 reads in 678 ms
[2015-09-30T22:56Z] INFO  23:56:52,196 MuTect - [MUTECT] Processed 78003706 reads in 806 ms
[2015-09-30T22:56Z] INFO  23:56:52,838 MuTect - [MUTECT] Processed 79003723 reads in 642 ms
[2015-09-30T22:56Z] INFO  23:56:53,155 MuTect - [MUTECT] Inspected 21000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:53,477 MuTect - [MUTECT] Processed 80003834 reads in 639 ms
[2015-09-30T22:56Z] WARNING(freebayes): Could not find any mapped reads in target region 1:1535392..1535455
[2015-09-30T22:56Z] INFO  23:56:54,132 MuTect - [MUTECT] Processed 81003903 reads in 655 ms
[2015-09-30T22:56Z] INFO  23:56:54,765 MuTect - [MUTECT] Processed 82003906 reads in 633 ms
[2015-09-30T22:56Z] INFO  23:56:55,233 MuTect - [MUTECT] Inspected 22000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:55,382 MuTect - [MUTECT] Processed 83003978 reads in 617 ms
[2015-09-30T22:56Z] INFO  23:56:56,020 MuTect - [MUTECT] Processed 84004020 reads in 638 ms
[2015-09-30T22:56Z] INFO  23:56:56,714 MuTect - [MUTECT] Processed 85004088 reads in 694 ms
[2015-09-30T22:56Z] INFO  23:56:57,359 MuTect - [MUTECT] Processed 86004169 reads in 645 ms
[2015-09-30T22:56Z] INFO  23:56:57,389 MuTect - [MUTECT] Inspected 23000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:58,021 MuTect - [MUTECT] Processed 87004273 reads in 662 ms
[2015-09-30T22:56Z] INFO  23:56:58,661 MuTect - [MUTECT] Processed 88004283 reads in 640 ms
[2015-09-30T22:56Z] INFO  23:56:59,311 MuTect - [MUTECT] Processed 89004361 reads in 650 ms
[2015-09-30T22:56Z] INFO  23:56:59,549 MuTect - [MUTECT] Inspected 24000 potential candidates
[2015-09-30T22:56Z] INFO  23:56:59,949 MuTect - [MUTECT] Processed 90004473 reads in 638 ms
[2015-09-30T22:57Z] INFO  23:57:00,643 MuTect - [MUTECT] Processed 91004566 reads in 694 ms
[2015-09-30T22:57Z] INFO  23:57:01,257 MuTect - [MUTECT] Processed 92004630 reads in 614 ms
[2015-09-30T22:57Z] INFO  23:57:01,868 MuTect - [MUTECT] Processed 93004710 reads in 611 ms
[2015-09-30T22:57Z] INFO  23:57:02,518 MuTect - [MUTECT] Processed 94004758 reads in 650 ms
[2015-09-30T22:57Z] INFO  23:57:03,124 MuTect - [MUTECT] Inspected 25000 potential candidates
[2015-09-30T22:57Z] INFO  23:57:03,151 MuTect - [MUTECT] Processed 95004888 reads in 632 ms
[2015-09-30T22:57Z] INFO  23:57:03,764 MuTect - [MUTECT] Processed 96004931 reads in 614 ms
[2015-09-30T22:57Z] INFO  23:57:04,440 MuTect - [MUTECT] Processed 97004974 reads in 676 ms
[2015-09-30T22:57Z] INFO  23:57:05,128 MuTect - [MUTECT] Processed 98005005 reads in 688 ms
[2015-09-30T22:57Z] INFO  23:57:05,352 MuTect - [MUTECT] Inspected 26000 potential candidates
[2015-09-30T22:57Z] INFO  23:57:05,764 MuTect - [MUTECT] Processed 99005107 reads in 636 ms
[2015-09-30T22:57Z] INFO  23:57:06,420 MuTect - [MUTECT] Processed 100005124 reads in 656 ms
[2015-09-30T22:57Z] INFO  23:57:06,880 ProgressMeter -     X:153692891        2.78e+06   70.0 s       25.0 s     87.2%        80.0 s    10.0 s
[2015-09-30T22:57Z] INFO  23:57:07,058 MuTect - [MUTECT] Processed 101005234 reads in 637 ms
[2015-09-30T22:57Z] WARNING(freebayes): Could not find any mapped reads in target region 1:2159758..2159904
[2015-09-30T22:57Z] WARNING(freebayes): Could not find any mapped reads in target region 1:2160000..2160095
[2015-09-30T22:57Z] INFO  23:57:07,526 MuTect - [MUTECT] Inspected 27000 potential candidates
[2015-09-30T22:57Z] INFO  23:57:07,689 MuTect - [MUTECT] Processed 102005357 reads in 632 ms
[2015-09-30T22:57Z] INFO  23:57:08,316 MuTect - [MUTECT] Processed 103005407 reads in 627 ms
[2015-09-30T22:57Z] INFO  23:57:08,962 MuTect - [MUTECT] Processed 104005470 reads in 646 ms
[2015-09-30T22:57Z] INFO  23:57:09,870 MuTect - [MUTECT] Processed 105005523 reads in 908 ms
[2015-09-30T22:57Z] INFO  23:57:10,482 MuTect - [MUTECT] Processed 106005533 reads in 612 ms
[2015-09-30T22:57Z] INFO  23:57:11,925 MuTect - [MUTECT] Inspected 28000 potential candidates
[2015-09-30T22:57Z] INFO  23:57:12,107 MuTect - [MUTECT] Processed 107005606 reads in 1624 ms
[2015-09-30T22:57Z] INFO  23:57:12,754 MuTect - [MUTECT] Processed 108005692 reads in 648 ms
[2015-09-30T22:57Z] INFO  23:57:13,398 MuTect - [MUTECT] Processed 109005789 reads in 644 ms
[2015-09-30T22:57Z] INFO  23:57:14,049 MuTect - [MUTECT] Processed 110005841 reads in 651 ms
[2015-09-30T22:57Z] INFO  23:57:14,390 MuTect - [MUTECT] Inspected 29000 potential candidates
[2015-09-30T22:57Z] INFO  23:57:14,735 MuTect - [MUTECT] Processed 111005887 reads in 686 ms
[2015-09-30T22:57Z] INFO  23:57:15,398 MuTect - [MUTECT] Processed 112005916 reads in 663 ms
[2015-09-30T22:57Z] INFO  23:57:16,023 MuTect - [MUTECT] Processed 113005979 reads in 625 ms
[2015-09-30T22:57Z] INFO  23:57:16,682 MuTect - [MUTECT] Processed 114006028 reads in 659 ms
[2015-09-30T22:57Z] INFO  23:57:17,186 MuTect - [MUTECT] Inspected 30000 potential candidates
[2015-09-30T22:57Z] INFO  23:57:17,354 MuTect - [MUTECT] Processed 115006173 reads in 672 ms
[2015-09-30T22:57Z] INFO  23:57:18,156 MuTect - [MUTECT] Processed 116006299 reads in 802 ms
[2015-09-30T22:57Z] INFO  23:57:18,175 Walker - [REDUCE RESULT] Traversal result is: 0
[2015-09-30T22:57Z] INFO  23:57:18,180 ProgressMeter -            done        3.20e+06   81.0 s       25.0 s    100.0%        81.0 s     0.0 s
[2015-09-30T22:57Z] INFO  23:57:18,180 ProgressMeter - Total runtime 81.30 secs, 1.36 min, 0.02 hours
[2015-09-30T22:57Z] INFO  23:57:18,247 MicroScheduler - 87394 reads were filtered out during the traversal out of approximately 1366007 total reads (6.40%)
[2015-09-30T22:57Z] INFO  23:57:18,247 MicroScheduler -   -> 64607 reads (4.73% of total) failing DuplicateReadFilter
[2015-09-30T22:57Z] INFO  23:57:18,247 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:57Z] INFO  23:57:18,247 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:57Z] INFO  23:57:18,247 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:57Z] INFO  23:57:18,247 MicroScheduler -   -> 22787 reads (1.67% of total) failing UnmappedReadFilter
[2015-09-30T22:57Z] INFO  23:57:19,375 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:57Z] bgzip syn3-X_125953527_155270560-raw-mutect.vcf
[2015-09-30T22:57Z] tabix index syn3-X_125953527_155270560-raw-mutect.vcf.gz
[2015-09-30T22:57Z] Genotyping paired variants with FreeBayes
[2015-09-30T22:57Z] WARNING(freebayes): Could not find any mapped reads in target region 1:6845789..6845861
[2015-09-30T22:58Z] tabix index syn3-1_62231753_93258244-raw.vcf.gz
[2015-09-30T22:58Z] GATK: VariantAnnotator
[2015-09-30T22:58Z] INFO  23:58:37,462 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:58Z] INFO  23:58:37,464 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T22:58Z] INFO  23:58:37,465 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:58Z] INFO  23:58:37,465 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:58Z] INFO  23:58:37,468 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/1/syn3-1_62231753_93258244-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/1/tx/tmp_s3cPJ/syn3-1_62231753_93258244-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/1/syn3-1_62231753_93258244-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_62231753_93258244-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T22:58Z] INFO  23:58:37,474 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T22:58Z] INFO  23:58:37,474 HelpFormatter - Date/Time: 2015/09/30 23:58:37
[2015-09-30T22:58Z] INFO  23:58:37,474 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:58Z] INFO  23:58:37,474 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:58Z] INFO  23:58:37,563 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:58Z] INFO  23:58:37,640 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T22:58Z] INFO  23:58:37,647 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:58Z] INFO  23:58:37,669 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:58Z] INFO  23:58:38,174 IntervalUtils - Processing 1554 bp from intervals
[2015-09-30T22:58Z] WARN  23:58:38,178 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:58Z] WARN  23:58:38,178 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:58Z] INFO  23:58:38,235 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:58Z] INFO  23:58:38,352 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:58Z] INFO  23:58:38,352 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:58Z] INFO  23:58:38,353 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T22:58Z] INFO  23:58:38,353 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T22:58Z] INFO  23:58:38,394 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T22:58Z] INFO  23:58:44,832 VariantAnnotator - Processed 1330 loci.
[2015-09-30T22:58Z]
[2015-09-30T22:58Z] INFO  23:58:44,863 ProgressMeter -            done      5439.0     6.0 s      19.9 m       99.9%     6.0 s       0.0 s
[2015-09-30T22:58Z] INFO  23:58:44,863 ProgressMeter - Total runtime 6.51 secs, 0.11 min, 0.00 hours
[2015-09-30T22:58Z] INFO  23:58:44,863 MicroScheduler - 3432 reads were filtered out during the traversal out of approximately 84752 total reads (4.05%)
[2015-09-30T22:58Z] INFO  23:58:44,863 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T22:58Z] INFO  23:58:44,864 MicroScheduler -   -> 3412 reads (4.03% of total) failing DuplicateReadFilter
[2015-09-30T22:58Z] INFO  23:58:44,864 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:58Z] INFO  23:58:44,864 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:58Z] INFO  23:58:44,864 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:58Z] INFO  23:58:44,865 MicroScheduler -   -> 20 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T22:58Z] INFO  23:58:45,795 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:58Z] Genotyping paired variants with FreeBayes
[2015-09-30T22:59Z] tabix index syn3-1_31187762_62229084-raw.vcf.gz
[2015-09-30T22:59Z] GATK: VariantAnnotator
[2015-09-30T22:59Z] INFO  23:59:35,679 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:59Z] INFO  23:59:35,681 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T22:59Z] INFO  23:59:35,681 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T22:59Z] INFO  23:59:35,681 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T22:59Z] INFO  23:59:35,685 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/1/syn3-1_31187762_62229084-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/1/tx/tmpWODAM1/syn3-1_31187762_62229084-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/1/syn3-1_31187762_62229084-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_31187762_62229084-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T22:59Z] INFO  23:59:35,691 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T22:59Z] INFO  23:59:35,691 HelpFormatter - Date/Time: 2015/09/30 23:59:35
[2015-09-30T22:59Z] INFO  23:59:35,691 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:59Z] INFO  23:59:35,691 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T22:59Z] INFO  23:59:35,752 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T22:59Z] INFO  23:59:35,823 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T22:59Z] INFO  23:59:35,831 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T22:59Z] INFO  23:59:35,852 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T22:59Z] INFO  23:59:36,417 IntervalUtils - Processing 2282 bp from intervals
[2015-09-30T22:59Z] WARN  23:59:36,421 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:59Z] WARN  23:59:36,421 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T22:59Z] INFO  23:59:36,474 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T22:59Z] INFO  23:59:36,601 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T22:59Z] INFO  23:59:36,601 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T22:59Z] INFO  23:59:36,601 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T22:59Z] INFO  23:59:36,602 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T22:59Z] INFO  23:59:36,640 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T22:59Z] INFO  23:59:48,257 VariantAnnotator - Processed 2018 loci.
[2015-09-30T22:59Z]
[2015-09-30T22:59Z] INFO  23:59:48,277 ProgressMeter -            done      9205.0    11.0 s      21.1 m      100.0%    11.0 s       0.0 s
[2015-09-30T22:59Z] INFO  23:59:48,277 ProgressMeter - Total runtime 11.68 secs, 0.19 min, 0.00 hours
[2015-09-30T22:59Z] INFO  23:59:48,278 MicroScheduler - 9654 reads were filtered out during the traversal out of approximately 189706 total reads (5.09%)
[2015-09-30T22:59Z] INFO  23:59:48,278 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T22:59Z] INFO  23:59:48,278 MicroScheduler -   -> 9599 reads (5.06% of total) failing DuplicateReadFilter
[2015-09-30T22:59Z] INFO  23:59:48,278 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T22:59Z] INFO  23:59:48,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T22:59Z] INFO  23:59:48,279 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T22:59Z] INFO  23:59:48,279 MicroScheduler -   -> 55 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T22:59Z] INFO  23:59:49,422 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T22:59Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:00Z] WARNING(freebayes): Could not find any mapped reads in target region 1:22469693..22469697
[2015-09-30T23:00Z] WARNING(freebayes): Could not find any mapped reads in target region 1:145803001..145803009
[2015-09-30T23:00Z] tabix index syn3-1_93297335_142653959-raw.vcf.gz
[2015-09-30T23:00Z] GATK: VariantAnnotator
[2015-09-30T23:00Z] INFO  00:00:34,334 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:00Z] INFO  00:00:34,336 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:00Z] INFO  00:00:34,336 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:00Z] INFO  00:00:34,336 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:00Z] INFO  00:00:34,340 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/1/syn3-1_93297335_142653959-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/1/tx/tmpsyQNg1/syn3-1_93297335_142653959-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/1/syn3-1_93297335_142653959-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_93297335_142653959-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:00Z] INFO  00:00:34,345 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:00Z] INFO  00:00:34,345 HelpFormatter - Date/Time: 2015/10/01 00:00:34
[2015-09-30T23:00Z] INFO  00:00:34,346 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:00Z] INFO  00:00:34,346 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:00Z] INFO  00:00:34,437 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:00Z] INFO  00:00:34,510 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:00Z] INFO  00:00:34,518 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:00Z] INFO  00:00:34,539 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:00Z] INFO  00:00:35,142 IntervalUtils - Processing 1667 bp from intervals
[2015-09-30T23:00Z] WARN  00:00:35,146 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:00Z] WARN  00:00:35,146 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:00Z] INFO  00:00:35,202 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:00Z] INFO  00:00:35,306 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:00Z] INFO  00:00:35,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:00Z] INFO  00:00:35,307 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:00Z] INFO  00:00:35,307 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:00Z] INFO  00:00:35,351 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:00Z] INFO  00:00:43,911 VariantAnnotator - Processed 1492 loci.
[2015-09-30T23:00Z]
[2015-09-30T23:00Z] INFO  00:00:43,934 ProgressMeter -            done      6027.0     8.0 s      23.9 m       99.9%     8.0 s       0.0 s
[2015-09-30T23:00Z] INFO  00:00:43,934 ProgressMeter - Total runtime 8.63 secs, 0.14 min, 0.00 hours
[2015-09-30T23:00Z] INFO  00:00:43,934 MicroScheduler - 5536 reads were filtered out during the traversal out of approximately 118620 total reads (4.67%)
[2015-09-30T23:00Z] INFO  00:00:43,935 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:00Z] INFO  00:00:43,935 MicroScheduler -   -> 5508 reads (4.64% of total) failing DuplicateReadFilter
[2015-09-30T23:00Z] INFO  00:00:43,935 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:00Z] INFO  00:00:43,935 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:00Z] INFO  00:00:43,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:00Z] INFO  00:00:43,936 MicroScheduler -   -> 28 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:00Z] INFO  00:00:44,878 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:00Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:01Z] WARNING(freebayes): Could not find any mapped reads in target region 1:152572902..152573781
[2015-09-30T23:01Z] tabix index syn3-1_0_31187470-raw.vcf.gz
[2015-09-30T23:01Z] GATK: VariantAnnotator
[2015-09-30T23:01Z] INFO  00:01:24,931 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:01Z] INFO  00:01:24,933 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:01Z] INFO  00:01:24,933 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:01Z] INFO  00:01:24,933 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:01Z] INFO  00:01:24,936 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/1/syn3-1_0_31187470-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/1/tx/tmpBKCgq1/syn3-1_0_31187470-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/1/syn3-1_0_31187470-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_0_31187470-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:01Z] INFO  00:01:24,942 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:01Z] INFO  00:01:24,942 HelpFormatter - Date/Time: 2015/10/01 00:01:24
[2015-09-30T23:01Z] INFO  00:01:24,942 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:01Z] INFO  00:01:24,942 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:01Z] INFO  00:01:25,014 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:01Z] INFO  00:01:25,116 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:01Z] INFO  00:01:25,124 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:01Z] INFO  00:01:25,145 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:01Z] INFO  00:01:25,872 IntervalUtils - Processing 4920 bp from intervals
[2015-09-30T23:01Z] WARN  00:01:25,877 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:01Z] WARN  00:01:25,877 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:01Z] INFO  00:01:25,932 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:01Z] INFO  00:01:26,103 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:01Z] INFO  00:01:26,103 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:01Z] INFO  00:01:26,103 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:01Z] INFO  00:01:26,104 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:01Z] INFO  00:01:26,142 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:01Z] INFO  00:01:49,208 VariantAnnotator - Processed 4402 loci.
[2015-09-30T23:01Z]
[2015-09-30T23:01Z] INFO  00:01:49,230 ProgressMeter -            done     40269.0    23.0 s       9.6 m      100.0%    23.0 s       0.0 s
[2015-09-30T23:01Z] INFO  00:01:49,230 ProgressMeter - Total runtime 23.13 secs, 0.39 min, 0.01 hours
[2015-09-30T23:01Z] INFO  00:01:49,231 MicroScheduler - 26160 reads were filtered out during the traversal out of approximately 468055 total reads (5.59%)
[2015-09-30T23:01Z] INFO  00:01:49,231 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:01Z] INFO  00:01:49,231 MicroScheduler -   -> 26037 reads (5.56% of total) failing DuplicateReadFilter
[2015-09-30T23:01Z] INFO  00:01:49,231 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:01Z] INFO  00:01:49,232 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:01Z] INFO  00:01:49,232 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:01Z] INFO  00:01:49,232 MicroScheduler -   -> 123 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:01Z] INFO  00:01:50,186 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:01Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:02Z] tabix index syn3-1_173702591_204798081-raw.vcf.gz
[2015-09-30T23:02Z] GATK: VariantAnnotator
[2015-09-30T23:02Z] INFO  00:02:50,966 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:02Z] INFO  00:02:50,968 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:02Z] INFO  00:02:50,969 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:02Z] INFO  00:02:50,969 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:02Z] INFO  00:02:50,973 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/1/syn3-1_173702591_204798081-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/1/tx/tmp8cn9Zo/syn3-1_173702591_204798081-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/1/syn3-1_173702591_204798081-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_173702591_204798081-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:02Z] INFO  00:02:50,979 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:02Z] INFO  00:02:50,979 HelpFormatter - Date/Time: 2015/10/01 00:02:50
[2015-09-30T23:02Z] INFO  00:02:50,979 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:02Z] INFO  00:02:50,980 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:02Z] INFO  00:02:51,054 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:02Z] INFO  00:02:51,139 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:02Z] INFO  00:02:51,147 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:02Z] INFO  00:02:51,169 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:02Z] INFO  00:02:51,729 IntervalUtils - Processing 1922 bp from intervals
[2015-09-30T23:02Z] WARN  00:02:51,734 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:02Z] WARN  00:02:51,734 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:02Z] INFO  00:02:51,791 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:02Z] INFO  00:02:51,952 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:02Z] INFO  00:02:51,953 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:02Z] INFO  00:02:51,953 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:02Z] INFO  00:02:51,953 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:02Z] INFO  00:02:51,994 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:03Z] INFO  00:03:01,675 VariantAnnotator - Processed 1696 loci.
[2015-09-30T23:03Z]
[2015-09-30T23:03Z] INFO  00:03:01,713 ProgressMeter -            done      8036.0     9.0 s      20.2 m       99.9%     9.0 s       0.0 s
[2015-09-30T23:03Z] INFO  00:03:01,713 ProgressMeter - Total runtime 9.76 secs, 0.16 min, 0.00 hours
[2015-09-30T23:03Z] INFO  00:03:01,713 MicroScheduler - 6512 reads were filtered out during the traversal out of approximately 136985 total reads (4.75%)
[2015-09-30T23:03Z] INFO  00:03:01,714 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:03Z] INFO  00:03:01,714 MicroScheduler -   -> 6495 reads (4.74% of total) failing DuplicateReadFilter
[2015-09-30T23:03Z] INFO  00:03:01,714 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:03Z] INFO  00:03:01,714 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:03Z] INFO  00:03:01,715 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:03Z] INFO  00:03:01,715 MicroScheduler -   -> 17 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:03Z] INFO  00:03:02,688 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:03Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:03Z] tabix index syn3-1_142666976_173685474-raw.vcf.gz
[2015-09-30T23:03Z] GATK: VariantAnnotator
[2015-09-30T23:03Z] INFO  00:03:48,684 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:03Z] INFO  00:03:48,686 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:03Z] INFO  00:03:48,686 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:03Z] INFO  00:03:48,686 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:03Z] INFO  00:03:48,690 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/1/syn3-1_142666976_173685474-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/1/tx/tmpOHb2wU/syn3-1_142666976_173685474-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/1/syn3-1_142666976_173685474-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_142666976_173685474-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:03Z] INFO  00:03:48,696 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:03Z] INFO  00:03:48,696 HelpFormatter - Date/Time: 2015/10/01 00:03:48
[2015-09-30T23:03Z] INFO  00:03:48,696 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:03Z] INFO  00:03:48,697 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:03Z] INFO  00:03:48,790 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:03Z] INFO  00:03:48,869 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:03Z] INFO  00:03:48,877 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:03Z] INFO  00:03:48,900 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:03Z] INFO  00:03:49,899 IntervalUtils - Processing 4081 bp from intervals
[2015-09-30T23:03Z] WARN  00:03:49,904 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:03Z] WARN  00:03:49,904 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:03Z] INFO  00:03:49,960 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:03Z] INFO  00:03:50,109 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:03Z] INFO  00:03:50,110 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:03Z] INFO  00:03:50,110 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:03Z] INFO  00:03:50,110 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:03Z] INFO  00:03:50,154 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:03Z] tabix index syn3-1_235865791_249250621-raw.vcf.gz
[2015-09-30T23:03Z] GATK: VariantAnnotator
[2015-09-30T23:03Z] INFO  00:03:54,168 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:03Z] INFO  00:03:54,171 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:03Z] INFO  00:03:54,171 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:03Z] INFO  00:03:54,171 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:03Z] INFO  00:03:54,175 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/1/syn3-1_235865791_249250621-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/1/tx/tmpkXeJUk/syn3-1_235865791_249250621-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/1/syn3-1_235865791_249250621-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_235865791_249250621-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:03Z] INFO  00:03:54,180 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:03Z] INFO  00:03:54,180 HelpFormatter - Date/Time: 2015/10/01 00:03:54
[2015-09-30T23:03Z] INFO  00:03:54,181 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:03Z] INFO  00:03:54,181 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:03Z] INFO  00:03:54,275 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:03Z] INFO  00:03:54,353 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:03Z] INFO  00:03:54,361 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:03Z] INFO  00:03:54,384 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:03Z] INFO  00:03:54,824 IntervalUtils - Processing 1188 bp from intervals
[2015-09-30T23:03Z] WARN  00:03:54,829 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:03Z] WARN  00:03:54,829 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:03Z] INFO  00:03:54,886 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:03Z] INFO  00:03:54,979 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:03Z] INFO  00:03:54,979 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:03Z] INFO  00:03:54,980 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:03Z] INFO  00:03:54,980 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:03Z] INFO  00:03:55,020 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:04Z] INFO  00:04:00,363 VariantAnnotator - Processed 1020 loci.
[2015-09-30T23:04Z]
[2015-09-30T23:04Z] INFO  00:04:00,388 ProgressMeter -            done      4882.0     5.0 s      18.5 m       99.8%     5.0 s       0.0 s
[2015-09-30T23:04Z] INFO  00:04:00,388 ProgressMeter - Total runtime 5.41 secs, 0.09 min, 0.00 hours
[2015-09-30T23:04Z] INFO  00:04:00,389 MicroScheduler - 4454 reads were filtered out during the traversal out of approximately 68725 total reads (6.48%)
[2015-09-30T23:04Z] INFO  00:04:00,389 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:04Z] INFO  00:04:00,389 MicroScheduler -   -> 4409 reads (6.42% of total) failing DuplicateReadFilter
[2015-09-30T23:04Z] INFO  00:04:00,389 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:04Z] INFO  00:04:00,390 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:04Z] INFO  00:04:00,390 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:04Z] INFO  00:04:00,390 MicroScheduler -   -> 45 reads (0.07% of total) failing UnmappedReadFilter
[2015-09-30T23:04Z] INFO  00:04:01,328 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:04Z] tabix index syn3-1_204839842_235860787-raw.vcf.gz
[2015-09-30T23:04Z] GATK: VariantAnnotator
[2015-09-30T23:04Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:04Z] INFO  00:04:04,845 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:04Z] INFO  00:04:04,847 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:04Z] INFO  00:04:04,847 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:04Z] INFO  00:04:04,848 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:04Z] INFO  00:04:04,851 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/1/syn3-1_204839842_235860787-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/1/tx/tmpJZPdKT/syn3-1_204839842_235860787-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/1/syn3-1_204839842_235860787-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/1/1_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/1/2_2014-08-13_dream-syn3-sort-1_204839842_235860787-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:04Z] INFO  00:04:04,856 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:04Z] INFO  00:04:04,857 HelpFormatter - Date/Time: 2015/10/01 00:04:04
[2015-09-30T23:04Z] INFO  00:04:04,857 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:04Z] INFO  00:04:04,857 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:04Z] INFO  00:04:04,944 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:04Z] INFO  00:04:05,021 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:04Z] INFO  00:04:05,029 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:04Z] INFO  00:04:05,053 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:04Z] INFO  00:04:05,828 IntervalUtils - Processing 2113 bp from intervals
[2015-09-30T23:04Z] WARN  00:04:05,832 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:04Z] WARN  00:04:05,832 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:04Z] INFO  00:04:05,887 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:04Z] INFO  00:04:06,023 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:04Z] INFO  00:04:06,024 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:04Z] INFO  00:04:06,024 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:04Z] INFO  00:04:06,025 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:04Z] INFO  00:04:06,068 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:04Z] INFO  00:04:09,316 VariantAnnotator - Processed 3688 loci.
[2015-09-30T23:04Z]
[2015-09-30T23:04Z] INFO  00:04:09,349 ProgressMeter -            done     29053.0    19.0 s      11.0 m      100.0%    19.0 s       0.0 s
[2015-09-30T23:04Z] INFO  00:04:09,350 ProgressMeter - Total runtime 19.24 secs, 0.32 min, 0.01 hours
[2015-09-30T23:04Z] INFO  00:04:09,350 MicroScheduler - 18223 reads were filtered out during the traversal out of approximately 365719 total reads (4.98%)
[2015-09-30T23:04Z] INFO  00:04:09,350 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:04Z] INFO  00:04:09,350 MicroScheduler -   -> 18155 reads (4.96% of total) failing DuplicateReadFilter
[2015-09-30T23:04Z] INFO  00:04:09,351 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:04Z] INFO  00:04:09,351 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:04Z] INFO  00:04:09,351 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:04Z] INFO  00:04:09,351 MicroScheduler -   -> 68 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:04Z] INFO  00:04:10,303 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:04Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:04Z] INFO  00:04:16,335 VariantAnnotator - Processed 1868 loci.
[2015-09-30T23:04Z]
[2015-09-30T23:04Z] INFO  00:04:16,362 ProgressMeter -            done      7932.0    10.0 s      21.7 m      100.0%    10.0 s       0.0 s
[2015-09-30T23:04Z] INFO  00:04:16,363 ProgressMeter - Total runtime 10.34 secs, 0.17 min, 0.00 hours
[2015-09-30T23:04Z] INFO  00:04:16,363 MicroScheduler - 7195 reads were filtered out during the traversal out of approximately 153088 total reads (4.70%)
[2015-09-30T23:04Z] INFO  00:04:16,363 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:04Z] INFO  00:04:16,363 MicroScheduler -   -> 7171 reads (4.68% of total) failing DuplicateReadFilter
[2015-09-30T23:04Z] INFO  00:04:16,364 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:04Z] INFO  00:04:16,364 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:04Z] INFO  00:04:16,364 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:04Z] INFO  00:04:16,364 MicroScheduler -   -> 24 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:04Z] INFO  00:04:17,295 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:04Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:05Z] tabix index syn3-2_31134801_62196287-raw.vcf.gz
[2015-09-30T23:05Z] GATK: VariantAnnotator
[2015-09-30T23:05Z] INFO  00:05:41,535 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:05Z] INFO  00:05:41,537 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:05Z] INFO  00:05:41,537 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:05Z] INFO  00:05:41,538 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:05Z] INFO  00:05:41,541 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/2/syn3-2_31134801_62196287-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/2/tx/tmpaXVNX1/syn3-2_31134801_62196287-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/2/syn3-2_31134801_62196287-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_31134801_62196287-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:05Z] INFO  00:05:41,547 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:05Z] INFO  00:05:41,547 HelpFormatter - Date/Time: 2015/10/01 00:05:41
[2015-09-30T23:05Z] INFO  00:05:41,547 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:05Z] INFO  00:05:41,547 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:05Z] INFO  00:05:41,681 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:05Z] INFO  00:05:41,828 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:05Z] INFO  00:05:41,836 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:05Z] INFO  00:05:41,880 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2015-09-30T23:05Z] INFO  00:05:42,380 IntervalUtils - Processing 1525 bp from intervals
[2015-09-30T23:05Z] WARN  00:05:42,385 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:05Z] WARN  00:05:42,385 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:05Z] INFO  00:05:42,440 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:05Z] INFO  00:05:42,550 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:05Z] INFO  00:05:42,551 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:05Z] INFO  00:05:42,558 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:05Z] INFO  00:05:42,558 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:05Z] INFO  00:05:42,597 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:05Z] INFO  00:05:49,424 VariantAnnotator - Processed 1335 loci.
[2015-09-30T23:05Z]
[2015-09-30T23:05Z] INFO  00:05:49,457 ProgressMeter -            done      5060.0     6.0 s      22.7 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:05Z] INFO  00:05:49,457 ProgressMeter - Total runtime 6.91 secs, 0.12 min, 0.00 hours
[2015-09-30T23:05Z] INFO  00:05:49,457 MicroScheduler - 4132 reads were filtered out during the traversal out of approximately 93647 total reads (4.41%)
[2015-09-30T23:05Z] INFO  00:05:49,458 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:05Z] INFO  00:05:49,458 MicroScheduler -   -> 4121 reads (4.40% of total) failing DuplicateReadFilter
[2015-09-30T23:05Z] INFO  00:05:49,458 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:05Z] INFO  00:05:49,458 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:05Z] INFO  00:05:49,458 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:05Z] INFO  00:05:49,459 MicroScheduler -   -> 11 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:05Z] INFO  00:05:50,397 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:05Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:05Z] tabix index syn3-2_0_31134137-raw.vcf.gz
[2015-09-30T23:05Z] GATK: VariantAnnotator
[2015-09-30T23:05Z] INFO  00:05:57,124 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:05Z] INFO  00:05:57,127 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:05Z] INFO  00:05:57,127 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:05Z] INFO  00:05:57,127 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:05Z] INFO  00:05:57,131 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/2/syn3-2_0_31134137-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/2/tx/tmpm9FMXK/syn3-2_0_31134137-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/2/syn3-2_0_31134137-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_0_31134137-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:05Z] INFO  00:05:57,137 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:05Z] INFO  00:05:57,137 HelpFormatter - Date/Time: 2015/10/01 00:05:57
[2015-09-30T23:05Z] INFO  00:05:57,138 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:05Z] INFO  00:05:57,138 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:05Z] INFO  00:05:57,529 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:05Z] INFO  00:05:57,603 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:05Z] INFO  00:05:57,611 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:05Z] INFO  00:05:57,632 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:05Z] INFO  00:05:58,217 IntervalUtils - Processing 1989 bp from intervals
[2015-09-30T23:05Z] WARN  00:05:58,222 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:05Z] WARN  00:05:58,222 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:05Z] INFO  00:05:58,278 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:05Z] INFO  00:05:58,416 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:05Z] INFO  00:05:58,417 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:05Z] INFO  00:05:58,417 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:05Z] INFO  00:05:58,418 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:05Z] INFO  00:05:58,455 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:06Z] INFO  00:06:07,368 VariantAnnotator - Processed 1739 loci.
[2015-09-30T23:06Z]
[2015-09-30T23:06Z] INFO  00:06:07,398 ProgressMeter -            done      8907.0     8.0 s      16.8 m       99.9%     8.0 s       0.0 s
[2015-09-30T23:06Z] INFO  00:06:07,399 ProgressMeter - Total runtime 8.98 secs, 0.15 min, 0.00 hours
[2015-09-30T23:06Z] INFO  00:06:07,399 MicroScheduler - 7453 reads were filtered out during the traversal out of approximately 150556 total reads (4.95%)
[2015-09-30T23:06Z] INFO  00:06:07,399 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:06Z] INFO  00:06:07,399 MicroScheduler -   -> 7424 reads (4.93% of total) failing DuplicateReadFilter
[2015-09-30T23:06Z] INFO  00:06:07,400 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:06Z] INFO  00:06:07,400 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:06Z] INFO  00:06:07,400 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:06Z] INFO  00:06:07,400 MicroScheduler -   -> 29 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:06Z] INFO  00:06:08,328 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:06Z] tabix index syn3-2_62227535_95457199-raw.vcf.gz
[2015-09-30T23:06Z] GATK: VariantAnnotator
[2015-09-30T23:06Z] INFO  00:06:10,311 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:06Z] INFO  00:06:10,313 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:06Z] INFO  00:06:10,313 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:06Z] INFO  00:06:10,313 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:06Z] INFO  00:06:10,317 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/2/syn3-2_62227535_95457199-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/2/tx/tmpxX8eJt/syn3-2_62227535_95457199-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/2/syn3-2_62227535_95457199-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_62227535_95457199-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:06Z] INFO  00:06:10,322 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:06Z] INFO  00:06:10,323 HelpFormatter - Date/Time: 2015/10/01 00:06:10
[2015-09-30T23:06Z] INFO  00:06:10,323 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:06Z] INFO  00:06:10,323 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:06Z] INFO  00:06:10,416 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:06Z] INFO  00:06:10,493 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:06Z] INFO  00:06:10,501 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:06Z] INFO  00:06:10,523 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:06Z] INFO  00:06:11,081 IntervalUtils - Processing 1949 bp from intervals
[2015-09-30T23:06Z] WARN  00:06:11,085 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:06Z] WARN  00:06:11,085 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:06Z] INFO  00:06:11,143 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:06Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:06Z] INFO  00:06:11,796 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:06Z] INFO  00:06:11,797 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:06Z] INFO  00:06:11,797 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:06Z] INFO  00:06:11,798 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:06Z] INFO  00:06:11,836 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:06Z] INFO  00:06:21,460 VariantAnnotator - Processed 1750 loci.
[2015-09-30T23:06Z]
[2015-09-30T23:06Z] INFO  00:06:21,482 ProgressMeter -            done     10538.0     9.0 s      15.3 m       99.9%     9.0 s       0.0 s
[2015-09-30T23:06Z] INFO  00:06:21,483 ProgressMeter - Total runtime 9.69 secs, 0.16 min, 0.00 hours
[2015-09-30T23:06Z] INFO  00:06:21,483 MicroScheduler - 8468 reads were filtered out during the traversal out of approximately 163158 total reads (5.19%)
[2015-09-30T23:06Z] INFO  00:06:21,483 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:06Z] INFO  00:06:21,483 MicroScheduler -   -> 8420 reads (5.16% of total) failing DuplicateReadFilter
[2015-09-30T23:06Z] INFO  00:06:21,484 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:06Z] INFO  00:06:21,484 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:06Z] INFO  00:06:21,484 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:06Z] INFO  00:06:21,484 MicroScheduler -   -> 48 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:06Z] INFO  00:06:22,403 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:06Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:07Z] WARNING(freebayes): Could not find any mapped reads in target region 2:176972384..176972400
[2015-09-30T23:07Z] tabix index syn3-2_127413596_158444156-raw.vcf.gz
[2015-09-30T23:07Z] GATK: VariantAnnotator
[2015-09-30T23:07Z] INFO  00:07:36,032 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:07Z] INFO  00:07:36,034 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:07Z] INFO  00:07:36,034 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:07Z] INFO  00:07:36,034 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:07Z] INFO  00:07:36,038 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/2/syn3-2_127413596_158444156-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/2/tx/tmpRjj_PA/syn3-2_127413596_158444156-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/2/syn3-2_127413596_158444156-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_127413596_158444156-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:07Z] INFO  00:07:36,043 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:07Z] INFO  00:07:36,043 HelpFormatter - Date/Time: 2015/10/01 00:07:36
[2015-09-30T23:07Z] INFO  00:07:36,044 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:07Z] INFO  00:07:36,044 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:07Z] INFO  00:07:36,130 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:07Z] INFO  00:07:36,204 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:07Z] INFO  00:07:36,212 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:07Z] INFO  00:07:36,233 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:07Z] INFO  00:07:36,743 IntervalUtils - Processing 1646 bp from intervals
[2015-09-30T23:07Z] WARN  00:07:36,747 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:07Z] WARN  00:07:36,747 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:07Z] INFO  00:07:36,803 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:07Z] INFO  00:07:36,902 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:07Z] INFO  00:07:36,902 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:07Z] INFO  00:07:36,902 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:07Z] INFO  00:07:36,903 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:07Z] INFO  00:07:36,942 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:07Z] INFO  00:07:45,359 VariantAnnotator - Processed 1481 loci.
[2015-09-30T23:07Z]
[2015-09-30T23:07Z] INFO  00:07:45,382 ProgressMeter -            done     19308.0     8.0 s       7.3 m       99.9%     8.0 s       0.0 s
[2015-09-30T23:07Z] INFO  00:07:45,382 ProgressMeter - Total runtime 8.48 secs, 0.14 min, 0.00 hours
[2015-09-30T23:07Z] INFO  00:07:45,382 MicroScheduler - 5858 reads were filtered out during the traversal out of approximately 109552 total reads (5.35%)
[2015-09-30T23:07Z] INFO  00:07:45,383 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:07Z] INFO  00:07:45,383 MicroScheduler -   -> 5812 reads (5.31% of total) failing DuplicateReadFilter
[2015-09-30T23:07Z] INFO  00:07:45,383 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:07Z] INFO  00:07:45,383 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:07Z] INFO  00:07:45,384 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:07Z] INFO  00:07:45,384 MicroScheduler -   -> 46 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T23:07Z] INFO  00:07:46,286 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:07Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:07Z] tabix index syn3-2_95457728_127315933-raw.vcf.gz
[2015-09-30T23:07Z] GATK: VariantAnnotator
[2015-09-30T23:07Z] INFO  00:07:50,586 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:07Z] INFO  00:07:50,589 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:07Z] INFO  00:07:50,589 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:07Z] INFO  00:07:50,589 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:07Z] INFO  00:07:50,593 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/2/syn3-2_95457728_127315933-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/2/tx/tmpVbrSMQ/syn3-2_95457728_127315933-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/2/syn3-2_95457728_127315933-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_95457728_127315933-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:07Z] INFO  00:07:50,599 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:07Z] INFO  00:07:50,599 HelpFormatter - Date/Time: 2015/10/01 00:07:50
[2015-09-30T23:07Z] INFO  00:07:50,599 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:07Z] INFO  00:07:50,599 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:07Z] INFO  00:07:50,916 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:07Z] INFO  00:07:51,017 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:07Z] INFO  00:07:51,025 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:07Z] INFO  00:07:51,048 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:07Z] INFO  00:07:51,647 IntervalUtils - Processing 2400 bp from intervals
[2015-09-30T23:07Z] WARN  00:07:51,651 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:07Z] WARN  00:07:51,651 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:07Z] INFO  00:07:51,709 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:07Z] INFO  00:07:51,831 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:07Z] INFO  00:07:51,831 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:07Z] INFO  00:07:51,832 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:07Z] INFO  00:07:51,832 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:07Z] INFO  00:07:51,872 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:08Z] tabix index syn3-2_158484801_189599894-raw.vcf.gz
[2015-09-30T23:08Z] GATK: VariantAnnotator
[2015-09-30T23:08Z] INFO  00:08:02,334 VariantAnnotator - Processed 2090 loci.
[2015-09-30T23:08Z]
[2015-09-30T23:08Z] INFO  00:08:02,356 ProgressMeter -            done     20466.0    10.0 s       8.6 m      100.0%    10.0 s       0.0 s
[2015-09-30T23:08Z] INFO  00:08:02,356 ProgressMeter - Total runtime 10.52 secs, 0.18 min, 0.00 hours
[2015-09-30T23:08Z] INFO  00:08:02,356 MicroScheduler - 7316 reads were filtered out during the traversal out of approximately 156199 total reads (4.68%)
[2015-09-30T23:08Z] INFO  00:08:02,357 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:08Z] INFO  00:08:02,357 MicroScheduler -   -> 7273 reads (4.66% of total) failing DuplicateReadFilter
[2015-09-30T23:08Z] INFO  00:08:02,357 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:08Z] INFO  00:08:02,357 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:08Z] INFO  00:08:02,358 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:08Z] INFO  00:08:02,358 MicroScheduler -   -> 43 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:08Z] INFO  00:08:02,534 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:08Z] INFO  00:08:02,536 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:08Z] INFO  00:08:02,536 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:08Z] INFO  00:08:02,536 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:08Z] INFO  00:08:02,540 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/2/syn3-2_158484801_189599894-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/2/tx/tmpYBwXju/syn3-2_158484801_189599894-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/2/syn3-2_158484801_189599894-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_158484801_189599894-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:08Z] INFO  00:08:02,545 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:08Z] INFO  00:08:02,545 HelpFormatter - Date/Time: 2015/10/01 00:08:02
[2015-09-30T23:08Z] INFO  00:08:02,545 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:08Z] INFO  00:08:02,545 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:08Z] INFO  00:08:02,639 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:08Z] INFO  00:08:02,833 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:08Z] INFO  00:08:02,840 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:08Z] INFO  00:08:02,862 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:08Z] INFO  00:08:03,307 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:08Z] INFO  00:08:03,418 IntervalUtils - Processing 1881 bp from intervals
[2015-09-30T23:08Z] WARN  00:08:03,422 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:08Z] WARN  00:08:03,422 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:08Z] INFO  00:08:03,482 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:08Z] INFO  00:08:03,619 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:08Z] INFO  00:08:03,620 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:08Z] INFO  00:08:03,620 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:08Z] INFO  00:08:03,620 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:08Z] INFO  00:08:03,662 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:08Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:08Z] INFO  00:08:12,421 VariantAnnotator - Processed 1617 loci.
[2015-09-30T23:08Z]
[2015-09-30T23:08Z] INFO  00:08:12,445 ProgressMeter -            done      6674.0     8.0 s      22.0 m       99.9%     8.0 s       0.0 s
[2015-09-30T23:08Z] INFO  00:08:12,446 ProgressMeter - Total runtime 8.83 secs, 0.15 min, 0.00 hours
[2015-09-30T23:08Z] INFO  00:08:12,446 MicroScheduler - 4308 reads were filtered out during the traversal out of approximately 106186 total reads (4.06%)
[2015-09-30T23:08Z] INFO  00:08:12,446 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:08Z] INFO  00:08:12,446 MicroScheduler -   -> 4283 reads (4.03% of total) failing DuplicateReadFilter
[2015-09-30T23:08Z] INFO  00:08:12,447 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:08Z] INFO  00:08:12,447 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:08Z] INFO  00:08:12,447 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:08Z] INFO  00:08:12,447 MicroScheduler -   -> 25 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:08Z] INFO  00:08:13,518 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:08Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:08Z] WARNING(freebayes): Could not find any mapped reads in target region 2:208395161..208395208
[2015-09-30T23:09Z] WARNING(freebayes): Could not find any mapped reads in target region 2:241507840..241507909
[2015-09-30T23:09Z] tabix index syn3-3_0_31203562-raw.vcf.gz
[2015-09-30T23:09Z] GATK: VariantAnnotator
[2015-09-30T23:09Z] INFO  00:09:48,516 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:09Z] INFO  00:09:48,518 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:09Z] INFO  00:09:48,518 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:09Z] INFO  00:09:48,519 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:09Z] INFO  00:09:48,522 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/3/syn3-3_0_31203562-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/3/tx/tmpKQs3Hz/syn3-3_0_31203562-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/3/syn3-3_0_31203562-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_0_31203562-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:09Z] INFO  00:09:48,528 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:09Z] INFO  00:09:48,528 HelpFormatter - Date/Time: 2015/10/01 00:09:48
[2015-09-30T23:09Z] INFO  00:09:48,529 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:09Z] INFO  00:09:48,529 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:09Z] INFO  00:09:48,623 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:09Z] INFO  00:09:48,701 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:09Z] INFO  00:09:48,709 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:09Z] INFO  00:09:48,731 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:09Z] INFO  00:09:49,252 IntervalUtils - Processing 1546 bp from intervals
[2015-09-30T23:09Z] WARN  00:09:49,257 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:09Z] WARN  00:09:49,257 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:09Z] INFO  00:09:49,311 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:09Z] INFO  00:09:49,413 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:09Z] INFO  00:09:49,413 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:09Z] INFO  00:09:49,414 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:09Z] INFO  00:09:49,414 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:09Z] INFO  00:09:49,453 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:09Z] INFO  00:09:57,490 VariantAnnotator - Processed 1393 loci.
[2015-09-30T23:09Z]
[2015-09-30T23:09Z] INFO  00:09:57,509 ProgressMeter -            done      7817.0     8.0 s      17.3 m       99.9%     8.0 s       0.0 s
[2015-09-30T23:09Z] INFO  00:09:57,509 ProgressMeter - Total runtime 8.10 secs, 0.13 min, 0.00 hours
[2015-09-30T23:09Z] INFO  00:09:57,509 MicroScheduler - 5470 reads were filtered out during the traversal out of approximately 113792 total reads (4.81%)
[2015-09-30T23:09Z] INFO  00:09:57,509 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:09Z] INFO  00:09:57,510 MicroScheduler -   -> 5454 reads (4.79% of total) failing DuplicateReadFilter
[2015-09-30T23:09Z] INFO  00:09:57,510 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:09Z] INFO  00:09:57,510 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:09Z] INFO  00:09:57,510 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:09Z] INFO  00:09:57,511 MicroScheduler -   -> 16 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:09Z] INFO  00:09:58,444 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:10Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:10Z] tabix index syn3-2_221341378_243199373-raw.vcf.gz
[2015-09-30T23:10Z] GATK: VariantAnnotator
[2015-09-30T23:10Z] tabix index syn3-2_189838937_221056966-raw.vcf.gz
[2015-09-30T23:10Z] GATK: VariantAnnotator
[2015-09-30T23:10Z] INFO  00:10:03,291 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:10Z] INFO  00:10:03,293 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:10Z] INFO  00:10:03,293 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:10Z] INFO  00:10:03,293 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:10Z] INFO  00:10:03,297 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/2/syn3-2_221341378_243199373-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/2/tx/tmp8oXDk0/syn3-2_221341378_243199373-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/2/syn3-2_221341378_243199373-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_221341378_243199373-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:10Z] INFO  00:10:03,302 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:10Z] INFO  00:10:03,302 HelpFormatter - Date/Time: 2015/10/01 00:10:03
[2015-09-30T23:10Z] INFO  00:10:03,302 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:10Z] INFO  00:10:03,303 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:10Z] INFO  00:10:03,396 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:10Z] INFO  00:10:03,599 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:10Z] INFO  00:10:03,607 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:10Z] INFO  00:10:03,630 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:10Z] INFO  00:10:04,350 IntervalUtils - Processing 2059 bp from intervals
[2015-09-30T23:10Z] WARN  00:10:04,354 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:10Z] WARN  00:10:04,354 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:10Z] INFO  00:10:04,412 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:10Z] INFO  00:10:04,534 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:10Z] INFO  00:10:04,536 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:10Z] INFO  00:10:04,536 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:10Z] INFO  00:10:04,536 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:10Z] INFO  00:10:04,537 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:10Z] INFO  00:10:04,538 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:10Z] INFO  00:10:04,538 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:10Z] INFO  00:10:04,538 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:10Z] INFO  00:10:04,540 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/2/syn3-2_189838937_221056966-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/2/tx/tmpVjfKVg/syn3-2_189838937_221056966-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/2/syn3-2_189838937_221056966-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/2/1_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/2/2_2014-08-13_dream-syn3-sort-2_189838937_221056966-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:10Z] INFO  00:10:04,545 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:10Z] INFO  00:10:04,546 HelpFormatter - Date/Time: 2015/10/01 00:10:04
[2015-09-30T23:10Z] INFO  00:10:04,546 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:10Z] INFO  00:10:04,546 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:10Z] INFO  00:10:04,581 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:10Z] INFO  00:10:04,643 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:10Z] INFO  00:10:04,719 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:10Z] INFO  00:10:04,727 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:10Z] INFO  00:10:04,750 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:10Z] INFO  00:10:05,404 IntervalUtils - Processing 2083 bp from intervals
[2015-09-30T23:10Z] WARN  00:10:05,408 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:10Z] WARN  00:10:05,409 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:10Z] INFO  00:10:05,466 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:10Z] INFO  00:10:05,605 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:10Z] INFO  00:10:05,606 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:10Z] INFO  00:10:05,606 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:10Z] INFO  00:10:05,606 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:10Z] INFO  00:10:05,649 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:10Z] INFO  00:10:15,026 VariantAnnotator - Processed 1781 loci.
[2015-09-30T23:10Z]
[2015-09-30T23:10Z] INFO  00:10:15,052 ProgressMeter -            done      9585.0    10.0 s      18.3 m      100.0%    10.0 s       0.0 s
[2015-09-30T23:10Z] INFO  00:10:15,052 ProgressMeter - Total runtime 10.51 secs, 0.18 min, 0.00 hours
[2015-09-30T23:10Z] INFO  00:10:15,052 MicroScheduler - 8646 reads were filtered out during the traversal out of approximately 165827 total reads (5.21%)
[2015-09-30T23:10Z] INFO  00:10:15,053 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:10Z] INFO  00:10:15,053 MicroScheduler -   -> 8608 reads (5.19% of total) failing DuplicateReadFilter
[2015-09-30T23:10Z] INFO  00:10:15,053 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:10Z] INFO  00:10:15,053 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:10Z] INFO  00:10:15,054 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:10Z] INFO  00:10:15,054 MicroScheduler -   -> 38 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:10Z] INFO  00:10:15,990 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:10Z] INFO  00:10:16,510 VariantAnnotator - Processed 1861 loci.
[2015-09-30T23:10Z]
[2015-09-30T23:10Z] INFO  00:10:16,535 ProgressMeter -            done      8222.0    10.0 s      22.2 m      100.0%    10.0 s       0.0 s
[2015-09-30T23:10Z] INFO  00:10:16,535 ProgressMeter - Total runtime 10.93 secs, 0.18 min, 0.00 hours
[2015-09-30T23:10Z] INFO  00:10:16,535 MicroScheduler - 6747 reads were filtered out during the traversal out of approximately 145809 total reads (4.63%)
[2015-09-30T23:10Z] INFO  00:10:16,536 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:10Z] INFO  00:10:16,536 MicroScheduler -   -> 6721 reads (4.61% of total) failing DuplicateReadFilter
[2015-09-30T23:10Z] INFO  00:10:16,536 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:10Z] INFO  00:10:16,536 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:10Z] INFO  00:10:16,537 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:10Z] INFO  00:10:16,537 MicroScheduler -   -> 26 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:10Z] INFO  00:10:17,457 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:10Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:10Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:10Z] WARNING(freebayes): Could not find any mapped reads in target region 3:63849654..63849685
[2015-09-30T23:10Z] tabix index syn3-3_62518267_93593495-raw.vcf.gz
[2015-09-30T23:10Z] GATK: VariantAnnotator
[2015-09-30T23:10Z] INFO  00:10:51,989 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:10Z] INFO  00:10:51,991 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:10Z] INFO  00:10:51,991 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:10Z] INFO  00:10:51,991 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:10Z] INFO  00:10:51,994 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/3/syn3-3_62518267_93593495-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/3/tx/tmpkCKS15/syn3-3_62518267_93593495-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/3/syn3-3_62518267_93593495-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_62518267_93593495-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:10Z] INFO  00:10:52,000 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:10Z] INFO  00:10:52,000 HelpFormatter - Date/Time: 2015/10/01 00:10:51
[2015-09-30T23:10Z] INFO  00:10:52,001 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:10Z] INFO  00:10:52,001 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:10Z] INFO  00:10:52,178 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:10Z] INFO  00:10:52,251 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:10Z] INFO  00:10:52,259 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:10Z] INFO  00:10:52,280 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:10Z] INFO  00:10:52,634 IntervalUtils - Processing 904 bp from intervals
[2015-09-30T23:10Z] WARN  00:10:52,638 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:10Z] WARN  00:10:52,639 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:10Z] INFO  00:10:52,748 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:10Z] INFO  00:10:52,820 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:10Z] INFO  00:10:52,821 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:10Z] INFO  00:10:52,821 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:10Z] INFO  00:10:52,822 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:10Z] INFO  00:10:52,862 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:10Z] INFO  00:10:57,503 VariantAnnotator - Processed 820 loci.
[2015-09-30T23:10Z]
[2015-09-30T23:10Z] INFO  00:10:57,533 ProgressMeter -            done     16245.0     4.0 s       4.8 m       99.9%     4.0 s       0.0 s
[2015-09-30T23:10Z] INFO  00:10:57,533 ProgressMeter - Total runtime 4.71 secs, 0.08 min, 0.00 hours
[2015-09-30T23:10Z] INFO  00:10:57,534 MicroScheduler - 6265 reads were filtered out during the traversal out of approximately 66985 total reads (9.35%)
[2015-09-30T23:10Z] INFO  00:10:57,534 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:10Z] INFO  00:10:57,534 MicroScheduler -   -> 6231 reads (9.30% of total) failing DuplicateReadFilter
[2015-09-30T23:10Z] INFO  00:10:57,534 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:10Z] INFO  00:10:57,534 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:10Z] INFO  00:10:57,535 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:10Z] INFO  00:10:57,535 MicroScheduler -   -> 34 reads (0.05% of total) failing UnmappedReadFilter
[2015-09-30T23:10Z] INFO  00:10:58,440 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:11Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:11Z] tabix index syn3-3_93595554_124625281-raw.vcf.gz
[2015-09-30T23:11Z] GATK: VariantAnnotator
[2015-09-30T23:11Z] INFO  00:11:48,057 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:11Z] INFO  00:11:48,059 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:11Z] INFO  00:11:48,059 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:11Z] INFO  00:11:48,059 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:11Z] INFO  00:11:48,062 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/3/syn3-3_93595554_124625281-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/3/tx/tmpP7PAJo/syn3-3_93595554_124625281-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/3/syn3-3_93595554_124625281-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_93595554_124625281-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:11Z] INFO  00:11:48,068 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:11Z] INFO  00:11:48,068 HelpFormatter - Date/Time: 2015/10/01 00:11:48
[2015-09-30T23:11Z] INFO  00:11:48,068 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:11Z] INFO  00:11:48,069 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:11Z] INFO  00:11:48,164 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:11Z] INFO  00:11:48,240 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:11Z] INFO  00:11:48,248 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:11Z] INFO  00:11:48,271 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:11Z] INFO  00:11:49,018 IntervalUtils - Processing 1745 bp from intervals
[2015-09-30T23:11Z] WARN  00:11:49,022 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:11Z] WARN  00:11:49,023 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:11Z] INFO  00:11:49,083 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:11Z] INFO  00:11:49,200 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:11Z] INFO  00:11:49,200 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:11Z] INFO  00:11:49,201 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:11Z] INFO  00:11:49,201 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:11Z] INFO  00:11:49,238 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:11Z] INFO  00:11:57,356 VariantAnnotator - Processed 1528 loci.
[2015-09-30T23:11Z]
[2015-09-30T23:11Z] INFO  00:11:57,966 ProgressMeter -            done      6057.0     8.0 s      24.1 m       99.9%     8.0 s       0.0 s
[2015-09-30T23:11Z] INFO  00:11:57,966 ProgressMeter - Total runtime 8.77 secs, 0.15 min, 0.00 hours
[2015-09-30T23:11Z] INFO  00:11:57,967 MicroScheduler - 4976 reads were filtered out during the traversal out of approximately 112559 total reads (4.42%)
[2015-09-30T23:11Z] INFO  00:11:57,967 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:11Z] INFO  00:11:57,967 MicroScheduler -   -> 4953 reads (4.40% of total) failing DuplicateReadFilter
[2015-09-30T23:11Z] INFO  00:11:57,967 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:11Z] INFO  00:11:57,968 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:11Z] INFO  00:11:57,968 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:11Z] INFO  00:11:57,968 MicroScheduler -   -> 23 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:11Z] INFO  00:11:58,909 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:12Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:12Z] WARNING(freebayes): Could not find any mapped reads in target region 3:167077957..167078017
[2015-09-30T23:12Z] tabix index syn3-3_124626733_155649953-raw.vcf.gz
[2015-09-30T23:12Z] GATK: VariantAnnotator
[2015-09-30T23:12Z] INFO  00:12:59,650 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:12Z] INFO  00:12:59,652 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:12Z] INFO  00:12:59,652 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:12Z] INFO  00:12:59,652 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:12Z] INFO  00:12:59,656 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/3/syn3-3_124626733_155649953-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/3/tx/tmpVdom1H/syn3-3_124626733_155649953-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/3/syn3-3_124626733_155649953-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_124626733_155649953-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:12Z] INFO  00:12:59,662 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:12Z] INFO  00:12:59,662 HelpFormatter - Date/Time: 2015/10/01 00:12:59
[2015-09-30T23:12Z] INFO  00:12:59,663 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:12Z] INFO  00:12:59,663 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:12Z] INFO  00:12:59,757 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:12Z] INFO  00:12:59,833 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:12Z] INFO  00:12:59,840 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:12Z] INFO  00:12:59,862 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:13Z] INFO  00:13:00,452 IntervalUtils - Processing 2176 bp from intervals
[2015-09-30T23:13Z] WARN  00:13:00,457 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:13Z] WARN  00:13:00,457 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:13Z] INFO  00:13:00,514 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:13Z] INFO  00:13:00,641 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:13Z] INFO  00:13:00,642 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:13Z] INFO  00:13:00,642 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:13Z] INFO  00:13:00,642 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:13Z] INFO  00:13:00,683 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:13Z] INFO  00:13:10,452 VariantAnnotator - Processed 1957 loci.
[2015-09-30T23:13Z]
[2015-09-30T23:13Z] INFO  00:13:10,475 ProgressMeter -            done     14362.0     9.0 s      11.4 m      100.0%     9.0 s       0.0 s
[2015-09-30T23:13Z] INFO  00:13:10,476 ProgressMeter - Total runtime 9.83 secs, 0.16 min, 0.00 hours
[2015-09-30T23:13Z] INFO  00:13:10,476 MicroScheduler - 7166 reads were filtered out during the traversal out of approximately 151445 total reads (4.73%)
[2015-09-30T23:13Z] INFO  00:13:10,476 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:13Z] INFO  00:13:10,476 MicroScheduler -   -> 7139 reads (4.71% of total) failing DuplicateReadFilter
[2015-09-30T23:13Z] INFO  00:13:10,477 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:13Z] INFO  00:13:10,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:13Z] INFO  00:13:10,477 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:13Z] INFO  00:13:10,477 MicroScheduler -   -> 27 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:13Z] INFO  00:13:11,412 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:13Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:13Z] tabix index syn3-3_155652401_186761310-raw.vcf.gz
[2015-09-30T23:13Z] GATK: VariantAnnotator
[2015-09-30T23:13Z] INFO  00:13:21,136 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:13Z] INFO  00:13:21,138 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:13Z] INFO  00:13:21,138 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:13Z] INFO  00:13:21,138 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:13Z] INFO  00:13:21,142 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/3/syn3-3_155652401_186761310-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/3/tx/tmpofjA7w/syn3-3_155652401_186761310-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/3/syn3-3_155652401_186761310-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_155652401_186761310-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:13Z] INFO  00:13:21,146 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:13Z] INFO  00:13:21,147 HelpFormatter - Date/Time: 2015/10/01 00:13:21
[2015-09-30T23:13Z] INFO  00:13:21,147 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:13Z] INFO  00:13:21,147 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:13Z] INFO  00:13:21,233 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:13Z] INFO  00:13:21,306 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:13Z] INFO  00:13:21,313 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:13Z] INFO  00:13:21,334 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:13Z] INFO  00:13:21,815 IntervalUtils - Processing 1377 bp from intervals
[2015-09-30T23:13Z] WARN  00:13:21,819 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:13Z] WARN  00:13:21,819 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:13Z] INFO  00:13:21,893 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:13Z] INFO  00:13:23,225 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:13Z] INFO  00:13:23,226 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:13Z] INFO  00:13:23,226 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:13Z] INFO  00:13:23,226 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:13Z] INFO  00:13:23,267 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:13Z] INFO  00:13:30,139 VariantAnnotator - Processed 1242 loci.
[2015-09-30T23:13Z]
[2015-09-30T23:13Z] INFO  00:13:30,165 ProgressMeter -            done      5024.0     6.0 s      23.0 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:13Z] INFO  00:13:30,165 ProgressMeter - Total runtime 6.94 secs, 0.12 min, 0.00 hours
[2015-09-30T23:13Z] INFO  00:13:30,166 MicroScheduler - 3881 reads were filtered out during the traversal out of approximately 87814 total reads (4.42%)
[2015-09-30T23:13Z] INFO  00:13:30,166 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:13Z] INFO  00:13:30,166 MicroScheduler -   -> 3855 reads (4.39% of total) failing DuplicateReadFilter
[2015-09-30T23:13Z] INFO  00:13:30,166 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:13Z] INFO  00:13:30,167 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:13Z] INFO  00:13:30,167 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:13Z] INFO  00:13:30,167 MicroScheduler -   -> 26 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:13Z] INFO  00:13:31,084 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:13Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:13Z] tabix index syn3-3_31494593_62516713-raw.vcf.gz
[2015-09-30T23:13Z] GATK: VariantAnnotator
[2015-09-30T23:13Z] INFO  00:13:41,057 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:13Z] INFO  00:13:41,059 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:13Z] INFO  00:13:41,059 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:13Z] INFO  00:13:41,060 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:13Z] INFO  00:13:41,063 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/3/syn3-3_31494593_62516713-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/3/tx/tmpiWUet2/syn3-3_31494593_62516713-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/3/syn3-3_31494593_62516713-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_31494593_62516713-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:13Z] INFO  00:13:41,069 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:13Z] INFO  00:13:41,069 HelpFormatter - Date/Time: 2015/10/01 00:13:41
[2015-09-30T23:13Z] INFO  00:13:41,069 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:13Z] INFO  00:13:41,069 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:13Z] INFO  00:13:41,162 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:13Z] INFO  00:13:41,237 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:13Z] INFO  00:13:41,244 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:13Z] INFO  00:13:41,266 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:13Z] INFO  00:13:41,890 IntervalUtils - Processing 2380 bp from intervals
[2015-09-30T23:13Z] WARN  00:13:41,894 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:13Z] WARN  00:13:41,894 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:13Z] INFO  00:13:41,949 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:13Z] INFO  00:13:42,089 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:13Z] INFO  00:13:42,090 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:13Z] INFO  00:13:42,090 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:13Z] INFO  00:13:42,091 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:13Z] INFO  00:13:42,130 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:13Z] INFO  00:13:54,597 VariantAnnotator - Processed 2043 loci.
[2015-09-30T23:13Z]
[2015-09-30T23:13Z] INFO  00:13:54,619 ProgressMeter -            done      8916.0    12.0 s      23.4 m      100.0%    12.0 s       0.0 s
[2015-09-30T23:13Z] INFO  00:13:54,620 ProgressMeter - Total runtime 12.53 secs, 0.21 min, 0.00 hours
[2015-09-30T23:13Z] INFO  00:13:54,620 MicroScheduler - 9437 reads were filtered out during the traversal out of approximately 190254 total reads (4.96%)
[2015-09-30T23:13Z] INFO  00:13:54,620 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:13Z] INFO  00:13:54,620 MicroScheduler -   -> 9407 reads (4.94% of total) failing DuplicateReadFilter
[2015-09-30T23:13Z] INFO  00:13:54,621 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:13Z] INFO  00:13:54,621 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:13Z] INFO  00:13:54,621 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:13Z] INFO  00:13:54,621 MicroScheduler -   -> 30 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:13Z] INFO  00:13:55,547 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:13Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:14Z] tabix index syn3-3_186768753_198022430-raw.vcf.gz
[2015-09-30T23:14Z] GATK: VariantAnnotator
[2015-09-30T23:14Z] INFO  00:14:09,309 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:14Z] INFO  00:14:09,311 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:14Z] INFO  00:14:09,311 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:14Z] INFO  00:14:09,311 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:14Z] INFO  00:14:09,314 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/3/syn3-3_186768753_198022430-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/3/tx/tmpEY8J8I/syn3-3_186768753_198022430-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/3/syn3-3_186768753_198022430-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/3/1_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/3/2_2014-08-13_dream-syn3-sort-3_186768753_198022430-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:14Z] INFO  00:14:09,320 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:14Z] INFO  00:14:09,320 HelpFormatter - Date/Time: 2015/10/01 00:14:09
[2015-09-30T23:14Z] INFO  00:14:09,320 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:14Z] INFO  00:14:09,321 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:14Z] INFO  00:14:09,414 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:14Z] INFO  00:14:09,491 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:14Z] INFO  00:14:09,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:14Z] INFO  00:14:09,521 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:14Z] INFO  00:14:10,040 IntervalUtils - Processing 1403 bp from intervals
[2015-09-30T23:14Z] WARN  00:14:10,045 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:14Z] WARN  00:14:10,045 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:14Z] INFO  00:14:10,101 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:14Z] INFO  00:14:10,209 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:14Z] INFO  00:14:10,210 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:14Z] INFO  00:14:10,210 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:14Z] INFO  00:14:10,210 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:14Z] INFO  00:14:10,250 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:14Z] INFO  00:14:17,010 VariantAnnotator - Processed 1310 loci.
[2015-09-30T23:14Z]
[2015-09-30T23:14Z] INFO  00:14:17,054 ProgressMeter -            done     23644.0     6.0 s       4.8 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:14Z] INFO  00:14:17,054 ProgressMeter - Total runtime 6.84 secs, 0.11 min, 0.00 hours
[2015-09-30T23:14Z] INFO  00:14:17,054 MicroScheduler - 5455 reads were filtered out during the traversal out of approximately 111571 total reads (4.89%)
[2015-09-30T23:14Z] INFO  00:14:17,055 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:14Z] INFO  00:14:17,055 MicroScheduler -   -> 5426 reads (4.86% of total) failing DuplicateReadFilter
[2015-09-30T23:14Z] INFO  00:14:17,055 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:14Z] INFO  00:14:17,055 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:14Z] INFO  00:14:17,055 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:14Z] INFO  00:14:17,056 MicroScheduler -   -> 29 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:14Z] INFO  00:14:18,094 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:14Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:14Z] WARNING(freebayes): Could not find any mapped reads in target region 4:9174623..9175048
[2015-09-30T23:14Z] WARNING(freebayes): Could not find any mapped reads in target region 4:9175080..9175166
[2015-09-30T23:14Z] tabix index syn3-4_31031389_62067173-raw.vcf.gz
[2015-09-30T23:14Z] GATK: VariantAnnotator
[2015-09-30T23:14Z] INFO  00:14:52,322 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:14Z] INFO  00:14:52,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:14Z] INFO  00:14:52,324 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:14Z] INFO  00:14:52,325 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:14Z] INFO  00:14:52,328 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/4/syn3-4_31031389_62067173-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/4/tx/tmpkRXm8f/syn3-4_31031389_62067173-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/4/syn3-4_31031389_62067173-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_31031389_62067173-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:14Z] INFO  00:14:52,334 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:14Z] INFO  00:14:52,334 HelpFormatter - Date/Time: 2015/10/01 00:14:52
[2015-09-30T23:14Z] INFO  00:14:52,335 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:14Z] INFO  00:14:52,335 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:14Z] INFO  00:14:52,407 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:14Z] INFO  00:14:52,491 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:14Z] INFO  00:14:52,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:14Z] INFO  00:14:52,520 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:14Z] INFO  00:14:52,954 IntervalUtils - Processing 977 bp from intervals
[2015-09-30T23:14Z] WARN  00:14:52,958 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:14Z] WARN  00:14:52,958 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:14Z] INFO  00:14:53,013 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:14Z] INFO  00:14:53,098 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:14Z] INFO  00:14:53,098 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:14Z] INFO  00:14:53,099 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:14Z] INFO  00:14:53,099 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:14Z] INFO  00:14:53,139 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:14Z] INFO  00:14:58,511 VariantAnnotator - Processed 887 loci.
[2015-09-30T23:14Z]
[2015-09-30T23:14Z] INFO  00:14:58,532 ProgressMeter -            done      3515.0     5.0 s      25.8 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:14Z] INFO  00:14:58,533 ProgressMeter - Total runtime 5.43 secs, 0.09 min, 0.00 hours
[2015-09-30T23:14Z] INFO  00:14:58,533 MicroScheduler - 2645 reads were filtered out during the traversal out of approximately 60533 total reads (4.37%)
[2015-09-30T23:14Z] INFO  00:14:58,533 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:14Z] INFO  00:14:58,534 MicroScheduler -   -> 2629 reads (4.34% of total) failing DuplicateReadFilter
[2015-09-30T23:14Z] INFO  00:14:58,534 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:14Z] INFO  00:14:58,534 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:14Z] INFO  00:14:58,534 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:14Z] INFO  00:14:58,535 MicroScheduler -   -> 16 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:14Z] INFO  00:14:59,529 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:15Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:15Z] WARNING(freebayes): Could not find any mapped reads in target region 4:84221877..84221951
[2015-09-30T23:15Z] tabix index syn3-4_0_31018607-raw.vcf.gz
[2015-09-30T23:15Z] GATK: VariantAnnotator
[2015-09-30T23:15Z] INFO  00:15:23,164 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:15Z] INFO  00:15:23,166 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:15Z] INFO  00:15:23,167 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:15Z] INFO  00:15:23,167 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:15Z] INFO  00:15:23,170 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/4/syn3-4_0_31018607-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/4/tx/tmpcBR92K/syn3-4_0_31018607-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/4/syn3-4_0_31018607-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_0_31018607-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:15Z] INFO  00:15:23,176 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:15Z] INFO  00:15:23,176 HelpFormatter - Date/Time: 2015/10/01 00:15:23
[2015-09-30T23:15Z] INFO  00:15:23,176 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:15Z] INFO  00:15:23,176 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:15Z] INFO  00:15:23,270 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:15Z] INFO  00:15:23,348 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:15Z] INFO  00:15:23,356 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:15Z] INFO  00:15:23,379 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:15Z] INFO  00:15:23,963 IntervalUtils - Processing 2133 bp from intervals
[2015-09-30T23:15Z] WARN  00:15:23,967 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:15Z] WARN  00:15:23,968 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:15Z] INFO  00:15:24,024 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:15Z] INFO  00:15:24,136 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:15Z] INFO  00:15:24,136 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:15Z] INFO  00:15:24,136 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:15Z] INFO  00:15:24,137 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:15Z] INFO  00:15:24,176 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:15Z] INFO  00:15:34,145 VariantAnnotator - Processed 1888 loci.
[2015-09-30T23:15Z]
[2015-09-30T23:15Z] INFO  00:15:34,166 ProgressMeter -            done     10474.0    10.0 s      16.0 m      100.0%    10.0 s       0.0 s
[2015-09-30T23:15Z] INFO  00:15:34,166 ProgressMeter - Total runtime 10.03 secs, 0.17 min, 0.00 hours
[2015-09-30T23:15Z] INFO  00:15:34,166 MicroScheduler - 9288 reads were filtered out during the traversal out of approximately 173430 total reads (5.36%)
[2015-09-30T23:15Z] INFO  00:15:34,166 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:15Z] INFO  00:15:34,167 MicroScheduler -   -> 9246 reads (5.33% of total) failing DuplicateReadFilter
[2015-09-30T23:15Z] INFO  00:15:34,167 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:15Z] INFO  00:15:34,167 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:15Z] INFO  00:15:34,167 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:15Z] INFO  00:15:34,167 MicroScheduler -   -> 42 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:15Z] INFO  00:15:35,069 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:15Z] tabix index syn3-4_62292837_93511697-raw.vcf.gz
[2015-09-30T23:15Z] GATK: VariantAnnotator
[2015-09-30T23:15Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:15Z] INFO  00:15:37,681 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:15Z] INFO  00:15:37,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:15Z] INFO  00:15:37,684 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:15Z] INFO  00:15:37,684 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:15Z] INFO  00:15:37,687 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/4/syn3-4_62292837_93511697-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/4/tx/tmpsyNOKf/syn3-4_62292837_93511697-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/4/syn3-4_62292837_93511697-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_62292837_93511697-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:15Z] INFO  00:15:37,693 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:15Z] INFO  00:15:37,693 HelpFormatter - Date/Time: 2015/10/01 00:15:37
[2015-09-30T23:15Z] INFO  00:15:37,693 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:15Z] INFO  00:15:37,693 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:15Z] INFO  00:15:38,216 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:15Z] INFO  00:15:38,300 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:15Z] INFO  00:15:38,309 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:15Z] INFO  00:15:38,332 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:15Z] INFO  00:15:38,855 IntervalUtils - Processing 1758 bp from intervals
[2015-09-30T23:15Z] WARN  00:15:38,859 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:15Z] WARN  00:15:38,860 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:15Z] INFO  00:15:39,241 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:15Z] INFO  00:15:39,350 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:15Z] INFO  00:15:39,351 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:15Z] INFO  00:15:39,351 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:15Z] INFO  00:15:39,352 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:15Z] INFO  00:15:39,391 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:15Z] INFO  00:15:46,183 VariantAnnotator - Processed 1472 loci.
[2015-09-30T23:15Z]
[2015-09-30T23:15Z] INFO  00:15:46,204 ProgressMeter -            done      8031.0     6.0 s      14.2 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:15Z] INFO  00:15:46,204 ProgressMeter - Total runtime 6.85 secs, 0.11 min, 0.00 hours
[2015-09-30T23:15Z] INFO  00:15:46,204 MicroScheduler - 3730 reads were filtered out during the traversal out of approximately 89091 total reads (4.19%)
[2015-09-30T23:15Z] INFO  00:15:46,205 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:15Z] INFO  00:15:46,205 MicroScheduler -   -> 3716 reads (4.17% of total) failing DuplicateReadFilter
[2015-09-30T23:15Z] INFO  00:15:46,205 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:15Z] INFO  00:15:46,205 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:15Z] INFO  00:15:46,205 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:15Z] INFO  00:15:46,206 MicroScheduler -   -> 14 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:15Z] INFO  00:15:47,123 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:15Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:15Z] tabix index syn3-4_94005855_125588163-raw.vcf.gz
[2015-09-30T23:15Z] GATK: VariantAnnotator
[2015-09-30T23:16Z] INFO  00:16:00,355 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:00,357 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:16Z] INFO  00:16:00,357 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:16Z] INFO  00:16:00,357 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:16Z] INFO  00:16:00,361 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/4/syn3-4_94005855_125588163-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/4/tx/tmpReZkxa/syn3-4_94005855_125588163-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/4/syn3-4_94005855_125588163-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_94005855_125588163-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:16Z] INFO  00:16:00,366 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:16Z] INFO  00:16:00,367 HelpFormatter - Date/Time: 2015/10/01 00:16:00
[2015-09-30T23:16Z] INFO  00:16:00,367 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:00,367 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:00,442 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:16Z] INFO  00:16:00,527 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:16Z] INFO  00:16:00,534 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:16Z] INFO  00:16:00,556 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:16Z] INFO  00:16:01,034 IntervalUtils - Processing 1233 bp from intervals
[2015-09-30T23:16Z] WARN  00:16:01,038 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:16Z] WARN  00:16:01,039 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:16Z] INFO  00:16:01,095 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:16Z] INFO  00:16:01,206 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:16Z] INFO  00:16:01,207 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:16Z] INFO  00:16:01,207 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:16Z] INFO  00:16:01,208 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:16Z] INFO  00:16:01,248 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:16Z] INFO  00:16:06,683 VariantAnnotator - Processed 1104 loci.
[2015-09-30T23:16Z]
[2015-09-30T23:16Z] INFO  00:16:06,704 ProgressMeter -            done      3881.0     5.0 s      23.6 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:16Z] INFO  00:16:06,704 ProgressMeter - Total runtime 5.50 secs, 0.09 min, 0.00 hours
[2015-09-30T23:16Z] INFO  00:16:06,705 MicroScheduler - 2762 reads were filtered out during the traversal out of approximately 66648 total reads (4.14%)
[2015-09-30T23:16Z] INFO  00:16:06,705 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:16Z] INFO  00:16:06,705 MicroScheduler -   -> 2746 reads (4.12% of total) failing DuplicateReadFilter
[2015-09-30T23:16Z] INFO  00:16:06,705 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:16Z] INFO  00:16:06,705 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:16Z] INFO  00:16:06,706 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:16Z] INFO  00:16:06,706 MicroScheduler -   -> 16 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:16Z] INFO  00:16:07,844 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:16Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:16Z] tabix index syn3-4_189012293_191154276-raw.vcf.gz
[2015-09-30T23:16Z] GATK: VariantAnnotator
[2015-09-30T23:16Z] INFO  00:16:18,000 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:18,002 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:16Z] INFO  00:16:18,003 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:16Z] INFO  00:16:18,003 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:16Z] INFO  00:16:18,006 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/4/syn3-4_189012293_191154276-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/4/tx/tmpSBZgkc/syn3-4_189012293_191154276-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/4/syn3-4_189012293_191154276-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_189012293_191154276-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:16Z] INFO  00:16:18,012 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:16Z] INFO  00:16:18,012 HelpFormatter - Date/Time: 2015/10/01 00:16:18
[2015-09-30T23:16Z] INFO  00:16:18,012 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:18,012 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:18,393 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:16Z] INFO  00:16:18,466 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:16Z] INFO  00:16:18,474 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:16Z] INFO  00:16:18,495 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:16Z] INFO  00:16:18,730 IntervalUtils - Processing 109 bp from intervals
[2015-09-30T23:16Z] WARN  00:16:18,734 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:16Z] WARN  00:16:18,734 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:16Z] INFO  00:16:18,791 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:16Z] INFO  00:16:18,838 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:16Z] INFO  00:16:18,839 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:16Z] INFO  00:16:18,839 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:16Z] INFO  00:16:18,840 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:16Z] INFO  00:16:18,880 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:16Z] INFO  00:16:20,567 VariantAnnotator - Processed 103 loci.
[2015-09-30T23:16Z]
[2015-09-30T23:16Z] INFO  00:16:20,929 ProgressMeter -            done       933.0     2.0 s      37.3 m       99.1%     2.0 s       0.0 s
[2015-09-30T23:16Z] INFO  00:16:20,929 ProgressMeter - Total runtime 2.09 secs, 0.03 min, 0.00 hours
[2015-09-30T23:16Z] INFO  00:16:20,930 MicroScheduler - 698 reads were filtered out during the traversal out of approximately 9529 total reads (7.33%)
[2015-09-30T23:16Z] INFO  00:16:20,930 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:16Z] INFO  00:16:20,930 MicroScheduler -   -> 687 reads (7.21% of total) failing DuplicateReadFilter
[2015-09-30T23:16Z] INFO  00:16:20,931 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:16Z] INFO  00:16:20,931 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:16Z] INFO  00:16:20,931 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:16Z] INFO  00:16:20,931 MicroScheduler -   -> 11 reads (0.12% of total) failing UnmappedReadFilter
[2015-09-30T23:16Z] INFO  00:16:21,917 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:16Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:16Z] tabix index syn3-4_125589908_156618518-raw.vcf.gz
[2015-09-30T23:16Z] GATK: VariantAnnotator
[2015-09-30T23:16Z] INFO  00:16:27,397 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:27,399 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:16Z] INFO  00:16:27,399 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:16Z] INFO  00:16:27,400 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:16Z] INFO  00:16:27,403 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/4/syn3-4_125589908_156618518-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/4/tx/tmpbxLj6x/syn3-4_125589908_156618518-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/4/syn3-4_125589908_156618518-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_125589908_156618518-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:16Z] INFO  00:16:27,408 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:16Z] INFO  00:16:27,408 HelpFormatter - Date/Time: 2015/10/01 00:16:27
[2015-09-30T23:16Z] INFO  00:16:27,409 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:27,409 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:27,495 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:16Z] INFO  00:16:27,569 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:16Z] INFO  00:16:27,576 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:16Z] INFO  00:16:27,597 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:16Z] INFO  00:16:27,950 IntervalUtils - Processing 862 bp from intervals
[2015-09-30T23:16Z] WARN  00:16:27,954 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:16Z] WARN  00:16:27,954 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:16Z] INFO  00:16:28,155 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:16Z] INFO  00:16:28,240 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:16Z] INFO  00:16:28,241 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:16Z] INFO  00:16:28,241 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:16Z] INFO  00:16:28,242 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:16Z] INFO  00:16:28,287 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:16Z] INFO  00:16:32,698 VariantAnnotator - Processed 769 loci.
[2015-09-30T23:16Z]
[2015-09-30T23:16Z] INFO  00:16:32,749 ProgressMeter -            done      2607.0     4.0 s      28.8 m       99.9%     4.0 s       0.0 s
[2015-09-30T23:16Z] INFO  00:16:32,749 ProgressMeter - Total runtime 4.51 secs, 0.08 min, 0.00 hours
[2015-09-30T23:16Z] INFO  00:16:32,750 MicroScheduler - 2109 reads were filtered out during the traversal out of approximately 50095 total reads (4.21%)
[2015-09-30T23:16Z] INFO  00:16:32,750 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:16Z] INFO  00:16:32,750 MicroScheduler -   -> 2097 reads (4.19% of total) failing DuplicateReadFilter
[2015-09-30T23:16Z] INFO  00:16:32,750 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:16Z] INFO  00:16:32,750 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:16Z] INFO  00:16:32,751 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:16Z] INFO  00:16:32,751 MicroScheduler -   -> 12 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:16Z] INFO  00:16:33,679 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:16Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:16Z] tabix index syn3-4_156624795_188926424-raw.vcf.gz
[2015-09-30T23:16Z] GATK: VariantAnnotator
[2015-09-30T23:16Z] INFO  00:16:43,127 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:43,129 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:16Z] INFO  00:16:43,130 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:16Z] INFO  00:16:43,130 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:16Z] INFO  00:16:43,133 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/4/syn3-4_156624795_188926424-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/4/tx/tmpHhvGE4/syn3-4_156624795_188926424-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/4/syn3-4_156624795_188926424-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/4/1_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/4/2_2014-08-13_dream-syn3-sort-4_156624795_188926424-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:16Z] INFO  00:16:43,139 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:16Z] INFO  00:16:43,139 HelpFormatter - Date/Time: 2015/10/01 00:16:43
[2015-09-30T23:16Z] INFO  00:16:43,139 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:43,139 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:16Z] INFO  00:16:43,203 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:16Z] INFO  00:16:43,276 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:16Z] INFO  00:16:43,284 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:16Z] INFO  00:16:43,305 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:16Z] INFO  00:16:43,747 IntervalUtils - Processing 1066 bp from intervals
[2015-09-30T23:16Z] WARN  00:16:43,751 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:16Z] WARN  00:16:43,751 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:16Z] INFO  00:16:43,807 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:16Z] INFO  00:16:43,899 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:16Z] INFO  00:16:43,900 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:16Z] INFO  00:16:43,900 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:16Z] INFO  00:16:43,901 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:16Z] INFO  00:16:43,940 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:16Z] INFO  00:16:49,234 VariantAnnotator - Processed 949 loci.
[2015-09-30T23:16Z]
[2015-09-30T23:16Z] INFO  00:16:49,257 ProgressMeter -            done      3648.0     5.0 s      24.5 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:16Z] INFO  00:16:49,257 ProgressMeter - Total runtime 5.36 secs, 0.09 min, 0.00 hours
[2015-09-30T23:16Z] INFO  00:16:49,257 MicroScheduler - 2599 reads were filtered out during the traversal out of approximately 60835 total reads (4.27%)
[2015-09-30T23:16Z] INFO  00:16:49,258 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:16Z] INFO  00:16:49,258 MicroScheduler -   -> 2590 reads (4.26% of total) failing DuplicateReadFilter
[2015-09-30T23:16Z] INFO  00:16:49,258 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:16Z] INFO  00:16:49,258 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:16Z] INFO  00:16:49,258 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:16Z] INFO  00:16:49,259 MicroScheduler -   -> 9 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:16Z] INFO  00:16:50,203 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:16Z] WARNING(freebayes): Could not find any mapped reads in target region 5:6713869..6713946
[2015-09-30T23:16Z] WARNING(freebayes): Could not find any mapped reads in target region 5:6713981..6714016
[2015-09-30T23:16Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:17Z] WARNING(freebayes): Could not find any mapped reads in target region 5:11385228..11385249
[2015-09-30T23:17Z] tabix index syn3-5_0_31268043-raw.vcf.gz
[2015-09-30T23:17Z] GATK: VariantAnnotator
[2015-09-30T23:17Z] INFO  00:17:20,137 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:17Z] INFO  00:17:20,139 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:17Z] INFO  00:17:20,139 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:17Z] INFO  00:17:20,139 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:17Z] INFO  00:17:20,143 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/5/syn3-5_0_31268043-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/5/tx/tmpikGjdf/syn3-5_0_31268043-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/5/syn3-5_0_31268043-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_0_31268043-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:17Z] INFO  00:17:20,148 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:17Z] INFO  00:17:20,149 HelpFormatter - Date/Time: 2015/10/01 00:17:20
[2015-09-30T23:17Z] INFO  00:17:20,149 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:17Z] INFO  00:17:20,149 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:17Z] INFO  00:17:20,527 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:17Z] INFO  00:17:20,738 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:17Z] INFO  00:17:20,746 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:17Z] INFO  00:17:20,892 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
[2015-09-30T23:17Z] INFO  00:17:21,703 IntervalUtils - Processing 1222 bp from intervals
[2015-09-30T23:17Z] WARN  00:17:21,707 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:17Z] WARN  00:17:21,707 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:17Z] INFO  00:17:21,763 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:17Z] INFO  00:17:21,842 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:17Z] INFO  00:17:21,843 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:17Z] INFO  00:17:21,843 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:17Z] INFO  00:17:21,843 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:17Z] INFO  00:17:21,883 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:17Z] INFO  00:17:28,129 VariantAnnotator - Processed 1035 loci.
[2015-09-30T23:17Z]
[2015-09-30T23:17Z] INFO  00:17:28,161 ProgressMeter -            done      7596.0     6.0 s      13.9 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:17Z] INFO  00:17:28,162 ProgressMeter - Total runtime 6.32 secs, 0.11 min, 0.00 hours
[2015-09-30T23:17Z] INFO  00:17:28,162 MicroScheduler - 4368 reads were filtered out during the traversal out of approximately 84943 total reads (5.14%)
[2015-09-30T23:17Z] INFO  00:17:28,162 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:17Z] INFO  00:17:28,163 MicroScheduler -   -> 4351 reads (5.12% of total) failing DuplicateReadFilter
[2015-09-30T23:17Z] INFO  00:17:28,163 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:17Z] INFO  00:17:28,163 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:17Z] INFO  00:17:28,163 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:17Z] INFO  00:17:28,163 MicroScheduler -   -> 17 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:17Z] INFO  00:17:29,105 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:17Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:17Z] WARNING(freebayes): Could not find any mapped reads in target region 5:60628561..60628600
[2015-09-30T23:17Z] tabix index syn3-5_31293868_62597714-raw.vcf.gz
[2015-09-30T23:17Z] GATK: VariantAnnotator
[2015-09-30T23:17Z] INFO  00:17:45,245 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:17Z] INFO  00:17:45,247 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:17Z] INFO  00:17:45,247 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:17Z] INFO  00:17:45,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:17Z] INFO  00:17:45,251 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/5/syn3-5_31293868_62597714-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/5/tx/tmpxAKcxj/syn3-5_31293868_62597714-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/5/syn3-5_31293868_62597714-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_31293868_62597714-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:17Z] INFO  00:17:45,257 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:17Z] INFO  00:17:45,257 HelpFormatter - Date/Time: 2015/10/01 00:17:45
[2015-09-30T23:17Z] INFO  00:17:45,257 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:17Z] INFO  00:17:45,257 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:17Z] INFO  00:17:45,331 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:17Z] INFO  00:17:45,413 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:17Z] INFO  00:17:45,420 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:17Z] INFO  00:17:45,441 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:17Z] INFO  00:17:45,902 IntervalUtils - Processing 1306 bp from intervals
[2015-09-30T23:17Z] WARN  00:17:45,906 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:17Z] WARN  00:17:45,906 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:17Z] INFO  00:17:45,962 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:17Z] INFO  00:17:46,056 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:17Z] INFO  00:17:46,056 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:17Z] INFO  00:17:46,057 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:17Z] INFO  00:17:46,057 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:17Z] INFO  00:17:46,094 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:17Z] INFO  00:17:52,320 VariantAnnotator - Processed 1158 loci.
[2015-09-30T23:17Z]
[2015-09-30T23:17Z] INFO  00:17:53,064 ProgressMeter -            done      4395.0     7.0 s      26.6 m       99.9%     7.0 s       0.0 s
[2015-09-30T23:17Z] INFO  00:17:53,065 ProgressMeter - Total runtime 7.01 secs, 0.12 min, 0.00 hours
[2015-09-30T23:17Z] INFO  00:17:53,065 MicroScheduler - 3506 reads were filtered out during the traversal out of approximately 81252 total reads (4.31%)
[2015-09-30T23:17Z] INFO  00:17:53,065 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:17Z] INFO  00:17:53,066 MicroScheduler -   -> 3495 reads (4.30% of total) failing DuplicateReadFilter
[2015-09-30T23:17Z] INFO  00:17:53,066 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:17Z] INFO  00:17:53,066 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:17Z] INFO  00:17:53,066 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:17Z] INFO  00:17:53,066 MicroScheduler -   -> 11 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:17Z] INFO  00:17:53,956 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:17Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:18Z] tabix index syn3-5_63256014_94276127-raw.vcf.gz
[2015-09-30T23:18Z] GATK: VariantAnnotator
[2015-09-30T23:18Z] INFO  00:18:06,910 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:18Z] INFO  00:18:06,912 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:18Z] INFO  00:18:06,912 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:18Z] INFO  00:18:06,912 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:18Z] INFO  00:18:06,916 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/5/syn3-5_63256014_94276127-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/5/tx/tmpYbb2rc/syn3-5_63256014_94276127-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/5/syn3-5_63256014_94276127-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_63256014_94276127-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:18Z] INFO  00:18:06,921 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:18Z] INFO  00:18:06,921 HelpFormatter - Date/Time: 2015/10/01 00:18:06
[2015-09-30T23:18Z] INFO  00:18:06,922 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:18Z] INFO  00:18:06,922 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:18Z] INFO  00:18:07,016 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:18Z] INFO  00:18:07,098 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:18Z] INFO  00:18:07,105 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:18Z] INFO  00:18:07,128 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:18Z] INFO  00:18:07,604 IntervalUtils - Processing 1288 bp from intervals
[2015-09-30T23:18Z] WARN  00:18:07,608 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:18Z] WARN  00:18:07,609 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:18Z] INFO  00:18:07,665 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:18Z] INFO  00:18:07,776 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:18Z] INFO  00:18:07,776 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:18Z] INFO  00:18:07,776 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:18Z] INFO  00:18:07,777 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:18Z] INFO  00:18:07,816 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:18Z] INFO  00:18:13,703 VariantAnnotator - Processed 1118 loci.
[2015-09-30T23:18Z]
[2015-09-30T23:18Z] INFO  00:18:13,751 ProgressMeter -            done      4558.0     5.0 s      21.8 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:18Z] INFO  00:18:13,751 ProgressMeter - Total runtime 5.98 secs, 0.10 min, 0.00 hours
[2015-09-30T23:18Z] INFO  00:18:13,752 MicroScheduler - 3293 reads were filtered out during the traversal out of approximately 77600 total reads (4.24%)
[2015-09-30T23:18Z] INFO  00:18:13,752 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:18Z] INFO  00:18:13,752 MicroScheduler -   -> 3283 reads (4.23% of total) failing DuplicateReadFilter
[2015-09-30T23:18Z] INFO  00:18:13,752 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:18Z] INFO  00:18:13,753 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:18Z] INFO  00:18:13,753 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:18Z] INFO  00:18:13,753 MicroScheduler -   -> 10 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:18Z] tabix index syn3-5_94277739_125696417-raw.vcf.gz
[2015-09-30T23:18Z] GATK: VariantAnnotator
[2015-09-30T23:18Z] INFO  00:18:14,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:18Z] INFO  00:18:15,992 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:18Z] INFO  00:18:15,994 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:18Z] INFO  00:18:15,994 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:18Z] INFO  00:18:15,995 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:18Z] INFO  00:18:15,998 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/5/syn3-5_94277739_125696417-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/5/tx/tmp76IaaQ/syn3-5_94277739_125696417-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/5/syn3-5_94277739_125696417-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_94277739_125696417-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:18Z] INFO  00:18:16,004 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:18Z] INFO  00:18:16,004 HelpFormatter - Date/Time: 2015/10/01 00:18:15
[2015-09-30T23:18Z] INFO  00:18:16,004 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:18Z] INFO  00:18:16,004 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:18Z] INFO  00:18:16,098 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:18Z] INFO  00:18:16,179 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:18Z] INFO  00:18:16,187 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:18Z] INFO  00:18:16,210 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:18Z] INFO  00:18:16,615 IntervalUtils - Processing 940 bp from intervals
[2015-09-30T23:18Z] WARN  00:18:16,619 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:18Z] WARN  00:18:16,619 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:18Z] INFO  00:18:16,879 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:18Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:18Z] INFO  00:18:16,980 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:18Z] INFO  00:18:16,981 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:18Z] INFO  00:18:16,981 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:18Z] INFO  00:18:16,982 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:18Z] INFO  00:18:17,029 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:18Z] INFO  00:18:21,794 VariantAnnotator - Processed 805 loci.
[2015-09-30T23:18Z]
[2015-09-30T23:18Z] INFO  00:18:22,015 ProgressMeter -            done      3602.0     5.0 s      23.3 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:18Z] INFO  00:18:22,015 ProgressMeter - Total runtime 5.03 secs, 0.08 min, 0.00 hours
[2015-09-30T23:18Z] INFO  00:18:22,016 MicroScheduler - 2178 reads were filtered out during the traversal out of approximately 51331 total reads (4.24%)
[2015-09-30T23:18Z] INFO  00:18:22,016 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:18Z] INFO  00:18:22,016 MicroScheduler -   -> 2168 reads (4.22% of total) failing DuplicateReadFilter
[2015-09-30T23:18Z] INFO  00:18:22,016 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:18Z] INFO  00:18:22,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:18Z] INFO  00:18:22,017 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:18Z] INFO  00:18:22,017 MicroScheduler -   -> 10 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:18Z] INFO  00:18:22,953 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:18Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:19Z] WARNING(freebayes): Could not find any mapped reads in target region 5:177099323..177099380
[2015-09-30T23:19Z] tabix index syn3-5_156785743_180915260-raw.vcf.gz
[2015-09-30T23:19Z] GATK: VariantAnnotator
[2015-09-30T23:19Z] INFO  00:19:55,427 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:19Z] INFO  00:19:55,429 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:19Z] INFO  00:19:55,429 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:19Z] INFO  00:19:55,429 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:19Z] INFO  00:19:55,433 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/5/syn3-5_156785743_180915260-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/5/tx/tmpmZeJUW/syn3-5_156785743_180915260-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/5/syn3-5_156785743_180915260-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_156785743_180915260-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:19Z] INFO  00:19:55,699 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:19Z] INFO  00:19:55,699 HelpFormatter - Date/Time: 2015/10/01 00:19:55
[2015-09-30T23:19Z] INFO  00:19:55,699 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:19Z] INFO  00:19:55,700 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:19Z] INFO  00:19:56,187 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:19Z] INFO  00:19:56,398 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:19Z] INFO  00:19:56,405 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:19Z] INFO  00:19:56,696 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.29
[2015-09-30T23:19Z] INFO  00:19:57,642 IntervalUtils - Processing 1613 bp from intervals
[2015-09-30T23:19Z] WARN  00:19:57,646 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:19Z] WARN  00:19:57,646 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:19Z] INFO  00:19:57,704 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:19Z] INFO  00:19:57,818 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:19Z] INFO  00:19:57,819 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:19Z] INFO  00:19:57,819 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:19Z] INFO  00:19:57,819 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:19Z] INFO  00:19:57,858 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:20Z] tabix index syn3-6_0_31080572-raw.vcf.gz
[2015-09-30T23:20Z] GATK: VariantAnnotator
[2015-09-30T23:20Z] INFO  00:20:06,211 VariantAnnotator - Processed 1426 loci.
[2015-09-30T23:20Z]
[2015-09-30T23:20Z] INFO  00:20:06,234 ProgressMeter -            done      7718.0     8.0 s      18.2 m       99.8%     8.0 s       0.0 s
[2015-09-30T23:20Z] INFO  00:20:06,235 ProgressMeter - Total runtime 8.42 secs, 0.14 min, 0.00 hours
[2015-09-30T23:20Z] INFO  00:20:06,235 MicroScheduler - 6731 reads were filtered out during the traversal out of approximately 129067 total reads (5.22%)
[2015-09-30T23:20Z] INFO  00:20:06,235 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:20Z] INFO  00:20:06,235 MicroScheduler -   -> 6692 reads (5.18% of total) failing DuplicateReadFilter
[2015-09-30T23:20Z] INFO  00:20:06,236 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:20Z] INFO  00:20:06,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:20Z] INFO  00:20:06,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:20Z] INFO  00:20:06,236 MicroScheduler -   -> 39 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:20Z] INFO  00:20:07,300 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:20Z] INFO  00:20:07,804 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:20Z] INFO  00:20:07,806 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:20Z] INFO  00:20:07,806 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:20Z] INFO  00:20:07,806 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:20Z] INFO  00:20:07,810 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/6/syn3-6_0_31080572-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/6/tx/tmpQFmqTQ/syn3-6_0_31080572-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/6/syn3-6_0_31080572-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_0_31080572-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:20Z] INFO  00:20:07,815 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:20Z] INFO  00:20:07,815 HelpFormatter - Date/Time: 2015/10/01 00:20:07
[2015-09-30T23:20Z] INFO  00:20:07,816 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:20Z] INFO  00:20:07,816 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:20Z] INFO  00:20:07,907 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:20Z] INFO  00:20:07,981 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:20Z] INFO  00:20:07,989 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:20Z] INFO  00:20:08,011 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:20Z] INFO  00:20:08,663 IntervalUtils - Processing 2480 bp from intervals
[2015-09-30T23:20Z] WARN  00:20:08,668 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:20Z] WARN  00:20:08,668 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:20Z] INFO  00:20:08,725 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:20Z] INFO  00:20:08,830 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:20Z] INFO  00:20:08,830 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:20Z] INFO  00:20:08,831 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:20Z] INFO  00:20:08,831 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:20Z] INFO  00:20:08,869 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:20Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:20Z] INFO  00:20:20,903 VariantAnnotator - Processed 2271 loci.
[2015-09-30T23:20Z]
[2015-09-30T23:20Z] INFO  00:20:20,932 ProgressMeter -            done     41370.0    12.0 s       4.9 m      100.0%    12.0 s       0.0 s
[2015-09-30T23:20Z] INFO  00:20:20,932 ProgressMeter - Total runtime 12.10 secs, 0.20 min, 0.00 hours
[2015-09-30T23:20Z] INFO  00:20:20,932 MicroScheduler - 7806 reads were filtered out during the traversal out of approximately 160231 total reads (4.87%)
[2015-09-30T23:20Z] INFO  00:20:20,933 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:20Z] INFO  00:20:20,933 MicroScheduler -   -> 7751 reads (4.84% of total) failing DuplicateReadFilter
[2015-09-30T23:20Z] INFO  00:20:20,933 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:20Z] INFO  00:20:20,933 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:20Z] INFO  00:20:20,933 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:20Z] INFO  00:20:20,934 MicroScheduler -   -> 55 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:20Z] INFO  00:20:21,897 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:20Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:20Z] tabix index syn3-5_125759062_156781785-raw.vcf.gz
[2015-09-30T23:20Z] GATK: VariantAnnotator
[2015-09-30T23:20Z] INFO  00:20:30,601 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:20Z] INFO  00:20:30,603 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:20Z] INFO  00:20:30,604 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:20Z] INFO  00:20:30,604 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:20Z] INFO  00:20:30,607 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/5/syn3-5_125759062_156781785-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/5/tx/tmpCpgw8u/syn3-5_125759062_156781785-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/5/syn3-5_125759062_156781785-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/5/1_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/5/2_2014-08-13_dream-syn3-sort-5_125759062_156781785-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:20Z] INFO  00:20:30,613 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:20Z] INFO  00:20:30,614 HelpFormatter - Date/Time: 2015/10/01 00:20:30
[2015-09-30T23:20Z] INFO  00:20:30,614 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:20Z] INFO  00:20:30,614 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:20Z] INFO  00:20:30,696 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:20Z] INFO  00:20:30,844 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:20Z] INFO  00:20:30,852 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:20Z] INFO  00:20:31,017 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17
[2015-09-30T23:20Z] INFO  00:20:31,602 IntervalUtils - Processing 2210 bp from intervals
[2015-09-30T23:20Z] WARN  00:20:31,607 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:20Z] WARN  00:20:31,607 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:20Z] INFO  00:20:31,664 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:20Z] INFO  00:20:31,782 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:20Z] INFO  00:20:31,783 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:20Z] INFO  00:20:31,783 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:20Z] INFO  00:20:31,783 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:20Z] INFO  00:20:31,824 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:20Z] INFO  00:20:42,656 VariantAnnotator - Processed 1907 loci.
[2015-09-30T23:20Z]
[2015-09-30T23:20Z] INFO  00:20:42,844 ProgressMeter -            done     10405.0    11.0 s      17.7 m      100.0%    11.0 s       0.0 s
[2015-09-30T23:20Z] INFO  00:20:42,844 ProgressMeter - Total runtime 11.06 secs, 0.18 min, 0.00 hours
[2015-09-30T23:20Z] INFO  00:20:42,844 MicroScheduler - 7915 reads were filtered out during the traversal out of approximately 163804 total reads (4.83%)
[2015-09-30T23:20Z] INFO  00:20:42,845 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:20Z] INFO  00:20:42,845 MicroScheduler -   -> 7882 reads (4.81% of total) failing DuplicateReadFilter
[2015-09-30T23:20Z] INFO  00:20:42,845 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:20Z] INFO  00:20:42,845 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:20Z] INFO  00:20:42,846 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:20Z] INFO  00:20:42,846 MicroScheduler -   -> 33 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:20Z] INFO  00:20:43,738 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:20Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:21Z] WARNING(freebayes): Could not find any mapped reads in target region 6:34205292..34205326
[2015-09-30T23:21Z] tabix index syn3-6_62389878_93953543-raw.vcf.gz
[2015-09-30T23:21Z] GATK: VariantAnnotator
[2015-09-30T23:21Z] INFO  00:21:19,418 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:21Z] INFO  00:21:19,420 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:21Z] INFO  00:21:19,420 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:21Z] INFO  00:21:19,420 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:21Z] INFO  00:21:19,424 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/6/syn3-6_62389878_93953543-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/6/tx/tmpdpj5g1/syn3-6_62389878_93953543-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/6/syn3-6_62389878_93953543-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_62389878_93953543-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:21Z] INFO  00:21:19,429 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:21Z] INFO  00:21:19,430 HelpFormatter - Date/Time: 2015/10/01 00:21:19
[2015-09-30T23:21Z] INFO  00:21:19,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:21Z] INFO  00:21:19,430 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:21Z] INFO  00:21:19,502 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:21Z] INFO  00:21:19,603 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:21Z] INFO  00:21:19,611 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:21Z] INFO  00:21:19,632 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:21Z] INFO  00:21:20,067 IntervalUtils - Processing 1016 bp from intervals
[2015-09-30T23:21Z] WARN  00:21:20,071 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:21Z] WARN  00:21:20,072 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:21Z] INFO  00:21:20,127 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:21Z] INFO  00:21:20,218 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:21Z] INFO  00:21:20,219 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:21Z] INFO  00:21:20,219 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:21Z] INFO  00:21:20,220 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:21Z] INFO  00:21:20,260 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:21Z] INFO  00:21:25,171 VariantAnnotator - Processed 891 loci.
[2015-09-30T23:21Z]
[2015-09-30T23:21Z] INFO  00:21:25,216 ProgressMeter -            done      3256.0     4.0 s      25.6 m       99.9%     4.0 s       0.0 s
[2015-09-30T23:21Z] INFO  00:21:25,217 ProgressMeter - Total runtime 5.00 secs, 0.08 min, 0.00 hours
[2015-09-30T23:21Z] INFO  00:21:25,217 MicroScheduler - 2406 reads were filtered out during the traversal out of approximately 57695 total reads (4.17%)
[2015-09-30T23:21Z] INFO  00:21:25,217 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:21Z] INFO  00:21:25,217 MicroScheduler -   -> 2396 reads (4.15% of total) failing DuplicateReadFilter
[2015-09-30T23:21Z] INFO  00:21:25,218 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:21Z] INFO  00:21:25,218 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:21Z] INFO  00:21:25,218 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:21Z] INFO  00:21:25,218 MicroScheduler -   -> 10 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:21Z] INFO  00:21:26,136 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:21Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:21Z] tabix index syn3-6_93954776_124979769-raw.vcf.gz
[2015-09-30T23:21Z] GATK: VariantAnnotator
[2015-09-30T23:21Z] INFO  00:21:45,065 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:21Z] INFO  00:21:45,067 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:21Z] INFO  00:21:45,067 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:21Z] INFO  00:21:45,067 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:21Z] INFO  00:21:45,070 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/6/syn3-6_93954776_124979769-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/6/tx/tmpREj2lB/syn3-6_93954776_124979769-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/6/syn3-6_93954776_124979769-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_93954776_124979769-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:21Z] INFO  00:21:45,076 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:21Z] INFO  00:21:45,076 HelpFormatter - Date/Time: 2015/10/01 00:21:45
[2015-09-30T23:21Z] INFO  00:21:45,076 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:21Z] INFO  00:21:45,076 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:21Z] INFO  00:21:45,250 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:21Z] INFO  00:21:45,322 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:21Z] INFO  00:21:45,330 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:21Z] INFO  00:21:45,350 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:21Z] INFO  00:21:45,793 IntervalUtils - Processing 1192 bp from intervals
[2015-09-30T23:21Z] WARN  00:21:45,797 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:21Z] WARN  00:21:45,797 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:21Z] INFO  00:21:45,850 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:21Z] INFO  00:21:45,954 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:21Z] INFO  00:21:45,954 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:21Z] INFO  00:21:45,955 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:21Z] INFO  00:21:45,955 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:21Z] INFO  00:21:45,993 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:21Z] INFO  00:21:51,168 VariantAnnotator - Processed 1061 loci.
[2015-09-30T23:21Z]
[2015-09-30T23:21Z] INFO  00:21:51,188 ProgressMeter -            done      4304.0     5.0 s      20.3 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:21Z] INFO  00:21:51,188 ProgressMeter - Total runtime 5.23 secs, 0.09 min, 0.00 hours
[2015-09-30T23:21Z] INFO  00:21:51,189 MicroScheduler - 2974 reads were filtered out during the traversal out of approximately 68242 total reads (4.36%)
[2015-09-30T23:21Z] INFO  00:21:51,189 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:21Z] INFO  00:21:51,189 MicroScheduler -   -> 2969 reads (4.35% of total) failing DuplicateReadFilter
[2015-09-30T23:21Z] INFO  00:21:51,189 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:21Z] INFO  00:21:51,190 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:21Z] INFO  00:21:51,190 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:21Z] INFO  00:21:51,190 MicroScheduler -   -> 5 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:21Z] INFO  00:21:52,131 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:21Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:21Z] WARNING(freebayes): Could not find any mapped reads in target region 6:157098873..157098933
[2015-09-30T23:22Z] WARNING(freebayes): Could not find any mapped reads in target region 6:163835534..163835583
[2015-09-30T23:22Z] tabix index syn3-6_125064552_156268261-raw.vcf.gz
[2015-09-30T23:22Z] GATK: VariantAnnotator
[2015-09-30T23:22Z] tabix index syn3-6_156275378_171115067-raw.vcf.gz
[2015-09-30T23:22Z] GATK: VariantAnnotator
[2015-09-30T23:22Z] INFO  00:22:46,966 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:22Z] INFO  00:22:46,968 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:22Z] INFO  00:22:46,968 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:22Z] INFO  00:22:46,968 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:22Z] INFO  00:22:46,972 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/6/syn3-6_125064552_156268261-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/6/tx/tmphj_bPk/syn3-6_125064552_156268261-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/6/syn3-6_125064552_156268261-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_125064552_156268261-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:22Z] INFO  00:22:46,978 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:22Z] INFO  00:22:46,979 HelpFormatter - Date/Time: 2015/10/01 00:22:46
[2015-09-30T23:22Z] INFO  00:22:46,979 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:22Z] INFO  00:22:46,979 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:22Z] INFO  00:22:47,072 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:22Z] INFO  00:22:47,253 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:22Z] INFO  00:22:47,261 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:22Z] INFO  00:22:47,284 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:22Z] INFO  00:22:47,785 IntervalUtils - Processing 1408 bp from intervals
[2015-09-30T23:22Z] WARN  00:22:47,789 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:22Z] WARN  00:22:47,790 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:22Z] INFO  00:22:47,847 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:22Z] INFO  00:22:47,956 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:22Z] INFO  00:22:47,956 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:22Z] INFO  00:22:47,957 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:22Z] INFO  00:22:47,957 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:22Z] INFO  00:22:48,001 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:22Z] INFO  00:22:48,371 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:22Z] INFO  00:22:48,373 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:22Z] INFO  00:22:48,373 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:22Z] INFO  00:22:48,373 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:22Z] INFO  00:22:48,377 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/6/syn3-6_156275378_171115067-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/6/tx/tmpIIeJBY/syn3-6_156275378_171115067-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/6/syn3-6_156275378_171115067-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_156275378_171115067-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:22Z] INFO  00:22:48,382 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:22Z] INFO  00:22:48,382 HelpFormatter - Date/Time: 2015/10/01 00:22:48
[2015-09-30T23:22Z] INFO  00:22:48,383 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:22Z] INFO  00:22:48,383 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:22Z] INFO  00:22:48,475 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:22Z] INFO  00:22:48,552 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:22Z] INFO  00:22:48,560 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:22Z] INFO  00:22:48,582 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:22Z] INFO  00:22:49,032 IntervalUtils - Processing 1088 bp from intervals
[2015-09-30T23:22Z] WARN  00:22:49,036 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:22Z] WARN  00:22:49,036 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:22Z] INFO  00:22:49,093 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:22Z] INFO  00:22:49,183 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:22Z] INFO  00:22:49,184 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:22Z] INFO  00:22:49,184 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:22Z] INFO  00:22:49,185 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:22Z] INFO  00:22:49,225 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:22Z] INFO  00:22:55,162 VariantAnnotator - Processed 889 loci.
[2015-09-30T23:22Z]
[2015-09-30T23:22Z] INFO  00:22:55,194 ProgressMeter -            done      4910.0     6.0 s      20.4 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:22Z] INFO  00:22:55,194 ProgressMeter - Total runtime 6.01 secs, 0.10 min, 0.00 hours
[2015-09-30T23:22Z] INFO  00:22:55,194 MicroScheduler - 4093 reads were filtered out during the traversal out of approximately 74824 total reads (5.47%)
[2015-09-30T23:22Z] INFO  00:22:55,195 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:22Z] INFO  00:22:55,195 MicroScheduler -   -> 4062 reads (5.43% of total) failing DuplicateReadFilter
[2015-09-30T23:22Z] INFO  00:22:55,195 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:22Z] INFO  00:22:55,195 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:22Z] INFO  00:22:55,195 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:22Z] INFO  00:22:55,196 MicroScheduler -   -> 31 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T23:22Z] INFO  00:22:55,414 VariantAnnotator - Processed 1240 loci.
[2015-09-30T23:22Z]
[2015-09-30T23:22Z] INFO  00:22:55,449 ProgressMeter -            done      4336.0     7.0 s      28.8 m       99.9%     7.0 s       0.0 s
[2015-09-30T23:22Z] INFO  00:22:55,450 ProgressMeter - Total runtime 7.49 secs, 0.12 min, 0.00 hours
[2015-09-30T23:22Z] INFO  00:22:55,450 MicroScheduler - 3652 reads were filtered out during the traversal out of approximately 85306 total reads (4.28%)
[2015-09-30T23:22Z] INFO  00:22:55,450 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:22Z] INFO  00:22:55,450 MicroScheduler -   -> 3640 reads (4.27% of total) failing DuplicateReadFilter
[2015-09-30T23:22Z] INFO  00:22:55,451 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:22Z] INFO  00:22:55,451 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:22Z] INFO  00:22:55,451 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:22Z] INFO  00:22:55,451 MicroScheduler -   -> 12 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:22Z] INFO  00:22:56,115 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:22Z] INFO  00:22:56,373 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:22Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:22Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:23Z] WARNING(freebayes): Could not find any mapped reads in target region 7:559441..559511
[2015-09-30T23:23Z] tabix index syn3-6_31082315_62284583-raw.vcf.gz
[2015-09-30T23:23Z] GATK: VariantAnnotator
[2015-09-30T23:23Z] INFO  00:23:30,937 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:23Z] INFO  00:23:30,939 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:23Z] INFO  00:23:30,939 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:23Z] INFO  00:23:30,939 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:23Z] INFO  00:23:30,943 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/6/syn3-6_31082315_62284583-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/6/tx/tmpw1cZr7/syn3-6_31082315_62284583-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/6/syn3-6_31082315_62284583-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/6/1_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/6/2_2014-08-13_dream-syn3-sort-6_31082315_62284583-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:23Z] INFO  00:23:30,948 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:23Z] INFO  00:23:30,949 HelpFormatter - Date/Time: 2015/10/01 00:23:30
[2015-09-30T23:23Z] INFO  00:23:30,949 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:23Z] INFO  00:23:30,949 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:23Z] INFO  00:23:31,046 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:23Z] INFO  00:23:31,123 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:23Z] INFO  00:23:31,130 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:23Z] INFO  00:23:31,152 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:23Z] INFO  00:23:31,888 IntervalUtils - Processing 5030 bp from intervals
[2015-09-30T23:23Z] WARN  00:23:31,892 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:23Z] WARN  00:23:31,893 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:23Z] INFO  00:23:31,949 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:23Z] INFO  00:23:32,079 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:23Z] INFO  00:23:32,079 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:23Z] INFO  00:23:32,080 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:23Z] INFO  00:23:32,080 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:23Z] INFO  00:23:32,119 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:23Z] WARNING(freebayes): Could not find any mapped reads in target region 7:45614099..45614143
[2015-09-30T23:23Z] INFO  00:23:54,680 VariantAnnotator - Processed 4581 loci.
[2015-09-30T23:23Z]
[2015-09-30T23:23Z] INFO  00:23:54,702 ProgressMeter -            done    188032.0    22.0 s     120.0 s      100.0%    22.0 s       0.0 s
[2015-09-30T23:23Z] INFO  00:23:54,702 ProgressMeter - Total runtime 22.62 secs, 0.38 min, 0.01 hours
[2015-09-30T23:23Z] INFO  00:23:54,703 MicroScheduler - 13770 reads were filtered out during the traversal out of approximately 277959 total reads (4.95%)
[2015-09-30T23:23Z] INFO  00:23:54,703 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:23Z] INFO  00:23:54,703 MicroScheduler -   -> 13674 reads (4.92% of total) failing DuplicateReadFilter
[2015-09-30T23:23Z] INFO  00:23:54,703 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:23Z] INFO  00:23:54,704 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:23Z] INFO  00:23:54,704 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:23Z] INFO  00:23:54,704 MicroScheduler -   -> 96 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:23Z] INFO  00:23:55,658 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:23Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:24Z] tabix index syn3-7_31022897_62585293-raw.vcf.gz
[2015-09-30T23:24Z] GATK: VariantAnnotator
[2015-09-30T23:24Z] INFO  00:24:21,723 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:24Z] INFO  00:24:21,725 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:24Z] INFO  00:24:21,725 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:24Z] INFO  00:24:21,725 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:24Z] INFO  00:24:21,729 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/7/syn3-7_31022897_62585293-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/7/tx/tmpsQ1OWb/syn3-7_31022897_62585293-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/7/syn3-7_31022897_62585293-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_31022897_62585293-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:24Z] INFO  00:24:21,734 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:24Z] INFO  00:24:21,734 HelpFormatter - Date/Time: 2015/10/01 00:24:21
[2015-09-30T23:24Z] INFO  00:24:21,735 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:24Z] INFO  00:24:21,735 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:24Z] INFO  00:24:21,844 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:24Z] INFO  00:24:22,061 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:24Z] INFO  00:24:22,069 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:24Z] INFO  00:24:22,187 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2015-09-30T23:24Z] INFO  00:24:22,768 IntervalUtils - Processing 1684 bp from intervals
[2015-09-30T23:24Z] WARN  00:24:22,772 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:24Z] WARN  00:24:22,772 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:24Z] INFO  00:24:22,832 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:24Z] INFO  00:24:24,712 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:24Z] INFO  00:24:24,713 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:24Z] INFO  00:24:24,713 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:24Z] INFO  00:24:24,713 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:24Z] INFO  00:24:24,752 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:24Z] INFO  00:24:33,739 VariantAnnotator - Processed 1558 loci.
[2015-09-30T23:24Z]
[2015-09-30T23:24Z] INFO  00:24:33,772 ProgressMeter -            done      9365.0     9.0 s      16.1 m       99.9%     9.0 s       0.0 s
[2015-09-30T23:24Z] INFO  00:24:33,773 ProgressMeter - Total runtime 9.06 secs, 0.15 min, 0.00 hours
[2015-09-30T23:24Z] INFO  00:24:33,773 MicroScheduler - 6218 reads were filtered out during the traversal out of approximately 124785 total reads (4.98%)
[2015-09-30T23:24Z] INFO  00:24:33,773 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:24Z] INFO  00:24:33,773 MicroScheduler -   -> 6186 reads (4.96% of total) failing DuplicateReadFilter
[2015-09-30T23:24Z] INFO  00:24:33,774 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:24Z] INFO  00:24:33,774 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:24Z] INFO  00:24:33,774 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:24Z] INFO  00:24:33,774 MicroScheduler -   -> 32 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:24Z] INFO  00:24:34,697 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:24Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:24Z] tabix index syn3-7_0_31019109-raw.vcf.gz
[2015-09-30T23:24Z] GATK: VariantAnnotator
[2015-09-30T23:24Z] INFO  00:24:49,869 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:24Z] INFO  00:24:49,871 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:24Z] INFO  00:24:49,871 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:24Z] INFO  00:24:49,871 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:24Z] INFO  00:24:49,874 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/7/syn3-7_0_31019109-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/7/tx/tmp5wWhqY/syn3-7_0_31019109-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/7/syn3-7_0_31019109-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_0_31019109-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:24Z] INFO  00:24:49,880 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:24Z] INFO  00:24:49,880 HelpFormatter - Date/Time: 2015/10/01 00:24:49
[2015-09-30T23:24Z] INFO  00:24:49,880 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:24Z] INFO  00:24:49,880 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:24Z] INFO  00:24:49,976 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:24Z] INFO  00:24:50,051 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:24Z] INFO  00:24:50,058 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:24Z] INFO  00:24:50,080 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:24Z] INFO  00:24:50,692 IntervalUtils - Processing 2422 bp from intervals
[2015-09-30T23:24Z] WARN  00:24:50,696 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:24Z] WARN  00:24:50,697 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:24Z] INFO  00:24:50,751 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:24Z] INFO  00:24:50,861 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:24Z] INFO  00:24:50,861 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:24Z] INFO  00:24:50,862 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:24Z] INFO  00:24:50,862 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:24Z] INFO  00:24:50,900 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:25Z] INFO  00:25:01,020 VariantAnnotator - Processed 2056 loci.
[2015-09-30T23:25Z]
[2015-09-30T23:25Z] INFO  00:25:01,039 ProgressMeter -            done     12030.0    10.0 s      14.1 m      100.0%    10.0 s       0.0 s
[2015-09-30T23:25Z] INFO  00:25:01,039 ProgressMeter - Total runtime 10.18 secs, 0.17 min, 0.00 hours
[2015-09-30T23:25Z] INFO  00:25:01,040 MicroScheduler - 8422 reads were filtered out during the traversal out of approximately 168608 total reads (5.00%)
[2015-09-30T23:25Z] INFO  00:25:01,040 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:25Z] INFO  00:25:01,040 MicroScheduler -   -> 8386 reads (4.97% of total) failing DuplicateReadFilter
[2015-09-30T23:25Z] INFO  00:25:01,040 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:25Z] INFO  00:25:01,041 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:25Z] INFO  00:25:01,041 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:25Z] INFO  00:25:01,041 MicroScheduler -   -> 36 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:25Z] INFO  00:25:01,960 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:25Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:25Z] tabix index syn3-7_62708318_93925745-raw.vcf.gz
[2015-09-30T23:25Z] GATK: VariantAnnotator
[2015-09-30T23:25Z] INFO  00:25:34,421 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:25Z] INFO  00:25:34,423 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:25Z] INFO  00:25:34,423 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:25Z] INFO  00:25:34,423 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:25Z] INFO  00:25:34,427 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/7/syn3-7_62708318_93925745-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/7/tx/tmpCzsOpw/syn3-7_62708318_93925745-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/7/syn3-7_62708318_93925745-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_62708318_93925745-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:25Z] INFO  00:25:34,432 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:25Z] INFO  00:25:34,432 HelpFormatter - Date/Time: 2015/10/01 00:25:34
[2015-09-30T23:25Z] INFO  00:25:34,432 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:25Z] INFO  00:25:34,433 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:25Z] INFO  00:25:34,672 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:25Z] INFO  00:25:34,747 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:25Z] INFO  00:25:34,754 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:25Z] INFO  00:25:34,776 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:25Z] INFO  00:25:35,312 IntervalUtils - Processing 1643 bp from intervals
[2015-09-30T23:25Z] WARN  00:25:35,316 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:25Z] WARN  00:25:35,316 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:25Z] INFO  00:25:35,374 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:25Z] INFO  00:25:35,480 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:25Z] INFO  00:25:35,480 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:25Z] INFO  00:25:35,481 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:25Z] INFO  00:25:35,481 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:25Z] INFO  00:25:35,519 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:25Z] INFO  00:25:43,209 VariantAnnotator - Processed 1472 loci.
[2015-09-30T23:25Z]
[2015-09-30T23:25Z] INFO  00:25:43,239 ProgressMeter -            done      7348.0     7.0 s      17.6 m       99.9%     7.0 s       0.0 s
[2015-09-30T23:25Z] INFO  00:25:43,239 ProgressMeter - Total runtime 7.76 secs, 0.13 min, 0.00 hours
[2015-09-30T23:25Z] INFO  00:25:43,239 MicroScheduler - 5294 reads were filtered out during the traversal out of approximately 113862 total reads (4.65%)
[2015-09-30T23:25Z] INFO  00:25:43,239 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:25Z] INFO  00:25:43,240 MicroScheduler -   -> 5273 reads (4.63% of total) failing DuplicateReadFilter
[2015-09-30T23:25Z] INFO  00:25:43,240 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:25Z] INFO  00:25:43,240 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:25Z] INFO  00:25:43,240 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:25Z] INFO  00:25:43,241 MicroScheduler -   -> 21 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:25Z] INFO  00:25:44,182 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:25Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:25Z] WARNING(freebayes): Could not find any mapped reads in target region 7:158380567..158380608
[2015-09-30T23:25Z] tabix index syn3-7_157155595_159138663-raw.vcf.gz
[2015-09-30T23:25Z] GATK: VariantAnnotator
[2015-09-30T23:25Z] INFO  00:25:59,694 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:25Z] INFO  00:25:59,697 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:25Z] INFO  00:25:59,697 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:25Z] INFO  00:25:59,697 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:25Z] INFO  00:25:59,700 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/7/syn3-7_157155595_159138663-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/7/tx/tmpK3m0cZ/syn3-7_157155595_159138663-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/7/syn3-7_157155595_159138663-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_157155595_159138663-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:25Z] INFO  00:25:59,705 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:25Z] INFO  00:25:59,706 HelpFormatter - Date/Time: 2015/10/01 00:25:59
[2015-09-30T23:25Z] INFO  00:25:59,706 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:25Z] INFO  00:25:59,706 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:26Z] INFO  00:26:00,022 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:26Z] INFO  00:26:00,099 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:26Z] INFO  00:26:00,107 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:26Z] INFO  00:26:00,129 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:26Z] INFO  00:26:00,433 IntervalUtils - Processing 271 bp from intervals
[2015-09-30T23:26Z] WARN  00:26:00,437 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:26Z] WARN  00:26:00,437 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:26Z] INFO  00:26:00,494 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:26Z] INFO  00:26:00,545 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:26Z] INFO  00:26:00,546 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:26Z] INFO  00:26:00,546 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:26Z] INFO  00:26:00,546 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:26Z] INFO  00:26:00,652 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:26Z] INFO  00:26:02,952 VariantAnnotator - Processed 244 loci.
[2015-09-30T23:26Z]
[2015-09-30T23:26Z] INFO  00:26:02,973 ProgressMeter -            done      1491.0     2.0 s      27.1 m       99.6%     2.0 s       0.0 s
[2015-09-30T23:26Z] INFO  00:26:02,973 ProgressMeter - Total runtime 2.43 secs, 0.04 min, 0.00 hours
[2015-09-30T23:26Z] INFO  00:26:02,974 MicroScheduler - 974 reads were filtered out during the traversal out of approximately 18747 total reads (5.20%)
[2015-09-30T23:26Z] INFO  00:26:02,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:26Z] INFO  00:26:02,974 MicroScheduler -   -> 969 reads (5.17% of total) failing DuplicateReadFilter
[2015-09-30T23:26Z] INFO  00:26:02,974 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:26Z] INFO  00:26:02,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:26Z] INFO  00:26:02,975 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:26Z] INFO  00:26:02,975 MicroScheduler -   -> 5 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:26Z] INFO  00:26:03,913 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:26Z] WARNING(freebayes): Could not find any mapped reads in target region 7:139477695..139477705
[2015-09-30T23:26Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:27Z] tabix index syn3-7_94024041_125680568-raw.vcf.gz
[2015-09-30T23:27Z] GATK: VariantAnnotator
[2015-09-30T23:27Z] INFO  00:27:19,724 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:27Z] INFO  00:27:19,726 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:27Z] INFO  00:27:19,726 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:27Z] INFO  00:27:19,727 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:27Z] INFO  00:27:19,730 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/7/syn3-7_94024041_125680568-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/7/tx/tmpPobEIW/syn3-7_94024041_125680568-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/7/syn3-7_94024041_125680568-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_94024041_125680568-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:27Z] INFO  00:27:19,736 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:27Z] INFO  00:27:19,736 HelpFormatter - Date/Time: 2015/10/01 00:27:19
[2015-09-30T23:27Z] INFO  00:27:19,737 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:27Z] INFO  00:27:19,737 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:27Z] INFO  00:27:19,829 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:27Z] INFO  00:27:19,905 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:27Z] INFO  00:27:19,912 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:27Z] INFO  00:27:19,934 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:27Z] INFO  00:27:20,578 IntervalUtils - Processing 2436 bp from intervals
[2015-09-30T23:27Z] WARN  00:27:20,583 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:27Z] WARN  00:27:20,583 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:27Z] INFO  00:27:20,638 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:27Z] INFO  00:27:20,760 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:27Z] INFO  00:27:20,761 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:27Z] INFO  00:27:20,761 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:27Z] INFO  00:27:20,762 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:27Z] INFO  00:27:20,800 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:27Z] WARNING(freebayes): Could not find any mapped reads in target region 7:154794719..154794783
[2015-09-30T23:27Z] INFO  00:27:32,137 VariantAnnotator - Processed 2159 loci.
[2015-09-30T23:27Z]
[2015-09-30T23:27Z] INFO  00:27:32,159 ProgressMeter -            done     58004.0    11.0 s       3.3 m      100.0%    11.0 s       0.0 s
[2015-09-30T23:27Z] INFO  00:27:32,159 ProgressMeter - Total runtime 11.40 secs, 0.19 min, 0.00 hours
[2015-09-30T23:27Z] INFO  00:27:32,160 MicroScheduler - 15556 reads were filtered out during the traversal out of approximately 191890 total reads (8.11%)
[2015-09-30T23:27Z] INFO  00:27:32,160 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:27Z] INFO  00:27:32,160 MicroScheduler -   -> 15207 reads (7.92% of total) failing DuplicateReadFilter
[2015-09-30T23:27Z] INFO  00:27:32,160 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:27Z] INFO  00:27:32,161 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:27Z] INFO  00:27:32,161 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:27Z] INFO  00:27:32,161 MicroScheduler -   -> 349 reads (0.18% of total) failing UnmappedReadFilter
[2015-09-30T23:27Z] INFO  00:27:33,155 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:27Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:27Z] WARNING(freebayes): Could not find any mapped reads in target region 7:156802678..156802704
[2015-09-30T23:27Z] tabix index syn3-7_126078434_157151579-raw.vcf.gz
[2015-09-30T23:27Z] GATK: VariantAnnotator
[2015-09-30T23:27Z] INFO  00:27:40,219 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:27Z] INFO  00:27:40,221 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:27Z] INFO  00:27:40,221 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:27Z] INFO  00:27:40,221 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:27Z] INFO  00:27:40,224 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/7/syn3-7_126078434_157151579-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/7/tx/tmpF7ltfu/syn3-7_126078434_157151579-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/7/syn3-7_126078434_157151579-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/7/1_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/7/2_2014-08-13_dream-syn3-sort-7_126078434_157151579-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:27Z] INFO  00:27:40,230 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:27Z] INFO  00:27:40,231 HelpFormatter - Date/Time: 2015/10/01 00:27:40
[2015-09-30T23:27Z] INFO  00:27:40,231 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:27Z] INFO  00:27:40,231 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:27Z] INFO  00:27:40,328 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:27Z] INFO  00:27:40,404 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:27Z] INFO  00:27:40,411 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:27Z] INFO  00:27:40,434 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:27Z] INFO  00:27:41,083 IntervalUtils - Processing 3081 bp from intervals
[2015-09-30T23:27Z] WARN  00:27:41,088 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:27Z] WARN  00:27:41,088 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:27Z] INFO  00:27:41,145 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:27Z] INFO  00:27:41,279 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:27Z] INFO  00:27:41,280 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:27Z] INFO  00:27:41,280 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:27Z] INFO  00:27:41,281 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:27Z] INFO  00:27:41,323 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:27Z] tabix index syn3-8_0_31024990-raw.vcf.gz
[2015-09-30T23:27Z] GATK: VariantAnnotator
[2015-09-30T23:27Z] INFO  00:27:53,897 VariantAnnotator - Processed 2715 loci.
[2015-09-30T23:27Z]
[2015-09-30T23:27Z] INFO  00:27:53,921 ProgressMeter -            done     34745.0    12.0 s       6.1 m      100.0%    12.0 s       0.0 s
[2015-09-30T23:27Z] INFO  00:27:53,922 ProgressMeter - Total runtime 12.64 secs, 0.21 min, 0.00 hours
[2015-09-30T23:27Z] INFO  00:27:53,922 MicroScheduler - 10990 reads were filtered out during the traversal out of approximately 207074 total reads (5.31%)
[2015-09-30T23:27Z] INFO  00:27:53,922 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:27Z] INFO  00:27:53,922 MicroScheduler -   -> 10917 reads (5.27% of total) failing DuplicateReadFilter
[2015-09-30T23:27Z] INFO  00:27:53,923 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:27Z] INFO  00:27:53,923 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:27Z] INFO  00:27:53,923 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:27Z] INFO  00:27:53,923 MicroScheduler -   -> 73 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T23:27Z] INFO  00:27:54,970 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:27Z] INFO  00:27:55,066 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:27Z] INFO  00:27:55,068 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:27Z] INFO  00:27:55,068 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:27Z] INFO  00:27:55,069 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:27Z] INFO  00:27:55,072 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/8/syn3-8_0_31024990-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/8/tx/tmprpYY5V/syn3-8_0_31024990-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/8/syn3-8_0_31024990-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_0_31024990-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:27Z] INFO  00:27:55,078 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:27Z] INFO  00:27:55,078 HelpFormatter - Date/Time: 2015/10/01 00:27:55
[2015-09-30T23:27Z] INFO  00:27:55,078 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:27Z] INFO  00:27:55,078 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:27Z] INFO  00:27:55,152 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:27Z] INFO  00:27:55,239 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:27Z] INFO  00:27:55,247 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:27Z] INFO  00:27:55,269 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:27Z] INFO  00:27:55,909 IntervalUtils - Processing 3032 bp from intervals
[2015-09-30T23:27Z] WARN  00:27:55,914 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:27Z] WARN  00:27:55,914 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:27Z] INFO  00:27:55,971 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:27Z] INFO  00:27:56,096 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:27Z] INFO  00:27:56,097 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:27Z] INFO  00:27:56,097 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:27Z] INFO  00:27:56,097 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:27Z] INFO  00:27:56,137 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:27Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:28Z] INFO  00:28:07,841 VariantAnnotator - Processed 2681 loci.
[2015-09-30T23:28Z]
[2015-09-30T23:28Z] INFO  00:28:07,862 ProgressMeter -            done     23348.0    11.0 s       8.4 m      100.0%    11.0 s       0.0 s
[2015-09-30T23:28Z] INFO  00:28:07,862 ProgressMeter - Total runtime 11.77 secs, 0.20 min, 0.00 hours
[2015-09-30T23:28Z] INFO  00:28:07,863 MicroScheduler - 9864 reads were filtered out during the traversal out of approximately 205519 total reads (4.80%)
[2015-09-30T23:28Z] INFO  00:28:07,863 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:28Z] INFO  00:28:07,863 MicroScheduler -   -> 9814 reads (4.78% of total) failing DuplicateReadFilter
[2015-09-30T23:28Z] INFO  00:28:07,863 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:28Z] INFO  00:28:07,864 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:28Z] INFO  00:28:07,864 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:28Z] INFO  00:28:07,864 MicroScheduler -   -> 50 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:28Z] INFO  00:28:08,795 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:28Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:28Z] tabix index syn3-8_31030285_62213090-raw.vcf.gz
[2015-09-30T23:28Z] GATK: VariantAnnotator
[2015-09-30T23:28Z] INFO  00:28:37,409 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:28Z] INFO  00:28:37,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:28Z] INFO  00:28:37,411 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:28Z] INFO  00:28:37,412 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:28Z] INFO  00:28:37,415 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/8/syn3-8_31030285_62213090-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/8/tx/tmpYHk_Xn/syn3-8_31030285_62213090-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/8/syn3-8_31030285_62213090-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_31030285_62213090-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:28Z] INFO  00:28:37,421 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:28Z] INFO  00:28:37,421 HelpFormatter - Date/Time: 2015/10/01 00:28:37
[2015-09-30T23:28Z] INFO  00:28:37,422 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:28Z] INFO  00:28:37,422 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:28Z] INFO  00:28:37,514 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:28Z] INFO  00:28:37,588 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:28Z] INFO  00:28:37,596 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:28Z] INFO  00:28:37,619 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:28Z] INFO  00:28:38,007 IntervalUtils - Processing 837 bp from intervals
[2015-09-30T23:28Z] WARN  00:28:38,012 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:28Z] WARN  00:28:38,012 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:28Z] INFO  00:28:38,069 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:28Z] INFO  00:28:38,392 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:28Z] INFO  00:28:38,393 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:28Z] INFO  00:28:38,393 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:28Z] INFO  00:28:38,393 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:28Z] INFO  00:28:38,433 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:28Z] INFO  00:28:42,951 VariantAnnotator - Processed 670 loci.
[2015-09-30T23:28Z]
[2015-09-30T23:28Z] INFO  00:28:43,020 ProgressMeter -            done      2507.0     4.0 s      30.8 m       99.9%     4.0 s       0.0 s
[2015-09-30T23:28Z] INFO  00:28:43,021 ProgressMeter - Total runtime 4.63 secs, 0.08 min, 0.00 hours
[2015-09-30T23:28Z] INFO  00:28:43,021 MicroScheduler - 2208 reads were filtered out during the traversal out of approximately 47955 total reads (4.60%)
[2015-09-30T23:28Z] INFO  00:28:43,021 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:28Z] INFO  00:28:43,022 MicroScheduler -   -> 2196 reads (4.58% of total) failing DuplicateReadFilter
[2015-09-30T23:28Z] INFO  00:28:43,022 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:28Z] INFO  00:28:43,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:28Z] INFO  00:28:43,022 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:28Z] INFO  00:28:43,022 MicroScheduler -   -> 12 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:28Z] INFO  00:28:43,968 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:28Z] tabix index syn3-8_62288979_93648031-raw.vcf.gz
[2015-09-30T23:28Z] GATK: VariantAnnotator
[2015-09-30T23:28Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:28Z] INFO  00:28:47,048 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:28Z] INFO  00:28:47,050 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:28Z] INFO  00:28:47,051 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:28Z] INFO  00:28:47,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:28Z] INFO  00:28:47,054 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/8/syn3-8_62288979_93648031-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/8/tx/tmp_S7vbF/syn3-8_62288979_93648031-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/8/syn3-8_62288979_93648031-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_62288979_93648031-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:28Z] INFO  00:28:47,060 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:28Z] INFO  00:28:47,060 HelpFormatter - Date/Time: 2015/10/01 00:28:47
[2015-09-30T23:28Z] INFO  00:28:47,061 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:28Z] INFO  00:28:47,061 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:28Z] INFO  00:28:47,157 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:28Z] INFO  00:28:47,248 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:28Z] INFO  00:28:47,257 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:28Z] INFO  00:28:47,281 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:28Z] INFO  00:28:47,640 IntervalUtils - Processing 932 bp from intervals
[2015-09-30T23:28Z] WARN  00:28:47,644 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:28Z] WARN  00:28:47,645 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:28Z] INFO  00:28:47,760 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:28Z] INFO  00:28:47,849 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:28Z] INFO  00:28:47,849 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:28Z] INFO  00:28:47,849 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:28Z] INFO  00:28:47,850 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:28Z] INFO  00:28:47,891 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:28Z] INFO  00:28:52,436 VariantAnnotator - Processed 763 loci.
[2015-09-30T23:28Z]
[2015-09-30T23:28Z] INFO  00:28:52,467 ProgressMeter -            done      2957.0     4.0 s      26.0 m       99.9%     4.0 s       0.0 s
[2015-09-30T23:28Z] INFO  00:28:52,467 ProgressMeter - Total runtime 4.62 secs, 0.08 min, 0.00 hours
[2015-09-30T23:28Z] INFO  00:28:52,467 MicroScheduler - 2116 reads were filtered out during the traversal out of approximately 51417 total reads (4.12%)
[2015-09-30T23:28Z] INFO  00:28:52,468 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:28Z] INFO  00:28:52,468 MicroScheduler -   -> 2106 reads (4.10% of total) failing DuplicateReadFilter
[2015-09-30T23:28Z] INFO  00:28:52,468 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:28Z] INFO  00:28:52,468 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:28Z] INFO  00:28:52,468 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:28Z] INFO  00:28:52,469 MicroScheduler -   -> 10 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:28Z] INFO  00:28:53,385 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:28Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:29Z] tabix index syn3-8_93896832_124968568-raw.vcf.gz
[2015-09-30T23:29Z] GATK: VariantAnnotator
[2015-09-30T23:29Z] INFO  00:29:13,564 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:29Z] INFO  00:29:13,566 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:29Z] INFO  00:29:13,566 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:29Z] INFO  00:29:13,566 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:29Z] INFO  00:29:13,570 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/8/syn3-8_93896832_124968568-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/8/tx/tmpWdLMsr/syn3-8_93896832_124968568-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/8/syn3-8_93896832_124968568-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_93896832_124968568-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:29Z] INFO  00:29:13,576 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:29Z] INFO  00:29:13,576 HelpFormatter - Date/Time: 2015/10/01 00:29:13
[2015-09-30T23:29Z] INFO  00:29:13,576 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:29Z] INFO  00:29:13,576 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:29Z] INFO  00:29:13,643 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:29Z] INFO  00:29:13,719 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:29Z] INFO  00:29:13,727 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:29Z] INFO  00:29:13,749 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:29Z] INFO  00:29:14,193 IntervalUtils - Processing 1078 bp from intervals
[2015-09-30T23:29Z] WARN  00:29:14,198 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:29Z] WARN  00:29:14,198 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:29Z] INFO  00:29:14,253 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:29Z] INFO  00:29:14,370 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:29Z] INFO  00:29:14,371 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:29Z] INFO  00:29:14,371 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:29Z] INFO  00:29:14,372 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:29Z] INFO  00:29:14,412 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:29Z] INFO  00:29:19,820 VariantAnnotator - Processed 934 loci.
[2015-09-30T23:29Z]
[2015-09-30T23:29Z] INFO  00:29:19,841 ProgressMeter -            done      3381.0     5.0 s      27.0 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:29Z] INFO  00:29:19,841 ProgressMeter - Total runtime 5.47 secs, 0.09 min, 0.00 hours
[2015-09-30T23:29Z] INFO  00:29:19,841 MicroScheduler - 2610 reads were filtered out during the traversal out of approximately 62294 total reads (4.19%)
[2015-09-30T23:29Z] INFO  00:29:19,842 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:29Z] INFO  00:29:19,842 MicroScheduler -   -> 2601 reads (4.18% of total) failing DuplicateReadFilter
[2015-09-30T23:29Z] INFO  00:29:19,842 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:29Z] INFO  00:29:19,842 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:29Z] INFO  00:29:19,843 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:29Z] INFO  00:29:19,843 MicroScheduler -   -> 9 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:29Z] INFO  00:29:20,751 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:29Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:29Z] WARNING(freebayes): Could not find any mapped reads in target region 8:143592003..143592127
[2015-09-30T23:29Z] tabix index syn3-9_0_32405837-raw.vcf.gz
[2015-09-30T23:29Z] GATK: VariantAnnotator
[2015-09-30T23:29Z] INFO  00:29:51,142 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:29Z] INFO  00:29:51,143 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:29Z] INFO  00:29:51,144 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:29Z] INFO  00:29:51,144 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:29Z] INFO  00:29:51,147 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/9/syn3-9_0_32405837-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/9/tx/tmp2YZ6VM/syn3-9_0_32405837-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/9/syn3-9_0_32405837-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_0_32405837-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:29Z] INFO  00:29:51,152 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:29Z] INFO  00:29:51,152 HelpFormatter - Date/Time: 2015/10/01 00:29:51
[2015-09-30T23:29Z] INFO  00:29:51,152 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:29Z] INFO  00:29:51,153 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:29Z] INFO  00:29:51,239 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:29Z] INFO  00:29:51,312 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:29Z] INFO  00:29:51,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:29Z] INFO  00:29:51,341 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:29Z] INFO  00:29:51,808 IntervalUtils - Processing 1228 bp from intervals
[2015-09-30T23:29Z] WARN  00:29:51,812 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:29Z] WARN  00:29:51,813 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:29Z] INFO  00:29:51,867 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:29Z] INFO  00:29:51,961 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:29Z] INFO  00:29:51,961 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:29Z] INFO  00:29:51,962 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:29Z] INFO  00:29:51,962 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:29Z] INFO  00:29:52,001 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:29Z] INFO  00:29:57,484 VariantAnnotator - Processed 1087 loci.
[2015-09-30T23:29Z]
[2015-09-30T23:29Z] INFO  00:29:57,502 ProgressMeter -            done      4262.0     5.0 s      21.7 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:29Z] INFO  00:29:57,503 ProgressMeter - Total runtime 5.54 secs, 0.09 min, 0.00 hours
[2015-09-30T23:29Z] INFO  00:29:57,503 MicroScheduler - 3242 reads were filtered out during the traversal out of approximately 73947 total reads (4.38%)
[2015-09-30T23:29Z] INFO  00:29:57,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:29Z] INFO  00:29:57,503 MicroScheduler -   -> 3222 reads (4.36% of total) failing DuplicateReadFilter
[2015-09-30T23:29Z] INFO  00:29:57,503 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:29Z] INFO  00:29:57,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:29Z] INFO  00:29:57,504 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:29Z] INFO  00:29:57,504 MicroScheduler -   -> 20 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:29Z] INFO  00:29:58,475 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:30Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:30Z] tabix index syn3-8_124975213_146364022-raw.vcf.gz
[2015-09-30T23:30Z] GATK: VariantAnnotator
[2015-09-30T23:30Z] INFO  00:30:16,154 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:30Z] INFO  00:30:16,156 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:30Z] INFO  00:30:16,156 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:30Z] INFO  00:30:16,156 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:30Z] INFO  00:30:16,160 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/8/syn3-8_124975213_146364022-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/8/tx/tmpqJU_dt/syn3-8_124975213_146364022-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/8/syn3-8_124975213_146364022-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/8/1_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/8/2_2014-08-13_dream-syn3-sort-8_124975213_146364022-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:30Z] INFO  00:30:16,165 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:30Z] INFO  00:30:16,166 HelpFormatter - Date/Time: 2015/10/01 00:30:16
[2015-09-30T23:30Z] INFO  00:30:16,166 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:30Z] INFO  00:30:16,166 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:30Z] INFO  00:30:16,264 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:30Z] INFO  00:30:16,338 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:30Z] INFO  00:30:16,346 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:30Z] INFO  00:30:16,367 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:30Z] INFO  00:30:16,853 IntervalUtils - Processing 1493 bp from intervals
[2015-09-30T23:30Z] WARN  00:30:16,857 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:30Z] WARN  00:30:16,857 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:30Z] INFO  00:30:16,912 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:30Z] INFO  00:30:17,006 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:30Z] INFO  00:30:17,006 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:30Z] INFO  00:30:17,007 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:30Z] INFO  00:30:17,007 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:30Z] INFO  00:30:17,046 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:30Z] INFO  00:30:25,057 VariantAnnotator - Processed 1329 loci.
[2015-09-30T23:30Z]
[2015-09-30T23:30Z] INFO  00:30:25,498 ProgressMeter -            done      8632.0     8.0 s      16.4 m       99.0%     8.0 s       0.0 s
[2015-09-30T23:30Z] INFO  00:30:25,498 ProgressMeter - Total runtime 8.49 secs, 0.14 min, 0.00 hours
[2015-09-30T23:30Z] INFO  00:30:25,498 MicroScheduler - 7830 reads were filtered out during the traversal out of approximately 139393 total reads (5.62%)
[2015-09-30T23:30Z] INFO  00:30:25,499 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:30Z] INFO  00:30:25,499 MicroScheduler -   -> 7796 reads (5.59% of total) failing DuplicateReadFilter
[2015-09-30T23:30Z] INFO  00:30:25,499 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:30Z] INFO  00:30:25,499 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:30Z] INFO  00:30:25,500 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:30Z] INFO  00:30:25,500 MicroScheduler -   -> 34 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:30Z] INFO  00:30:26,485 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:30Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:30Z] tabix index syn3-9_32406980_65488652-raw.vcf.gz
[2015-09-30T23:30Z] GATK: VariantAnnotator
[2015-09-30T23:30Z] INFO  00:30:32,287 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:30Z] INFO  00:30:32,289 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:30Z] INFO  00:30:32,290 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:30Z] INFO  00:30:32,290 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:30Z] INFO  00:30:32,293 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/9/syn3-9_32406980_65488652-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/9/tx/tmppfWsh2/syn3-9_32406980_65488652-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/9/syn3-9_32406980_65488652-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_32406980_65488652-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:30Z] INFO  00:30:32,299 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:30Z] INFO  00:30:32,299 HelpFormatter - Date/Time: 2015/10/01 00:30:32
[2015-09-30T23:30Z] INFO  00:30:32,299 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:30Z] INFO  00:30:32,300 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:30Z] INFO  00:30:32,395 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:30Z] INFO  00:30:32,468 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:30Z] INFO  00:30:32,476 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:30Z] INFO  00:30:32,497 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:30Z] INFO  00:30:33,256 IntervalUtils - Processing 1302 bp from intervals
[2015-09-30T23:30Z] WARN  00:30:33,260 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:30Z] WARN  00:30:33,260 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:30Z] INFO  00:30:33,314 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:30Z] INFO  00:30:33,390 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:30Z] INFO  00:30:33,390 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:30Z] INFO  00:30:33,390 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:30Z] INFO  00:30:33,391 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:30Z] INFO  00:30:33,428 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:30Z] INFO  00:30:39,838 VariantAnnotator - Processed 1203 loci.
[2015-09-30T23:30Z]
[2015-09-30T23:30Z] INFO  00:30:39,857 ProgressMeter -            done     17783.0     6.0 s       6.1 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:30Z] INFO  00:30:39,858 ProgressMeter - Total runtime 6.47 secs, 0.11 min, 0.00 hours
[2015-09-30T23:30Z] INFO  00:30:39,858 MicroScheduler - 4400 reads were filtered out during the traversal out of approximately 88854 total reads (4.95%)
[2015-09-30T23:30Z] INFO  00:30:39,858 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:30Z] INFO  00:30:39,858 MicroScheduler -   -> 4374 reads (4.92% of total) failing DuplicateReadFilter
[2015-09-30T23:30Z] INFO  00:30:39,859 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:30Z] INFO  00:30:39,859 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:30Z] INFO  00:30:39,859 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:30Z] INFO  00:30:39,859 MicroScheduler -   -> 26 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:30Z] INFO  00:30:40,807 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:30Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:31Z] tabix index syn3-9_65505265_96581951-raw.vcf.gz
[2015-09-30T23:31Z] GATK: VariantAnnotator
[2015-09-30T23:31Z] INFO  00:31:32,177 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:31Z] INFO  00:31:32,179 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:31Z] INFO  00:31:32,180 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:31Z] INFO  00:31:32,180 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:31Z] INFO  00:31:32,183 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/9/syn3-9_65505265_96581951-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/9/tx/tmp2mSlnm/syn3-9_65505265_96581951-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/9/syn3-9_65505265_96581951-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_65505265_96581951-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:31Z] INFO  00:31:32,189 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:31Z] INFO  00:31:32,189 HelpFormatter - Date/Time: 2015/10/01 00:31:32
[2015-09-30T23:31Z] INFO  00:31:32,190 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:31Z] INFO  00:31:32,190 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:31Z] INFO  00:31:32,266 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:31Z] INFO  00:31:32,354 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:31Z] INFO  00:31:32,361 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:31Z] INFO  00:31:32,383 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:31Z] INFO  00:31:32,941 IntervalUtils - Processing 1928 bp from intervals
[2015-09-30T23:31Z] WARN  00:31:32,945 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:31Z] WARN  00:31:32,946 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:31Z] INFO  00:31:33,003 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:31Z] INFO  00:31:33,109 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:31Z] INFO  00:31:33,110 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:31Z] INFO  00:31:33,110 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:31Z] INFO  00:31:33,111 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:31Z] INFO  00:31:33,149 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:31Z] INFO  00:31:42,487 VariantAnnotator - Processed 1718 loci.
[2015-09-30T23:31Z]
[2015-09-30T23:31Z] INFO  00:31:42,510 ProgressMeter -            done     15639.0     9.0 s      10.0 m       99.9%     9.0 s       0.0 s
[2015-09-30T23:31Z] INFO  00:31:42,510 ProgressMeter - Total runtime 9.40 secs, 0.16 min, 0.00 hours
[2015-09-30T23:31Z] INFO  00:31:42,511 MicroScheduler - 9048 reads were filtered out during the traversal out of approximately 166747 total reads (5.43%)
[2015-09-30T23:31Z] INFO  00:31:42,511 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:31Z] INFO  00:31:42,511 MicroScheduler -   -> 8986 reads (5.39% of total) failing DuplicateReadFilter
[2015-09-30T23:31Z] INFO  00:31:42,511 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:31Z] INFO  00:31:42,512 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:31Z] INFO  00:31:42,512 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:31Z] INFO  00:31:42,512 MicroScheduler -   -> 62 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T23:31Z] INFO  00:31:43,448 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:31Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:32Z] WARNING(freebayes): Could not find any mapped reads in target region 9:134615452..134615454
[2015-09-30T23:32Z] WARNING(freebayes): Could not find any mapped reads in target region 9:127020246..127020274
[2015-09-30T23:32Z] tabix index syn3-9_96714155_127734373-raw.vcf.gz
[2015-09-30T23:32Z] GATK: VariantAnnotator
[2015-09-30T23:32Z] INFO  00:32:33,291 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:32Z] INFO  00:32:33,293 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:32Z] INFO  00:32:33,293 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:32Z] INFO  00:32:33,293 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:32Z] INFO  00:32:33,297 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/9/syn3-9_96714155_127734373-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/9/tx/tmps9_azy/syn3-9_96714155_127734373-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/9/syn3-9_96714155_127734373-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_96714155_127734373-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:32Z] INFO  00:32:33,302 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:32Z] INFO  00:32:33,302 HelpFormatter - Date/Time: 2015/10/01 00:32:33
[2015-09-30T23:32Z] INFO  00:32:33,302 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:32Z] INFO  00:32:33,303 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:32Z] INFO  00:32:33,395 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:32Z] INFO  00:32:33,472 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:32Z] INFO  00:32:33,480 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:32Z] INFO  00:32:33,502 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:32Z] INFO  00:32:34,137 IntervalUtils - Processing 1914 bp from intervals
[2015-09-30T23:32Z] WARN  00:32:34,141 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:32Z] WARN  00:32:34,141 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:32Z] INFO  00:32:34,198 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:32Z] INFO  00:32:34,367 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:32Z] INFO  00:32:34,368 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:32Z] INFO  00:32:34,368 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:32Z] INFO  00:32:34,369 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:32Z] INFO  00:32:34,412 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:32Z] WARNING(freebayes): Could not find any mapped reads in target region 9:137218195..137218214
[2015-09-30T23:32Z] WARNING(freebayes): Could not find any mapped reads in target region 9:137218289..137218335
[2015-09-30T23:32Z] WARNING(freebayes): Could not find any mapped reads in target region 9:137218457..137218512
[2015-09-30T23:32Z] WARNING(freebayes): Could not find any mapped reads in target region 9:137218577..137218687
[2015-09-30T23:32Z] INFO  00:32:43,480 VariantAnnotator - Processed 1690 loci.
[2015-09-30T23:32Z]
[2015-09-30T23:32Z] INFO  00:32:43,502 ProgressMeter -            done      6731.0     9.0 s      22.6 m       99.9%     9.0 s       0.0 s
[2015-09-30T23:32Z] INFO  00:32:43,502 ProgressMeter - Total runtime 9.13 secs, 0.15 min, 0.00 hours
[2015-09-30T23:32Z] INFO  00:32:43,502 MicroScheduler - 6884 reads were filtered out during the traversal out of approximately 141585 total reads (4.86%)
[2015-09-30T23:32Z] INFO  00:32:43,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:32Z] INFO  00:32:43,503 MicroScheduler -   -> 6862 reads (4.85% of total) failing DuplicateReadFilter
[2015-09-30T23:32Z] INFO  00:32:43,503 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:32Z] INFO  00:32:43,503 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:32Z] INFO  00:32:43,504 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:32Z] INFO  00:32:43,504 MicroScheduler -   -> 22 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:32Z] INFO  00:32:44,470 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:32Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:33Z] tabix index syn3-10_0_31134673-raw.vcf.gz
[2015-09-30T23:33Z] GATK: VariantAnnotator
[2015-09-30T23:33Z] INFO  00:33:15,393 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:33Z] INFO  00:33:15,395 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:33Z] INFO  00:33:15,395 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:33Z] INFO  00:33:15,395 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:33Z] INFO  00:33:15,398 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/10/syn3-10_0_31134673-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/10/tx/tmpso5hrk/syn3-10_0_31134673-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/10/syn3-10_0_31134673-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_0_31134673-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:33Z] INFO  00:33:15,404 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:33Z] INFO  00:33:15,404 HelpFormatter - Date/Time: 2015/10/01 00:33:15
[2015-09-30T23:33Z] INFO  00:33:15,404 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:33Z] INFO  00:33:15,404 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:33Z] INFO  00:33:15,496 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:33Z] INFO  00:33:15,571 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:33Z] INFO  00:33:15,579 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:33Z] INFO  00:33:15,600 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:33Z] INFO  00:33:16,174 IntervalUtils - Processing 2138 bp from intervals
[2015-09-30T23:33Z] WARN  00:33:16,178 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:33Z] WARN  00:33:16,178 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:33Z] INFO  00:33:16,235 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:33Z] INFO  00:33:16,377 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:33Z] INFO  00:33:16,378 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:33Z] INFO  00:33:16,378 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:33Z] INFO  00:33:16,379 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:33Z] INFO  00:33:16,417 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:33Z] INFO  00:33:25,656 VariantAnnotator - Processed 1872 loci.
[2015-09-30T23:33Z]
[2015-09-30T23:33Z] INFO  00:33:25,677 ProgressMeter -            done     10174.0     9.0 s      15.2 m      100.0%     9.0 s       0.0 s
[2015-09-30T23:33Z] INFO  00:33:25,677 ProgressMeter - Total runtime 9.30 secs, 0.15 min, 0.00 hours
[2015-09-30T23:33Z] INFO  00:33:25,677 MicroScheduler - 6390 reads were filtered out during the traversal out of approximately 139260 total reads (4.59%)
[2015-09-30T23:33Z] INFO  00:33:25,678 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:33Z] INFO  00:33:25,678 MicroScheduler -   -> 6366 reads (4.57% of total) failing DuplicateReadFilter
[2015-09-30T23:33Z] INFO  00:33:25,678 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:33Z] INFO  00:33:25,678 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:33Z] INFO  00:33:25,679 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:33Z] INFO  00:33:25,679 MicroScheduler -   -> 24 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:33Z] INFO  00:33:26,585 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:33Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:33Z] tabix index syn3-9_127737328_141213431-raw.vcf.gz
[2015-09-30T23:33Z] GATK: VariantAnnotator
[2015-09-30T23:33Z] INFO  00:33:49,521 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:33Z] INFO  00:33:49,523 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:33Z] INFO  00:33:49,524 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:33Z] INFO  00:33:49,524 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:33Z] INFO  00:33:49,527 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/9/syn3-9_127737328_141213431-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/9/tx/tmp85uqDb/syn3-9_127737328_141213431-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/9/syn3-9_127737328_141213431-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/9/1_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/9/2_2014-08-13_dream-syn3-sort-9_127737328_141213431-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:33Z] INFO  00:33:49,533 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:33Z] INFO  00:33:49,534 HelpFormatter - Date/Time: 2015/10/01 00:33:49
[2015-09-30T23:33Z] INFO  00:33:49,534 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:33Z] INFO  00:33:49,534 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:33Z] INFO  00:33:49,629 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:33Z] INFO  00:33:49,705 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:33Z] INFO  00:33:49,713 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:33Z] INFO  00:33:49,735 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:33Z] INFO  00:33:50,349 IntervalUtils - Processing 2747 bp from intervals
[2015-09-30T23:33Z] WARN  00:33:50,354 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:33Z] WARN  00:33:50,354 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:33Z] INFO  00:33:50,410 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:33Z] INFO  00:33:50,522 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:33Z] INFO  00:33:50,522 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:33Z] INFO  00:33:50,523 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:33Z] INFO  00:33:50,523 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:33Z] INFO  00:33:50,566 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:33Z] tabix index syn3-10_31137165_62208748-raw.vcf.gz
[2015-09-30T23:33Z] GATK: VariantAnnotator
[2015-09-30T23:33Z] INFO  00:33:54,914 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:33Z] INFO  00:33:54,916 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:33Z] INFO  00:33:54,916 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:33Z] INFO  00:33:54,917 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:33Z] INFO  00:33:54,920 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/10/syn3-10_31137165_62208748-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/10/tx/tmpUqpecp/syn3-10_31137165_62208748-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/10/syn3-10_31137165_62208748-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_31137165_62208748-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:33Z] INFO  00:33:54,926 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:33Z] INFO  00:33:54,926 HelpFormatter - Date/Time: 2015/10/01 00:33:54
[2015-09-30T23:33Z] INFO  00:33:54,926 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:33Z] INFO  00:33:54,926 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:33Z] INFO  00:33:55,002 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:33Z] INFO  00:33:55,105 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:33Z] INFO  00:33:55,112 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:33Z] INFO  00:33:55,134 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:33Z] INFO  00:33:55,660 IntervalUtils - Processing 1593 bp from intervals
[2015-09-30T23:33Z] WARN  00:33:55,664 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:33Z] WARN  00:33:55,664 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:33Z] INFO  00:33:55,728 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:33Z] INFO  00:33:55,820 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:33Z] INFO  00:33:55,821 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:33Z] INFO  00:33:55,821 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:33Z] INFO  00:33:55,822 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:33Z] INFO  00:33:55,860 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:34Z] INFO  00:34:03,000 VariantAnnotator - Processed 1457 loci.
[2015-09-30T23:34Z]
[2015-09-30T23:34Z] INFO  00:34:03,039 ProgressMeter -            done      9522.0     7.0 s      12.6 m       99.9%     7.0 s       0.0 s
[2015-09-30T23:34Z] INFO  00:34:03,040 ProgressMeter - Total runtime 7.22 secs, 0.12 min, 0.00 hours
[2015-09-30T23:34Z] INFO  00:34:03,040 MicroScheduler - 5264 reads were filtered out during the traversal out of approximately 109678 total reads (4.80%)
[2015-09-30T23:34Z] INFO  00:34:03,040 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:34Z] INFO  00:34:03,040 MicroScheduler -   -> 5241 reads (4.78% of total) failing DuplicateReadFilter
[2015-09-30T23:34Z] INFO  00:34:03,041 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:34Z] INFO  00:34:03,041 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:34Z] INFO  00:34:03,041 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:34Z] INFO  00:34:03,041 MicroScheduler -   -> 23 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:34Z] INFO  00:34:03,963 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:34Z] INFO  00:34:05,419 VariantAnnotator - Processed 2363 loci.
[2015-09-30T23:34Z]
[2015-09-30T23:34Z] INFO  00:34:05,443 ProgressMeter -            done     22510.0    14.0 s      11.0 m      100.0%    14.0 s       0.0 s
[2015-09-30T23:34Z] INFO  00:34:05,443 ProgressMeter - Total runtime 14.92 secs, 0.25 min, 0.00 hours
[2015-09-30T23:34Z] INFO  00:34:05,443 MicroScheduler - 13613 reads were filtered out during the traversal out of approximately 245106 total reads (5.55%)
[2015-09-30T23:34Z] INFO  00:34:05,443 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:34Z] INFO  00:34:05,444 MicroScheduler -   -> 13546 reads (5.53% of total) failing DuplicateReadFilter
[2015-09-30T23:34Z] INFO  00:34:05,444 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:34Z] INFO  00:34:05,444 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:34Z] INFO  00:34:05,444 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:34Z] INFO  00:34:05,445 MicroScheduler -   -> 67 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:34Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:34Z] INFO  00:34:06,390 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:34Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:35Z] tabix index syn3-10_124438084_135534747-raw.vcf.gz
[2015-09-30T23:35Z] GATK: VariantAnnotator
[2015-09-30T23:35Z] INFO  00:35:08,081 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:35Z] INFO  00:35:08,083 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:35Z] INFO  00:35:08,084 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:35Z] INFO  00:35:08,084 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:35Z] INFO  00:35:08,087 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/10/syn3-10_124438084_135534747-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/10/tx/tmpmEBy62/syn3-10_124438084_135534747-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/10/syn3-10_124438084_135534747-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_124438084_135534747-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:35Z] INFO  00:35:08,093 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:35Z] INFO  00:35:08,094 HelpFormatter - Date/Time: 2015/10/01 00:35:08
[2015-09-30T23:35Z] INFO  00:35:08,094 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:35Z] INFO  00:35:08,094 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:35Z] INFO  00:35:08,169 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:35Z] INFO  00:35:08,252 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:35Z] INFO  00:35:08,260 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:35Z] INFO  00:35:08,283 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:35Z] INFO  00:35:08,761 IntervalUtils - Processing 1183 bp from intervals
[2015-09-30T23:35Z] WARN  00:35:08,766 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:35Z] WARN  00:35:08,766 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:35Z] INFO  00:35:08,822 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:35Z] INFO  00:35:09,177 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:35Z] INFO  00:35:09,177 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:35Z] INFO  00:35:09,177 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:35Z] INFO  00:35:09,178 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:35Z] INFO  00:35:09,218 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:35Z] tabix index syn3-10_62267938_93388847-raw.vcf.gz
[2015-09-30T23:35Z] GATK: VariantAnnotator
[2015-09-30T23:35Z] INFO  00:35:15,861 VariantAnnotator - Processed 1038 loci.
[2015-09-30T23:35Z]
[2015-09-30T23:35Z] INFO  00:35:15,883 ProgressMeter -            done      9293.0     6.0 s      12.0 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:35Z] INFO  00:35:15,883 ProgressMeter - Total runtime 6.71 secs, 0.11 min, 0.00 hours
[2015-09-30T23:35Z] INFO  00:35:15,884 MicroScheduler - 4875 reads were filtered out during the traversal out of approximately 88600 total reads (5.50%)
[2015-09-30T23:35Z] INFO  00:35:15,884 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:35Z] INFO  00:35:15,884 MicroScheduler -   -> 4856 reads (5.48% of total) failing DuplicateReadFilter
[2015-09-30T23:35Z] INFO  00:35:15,885 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:35Z] INFO  00:35:15,885 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:35Z] INFO  00:35:15,885 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:35Z] INFO  00:35:15,885 MicroScheduler -   -> 19 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:35Z] INFO  00:35:16,870 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:35Z] INFO  00:35:17,231 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:35Z] INFO  00:35:17,233 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:35Z] INFO  00:35:17,234 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:35Z] INFO  00:35:17,234 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:35Z] INFO  00:35:17,238 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/10/syn3-10_62267938_93388847-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/10/tx/tmpF5lfFP/syn3-10_62267938_93388847-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/10/syn3-10_62267938_93388847-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_62267938_93388847-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:35Z] INFO  00:35:17,243 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:35Z] INFO  00:35:17,244 HelpFormatter - Date/Time: 2015/10/01 00:35:17
[2015-09-30T23:35Z] INFO  00:35:17,244 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:35Z] INFO  00:35:17,244 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:35Z] INFO  00:35:17,318 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:35Z] INFO  00:35:17,395 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:35Z] INFO  00:35:17,402 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:35Z] INFO  00:35:17,425 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:35Z] INFO  00:35:18,305 IntervalUtils - Processing 1884 bp from intervals
[2015-09-30T23:35Z] WARN  00:35:18,310 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:35Z] WARN  00:35:18,310 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:35Z] INFO  00:35:18,368 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:35Z] INFO  00:35:18,482 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:35Z] INFO  00:35:18,483 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:35Z] INFO  00:35:18,483 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:35Z] INFO  00:35:18,484 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:35Z] INFO  00:35:18,523 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:35Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:35Z] WARNING(freebayes): Could not find any mapped reads in target region 11:369548..369701
[2015-09-30T23:35Z] WARNING(freebayes): Could not find any mapped reads in target region 11:369756..369841
[2015-09-30T23:35Z] WARNING(freebayes): Could not find any mapped reads in target region 11:369875..369954
[2015-09-30T23:35Z] INFO  00:35:27,978 VariantAnnotator - Processed 1671 loci.
[2015-09-30T23:35Z]
[2015-09-30T23:35Z] INFO  00:35:28,001 ProgressMeter -            done      7364.0     9.0 s      21.5 m       99.9%     9.0 s       0.0 s
[2015-09-30T23:35Z] INFO  00:35:28,001 ProgressMeter - Total runtime 9.52 secs, 0.16 min, 0.00 hours
[2015-09-30T23:35Z] INFO  00:35:28,001 MicroScheduler - 6856 reads were filtered out during the traversal out of approximately 141980 total reads (4.83%)
[2015-09-30T23:35Z] INFO  00:35:28,002 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:35Z] INFO  00:35:28,002 MicroScheduler -   -> 6818 reads (4.80% of total) failing DuplicateReadFilter
[2015-09-30T23:35Z] INFO  00:35:28,002 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:35Z] INFO  00:35:28,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:35Z] INFO  00:35:28,003 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:35Z] INFO  00:35:28,003 MicroScheduler -   -> 38 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:35Z] INFO  00:35:28,948 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:35Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:36Z] tabix index syn3-10_93389481_124436664-raw.vcf.gz
[2015-09-30T23:36Z] GATK: VariantAnnotator
[2015-09-30T23:36Z] INFO  00:36:43,565 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:36Z] INFO  00:36:43,567 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:36Z] INFO  00:36:43,567 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:36Z] INFO  00:36:43,567 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:36Z] INFO  00:36:43,571 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/10/syn3-10_93389481_124436664-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/10/tx/tmpKNfS9B/syn3-10_93389481_124436664-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/10/syn3-10_93389481_124436664-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/10/1_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/10/2_2014-08-13_dream-syn3-sort-10_93389481_124436664-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:36Z] INFO  00:36:43,576 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:36Z] INFO  00:36:43,576 HelpFormatter - Date/Time: 2015/10/01 00:36:43
[2015-09-30T23:36Z] INFO  00:36:43,576 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:36Z] INFO  00:36:43,577 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:36Z] INFO  00:36:43,860 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:36Z] INFO  00:36:43,938 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:36Z] INFO  00:36:43,946 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:36Z] INFO  00:36:43,968 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:36Z] INFO  00:36:44,654 IntervalUtils - Processing 2538 bp from intervals
[2015-09-30T23:36Z] WARN  00:36:44,658 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:36Z] WARN  00:36:44,659 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:36Z] INFO  00:36:44,789 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:36Z] INFO  00:36:44,923 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:36Z] INFO  00:36:44,924 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:36Z] INFO  00:36:44,924 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:36Z] INFO  00:36:44,925 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:36Z] INFO  00:36:44,964 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:36Z] INFO  00:36:56,481 VariantAnnotator - Processed 2190 loci.
[2015-09-30T23:36Z]
[2015-09-30T23:36Z] INFO  00:36:56,512 ProgressMeter -            done     10839.0    11.0 s      17.8 m      100.0%    11.0 s       0.0 s
[2015-09-30T23:36Z] INFO  00:36:56,512 ProgressMeter - Total runtime 11.59 secs, 0.19 min, 0.00 hours
[2015-09-30T23:36Z] INFO  00:36:56,512 MicroScheduler - 8829 reads were filtered out during the traversal out of approximately 182595 total reads (4.84%)
[2015-09-30T23:36Z] INFO  00:36:56,512 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:36Z] INFO  00:36:56,513 MicroScheduler -   -> 8797 reads (4.82% of total) failing DuplicateReadFilter
[2015-09-30T23:36Z] INFO  00:36:56,513 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:36Z] INFO  00:36:56,513 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:36Z] INFO  00:36:56,513 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:36Z] INFO  00:36:56,513 MicroScheduler -   -> 32 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:36Z] INFO  00:36:57,460 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:37Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:37Z] tabix index syn3-11_31085657_62105890-raw.vcf.gz
[2015-09-30T23:37Z] GATK: VariantAnnotator
[2015-09-30T23:37Z] INFO  00:37:34,979 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:37Z] INFO  00:37:34,981 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:37Z] INFO  00:37:34,981 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:37Z] INFO  00:37:34,981 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:37Z] INFO  00:37:34,985 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/11/syn3-11_31085657_62105890-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/11/tx/tmp3hG8hZ/syn3-11_31085657_62105890-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/11/syn3-11_31085657_62105890-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_31085657_62105890-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:37Z] INFO  00:37:34,991 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:37Z] INFO  00:37:34,991 HelpFormatter - Date/Time: 2015/10/01 00:37:34
[2015-09-30T23:37Z] INFO  00:37:34,991 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:37Z] INFO  00:37:34,991 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:37Z] INFO  00:37:35,084 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:37Z] INFO  00:37:35,160 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:37Z] INFO  00:37:35,168 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:37Z] INFO  00:37:35,190 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:37Z] INFO  00:37:35,839 IntervalUtils - Processing 2253 bp from intervals
[2015-09-30T23:37Z] WARN  00:37:35,843 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:37Z] WARN  00:37:35,844 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:37Z] INFO  00:37:35,899 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:37Z] INFO  00:37:36,407 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:37Z] INFO  00:37:36,407 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:37Z] INFO  00:37:36,408 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:37Z] INFO  00:37:36,408 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:37Z] INFO  00:37:36,447 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:37Z] INFO  00:37:47,059 VariantAnnotator - Processed 2066 loci.
[2015-09-30T23:37Z]
[2015-09-30T23:37Z] INFO  00:37:47,091 ProgressMeter -            done     21427.0    10.0 s       8.3 m      100.0%    10.0 s       0.0 s
[2015-09-30T23:37Z] INFO  00:37:47,091 ProgressMeter - Total runtime 10.68 secs, 0.18 min, 0.00 hours
[2015-09-30T23:37Z] INFO  00:37:47,092 MicroScheduler - 7579 reads were filtered out during the traversal out of approximately 156586 total reads (4.84%)
[2015-09-30T23:37Z] INFO  00:37:47,092 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:37Z] INFO  00:37:47,092 MicroScheduler -   -> 7524 reads (4.81% of total) failing DuplicateReadFilter
[2015-09-30T23:37Z] INFO  00:37:47,092 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:37Z] INFO  00:37:47,092 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:37Z] INFO  00:37:47,093 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:37Z] INFO  00:37:47,093 MicroScheduler -   -> 55 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T23:37Z] INFO  00:37:48,078 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:37Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:38Z] tabix index syn3-11_0_31082819-raw.vcf.gz
[2015-09-30T23:38Z] GATK: VariantAnnotator
[2015-09-30T23:38Z] INFO  00:38:17,685 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:38Z] INFO  00:38:17,687 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:38Z] INFO  00:38:17,687 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:38Z] INFO  00:38:17,687 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:38Z] INFO  00:38:17,691 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/11/syn3-11_0_31082819-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/11/tx/tmp7SQ6j2/syn3-11_0_31082819-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/11/syn3-11_0_31082819-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_0_31082819-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:38Z] INFO  00:38:17,696 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:38Z] INFO  00:38:17,696 HelpFormatter - Date/Time: 2015/10/01 00:38:17
[2015-09-30T23:38Z] INFO  00:38:17,696 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:38Z] INFO  00:38:17,697 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:38Z] INFO  00:38:17,789 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:38Z] INFO  00:38:17,865 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:38Z] INFO  00:38:17,873 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:38Z] INFO  00:38:17,895 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:38Z] INFO  00:38:18,775 IntervalUtils - Processing 3588 bp from intervals
[2015-09-30T23:38Z] WARN  00:38:18,779 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:38Z] WARN  00:38:18,779 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:38Z] INFO  00:38:18,838 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:38Z] INFO  00:38:18,974 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:38Z] INFO  00:38:18,974 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:38Z] INFO  00:38:18,975 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:38Z] INFO  00:38:18,975 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:38Z] INFO  00:38:19,014 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:38Z] INFO  00:38:35,970 VariantAnnotator - Processed 3207 loci.
[2015-09-30T23:38Z]
[2015-09-30T23:38Z] INFO  00:38:36,026 ProgressMeter -            done     33669.0    17.0 s       8.4 m      100.0%    17.0 s       0.0 s
[2015-09-30T23:38Z] INFO  00:38:36,026 ProgressMeter - Total runtime 17.05 secs, 0.28 min, 0.00 hours
[2015-09-30T23:38Z] INFO  00:38:36,026 MicroScheduler - 18049 reads were filtered out during the traversal out of approximately 302417 total reads (5.97%)
[2015-09-30T23:38Z] INFO  00:38:36,026 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:38Z] INFO  00:38:36,027 MicroScheduler -   -> 17903 reads (5.92% of total) failing DuplicateReadFilter
[2015-09-30T23:38Z] INFO  00:38:36,027 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:38Z] INFO  00:38:36,027 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:38Z] INFO  00:38:36,027 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:38Z] INFO  00:38:36,027 MicroScheduler -   -> 146 reads (0.05% of total) failing UnmappedReadFilter
[2015-09-30T23:38Z] INFO  00:38:36,997 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:38Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:39Z] tabix index syn3-11_124188917_135006516-raw.vcf.gz
[2015-09-30T23:39Z] GATK: VariantAnnotator
[2015-09-30T23:39Z] INFO  00:39:22,382 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:39Z] INFO  00:39:22,384 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:39Z] INFO  00:39:22,384 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:39Z] INFO  00:39:22,385 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:39Z] INFO  00:39:22,388 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/11/syn3-11_124188917_135006516-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/11/tx/tmpmKAKXN/syn3-11_124188917_135006516-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/11/syn3-11_124188917_135006516-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_124188917_135006516-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:39Z] INFO  00:39:22,394 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:39Z] INFO  00:39:22,395 HelpFormatter - Date/Time: 2015/10/01 00:39:22
[2015-09-30T23:39Z] INFO  00:39:22,395 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:39Z] INFO  00:39:22,395 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:39Z] INFO  00:39:22,472 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:39Z] INFO  00:39:22,570 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:39Z] INFO  00:39:22,578 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:39Z] INFO  00:39:22,601 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:39Z] INFO  00:39:22,948 IntervalUtils - Processing 661 bp from intervals
[2015-09-30T23:39Z] WARN  00:39:22,952 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:39Z] WARN  00:39:22,953 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:39Z] INFO  00:39:23,151 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:39Z] INFO  00:39:23,228 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:39Z] INFO  00:39:23,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:39Z] INFO  00:39:23,229 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:39Z] INFO  00:39:23,229 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:39Z] INFO  00:39:23,270 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:39Z] INFO  00:39:27,767 VariantAnnotator - Processed 604 loci.
[2015-09-30T23:39Z]
[2015-09-30T23:39Z] INFO  00:39:27,793 ProgressMeter -            done      3152.0     4.0 s      24.1 m       99.8%     4.0 s       0.0 s
[2015-09-30T23:39Z] INFO  00:39:27,793 ProgressMeter - Total runtime 4.57 secs, 0.08 min, 0.00 hours
[2015-09-30T23:39Z] INFO  00:39:27,794 MicroScheduler - 2661 reads were filtered out during the traversal out of approximately 52797 total reads (5.04%)
[2015-09-30T23:39Z] INFO  00:39:27,794 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:39Z] INFO  00:39:27,794 MicroScheduler -   -> 2645 reads (5.01% of total) failing DuplicateReadFilter
[2015-09-30T23:39Z] INFO  00:39:27,794 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:39Z] INFO  00:39:27,795 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:39Z] INFO  00:39:27,795 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:39Z] INFO  00:39:27,795 MicroScheduler -   -> 16 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:39Z] INFO  00:39:28,733 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:39Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:39Z] tabix index syn3-11_93147865_124180877-raw.vcf.gz
[2015-09-30T23:39Z] GATK: VariantAnnotator
[2015-09-30T23:39Z] INFO  00:39:55,084 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:39Z] INFO  00:39:55,086 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:39Z] INFO  00:39:55,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:39Z] INFO  00:39:55,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:39Z] INFO  00:39:55,089 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/11/syn3-11_93147865_124180877-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/11/tx/tmprrLc37/syn3-11_93147865_124180877-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/11/syn3-11_93147865_124180877-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_93147865_124180877-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:39Z] INFO  00:39:55,095 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:39Z] INFO  00:39:55,095 HelpFormatter - Date/Time: 2015/10/01 00:39:55
[2015-09-30T23:39Z] INFO  00:39:55,095 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:39Z] INFO  00:39:55,095 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:39Z] INFO  00:39:55,186 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:39Z] INFO  00:39:55,260 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:39Z] INFO  00:39:55,268 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:39Z] INFO  00:39:55,290 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:39Z] INFO  00:39:55,844 IntervalUtils - Processing 2024 bp from intervals
[2015-09-30T23:39Z] WARN  00:39:55,848 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:39Z] WARN  00:39:55,848 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:39Z] INFO  00:39:55,905 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:39Z] INFO  00:39:56,028 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:39Z] INFO  00:39:56,029 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:39Z] INFO  00:39:56,029 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:39Z] INFO  00:39:56,029 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:39Z] INFO  00:39:56,068 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:40Z] INFO  00:40:05,867 VariantAnnotator - Processed 1799 loci.
[2015-09-30T23:40Z]
[2015-09-30T23:40Z] INFO  00:40:05,899 ProgressMeter -            done      8058.0     9.0 s      20.4 m      100.0%     9.0 s       0.0 s
[2015-09-30T23:40Z] INFO  00:40:05,899 ProgressMeter - Total runtime 9.87 secs, 0.16 min, 0.00 hours
[2015-09-30T23:40Z] INFO  00:40:05,900 MicroScheduler - 6879 reads were filtered out during the traversal out of approximately 143925 total reads (4.78%)
[2015-09-30T23:40Z] INFO  00:40:05,900 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:40Z] INFO  00:40:05,900 MicroScheduler -   -> 6842 reads (4.75% of total) failing DuplicateReadFilter
[2015-09-30T23:40Z] INFO  00:40:05,900 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:40Z] INFO  00:40:05,901 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:40Z] INFO  00:40:05,901 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:40Z] INFO  00:40:05,901 MicroScheduler -   -> 37 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:40Z] INFO  00:40:06,873 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:40Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:40Z] tabix index syn3-11_62123540_93141822-raw.vcf.gz
[2015-09-30T23:40Z] GATK: VariantAnnotator
[2015-09-30T23:40Z] INFO  00:40:28,485 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:40Z] INFO  00:40:28,487 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:40Z] INFO  00:40:28,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:40Z] INFO  00:40:28,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:40Z] INFO  00:40:28,491 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/11/syn3-11_62123540_93141822-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/11/tx/tmpcYPi6i/syn3-11_62123540_93141822-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/11/syn3-11_62123540_93141822-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/11/1_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/11/2_2014-08-13_dream-syn3-sort-11_62123540_93141822-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:40Z] INFO  00:40:28,496 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:40Z] INFO  00:40:28,496 HelpFormatter - Date/Time: 2015/10/01 00:40:28
[2015-09-30T23:40Z] INFO  00:40:28,497 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:40Z] INFO  00:40:28,497 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:40Z] INFO  00:40:28,586 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:40Z] INFO  00:40:28,660 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:40Z] INFO  00:40:28,667 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:40Z] INFO  00:40:28,689 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:40Z] INFO  00:40:29,348 IntervalUtils - Processing 2479 bp from intervals
[2015-09-30T23:40Z] WARN  00:40:29,352 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:40Z] WARN  00:40:29,353 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:40Z] INFO  00:40:29,408 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:40Z] INFO  00:40:29,544 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:40Z] INFO  00:40:29,544 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:40Z] INFO  00:40:29,545 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:40Z] INFO  00:40:29,545 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:40Z] INFO  00:40:29,586 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:40Z] WARNING(freebayes): Could not find any mapped reads in target region 12:46124159..46124162
[2015-09-30T23:40Z] INFO  00:40:43,024 VariantAnnotator - Processed 2215 loci.
[2015-09-30T23:40Z]
[2015-09-30T23:40Z] INFO  00:40:43,047 ProgressMeter -            done     12070.0    13.0 s      18.6 m      100.0%    13.0 s       0.0 s
[2015-09-30T23:40Z] INFO  00:40:43,047 ProgressMeter - Total runtime 13.50 secs, 0.23 min, 0.00 hours
[2015-09-30T23:40Z] INFO  00:40:43,048 MicroScheduler - 11380 reads were filtered out during the traversal out of approximately 213813 total reads (5.32%)
[2015-09-30T23:40Z] INFO  00:40:43,048 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:40Z] INFO  00:40:43,048 MicroScheduler -   -> 11344 reads (5.31% of total) failing DuplicateReadFilter
[2015-09-30T23:40Z] INFO  00:40:43,048 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:40Z] INFO  00:40:43,049 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:40Z] INFO  00:40:43,049 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:40Z] INFO  00:40:43,049 MicroScheduler -   -> 36 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:40Z] INFO  00:40:44,143 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:40Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:41Z] tabix index syn3-12_62147092_93167456-raw.vcf.gz
[2015-09-30T23:41Z] GATK: VariantAnnotator
[2015-09-30T23:41Z] INFO  00:41:43,209 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:41Z] INFO  00:41:43,211 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:41Z] INFO  00:41:43,211 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:41Z] INFO  00:41:43,211 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:41Z] INFO  00:41:43,215 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/12/syn3-12_62147092_93167456-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/12/tx/tmpqgkQea/syn3-12_62147092_93167456-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/12/syn3-12_62147092_93167456-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_62147092_93167456-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:41Z] INFO  00:41:43,220 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:41Z] INFO  00:41:43,220 HelpFormatter - Date/Time: 2015/10/01 00:41:43
[2015-09-30T23:41Z] INFO  00:41:43,221 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:41Z] INFO  00:41:43,221 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:41Z] INFO  00:41:43,314 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:41Z] INFO  00:41:43,389 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:41Z] INFO  00:41:43,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:41Z] INFO  00:41:43,419 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:41Z] INFO  00:41:43,852 IntervalUtils - Processing 1056 bp from intervals
[2015-09-30T23:41Z] WARN  00:41:43,856 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:41Z] WARN  00:41:43,856 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:41Z] INFO  00:41:43,912 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:41Z] INFO  00:41:44,004 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:41Z] INFO  00:41:44,004 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:41Z] INFO  00:41:44,005 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:41Z] INFO  00:41:44,005 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:41Z] INFO  00:41:44,044 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:41Z] INFO  00:41:48,890 VariantAnnotator - Processed 894 loci.
[2015-09-30T23:41Z]
[2015-09-30T23:41Z] INFO  00:41:48,912 ProgressMeter -            done      3203.0     4.0 s      25.5 m       99.9%     4.0 s       0.0 s
[2015-09-30T23:41Z] INFO  00:41:48,912 ProgressMeter - Total runtime 4.91 secs, 0.08 min, 0.00 hours
[2015-09-30T23:41Z] INFO  00:41:48,913 MicroScheduler - 2071 reads were filtered out during the traversal out of approximately 53901 total reads (3.84%)
[2015-09-30T23:41Z] INFO  00:41:48,913 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:41Z] INFO  00:41:48,913 MicroScheduler -   -> 2060 reads (3.82% of total) failing DuplicateReadFilter
[2015-09-30T23:41Z] INFO  00:41:48,913 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:41Z] INFO  00:41:48,913 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:41Z] INFO  00:41:48,914 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:41Z] INFO  00:41:48,914 MicroScheduler -   -> 11 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:41Z] tabix index syn3-12_0_31107241-raw.vcf.gz
[2015-09-30T23:41Z] GATK: VariantAnnotator
[2015-09-30T23:41Z] INFO  00:41:49,844 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:41Z] INFO  00:41:51,272 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:41Z] INFO  00:41:51,274 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:41Z] INFO  00:41:51,274 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:41Z] INFO  00:41:51,274 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:41Z] INFO  00:41:51,278 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/12/syn3-12_0_31107241-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/12/tx/tmp883gIK/syn3-12_0_31107241-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/12/syn3-12_0_31107241-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_0_31107241-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:41Z] INFO  00:41:51,283 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:41Z] INFO  00:41:51,284 HelpFormatter - Date/Time: 2015/10/01 00:41:51
[2015-09-30T23:41Z] INFO  00:41:51,284 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:41Z] INFO  00:41:51,284 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:41Z] INFO  00:41:51,377 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:41Z] INFO  00:41:51,454 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:41Z] INFO  00:41:51,462 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:41Z] INFO  00:41:51,484 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:41Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:41Z] INFO  00:41:52,183 IntervalUtils - Processing 3394 bp from intervals
[2015-09-30T23:41Z] WARN  00:41:52,187 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:41Z] WARN  00:41:52,187 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:41Z] INFO  00:41:52,246 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:41Z] INFO  00:41:52,406 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:41Z] INFO  00:41:52,407 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:41Z] INFO  00:41:52,407 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:41Z] INFO  00:41:52,407 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:41Z] INFO  00:41:52,449 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:42Z] INFO  00:42:05,831 VariantAnnotator - Processed 2951 loci.
[2015-09-30T23:42Z]
[2015-09-30T23:42Z] INFO  00:42:05,852 ProgressMeter -            done     20796.0    13.0 s      10.8 m      100.0%    13.0 s       0.0 s
[2015-09-30T23:42Z] INFO  00:42:05,852 ProgressMeter - Total runtime 13.45 secs, 0.22 min, 0.00 hours
[2015-09-30T23:42Z] INFO  00:42:05,853 MicroScheduler - 10068 reads were filtered out during the traversal out of approximately 218309 total reads (4.61%)
[2015-09-30T23:42Z] INFO  00:42:05,853 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:42Z] INFO  00:42:05,853 MicroScheduler -   -> 10018 reads (4.59% of total) failing DuplicateReadFilter
[2015-09-30T23:42Z] INFO  00:42:05,853 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:42Z] INFO  00:42:05,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:42Z] INFO  00:42:05,854 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:42Z] INFO  00:42:05,854 MicroScheduler -   -> 50 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:42Z] INFO  00:42:06,774 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:42Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:42Z] WARNING(freebayes): Could not find any mapped reads in target region 12:56136991..56137005
[2015-09-30T23:42Z] tabix index syn3-12_124191013_133851895-raw.vcf.gz
[2015-09-30T23:42Z] GATK: VariantAnnotator
[2015-09-30T23:42Z] INFO  00:42:59,093 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:42Z] INFO  00:42:59,096 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:42Z] INFO  00:42:59,096 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:42Z] INFO  00:42:59,096 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:42Z] INFO  00:42:59,100 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/12/syn3-12_124191013_133851895-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/12/tx/tmp0t7w4x/syn3-12_124191013_133851895-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/12/syn3-12_124191013_133851895-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_124191013_133851895-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:42Z] INFO  00:42:59,107 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:42Z] INFO  00:42:59,107 HelpFormatter - Date/Time: 2015/10/01 00:42:59
[2015-09-30T23:42Z] INFO  00:42:59,107 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:42Z] INFO  00:42:59,107 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:42Z] INFO  00:42:59,182 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:42Z] INFO  00:42:59,259 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:42Z] INFO  00:42:59,267 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:42Z] INFO  00:42:59,290 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:42Z] INFO  00:42:59,708 IntervalUtils - Processing 929 bp from intervals
[2015-09-30T23:42Z] WARN  00:42:59,712 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:42Z] WARN  00:42:59,712 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:42Z] INFO  00:42:59,770 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:42Z] INFO  00:42:59,838 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:42Z] INFO  00:42:59,839 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:42Z] INFO  00:42:59,839 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:42Z] INFO  00:42:59,839 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:42Z] INFO  00:42:59,881 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:43Z] INFO  00:43:04,913 VariantAnnotator - Processed 781 loci.
[2015-09-30T23:43Z]
[2015-09-30T23:43Z] INFO  00:43:04,935 ProgressMeter -            done      4444.0     5.0 s      19.1 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:43Z] INFO  00:43:04,936 ProgressMeter - Total runtime 5.10 secs, 0.08 min, 0.00 hours
[2015-09-30T23:43Z] INFO  00:43:04,936 MicroScheduler - 3981 reads were filtered out during the traversal out of approximately 72939 total reads (5.46%)
[2015-09-30T23:43Z] INFO  00:43:04,936 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:43Z] INFO  00:43:04,937 MicroScheduler -   -> 3965 reads (5.44% of total) failing DuplicateReadFilter
[2015-09-30T23:43Z] INFO  00:43:04,937 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:43Z] INFO  00:43:04,937 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:43Z] INFO  00:43:04,937 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:43Z] INFO  00:43:04,937 MicroScheduler -   -> 16 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:43Z] INFO  00:43:05,876 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:43Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:43Z] tabix index syn3-12_31116488_62142833-raw.vcf.gz
[2015-09-30T23:43Z] GATK: VariantAnnotator
[2015-09-30T23:43Z] INFO  00:43:12,516 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:43Z] INFO  00:43:12,518 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:43Z] INFO  00:43:12,518 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:43Z] INFO  00:43:12,518 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:43Z] INFO  00:43:12,522 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/12/syn3-12_31116488_62142833-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/12/tx/tmpzyyXC6/syn3-12_31116488_62142833-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/12/syn3-12_31116488_62142833-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_31116488_62142833-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:43Z] INFO  00:43:12,528 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:43Z] INFO  00:43:12,528 HelpFormatter - Date/Time: 2015/10/01 00:43:12
[2015-09-30T23:43Z] INFO  00:43:12,528 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:43Z] INFO  00:43:12,528 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:43Z] INFO  00:43:12,603 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:43Z] INFO  00:43:12,702 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:43Z] INFO  00:43:12,710 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:43Z] INFO  00:43:12,732 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:43Z] INFO  00:43:13,377 IntervalUtils - Processing 2694 bp from intervals
[2015-09-30T23:43Z] WARN  00:43:13,381 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:43Z] WARN  00:43:13,382 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:43Z] INFO  00:43:13,438 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:43Z] INFO  00:43:13,560 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:43Z] INFO  00:43:13,561 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:43Z] INFO  00:43:13,561 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:43Z] INFO  00:43:13,562 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:43Z] INFO  00:43:13,601 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:43Z] INFO  00:43:26,259 VariantAnnotator - Processed 2386 loci.
[2015-09-30T23:43Z]
[2015-09-30T23:43Z] INFO  00:43:26,280 ProgressMeter -            done     20376.0    12.0 s      10.4 m      100.0%    12.0 s       0.0 s
[2015-09-30T23:43Z] INFO  00:43:26,281 ProgressMeter - Total runtime 12.72 secs, 0.21 min, 0.00 hours
[2015-09-30T23:43Z] INFO  00:43:26,281 MicroScheduler - 9726 reads were filtered out during the traversal out of approximately 197287 total reads (4.93%)
[2015-09-30T23:43Z] INFO  00:43:26,281 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:43Z] INFO  00:43:26,281 MicroScheduler -   -> 9684 reads (4.91% of total) failing DuplicateReadFilter
[2015-09-30T23:43Z] INFO  00:43:26,282 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:43Z] INFO  00:43:26,282 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:43Z] INFO  00:43:26,282 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:43Z] INFO  00:43:26,282 MicroScheduler -   -> 42 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:43Z] INFO  00:43:27,215 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:43Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:43Z] WARNING(freebayes): Could not find any mapped reads in target region 13:33590554..33590565
[2015-09-30T23:43Z] tabix index syn3-13_0_31036104-raw.vcf.gz
[2015-09-30T23:43Z] GATK: VariantAnnotator
[2015-09-30T23:43Z] INFO  00:43:49,075 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:43Z] INFO  00:43:49,077 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:43Z] INFO  00:43:49,077 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:43Z] INFO  00:43:49,077 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:43Z] INFO  00:43:49,080 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/13/syn3-13_0_31036104-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/13/tx/tmpTgXRAB/syn3-13_0_31036104-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/13/syn3-13_0_31036104-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_0_31036104-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:43Z] INFO  00:43:49,086 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:43Z] INFO  00:43:49,086 HelpFormatter - Date/Time: 2015/10/01 00:43:49
[2015-09-30T23:43Z] INFO  00:43:49,086 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:43Z] INFO  00:43:49,086 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:43Z] INFO  00:43:49,178 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:43Z] INFO  00:43:49,250 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:43Z] INFO  00:43:49,257 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:43Z] INFO  00:43:49,278 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:43Z] INFO  00:43:49,752 IntervalUtils - Processing 1139 bp from intervals
[2015-09-30T23:43Z] WARN  00:43:49,756 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:43Z] WARN  00:43:49,757 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:43Z] INFO  00:43:49,813 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:43Z] INFO  00:43:49,881 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:43Z] INFO  00:43:49,881 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:43Z] INFO  00:43:49,881 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:43Z] INFO  00:43:49,882 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:43Z] INFO  00:43:49,920 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:43Z] INFO  00:43:55,286 VariantAnnotator - Processed 1020 loci.
[2015-09-30T23:43Z]
[2015-09-30T23:43Z] INFO  00:43:55,304 ProgressMeter -            done      7338.0     5.0 s      12.3 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:43Z] INFO  00:43:55,305 ProgressMeter - Total runtime 5.42 secs, 0.09 min, 0.00 hours
[2015-09-30T23:43Z] INFO  00:43:55,305 MicroScheduler - 2706 reads were filtered out during the traversal out of approximately 62179 total reads (4.35%)
[2015-09-30T23:43Z] INFO  00:43:55,305 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:43Z] INFO  00:43:55,306 MicroScheduler -   -> 2689 reads (4.32% of total) failing DuplicateReadFilter
[2015-09-30T23:43Z] INFO  00:43:55,306 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:43Z] INFO  00:43:55,306 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:43Z] INFO  00:43:55,306 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:43Z] INFO  00:43:55,306 MicroScheduler -   -> 17 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:43Z] INFO  00:43:56,222 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:43Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:44Z] WARNING(freebayes): Could not find any mapped reads in target region 13:42756063..42756159
[2015-09-30T23:44Z] WARNING(freebayes): Could not find any mapped reads in target region 12:120806960..120807099
[2015-09-30T23:44Z] tabix index syn3-13_63745563_94765401-raw.vcf.gz
[2015-09-30T23:44Z] GATK: VariantAnnotator
[2015-09-30T23:44Z] INFO  00:44:19,574 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:44Z] INFO  00:44:19,576 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:44Z] INFO  00:44:19,576 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:44Z] INFO  00:44:19,577 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:44Z] INFO  00:44:19,580 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/13/syn3-13_63745563_94765401-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/13/tx/tmp3nEgav/syn3-13_63745563_94765401-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/13/syn3-13_63745563_94765401-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_63745563_94765401-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:44Z] INFO  00:44:19,586 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:44Z] INFO  00:44:19,586 HelpFormatter - Date/Time: 2015/10/01 00:44:19
[2015-09-30T23:44Z] INFO  00:44:19,586 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:44Z] INFO  00:44:19,587 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:44Z] INFO  00:44:19,662 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:44Z] INFO  00:44:19,749 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:44Z] INFO  00:44:19,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:44Z] INFO  00:44:19,778 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:44Z] INFO  00:44:20,079 IntervalUtils - Processing 394 bp from intervals
[2015-09-30T23:44Z] WARN  00:44:20,083 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:44Z] WARN  00:44:20,084 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:44Z] INFO  00:44:20,138 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:44Z] INFO  00:44:20,283 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:44Z] INFO  00:44:20,283 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:44Z] INFO  00:44:20,284 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:44Z] INFO  00:44:20,284 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:44Z] INFO  00:44:20,323 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:44Z] INFO  00:44:22,957 VariantAnnotator - Processed 333 loci.
[2015-09-30T23:44Z]
[2015-09-30T23:44Z] INFO  00:44:22,988 ProgressMeter -            done       976.0     2.0 s      46.2 m       99.7%     2.0 s       0.0 s
[2015-09-30T23:44Z] INFO  00:44:22,988 ProgressMeter - Total runtime 2.71 secs, 0.05 min, 0.00 hours
[2015-09-30T23:44Z] INFO  00:44:22,989 MicroScheduler - 822 reads were filtered out during the traversal out of approximately 19974 total reads (4.12%)
[2015-09-30T23:44Z] INFO  00:44:22,989 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:44Z] INFO  00:44:22,989 MicroScheduler -   -> 818 reads (4.10% of total) failing DuplicateReadFilter
[2015-09-30T23:44Z] INFO  00:44:22,989 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:44Z] INFO  00:44:22,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:44Z] INFO  00:44:22,990 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:44Z] INFO  00:44:22,990 MicroScheduler -   -> 4 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:44Z] INFO  00:44:23,914 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:44Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:44Z] tabix index syn3-13_31036377_62334609-raw.vcf.gz
[2015-09-30T23:44Z] GATK: VariantAnnotator
[2015-09-30T23:44Z] INFO  00:44:38,418 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:44Z] INFO  00:44:38,420 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:44Z] INFO  00:44:38,420 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:44Z] INFO  00:44:38,420 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:44Z] INFO  00:44:38,424 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/13/syn3-13_31036377_62334609-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/13/tx/tmp_8RhTg/syn3-13_31036377_62334609-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/13/syn3-13_31036377_62334609-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_31036377_62334609-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:44Z] INFO  00:44:38,429 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:44Z] INFO  00:44:38,429 HelpFormatter - Date/Time: 2015/10/01 00:44:38
[2015-09-30T23:44Z] INFO  00:44:38,429 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:44Z] INFO  00:44:38,429 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:44Z] INFO  00:44:38,516 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:44Z] INFO  00:44:38,589 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:44Z] INFO  00:44:38,596 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:44Z] INFO  00:44:38,617 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:44Z] INFO  00:44:39,095 IntervalUtils - Processing 1354 bp from intervals
[2015-09-30T23:44Z] WARN  00:44:39,099 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:44Z] WARN  00:44:39,100 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:44Z] INFO  00:44:39,154 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:44Z] INFO  00:44:39,258 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:44Z] INFO  00:44:39,259 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:44Z] INFO  00:44:39,259 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:44Z] INFO  00:44:39,260 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:44Z] INFO  00:44:39,298 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:44Z] INFO  00:44:45,542 VariantAnnotator - Processed 1185 loci.
[2015-09-30T23:44Z]
[2015-09-30T23:44Z] INFO  00:44:45,562 ProgressMeter -            done      4529.0     6.0 s      23.2 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:44Z] INFO  00:44:45,562 ProgressMeter - Total runtime 6.30 secs, 0.11 min, 0.00 hours
[2015-09-30T23:44Z] INFO  00:44:45,563 MicroScheduler - 3343 reads were filtered out during the traversal out of approximately 79538 total reads (4.20%)
[2015-09-30T23:44Z] INFO  00:44:45,563 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:44Z] INFO  00:44:45,563 MicroScheduler -   -> 3327 reads (4.18% of total) failing DuplicateReadFilter
[2015-09-30T23:44Z] INFO  00:44:45,563 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:44Z] INFO  00:44:45,563 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:44Z] INFO  00:44:45,564 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:44Z] INFO  00:44:45,564 MicroScheduler -   -> 16 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:44Z] WARNING(freebayes): Could not find any mapped reads in target region 12:124018208..124018264
[2015-09-30T23:44Z] INFO  00:44:46,473 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:44Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:44Z] tabix index syn3-12_93169109_124189486-raw.vcf.gz
[2015-09-30T23:44Z] GATK: VariantAnnotator
[2015-09-30T23:44Z] INFO  00:44:51,148 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:44Z] INFO  00:44:51,150 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:44Z] INFO  00:44:51,150 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:44Z] INFO  00:44:51,150 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:44Z] INFO  00:44:51,154 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/12/syn3-12_93169109_124189486-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/12/tx/tmpPZjaY7/syn3-12_93169109_124189486-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/12/syn3-12_93169109_124189486-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/12/1_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/12/2_2014-08-13_dream-syn3-sort-12_93169109_124189486-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:44Z] INFO  00:44:51,159 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:44Z] INFO  00:44:51,159 HelpFormatter - Date/Time: 2015/10/01 00:44:51
[2015-09-30T23:44Z] INFO  00:44:51,160 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:44Z] INFO  00:44:51,160 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:44Z] INFO  00:44:51,253 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:44Z] INFO  00:44:51,328 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:44Z] INFO  00:44:51,335 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:44Z] INFO  00:44:51,358 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:44Z] INFO  00:44:52,034 IntervalUtils - Processing 2405 bp from intervals
[2015-09-30T23:44Z] WARN  00:44:52,038 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:44Z] WARN  00:44:52,038 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:44Z] INFO  00:44:52,095 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:44Z] INFO  00:44:52,233 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:44Z] INFO  00:44:52,234 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:44Z] INFO  00:44:52,234 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:44Z] INFO  00:44:52,235 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:44Z] INFO  00:44:52,275 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:45Z] INFO  00:45:03,892 VariantAnnotator - Processed 2154 loci.
[2015-09-30T23:45Z]
[2015-09-30T23:45Z] INFO  00:45:03,913 ProgressMeter -            done      9315.0    11.0 s      20.9 m      100.0%    11.0 s       0.0 s
[2015-09-30T23:45Z] INFO  00:45:03,914 ProgressMeter - Total runtime 11.68 secs, 0.19 min, 0.00 hours
[2015-09-30T23:45Z] INFO  00:45:03,914 MicroScheduler - 8846 reads were filtered out during the traversal out of approximately 183548 total reads (4.82%)
[2015-09-30T23:45Z] INFO  00:45:03,914 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:45Z] INFO  00:45:03,914 MicroScheduler -   -> 8810 reads (4.80% of total) failing DuplicateReadFilter
[2015-09-30T23:45Z] INFO  00:45:03,915 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:45Z] INFO  00:45:03,915 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:45Z] INFO  00:45:03,915 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:45Z] INFO  00:45:03,915 MicroScheduler -   -> 36 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:45Z] INFO  00:45:04,933 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:45Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:45Z] tabix index syn3-13_94938309_115169878-raw.vcf.gz
[2015-09-30T23:45Z] GATK: VariantAnnotator
[2015-09-30T23:45Z] INFO  00:45:32,540 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:45Z] INFO  00:45:32,542 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:45Z] INFO  00:45:32,542 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:45Z] INFO  00:45:32,542 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:45Z] INFO  00:45:32,546 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/13/syn3-13_94938309_115169878-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/13/tx/tmpXpkXPm/syn3-13_94938309_115169878-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/13/syn3-13_94938309_115169878-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/13/1_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/13/2_2014-08-13_dream-syn3-sort-13_94938309_115169878-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:45Z] INFO  00:45:32,551 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:45Z] INFO  00:45:32,551 HelpFormatter - Date/Time: 2015/10/01 00:45:32
[2015-09-30T23:45Z] INFO  00:45:32,551 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:45Z] INFO  00:45:32,552 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:45Z] INFO  00:45:32,643 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:45Z] INFO  00:45:32,722 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:45Z] INFO  00:45:32,730 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:45Z] INFO  00:45:32,752 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:45Z] INFO  00:45:33,284 IntervalUtils - Processing 1424 bp from intervals
[2015-09-30T23:45Z] WARN  00:45:33,288 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:45Z] WARN  00:45:33,288 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:45Z] INFO  00:45:33,343 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:45Z] INFO  00:45:33,444 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:45Z] INFO  00:45:33,444 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:45Z] INFO  00:45:33,444 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:45Z] INFO  00:45:33,445 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:45Z] INFO  00:45:33,485 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:45Z] INFO  00:45:40,197 VariantAnnotator - Processed 1258 loci.
[2015-09-30T23:45Z]
[2015-09-30T23:45Z] INFO  00:45:40,218 ProgressMeter -            done      8712.0     6.0 s      13.0 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:45Z] INFO  00:45:40,218 ProgressMeter - Total runtime 6.77 secs, 0.11 min, 0.00 hours
[2015-09-30T23:45Z] INFO  00:45:40,218 MicroScheduler - 5298 reads were filtered out during the traversal out of approximately 104713 total reads (5.06%)
[2015-09-30T23:45Z] INFO  00:45:40,218 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:45Z] INFO  00:45:40,219 MicroScheduler -   -> 5280 reads (5.04% of total) failing DuplicateReadFilter
[2015-09-30T23:45Z] INFO  00:45:40,219 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:45Z] INFO  00:45:40,219 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:45Z] INFO  00:45:40,219 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:45Z] INFO  00:45:40,219 MicroScheduler -   -> 18 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:45Z] INFO  00:45:41,307 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:45Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:45Z] WARNING(freebayes): Could not find any mapped reads in target region 14:28102367..28102404
[2015-09-30T23:45Z] tabix index syn3-14_0_31050569-raw.vcf.gz
[2015-09-30T23:45Z] GATK: VariantAnnotator
[2015-09-30T23:46Z] INFO  00:46:00,643 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:46Z] INFO  00:46:00,644 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:46Z] INFO  00:46:00,645 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:46Z] INFO  00:46:00,645 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:46Z] INFO  00:46:00,648 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/14/syn3-14_0_31050569-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/14/tx/tmpEhbL1t/syn3-14_0_31050569-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/14/syn3-14_0_31050569-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_0_31050569-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:46Z] INFO  00:46:00,653 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:46Z] INFO  00:46:00,654 HelpFormatter - Date/Time: 2015/10/01 00:46:00
[2015-09-30T23:46Z] INFO  00:46:00,654 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:46Z] INFO  00:46:00,654 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:46Z] INFO  00:46:00,743 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:46Z] INFO  00:46:00,817 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:46Z] INFO  00:46:00,825 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:46Z] INFO  00:46:00,847 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:46Z] INFO  00:46:01,333 IntervalUtils - Processing 1306 bp from intervals
[2015-09-30T23:46Z] WARN  00:46:01,337 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:46Z] WARN  00:46:01,338 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:46Z] INFO  00:46:01,414 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:46Z] INFO  00:46:01,484 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:46Z] INFO  00:46:01,485 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:46Z] INFO  00:46:01,485 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:46Z] INFO  00:46:01,485 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:46Z] INFO  00:46:01,523 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:46Z] INFO  00:46:08,712 VariantAnnotator - Processed 1173 loci.
[2015-09-30T23:46Z]
[2015-09-30T23:46Z] INFO  00:46:08,762 ProgressMeter -            done      7477.0     7.0 s      16.2 m       99.9%     7.0 s       0.0 s
[2015-09-30T23:46Z] INFO  00:46:08,763 ProgressMeter - Total runtime 7.28 secs, 0.12 min, 0.00 hours
[2015-09-30T23:46Z] INFO  00:46:08,763 MicroScheduler - 5176 reads were filtered out during the traversal out of approximately 105400 total reads (4.91%)
[2015-09-30T23:46Z] INFO  00:46:08,763 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:46Z] INFO  00:46:08,763 MicroScheduler -   -> 5156 reads (4.89% of total) failing DuplicateReadFilter
[2015-09-30T23:46Z] INFO  00:46:08,764 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:46Z] INFO  00:46:08,764 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:46Z] INFO  00:46:08,764 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:46Z] INFO  00:46:08,764 MicroScheduler -   -> 20 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:46Z] INFO  00:46:09,684 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:46Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:46Z] tabix index syn3-14_31055710_62162825-raw.vcf.gz
[2015-09-30T23:46Z] GATK: VariantAnnotator
[2015-09-30T23:46Z] INFO  00:46:22,301 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:46Z] INFO  00:46:22,304 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:46Z] INFO  00:46:22,304 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:46Z] INFO  00:46:22,304 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:46Z] INFO  00:46:22,307 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/14/syn3-14_31055710_62162825-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/14/tx/tmpgn1yFD/syn3-14_31055710_62162825-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/14/syn3-14_31055710_62162825-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_31055710_62162825-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:46Z] INFO  00:46:22,314 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:46Z] INFO  00:46:22,314 HelpFormatter - Date/Time: 2015/10/01 00:46:22
[2015-09-30T23:46Z] INFO  00:46:22,314 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:46Z] INFO  00:46:22,314 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:46Z] INFO  00:46:22,389 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:46Z] INFO  00:46:22,475 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:46Z] INFO  00:46:22,483 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:46Z] INFO  00:46:22,505 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:46Z] INFO  00:46:23,004 IntervalUtils - Processing 1515 bp from intervals
[2015-09-30T23:46Z] WARN  00:46:23,008 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:46Z] WARN  00:46:23,008 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:46Z] INFO  00:46:23,065 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:46Z] INFO  00:46:23,170 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:46Z] INFO  00:46:23,170 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:46Z] INFO  00:46:23,171 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:46Z] INFO  00:46:23,171 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:46Z] INFO  00:46:23,211 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:46Z] INFO  00:46:29,665 VariantAnnotator - Processed 1324 loci.
[2015-09-30T23:46Z]
[2015-09-30T23:46Z] INFO  00:46:29,686 ProgressMeter -            done      4786.0     6.0 s      22.7 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:46Z] INFO  00:46:29,686 ProgressMeter - Total runtime 6.52 secs, 0.11 min, 0.00 hours
[2015-09-30T23:46Z] INFO  00:46:29,687 MicroScheduler - 3633 reads were filtered out during the traversal out of approximately 84692 total reads (4.29%)
[2015-09-30T23:46Z] INFO  00:46:29,687 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:46Z] INFO  00:46:29,687 MicroScheduler -   -> 3616 reads (4.27% of total) failing DuplicateReadFilter
[2015-09-30T23:46Z] INFO  00:46:29,687 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:46Z] INFO  00:46:29,688 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:46Z] INFO  00:46:29,688 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:46Z] INFO  00:46:29,688 MicroScheduler -   -> 17 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:46Z] INFO  00:46:30,637 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:46Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:47Z] tabix index syn3-15_0_31041107-raw.vcf.gz
[2015-09-30T23:47Z] GATK: VariantAnnotator
[2015-09-30T23:47Z] INFO  00:47:21,391 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:47Z] INFO  00:47:21,393 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:47Z] INFO  00:47:21,393 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:47Z] INFO  00:47:21,394 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:47Z] INFO  00:47:21,397 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/15/syn3-15_0_31041107-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/15/tx/tmp9AeSAU/syn3-15_0_31041107-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/15/syn3-15_0_31041107-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_0_31041107-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:47Z] INFO  00:47:21,403 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:47Z] INFO  00:47:21,403 HelpFormatter - Date/Time: 2015/10/01 00:47:21
[2015-09-30T23:47Z] INFO  00:47:21,403 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:47Z] INFO  00:47:21,403 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:47Z] INFO  00:47:21,492 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:47Z] INFO  00:47:21,567 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:47Z] INFO  00:47:21,574 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:47Z] INFO  00:47:21,596 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:47Z] INFO  00:47:22,082 IntervalUtils - Processing 1052 bp from intervals
[2015-09-30T23:47Z] WARN  00:47:22,086 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:47Z] WARN  00:47:22,086 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:47Z] INFO  00:47:22,140 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:47Z] INFO  00:47:22,213 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:47Z] INFO  00:47:22,213 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:47Z] INFO  00:47:22,213 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:47Z] INFO  00:47:22,214 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:47Z] INFO  00:47:22,251 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:105634845..105634858
[2015-09-30T23:47Z] INFO  00:47:27,811 VariantAnnotator - Processed 994 loci.
[2015-09-30T23:47Z]
[2015-09-30T23:47Z] INFO  00:47:27,831 ProgressMeter -            done      8722.0     5.0 s      10.7 m       99.9%     5.0 s       0.0 s
[2015-09-30T23:47Z] INFO  00:47:27,831 ProgressMeter - Total runtime 5.62 secs, 0.09 min, 0.00 hours
[2015-09-30T23:47Z] INFO  00:47:27,831 MicroScheduler - 4341 reads were filtered out during the traversal out of approximately 91570 total reads (4.74%)
[2015-09-30T23:47Z] INFO  00:47:27,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:47Z] INFO  00:47:27,832 MicroScheduler -   -> 4327 reads (4.73% of total) failing DuplicateReadFilter
[2015-09-30T23:47Z] INFO  00:47:27,832 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:47Z] INFO  00:47:27,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:47Z] INFO  00:47:27,832 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:47Z] INFO  00:47:27,833 MicroScheduler -   -> 14 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:47Z] INFO  00:47:28,916 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:105781083..105781157
[2015-09-30T23:47Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:105886259..105886306
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106251619..106252405
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106303211..106304140
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106304414..106305019
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106306541..106307651
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106307959..106308538
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106310870..106312270
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106317994..106318823
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106320192..106322551
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106346621..106347691
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106350448..106351026
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106359120..106359690
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106360066..106360663
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106363538..106364104
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106366206..106367299
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106368207..106368796
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106369169..106369769
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106370067..106370813
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106375476..106376551
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106377836..106378402
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106378800..106379378
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106379940..106380521
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106382387..106382995
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106385059..106385616
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106387809..106388688
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106405241..106405428
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106405447..106406219
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106411134..106411701
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106444359..106444525
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106452404..106452447
[2015-09-30T23:47Z] WARNING(freebayes): Could not find any mapped reads in target region 14:106518118..106518128
[2015-09-30T23:47Z] tabix index syn3-14_62186823_93262365-raw.vcf.gz
[2015-09-30T23:47Z] GATK: VariantAnnotator
[2015-09-30T23:47Z] tabix index syn3-14_93263525_107349540-raw.vcf.gz
[2015-09-30T23:47Z] GATK: VariantAnnotator
[2015-09-30T23:47Z] INFO  00:47:44,448 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:47Z] INFO  00:47:44,450 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:47Z] INFO  00:47:44,450 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:47Z] INFO  00:47:44,450 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:47Z] INFO  00:47:44,454 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/14/syn3-14_62186823_93262365-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/14/tx/tmpicY7Ah/syn3-14_62186823_93262365-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/14/syn3-14_62186823_93262365-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_62186823_93262365-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:47Z] INFO  00:47:44,460 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:47Z] INFO  00:47:44,460 HelpFormatter - Date/Time: 2015/10/01 00:47:44
[2015-09-30T23:47Z] INFO  00:47:44,460 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:47Z] INFO  00:47:44,460 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:47Z] INFO  00:47:44,552 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:47Z] INFO  00:47:44,629 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:47Z] INFO  00:47:44,637 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:47Z] INFO  00:47:44,660 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:47Z] INFO  00:47:45,332 IntervalUtils - Processing 1765 bp from intervals
[2015-09-30T23:47Z] WARN  00:47:45,336 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:47Z] WARN  00:47:45,336 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:47Z] INFO  00:47:45,341 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:47Z] INFO  00:47:45,343 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:47Z] INFO  00:47:45,344 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:47Z] INFO  00:47:45,344 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:47Z] INFO  00:47:45,347 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/14/syn3-14_93263525_107349540-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/14/tx/tmpdj8yPR/syn3-14_93263525_107349540-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/14/syn3-14_93263525_107349540-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/14/1_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/14/2_2014-08-13_dream-syn3-sort-14_93263525_107349540-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:47Z] INFO  00:47:45,353 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:47Z] INFO  00:47:45,353 HelpFormatter - Date/Time: 2015/10/01 00:47:45
[2015-09-30T23:47Z] INFO  00:47:45,353 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:47Z] INFO  00:47:45,353 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:47Z] INFO  00:47:45,393 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:47Z] INFO  00:47:45,447 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:47Z] INFO  00:47:45,513 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:47Z] INFO  00:47:45,513 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:47Z] INFO  00:47:45,514 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:47Z] INFO  00:47:45,514 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:47Z] INFO  00:47:45,523 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:47Z] INFO  00:47:45,530 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:47Z] INFO  00:47:45,553 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:47Z] INFO  00:47:45,555 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:47Z] INFO  00:47:46,147 IntervalUtils - Processing 2231 bp from intervals
[2015-09-30T23:47Z] WARN  00:47:46,151 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:47Z] WARN  00:47:46,151 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:47Z] INFO  00:47:46,207 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:47Z] INFO  00:47:46,307 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:47Z] INFO  00:47:46,308 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:47Z] INFO  00:47:46,308 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:47Z] INFO  00:47:46,308 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:47Z] INFO  00:47:46,347 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:47Z] INFO  00:47:54,324 VariantAnnotator - Processed 1549 loci.
[2015-09-30T23:47Z]
[2015-09-30T23:47Z] INFO  00:47:54,616 ProgressMeter -            done      5939.0     9.0 s      25.5 m       99.9%     9.0 s       0.0 s
[2015-09-30T23:47Z] INFO  00:47:54,616 ProgressMeter - Total runtime 9.10 secs, 0.15 min, 0.00 hours
[2015-09-30T23:47Z] INFO  00:47:54,617 MicroScheduler - 6089 reads were filtered out during the traversal out of approximately 128730 total reads (4.73%)
[2015-09-30T23:47Z] INFO  00:47:54,617 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:47Z] INFO  00:47:54,617 MicroScheduler -   -> 6061 reads (4.71% of total) failing DuplicateReadFilter
[2015-09-30T23:47Z] INFO  00:47:54,617 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:47Z] INFO  00:47:54,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:47Z] INFO  00:47:54,618 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:47Z] INFO  00:47:54,618 MicroScheduler -   -> 28 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:47Z] INFO  00:47:55,688 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:47Z] INFO  00:47:55,958 VariantAnnotator - Processed 2030 loci.
[2015-09-30T23:47Z]
[2015-09-30T23:47Z] INFO  00:47:55,989 ProgressMeter -            done     23422.0     9.0 s       6.9 m      100.0%     9.0 s       0.0 s
[2015-09-30T23:47Z] INFO  00:47:55,989 ProgressMeter - Total runtime 9.68 secs, 0.16 min, 0.00 hours
[2015-09-30T23:47Z] INFO  00:47:55,989 MicroScheduler - 8011 reads were filtered out during the traversal out of approximately 146600 total reads (5.46%)
[2015-09-30T23:47Z] INFO  00:47:55,990 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:47Z] INFO  00:47:55,990 MicroScheduler -   -> 7975 reads (5.44% of total) failing DuplicateReadFilter
[2015-09-30T23:47Z] INFO  00:47:55,990 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:47Z] INFO  00:47:55,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:47Z] INFO  00:47:55,991 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:47Z] INFO  00:47:55,991 MicroScheduler -   -> 36 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:47Z] INFO  00:47:56,924 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:47Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:47Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:48Z] tabix index syn3-15_93173163_102531392-raw.vcf.gz
[2015-09-30T23:48Z] GATK: VariantAnnotator
[2015-09-30T23:48Z] INFO  00:48:26,744 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:48Z] INFO  00:48:26,746 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:48Z] INFO  00:48:26,746 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:48Z] INFO  00:48:26,746 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:48Z] INFO  00:48:26,750 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/15/syn3-15_93173163_102531392-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/15/tx/tmpJIpSMF/syn3-15_93173163_102531392-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/15/syn3-15_93173163_102531392-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_93173163_102531392-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:48Z] INFO  00:48:26,755 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:48Z] INFO  00:48:26,755 HelpFormatter - Date/Time: 2015/10/01 00:48:26
[2015-09-30T23:48Z] INFO  00:48:26,755 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:48Z] INFO  00:48:26,755 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:48Z] INFO  00:48:26,843 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:48Z] INFO  00:48:26,916 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:48Z] INFO  00:48:26,924 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:48Z] INFO  00:48:26,945 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:48Z] INFO  00:48:27,259 IntervalUtils - Processing 576 bp from intervals
[2015-09-30T23:48Z] WARN  00:48:27,263 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:48Z] WARN  00:48:27,263 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:48Z] INFO  00:48:27,317 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:48Z] INFO  00:48:27,847 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:48Z] INFO  00:48:27,848 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:48Z] INFO  00:48:27,848 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:48Z] INFO  00:48:27,848 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:48Z] INFO  00:48:27,890 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:48Z] INFO  00:48:31,600 VariantAnnotator - Processed 529 loci.
[2015-09-30T23:48Z]
[2015-09-30T23:48Z] INFO  00:48:31,620 ProgressMeter -            done      2457.0     3.0 s      25.6 m       99.8%     3.0 s       0.0 s
[2015-09-30T23:48Z] INFO  00:48:31,621 ProgressMeter - Total runtime 3.77 secs, 0.06 min, 0.00 hours
[2015-09-30T23:48Z] INFO  00:48:31,621 MicroScheduler - 2481 reads were filtered out during the traversal out of approximately 47749 total reads (5.20%)
[2015-09-30T23:48Z] INFO  00:48:31,621 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:48Z] INFO  00:48:31,621 MicroScheduler -   -> 2475 reads (5.18% of total) failing DuplicateReadFilter
[2015-09-30T23:48Z] INFO  00:48:31,622 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:48Z] INFO  00:48:31,622 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:48Z] INFO  00:48:31,622 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:48Z] INFO  00:48:31,622 MicroScheduler -   -> 6 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:48Z] INFO  00:48:32,624 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:48Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:49Z] WARNING(freebayes): Could not find any mapped reads in target region 16:1664389..1664448
[2015-09-30T23:49Z] WARNING(freebayes): Could not find any mapped reads in target region 16:2246560..2246597
[2015-09-30T23:49Z] WARNING(freebayes): Could not find any mapped reads in target region 16:2246686..2246693
[2015-09-30T23:49Z] WARNING(freebayes): Could not find any mapped reads in target region 15:52311678..52311784
[2015-09-30T23:50Z] tabix index syn3-15_31042312_62147370-raw.vcf.gz
[2015-09-30T23:50Z] GATK: VariantAnnotator
[2015-09-30T23:50Z] INFO  00:50:09,441 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:50Z] INFO  00:50:09,443 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:50Z] INFO  00:50:09,443 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:50Z] INFO  00:50:09,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:50Z] INFO  00:50:09,447 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/15/syn3-15_31042312_62147370-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/15/tx/tmpBr4uSK/syn3-15_31042312_62147370-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/15/syn3-15_31042312_62147370-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_31042312_62147370-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:50Z] INFO  00:50:09,452 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:50Z] INFO  00:50:09,452 HelpFormatter - Date/Time: 2015/10/01 00:50:09
[2015-09-30T23:50Z] INFO  00:50:09,453 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:50Z] INFO  00:50:09,453 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:50Z] INFO  00:50:09,544 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:50Z] INFO  00:50:09,621 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:50Z] INFO  00:50:09,629 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:50Z] INFO  00:50:09,651 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:50Z] INFO  00:50:10,272 IntervalUtils - Processing 2561 bp from intervals
[2015-09-30T23:50Z] WARN  00:50:10,276 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:50Z] WARN  00:50:10,277 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:50Z] INFO  00:50:10,334 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:50Z] INFO  00:50:10,467 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:50Z] INFO  00:50:10,467 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:50Z] INFO  00:50:10,468 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:50Z] INFO  00:50:10,468 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:50Z] INFO  00:50:10,507 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:50Z] INFO  00:50:22,683 VariantAnnotator - Processed 2296 loci.
[2015-09-30T23:50Z]
[2015-09-30T23:50Z] INFO  00:50:22,705 ProgressMeter -            done     10230.0    12.0 s      19.9 m      100.0%    12.0 s       0.0 s
[2015-09-30T23:50Z] INFO  00:50:22,705 ProgressMeter - Total runtime 12.24 secs, 0.20 min, 0.00 hours
[2015-09-30T23:50Z] INFO  00:50:22,705 MicroScheduler - 8524 reads were filtered out during the traversal out of approximately 184405 total reads (4.62%)
[2015-09-30T23:50Z] INFO  00:50:22,706 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:50Z] INFO  00:50:22,706 MicroScheduler -   -> 8483 reads (4.60% of total) failing DuplicateReadFilter
[2015-09-30T23:50Z] INFO  00:50:22,706 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:50Z] INFO  00:50:22,706 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:50Z] INFO  00:50:22,707 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:50Z] INFO  00:50:22,707 MicroScheduler -   -> 41 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:50Z] INFO  00:50:23,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:50Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:50Z] WARNING(freebayes): Could not find any mapped reads in target region 16:9057250..9057279
[2015-09-30T23:50Z] WARNING(freebayes): Could not find any mapped reads in target region 16:33778259..33778338
[2015-09-30T23:51Z] tabix index syn3-15_62148224_93170844-raw.vcf.gz
[2015-09-30T23:51Z] GATK: VariantAnnotator
[2015-09-30T23:51Z] INFO  00:51:04,572 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:51Z] INFO  00:51:04,574 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:51Z] INFO  00:51:04,574 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:51Z] INFO  00:51:04,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:51Z] INFO  00:51:04,578 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/15/syn3-15_62148224_93170844-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/15/tx/tmpUk4NWR/syn3-15_62148224_93170844-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/15/syn3-15_62148224_93170844-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/15/1_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/15/2_2014-08-13_dream-syn3-sort-15_62148224_93170844-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:51Z] INFO  00:51:04,583 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:51Z] INFO  00:51:04,584 HelpFormatter - Date/Time: 2015/10/01 00:51:04
[2015-09-30T23:51Z] INFO  00:51:04,584 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:51Z] INFO  00:51:04,584 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:51Z] INFO  00:51:04,677 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:51Z] INFO  00:51:04,756 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:51Z] INFO  00:51:04,763 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:51Z] INFO  00:51:04,786 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:51Z] INFO  00:51:05,403 IntervalUtils - Processing 2753 bp from intervals
[2015-09-30T23:51Z] WARN  00:51:05,407 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:51Z] WARN  00:51:05,407 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:51Z] INFO  00:51:05,462 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:51Z] INFO  00:51:05,598 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:51Z] INFO  00:51:05,598 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:51Z] INFO  00:51:05,598 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:51Z] INFO  00:51:05,599 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:51Z] INFO  00:51:05,637 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:51Z] INFO  00:51:19,524 VariantAnnotator - Processed 2414 loci.
[2015-09-30T23:51Z]
[2015-09-30T23:51Z] INFO  00:51:19,548 ProgressMeter -            done     13018.0    13.0 s      17.9 m      100.0%    13.0 s       0.0 s
[2015-09-30T23:51Z] INFO  00:51:19,548 ProgressMeter - Total runtime 13.95 secs, 0.23 min, 0.00 hours
[2015-09-30T23:51Z] INFO  00:51:19,549 MicroScheduler - 11728 reads were filtered out during the traversal out of approximately 227798 total reads (5.15%)
[2015-09-30T23:51Z] INFO  00:51:19,549 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:51Z] INFO  00:51:19,549 MicroScheduler -   -> 11679 reads (5.13% of total) failing DuplicateReadFilter
[2015-09-30T23:51Z] INFO  00:51:19,549 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:51Z] INFO  00:51:19,550 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:51Z] INFO  00:51:19,550 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:51Z] INFO  00:51:19,550 MicroScheduler -   -> 49 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:51Z] INFO  00:51:20,500 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:51Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:51Z] WARNING(freebayes): Could not find any mapped reads in target region 16:55813355..55813915
[2015-09-30T23:51Z] WARNING(freebayes): Could not find any mapped reads in target region 16:66730586..66730596
[2015-09-30T23:51Z] WARNING(freebayes): Could not find any mapped reads in target region 16:58231711..58231775
[2015-09-30T23:51Z] WARNING(freebayes): Could not find any mapped reads in target region 16:58231836..58231854
[2015-09-30T23:52Z] tabix index syn3-16_31044089_62860191-raw.vcf.gz
[2015-09-30T23:52Z] GATK: VariantAnnotator
[2015-09-30T23:52Z] INFO  00:52:03,459 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:52Z] INFO  00:52:03,461 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:52Z] INFO  00:52:03,461 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:52Z] INFO  00:52:03,461 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:52Z] INFO  00:52:03,465 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/16/syn3-16_31044089_62860191-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/16/tx/tmpBnHupw/syn3-16_31044089_62860191-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/16/syn3-16_31044089_62860191-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_31044089_62860191-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:52Z] INFO  00:52:03,470 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:52Z] INFO  00:52:03,470 HelpFormatter - Date/Time: 2015/10/01 00:52:03
[2015-09-30T23:52Z] INFO  00:52:03,471 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:52Z] INFO  00:52:03,471 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:52Z] INFO  00:52:03,562 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:52Z] INFO  00:52:03,640 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:52Z] INFO  00:52:03,648 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:52Z] INFO  00:52:03,670 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:52Z] INFO  00:52:04,206 IntervalUtils - Processing 1694 bp from intervals
[2015-09-30T23:52Z] WARN  00:52:04,211 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:52Z] WARN  00:52:04,211 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:52Z] INFO  00:52:04,273 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:52Z] INFO  00:52:04,366 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:52Z] INFO  00:52:04,367 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:52Z] INFO  00:52:04,367 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:52Z] INFO  00:52:04,368 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:52Z] INFO  00:52:04,407 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:52Z] INFO  00:52:13,868 VariantAnnotator - Processed 1548 loci.
[2015-09-30T23:52Z]
[2015-09-30T23:52Z] INFO  00:52:13,903 ProgressMeter -            done     13107.0     9.0 s      12.1 m       99.9%     9.0 s       0.0 s
[2015-09-30T23:52Z] INFO  00:52:13,903 ProgressMeter - Total runtime 9.54 secs, 0.16 min, 0.00 hours
[2015-09-30T23:52Z] INFO  00:52:13,904 MicroScheduler - 7666 reads were filtered out during the traversal out of approximately 143944 total reads (5.33%)
[2015-09-30T23:52Z] INFO  00:52:13,904 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:52Z] INFO  00:52:13,904 MicroScheduler -   -> 7603 reads (5.28% of total) failing DuplicateReadFilter
[2015-09-30T23:52Z] INFO  00:52:13,904 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:52Z] INFO  00:52:13,905 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:52Z] INFO  00:52:13,905 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:52Z] INFO  00:52:13,905 MicroScheduler -   -> 63 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T23:52Z] INFO  00:52:14,835 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:52Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:53Z] WARNING(freebayes): Could not find any mapped reads in target region 16:80837887..80837951
[2015-09-30T23:53Z] tabix index syn3-16_0_31021934-raw.vcf.gz
[2015-09-30T23:53Z] GATK: VariantAnnotator
[2015-09-30T23:53Z] INFO  00:53:10,502 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:53Z] INFO  00:53:10,504 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:53Z] INFO  00:53:10,504 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:53Z] INFO  00:53:10,504 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:53Z] INFO  00:53:10,508 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/16/syn3-16_0_31021934-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/16/tx/tmpJYleHw/syn3-16_0_31021934-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/16/syn3-16_0_31021934-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_0_31021934-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:53Z] INFO  00:53:10,514 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:53Z] INFO  00:53:10,514 HelpFormatter - Date/Time: 2015/10/01 00:53:10
[2015-09-30T23:53Z] INFO  00:53:10,514 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:53Z] INFO  00:53:10,514 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:53Z] INFO  00:53:10,752 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:53Z] INFO  00:53:10,828 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:53Z] INFO  00:53:10,836 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:53Z] INFO  00:53:10,858 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:53Z] INFO  00:53:11,527 IntervalUtils - Processing 3784 bp from intervals
[2015-09-30T23:53Z] WARN  00:53:11,532 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:53Z] WARN  00:53:11,532 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:53Z] INFO  00:53:11,589 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:53Z] INFO  00:53:11,738 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:53Z] INFO  00:53:11,739 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:53Z] INFO  00:53:11,739 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:53Z] INFO  00:53:11,739 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:53Z] INFO  00:53:11,778 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:53Z] WARNING(freebayes): Could not find any mapped reads in target region 16:84002199..84002213
[2015-09-30T23:53Z] INFO  00:53:31,066 VariantAnnotator - Processed 3389 loci.
[2015-09-30T23:53Z]
[2015-09-30T23:53Z] INFO  00:53:31,088 ProgressMeter -            done     22991.0    19.0 s      14.0 m      100.0%    19.0 s       0.0 s
[2015-09-30T23:53Z] INFO  00:53:31,088 ProgressMeter - Total runtime 19.35 secs, 0.32 min, 0.01 hours
[2015-09-30T23:53Z] INFO  00:53:31,088 MicroScheduler - 18416 reads were filtered out during the traversal out of approximately 336937 total reads (5.47%)
[2015-09-30T23:53Z] INFO  00:53:31,089 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:53Z] INFO  00:53:31,089 MicroScheduler -   -> 18351 reads (5.45% of total) failing DuplicateReadFilter
[2015-09-30T23:53Z] INFO  00:53:31,089 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:53Z] INFO  00:53:31,089 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:53Z] INFO  00:53:31,090 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:53Z] INFO  00:53:31,090 MicroScheduler -   -> 65 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:53Z] INFO  00:53:32,140 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:53Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:53Z] WARNING(freebayes): Could not find any mapped reads in target region 16:87526030..87526047
[2015-09-30T23:54Z] tabix index syn3-16_64294277_90354753-raw.vcf.gz
[2015-09-30T23:54Z] GATK: VariantAnnotator
[2015-09-30T23:54Z] INFO  00:54:16,886 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:54Z] INFO  00:54:16,888 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:54Z] INFO  00:54:16,888 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:54Z] INFO  00:54:16,888 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:54Z] INFO  00:54:16,892 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/16/syn3-16_64294277_90354753-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/16/tx/tmp2jf1E_/syn3-16_64294277_90354753-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/16/syn3-16_64294277_90354753-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/16/1_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/16/2_2014-08-13_dream-syn3-sort-16_64294277_90354753-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:54Z] INFO  00:54:16,897 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:54Z] INFO  00:54:16,897 HelpFormatter - Date/Time: 2015/10/01 00:54:16
[2015-09-30T23:54Z] INFO  00:54:16,898 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:54Z] INFO  00:54:16,898 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:54Z] INFO  00:54:16,991 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:54Z] INFO  00:54:17,068 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:54Z] INFO  00:54:17,076 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:54Z] INFO  00:54:17,098 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:54Z] INFO  00:54:17,739 IntervalUtils - Processing 2771 bp from intervals
[2015-09-30T23:54Z] WARN  00:54:17,744 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:54Z] WARN  00:54:17,744 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:54Z] INFO  00:54:17,800 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:54Z] INFO  00:54:17,938 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:54Z] INFO  00:54:17,938 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:54Z] INFO  00:54:17,939 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:54Z] INFO  00:54:17,939 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:54Z] INFO  00:54:17,978 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:54Z] INFO  00:54:31,690 VariantAnnotator - Processed 2512 loci.
[2015-09-30T23:54Z]
[2015-09-30T23:54Z] INFO  00:54:31,727 ProgressMeter -            done     17108.0    13.0 s      13.4 m      100.0%    13.0 s       0.0 s
[2015-09-30T23:54Z] INFO  00:54:31,728 ProgressMeter - Total runtime 13.79 secs, 0.23 min, 0.00 hours
[2015-09-30T23:54Z] INFO  00:54:31,728 MicroScheduler - 12419 reads were filtered out during the traversal out of approximately 237507 total reads (5.23%)
[2015-09-30T23:54Z] INFO  00:54:31,728 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:54Z] INFO  00:54:31,728 MicroScheduler -   -> 12372 reads (5.21% of total) failing DuplicateReadFilter
[2015-09-30T23:54Z] INFO  00:54:31,729 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:54Z] INFO  00:54:31,729 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:54Z] INFO  00:54:31,729 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:54Z] INFO  00:54:31,729 MicroScheduler -   -> 47 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:54Z] INFO  00:54:32,653 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:54Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:55Z] WARNING(freebayes): Could not find any mapped reads in target region 17:68908694..68908703
[2015-09-30T23:56Z] tabix index syn3-17_0_31039439-raw.vcf.gz
[2015-09-30T23:56Z] GATK: VariantAnnotator
[2015-09-30T23:56Z] INFO  00:56:46,481 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:56Z] INFO  00:56:46,483 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:56Z] INFO  00:56:46,483 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:56Z] INFO  00:56:46,483 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:56Z] INFO  00:56:46,487 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/17/syn3-17_0_31039439-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/17/tx/tmptQpH2g/syn3-17_0_31039439-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/17/syn3-17_0_31039439-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_0_31039439-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:56Z] INFO  00:56:46,493 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:56Z] INFO  00:56:46,493 HelpFormatter - Date/Time: 2015/10/01 00:56:46
[2015-09-30T23:56Z] INFO  00:56:46,493 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:56Z] INFO  00:56:46,493 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:56Z] INFO  00:56:46,582 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:56Z] INFO  00:56:46,658 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:56Z] INFO  00:56:46,666 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:56Z] INFO  00:56:46,688 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:56Z] INFO  00:56:47,389 IntervalUtils - Processing 4378 bp from intervals
[2015-09-30T23:56Z] WARN  00:56:47,393 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:56Z] WARN  00:56:47,394 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:56Z] INFO  00:56:47,449 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:56Z] INFO  00:56:47,622 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:56Z] INFO  00:56:47,622 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:56Z] INFO  00:56:47,622 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:56Z] INFO  00:56:47,623 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:56Z] INFO  00:56:47,661 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:57Z] INFO  00:57:07,362 VariantAnnotator - Processed 3827 loci.
[2015-09-30T23:57Z]
[2015-09-30T23:57Z] INFO  00:57:07,556 ProgressMeter -            done     53195.0    19.0 s       6.2 m      100.0%    19.0 s       0.0 s
[2015-09-30T23:57Z] INFO  00:57:07,558 ProgressMeter - Total runtime 19.94 secs, 0.33 min, 0.01 hours
[2015-09-30T23:57Z] INFO  00:57:07,559 MicroScheduler - 19081 reads were filtered out during the traversal out of approximately 356756 total reads (5.35%)
[2015-09-30T23:57Z] INFO  00:57:07,559 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:57Z] INFO  00:57:07,560 MicroScheduler -   -> 18971 reads (5.32% of total) failing DuplicateReadFilter
[2015-09-30T23:57Z] INFO  00:57:07,560 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:57Z] INFO  00:57:07,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:57Z] INFO  00:57:07,561 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:57Z] INFO  00:57:07,561 MicroScheduler -   -> 110 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:57Z] INFO  00:57:08,619 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:57Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:57Z] tabix index syn3-17_62078196_81195210-raw.vcf.gz
[2015-09-30T23:57Z] GATK: VariantAnnotator
[2015-09-30T23:57Z] INFO  00:57:33,736 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:57Z] INFO  00:57:33,738 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:57Z] INFO  00:57:33,738 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:57Z] INFO  00:57:33,738 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:57Z] INFO  00:57:33,742 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/17/syn3-17_62078196_81195210-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/17/tx/tmpA3NHZh/syn3-17_62078196_81195210-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/17/syn3-17_62078196_81195210-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_62078196_81195210-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:57Z] INFO  00:57:33,748 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:57Z] INFO  00:57:33,748 HelpFormatter - Date/Time: 2015/10/01 00:57:33
[2015-09-30T23:57Z] INFO  00:57:33,748 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:57Z] INFO  00:57:33,749 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:57Z] INFO  00:57:33,983 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:57Z] INFO  00:57:34,057 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:57Z] INFO  00:57:34,065 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:57Z] INFO  00:57:34,087 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:57Z] INFO  00:57:34,762 IntervalUtils - Processing 2973 bp from intervals
[2015-09-30T23:57Z] WARN  00:57:34,767 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:57Z] WARN  00:57:34,767 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:57Z] INFO  00:57:34,822 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:57Z] INFO  00:57:34,944 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:57Z] INFO  00:57:34,944 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:57Z] INFO  00:57:34,945 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:57Z] INFO  00:57:34,945 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:57Z] INFO  00:57:34,983 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:57Z] WARNING(freebayes): Could not find any mapped reads in target region 18:9614624..9614655
[2015-09-30T23:57Z] INFO  00:57:49,194 VariantAnnotator - Processed 2628 loci.
[2015-09-30T23:57Z]
[2015-09-30T23:57Z] INFO  00:57:49,216 ProgressMeter -            done     18007.0    14.0 s      13.2 m      100.0%    14.0 s       0.0 s
[2015-09-30T23:57Z] INFO  00:57:49,216 ProgressMeter - Total runtime 14.27 secs, 0.24 min, 0.00 hours
[2015-09-30T23:57Z] INFO  00:57:49,217 MicroScheduler - 14329 reads were filtered out during the traversal out of approximately 263160 total reads (5.44%)
[2015-09-30T23:57Z] INFO  00:57:49,217 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:57Z] INFO  00:57:49,217 MicroScheduler -   -> 14269 reads (5.42% of total) failing DuplicateReadFilter
[2015-09-30T23:57Z] INFO  00:57:49,217 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:57Z] INFO  00:57:49,218 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:57Z] INFO  00:57:49,218 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:57Z] INFO  00:57:49,218 MicroScheduler -   -> 60 reads (0.02% of total) failing UnmappedReadFilter
[2015-09-30T23:57Z] INFO  00:57:50,156 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:57Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:58Z] tabix index syn3-17_31047756_62076645-raw.vcf.gz
[2015-09-30T23:58Z] GATK: VariantAnnotator
[2015-09-30T23:58Z] INFO  00:58:05,132 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:05,134 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:58Z] INFO  00:58:05,134 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:58Z] INFO  00:58:05,135 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:58Z] INFO  00:58:05,138 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/17/syn3-17_31047756_62076645-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/17/tx/tmpeeve1D/syn3-17_31047756_62076645-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/17/syn3-17_31047756_62076645-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/17/1_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/17/2_2014-08-13_dream-syn3-sort-17_31047756_62076645-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:58Z] INFO  00:58:05,157 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:58Z] INFO  00:58:05,157 HelpFormatter - Date/Time: 2015/10/01 00:58:05
[2015-09-30T23:58Z] INFO  00:58:05,158 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:05,158 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:05,249 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:58Z] INFO  00:58:05,327 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:58Z] INFO  00:58:05,335 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:58Z] INFO  00:58:05,358 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:58Z] INFO  00:58:06,051 IntervalUtils - Processing 3522 bp from intervals
[2015-09-30T23:58Z] WARN  00:58:06,056 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:58Z] WARN  00:58:06,056 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:58Z] INFO  00:58:06,113 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:58Z] INFO  00:58:06,266 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:58Z] INFO  00:58:06,266 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:58Z] INFO  00:58:06,267 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:58Z] INFO  00:58:06,267 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:58Z] INFO  00:58:06,337 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:58Z] INFO  00:58:24,299 VariantAnnotator - Processed 3132 loci.
[2015-09-30T23:58Z]
[2015-09-30T23:58Z] INFO  00:58:24,331 ProgressMeter -            done     17483.0    18.0 s      17.2 m      100.0%    18.0 s       0.0 s
[2015-09-30T23:58Z] INFO  00:58:24,331 ProgressMeter - Total runtime 18.07 secs, 0.30 min, 0.01 hours
[2015-09-30T23:58Z] INFO  00:58:24,331 MicroScheduler - 16922 reads were filtered out during the traversal out of approximately 298698 total reads (5.67%)
[2015-09-30T23:58Z] INFO  00:58:24,332 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:58Z] INFO  00:58:24,332 MicroScheduler -   -> 16814 reads (5.63% of total) failing DuplicateReadFilter
[2015-09-30T23:58Z] INFO  00:58:24,332 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:58Z] INFO  00:58:24,332 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:58Z] INFO  00:58:24,333 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:58Z] INFO  00:58:24,333 MicroScheduler -   -> 108 reads (0.04% of total) failing UnmappedReadFilter
[2015-09-30T23:58Z] INFO  00:58:25,454 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:58Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:58Z] tabix index syn3-18_0_31142016-raw.vcf.gz
[2015-09-30T23:58Z] GATK: VariantAnnotator
[2015-09-30T23:58Z] INFO  00:58:30,165 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:30,167 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:58Z] INFO  00:58:30,167 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:58Z] INFO  00:58:30,167 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:58Z] INFO  00:58:30,170 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/18/syn3-18_0_31142016-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/18/tx/tmpji9zPY/syn3-18_0_31142016-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/18/syn3-18_0_31142016-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_0_31142016-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:58Z] INFO  00:58:30,176 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:58Z] INFO  00:58:30,176 HelpFormatter - Date/Time: 2015/10/01 00:58:30
[2015-09-30T23:58Z] INFO  00:58:30,176 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:30,176 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:30,266 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:58Z] INFO  00:58:30,346 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:58Z] INFO  00:58:30,354 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:58Z] INFO  00:58:30,376 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:58Z] INFO  00:58:31,155 IntervalUtils - Processing 1615 bp from intervals
[2015-09-30T23:58Z] WARN  00:58:31,159 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:58Z] WARN  00:58:31,159 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:58Z] INFO  00:58:31,219 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:58Z] INFO  00:58:31,316 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:58Z] INFO  00:58:31,316 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:58Z] INFO  00:58:31,317 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:58Z] INFO  00:58:31,317 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:58Z] INFO  00:58:31,357 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:58Z] INFO  00:58:38,627 VariantAnnotator - Processed 1445 loci.
[2015-09-30T23:58Z]
[2015-09-30T23:58Z] INFO  00:58:38,647 ProgressMeter -            done      7316.0     7.0 s      16.7 m       99.9%     7.0 s       0.0 s
[2015-09-30T23:58Z] INFO  00:58:38,647 ProgressMeter - Total runtime 7.33 secs, 0.12 min, 0.00 hours
[2015-09-30T23:58Z] INFO  00:58:38,647 MicroScheduler - 4420 reads were filtered out during the traversal out of approximately 99078 total reads (4.46%)
[2015-09-30T23:58Z] INFO  00:58:38,648 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:58Z] INFO  00:58:38,648 MicroScheduler -   -> 4406 reads (4.45% of total) failing DuplicateReadFilter
[2015-09-30T23:58Z] INFO  00:58:38,648 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:58Z] INFO  00:58:38,648 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:58Z] INFO  00:58:38,648 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:58Z] INFO  00:58:38,649 MicroScheduler -   -> 14 reads (0.01% of total) failing UnmappedReadFilter
[2015-09-30T23:58Z] INFO  00:58:39,662 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:58Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:58Z] tabix index syn3-18_63476668_78077248-raw.vcf.gz
[2015-09-30T23:58Z] GATK: VariantAnnotator
[2015-09-30T23:58Z] WARNING(freebayes): Could not find any mapped reads in target region 19:589883..589991
[2015-09-30T23:58Z] INFO  00:58:49,925 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:49,927 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:58Z] INFO  00:58:49,928 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:58Z] INFO  00:58:49,928 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:58Z] INFO  00:58:49,931 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/18/syn3-18_63476668_78077248-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/18/tx/tmpUqMe7_/syn3-18_63476668_78077248-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/18/syn3-18_63476668_78077248-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_63476668_78077248-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:58Z] INFO  00:58:49,937 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:58Z] INFO  00:58:49,937 HelpFormatter - Date/Time: 2015/10/01 00:58:49
[2015-09-30T23:58Z] INFO  00:58:49,937 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:49,937 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:50,028 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:58Z] INFO  00:58:50,101 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:58Z] INFO  00:58:50,108 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:58Z] INFO  00:58:50,129 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:58Z] INFO  00:58:50,423 IntervalUtils - Processing 424 bp from intervals
[2015-09-30T23:58Z] WARN  00:58:50,427 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:58Z] WARN  00:58:50,427 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:58Z] INFO  00:58:50,481 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:58Z] INFO  00:58:50,534 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:58Z] INFO  00:58:50,534 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:58Z] INFO  00:58:50,534 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:58Z] INFO  00:58:50,535 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:58Z] INFO  00:58:50,638 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:58Z] WARNING(freebayes): Could not find any mapped reads in target region 19:708893..708991
[2015-09-30T23:58Z] INFO  00:58:53,737 VariantAnnotator - Processed 364 loci.
[2015-09-30T23:58Z]
[2015-09-30T23:58Z] INFO  00:58:53,757 ProgressMeter -            done      1422.0     3.0 s      37.8 m       99.8%     3.0 s       0.0 s
[2015-09-30T23:58Z] INFO  00:58:53,757 ProgressMeter - Total runtime 3.22 secs, 0.05 min, 0.00 hours
[2015-09-30T23:58Z] INFO  00:58:53,757 MicroScheduler - 1456 reads were filtered out during the traversal out of approximately 29142 total reads (5.00%)
[2015-09-30T23:58Z] INFO  00:58:53,758 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:58Z] INFO  00:58:53,758 MicroScheduler -   -> 1447 reads (4.97% of total) failing DuplicateReadFilter
[2015-09-30T23:58Z] INFO  00:58:53,758 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:58Z] INFO  00:58:53,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:58Z] INFO  00:58:53,758 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:58Z] INFO  00:58:53,759 MicroScheduler -   -> 9 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:58Z] INFO  00:58:54,688 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:58Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:58Z] tabix index syn3-18_31158315_63430522-raw.vcf.gz
[2015-09-30T23:58Z] GATK: VariantAnnotator
[2015-09-30T23:58Z] INFO  00:58:59,405 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:59,407 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-09-30T23:58Z] INFO  00:58:59,407 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-09-30T23:58Z] INFO  00:58:59,407 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-09-30T23:58Z] INFO  00:58:59,411 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/18/syn3-18_31158315_63430522-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/18/tx/tmpXJiyTU/syn3-18_31158315_63430522-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/18/syn3-18_31158315_63430522-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/18/1_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/18/2_2014-08-13_dream-syn3-sort-18_31158315_63430522-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-09-30T23:58Z] INFO  00:58:59,417 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-09-30T23:58Z] INFO  00:58:59,417 HelpFormatter - Date/Time: 2015/10/01 00:58:59
[2015-09-30T23:58Z] INFO  00:58:59,417 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:59,417 HelpFormatter - --------------------------------------------------------------------------------
[2015-09-30T23:58Z] INFO  00:58:59,698 GenomeAnalysisEngine - Strictness is SILENT
[2015-09-30T23:58Z] INFO  00:58:59,771 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-09-30T23:58Z] INFO  00:58:59,778 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-09-30T23:58Z] INFO  00:58:59,799 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-09-30T23:59Z] INFO  00:59:00,273 IntervalUtils - Processing 1296 bp from intervals
[2015-09-30T23:59Z] WARN  00:59:00,277 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:59Z] WARN  00:59:00,277 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-09-30T23:59Z] INFO  00:59:00,332 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-09-30T23:59Z] INFO  00:59:00,425 GenomeAnalysisEngine - Done preparing for traversal
[2015-09-30T23:59Z] INFO  00:59:00,426 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-09-30T23:59Z] INFO  00:59:00,426 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-09-30T23:59Z] INFO  00:59:00,426 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-09-30T23:59Z] INFO  00:59:00,465 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-09-30T23:59Z] INFO  00:59:06,596 VariantAnnotator - Processed 1127 loci.
[2015-09-30T23:59Z]
[2015-09-30T23:59Z] INFO  00:59:06,617 ProgressMeter -            done      5312.0     6.0 s      19.4 m       99.9%     6.0 s       0.0 s
[2015-09-30T23:59Z] INFO  00:59:06,618 ProgressMeter - Total runtime 6.19 secs, 0.10 min, 0.00 hours
[2015-09-30T23:59Z] INFO  00:59:06,618 MicroScheduler - 3935 reads were filtered out during the traversal out of approximately 86318 total reads (4.56%)
[2015-09-30T23:59Z] INFO  00:59:06,618 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-09-30T23:59Z] INFO  00:59:06,618 MicroScheduler -   -> 3913 reads (4.53% of total) failing DuplicateReadFilter
[2015-09-30T23:59Z] INFO  00:59:06,619 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-09-30T23:59Z] INFO  00:59:06,619 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-09-30T23:59Z] INFO  00:59:06,619 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-09-30T23:59Z] INFO  00:59:06,619 MicroScheduler -   -> 22 reads (0.03% of total) failing UnmappedReadFilter
[2015-09-30T23:59Z] INFO  00:59:07,573 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-09-30T23:59Z] Genotyping paired variants with FreeBayes
[2015-09-30T23:59Z] WARNING(freebayes): Could not find any mapped reads in target region 19:1568031..1568072
[2015-09-30T23:59Z] WARNING(freebayes): Could not find any mapped reads in target region 19:1568128..1568159
[2015-09-30T23:59Z] WARNING(freebayes): Could not find any mapped reads in target region 20:1568934..1569518
[2015-09-30T23:59Z] WARNING(freebayes): Could not find any mapped reads in target region 20:1579163..1579830
[2015-09-30T23:59Z] WARNING(freebayes): Could not find any mapped reads in target region 19:36208893..36208960
[2015-09-30T23:59Z] WARNING(freebayes): Could not find any mapped reads in target region 19:3224670..3224684
[2015-10-01T00:01Z] tabix index syn3-20_0_31018105-raw.vcf.gz
[2015-10-01T00:01Z] GATK: VariantAnnotator
[2015-10-01T00:01Z] WARNING(freebayes): Could not find any mapped reads in target region 19:7581083..7581155
[2015-10-01T00:01Z] INFO  01:01:05,393 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:01Z] INFO  01:01:05,395 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:01Z] INFO  01:01:05,395 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:01Z] INFO  01:01:05,395 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:01Z] INFO  01:01:05,399 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/20/syn3-20_0_31018105-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/20/tx/tmpFQgCcw/syn3-20_0_31018105-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/20/syn3-20_0_31018105-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_0_31018105-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:01Z] INFO  01:01:05,404 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:01Z] INFO  01:01:05,405 HelpFormatter - Date/Time: 2015/10/01 01:01:05
[2015-10-01T00:01Z] INFO  01:01:05,405 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:01Z] INFO  01:01:05,405 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:01Z] INFO  01:01:05,491 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:01Z] INFO  01:01:05,563 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:01Z] INFO  01:01:05,571 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:01Z] INFO  01:01:05,592 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:01Z] INFO  01:01:06,156 IntervalUtils - Processing 2494 bp from intervals
[2015-10-01T00:01Z] WARN  01:01:06,160 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:01Z] WARN  01:01:06,160 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:01Z] INFO  01:01:06,214 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:01Z] INFO  01:01:06,318 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:01Z] INFO  01:01:06,319 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:01Z] INFO  01:01:06,319 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:01Z] INFO  01:01:06,319 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:01Z] INFO  01:01:06,360 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:01Z] INFO  01:01:18,112 VariantAnnotator - Processed 2188 loci.
[2015-10-01T00:01Z]
[2015-10-01T00:01Z] INFO  01:01:18,133 ProgressMeter -            done     29018.0    11.0 s       6.8 m      100.0%    11.0 s       0.0 s
[2015-10-01T00:01Z] INFO  01:01:18,133 ProgressMeter - Total runtime 11.82 secs, 0.20 min, 0.00 hours
[2015-10-01T00:01Z] INFO  01:01:18,134 MicroScheduler - 9706 reads were filtered out during the traversal out of approximately 186001 total reads (5.22%)
[2015-10-01T00:01Z] INFO  01:01:18,134 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:01Z] INFO  01:01:18,134 MicroScheduler -   -> 9648 reads (5.19% of total) failing DuplicateReadFilter
[2015-10-01T00:01Z] INFO  01:01:18,134 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:01Z] INFO  01:01:18,135 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:01Z] INFO  01:01:18,135 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:01Z] INFO  01:01:18,135 MicroScheduler -   -> 58 reads (0.03% of total) failing UnmappedReadFilter
[2015-10-01T00:01Z] INFO  01:01:19,065 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:01Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:02Z] WARNING(freebayes): Could not find any mapped reads in target region 19:46476755..46476799
[2015-10-01T00:02Z] WARNING(freebayes): Could not find any mapped reads in target region 19:10982206..10982239
[2015-10-01T00:02Z] WARNING(freebayes): Could not find any mapped reads in target region 19:10982361..10982381
[2015-10-01T00:02Z] WARNING(freebayes): Could not find any mapped reads in target region 20:41818591..41818604
[2015-10-01T00:02Z] WARNING(freebayes): Could not find any mapped reads in target region 20:43438967..43439130
[2015-10-01T00:03Z] WARNING(freebayes): Could not find any mapped reads in target region 20:50384992..50385130
[2015-10-01T00:03Z] WARNING(freebayes): Could not find any mapped reads in target region 19:52146326..52147519
[2015-10-01T00:03Z] WARNING(freebayes): Could not find any mapped reads in target region 19:52148506..52148949
[2015-10-01T00:04Z] tabix index syn3-20_31018873_62038916-raw.vcf.gz
[2015-10-01T00:04Z] GATK: VariantAnnotator
[2015-10-01T00:04Z] INFO  01:04:39,289 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:04Z] INFO  01:04:39,291 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:04Z] INFO  01:04:39,291 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:04Z] INFO  01:04:39,291 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:04Z] INFO  01:04:39,295 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/20/syn3-20_31018873_62038916-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/20/tx/tmpqEXk5V/syn3-20_31018873_62038916-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/20/syn3-20_31018873_62038916-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_31018873_62038916-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:04Z] INFO  01:04:39,302 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:04Z] INFO  01:04:39,302 HelpFormatter - Date/Time: 2015/10/01 01:04:39
[2015-10-01T00:04Z] INFO  01:04:39,302 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:04Z] INFO  01:04:39,302 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:04Z] INFO  01:04:39,396 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:04Z] INFO  01:04:39,472 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:04Z] INFO  01:04:39,479 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:04Z] INFO  01:04:39,502 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:04Z] INFO  01:04:40,190 IntervalUtils - Processing 2715 bp from intervals
[2015-10-01T00:04Z] WARN  01:04:40,195 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:04Z] WARN  01:04:40,195 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:04Z] INFO  01:04:40,252 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:04Z] INFO  01:04:40,396 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:04Z] INFO  01:04:40,396 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:04Z] INFO  01:04:40,396 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:04Z] INFO  01:04:40,397 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:04Z] INFO  01:04:40,437 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:04Z] tabix index syn3-19_0_31026185-raw.vcf.gz
[2015-10-01T00:04Z] GATK: VariantAnnotator
[2015-10-01T00:04Z] INFO  01:04:46,446 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:04Z] INFO  01:04:46,448 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:04Z] INFO  01:04:46,449 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:04Z] INFO  01:04:46,449 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:04Z] INFO  01:04:46,452 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/19/syn3-19_0_31026185-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/19/tx/tmp43sA72/syn3-19_0_31026185-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/19/syn3-19_0_31026185-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_0_31026185-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:04Z] INFO  01:04:46,458 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:04Z] INFO  01:04:46,458 HelpFormatter - Date/Time: 2015/10/01 01:04:46
[2015-10-01T00:04Z] INFO  01:04:46,458 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:04Z] INFO  01:04:46,458 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:04Z] INFO  01:04:46,553 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:04Z] INFO  01:04:46,629 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:04Z] INFO  01:04:46,636 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:04Z] INFO  01:04:46,658 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:04Z] INFO  01:04:47,430 IntervalUtils - Processing 5798 bp from intervals
[2015-10-01T00:04Z] WARN  01:04:47,434 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:04Z] WARN  01:04:47,434 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:04Z] INFO  01:04:47,491 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:04Z] INFO  01:04:47,662 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:04Z] INFO  01:04:47,663 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:04Z] INFO  01:04:47,663 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:04Z] INFO  01:04:47,663 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:04Z] INFO  01:04:47,701 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:04Z] INFO  01:04:53,950 VariantAnnotator - Processed 2299 loci.
[2015-10-01T00:04Z]
[2015-10-01T00:04Z] INFO  01:04:53,976 ProgressMeter -            done     13058.0    13.0 s      17.3 m      100.0%    13.0 s       0.0 s
[2015-10-01T00:04Z] INFO  01:04:53,976 ProgressMeter - Total runtime 13.58 secs, 0.23 min, 0.00 hours
[2015-10-01T00:04Z] INFO  01:04:53,976 MicroScheduler - 12184 reads were filtered out during the traversal out of approximately 230579 total reads (5.28%)
[2015-10-01T00:04Z] INFO  01:04:53,976 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:04Z] INFO  01:04:53,977 MicroScheduler -   -> 12131 reads (5.26% of total) failing DuplicateReadFilter
[2015-10-01T00:04Z] INFO  01:04:53,977 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:04Z] INFO  01:04:53,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:04Z] INFO  01:04:53,977 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:04Z] INFO  01:04:53,977 MicroScheduler -   -> 53 reads (0.02% of total) failing UnmappedReadFilter
[2015-10-01T00:04Z] INFO  01:04:54,962 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:04Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:05Z] INFO  01:05:14,512 VariantAnnotator - Processed 5150 loci.
[2015-10-01T00:05Z]
[2015-10-01T00:05Z] INFO  01:05:14,533 ProgressMeter -            done     50855.0    26.0 s       8.8 m      100.0%    26.0 s       0.0 s
[2015-10-01T00:05Z] INFO  01:05:14,534 ProgressMeter - Total runtime 26.87 secs, 0.45 min, 0.01 hours
[2015-10-01T00:05Z] INFO  01:05:14,534 MicroScheduler - 29414 reads were filtered out during the traversal out of approximately 502663 total reads (5.85%)
[2015-10-01T00:05Z] INFO  01:05:14,534 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:05Z] INFO  01:05:14,534 MicroScheduler -   -> 29265 reads (5.82% of total) failing DuplicateReadFilter
[2015-10-01T00:05Z] INFO  01:05:14,535 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:05Z] INFO  01:05:14,535 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:05Z] INFO  01:05:14,535 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:05Z] INFO  01:05:14,535 MicroScheduler -   -> 149 reads (0.03% of total) failing UnmappedReadFilter
[2015-10-01T00:05Z] INFO  01:05:15,751 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:05Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:05Z] tabix index syn3-20_62039427_63025520-raw.vcf.gz
[2015-10-01T00:05Z] GATK: VariantAnnotator
[2015-10-01T00:05Z] tabix index syn3-19_31038548_59128983-raw.vcf.gz
[2015-10-01T00:05Z] GATK: VariantAnnotator
[2015-10-01T00:05Z] INFO  01:05:20,347 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:05Z] INFO  01:05:20,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:05Z] INFO  01:05:20,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:05Z] INFO  01:05:20,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:05Z] INFO  01:05:20,352 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/20/syn3-20_62039427_63025520-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/20/tx/tmpmvyU15/syn3-20_62039427_63025520-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/20/syn3-20_62039427_63025520-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/20/1_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/20/2_2014-08-13_dream-syn3-sort-20_62039427_63025520-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:05Z] INFO  01:05:20,358 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:05Z] INFO  01:05:20,358 HelpFormatter - Date/Time: 2015/10/01 01:05:20
[2015-10-01T00:05Z] INFO  01:05:20,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:05Z] INFO  01:05:20,358 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:05Z] INFO  01:05:20,454 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:05Z] INFO  01:05:20,530 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:05Z] INFO  01:05:20,538 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:05Z] INFO  01:05:20,560 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:05Z] INFO  01:05:20,877 IntervalUtils - Processing 297 bp from intervals
[2015-10-01T00:05Z] WARN  01:05:20,881 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:05Z] WARN  01:05:20,881 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:05Z] INFO  01:05:20,937 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:05Z] INFO  01:05:20,972 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:05Z] INFO  01:05:20,972 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:05Z] INFO  01:05:20,973 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:05Z] INFO  01:05:20,973 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:05Z] INFO  01:05:21,083 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:05Z] INFO  01:05:21,196 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:05Z] INFO  01:05:21,198 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:05Z] INFO  01:05:21,198 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:05Z] INFO  01:05:21,199 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:05Z] INFO  01:05:21,202 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/19/syn3-19_31038548_59128983-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/19/tx/tmpJMKXhC/syn3-19_31038548_59128983-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/19/syn3-19_31038548_59128983-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/19/1_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/19/2_2014-08-13_dream-syn3-sort-19_31038548_59128983-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:05Z] INFO  01:05:21,208 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:05Z] INFO  01:05:21,208 HelpFormatter - Date/Time: 2015/10/01 01:05:21
[2015-10-01T00:05Z] INFO  01:05:21,208 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:05Z] INFO  01:05:21,209 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:05Z] INFO  01:05:21,305 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:05Z] INFO  01:05:21,379 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:05Z] INFO  01:05:21,386 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:05Z] INFO  01:05:21,407 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:05Z] INFO  01:05:22,249 IntervalUtils - Processing 6147 bp from intervals
[2015-10-01T00:05Z] WARN  01:05:22,254 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:05Z] WARN  01:05:22,254 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:05Z] INFO  01:05:22,310 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:05Z] INFO  01:05:22,493 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:05Z] INFO  01:05:22,493 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:05Z] INFO  01:05:22,493 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:05Z] INFO  01:05:22,494 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:05Z] INFO  01:05:22,531 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:05Z] INFO  01:05:24,025 VariantAnnotator - Processed 287 loci.
[2015-10-01T00:05Z]
[2015-10-01T00:05Z] INFO  01:05:24,057 ProgressMeter -            done      2160.0     3.0 s      23.8 m       99.7%     3.0 s       0.0 s
[2015-10-01T00:05Z] INFO  01:05:24,058 ProgressMeter - Total runtime 3.09 secs, 0.05 min, 0.00 hours
[2015-10-01T00:05Z] INFO  01:05:24,058 MicroScheduler - 1940 reads were filtered out during the traversal out of approximately 32200 total reads (6.02%)
[2015-10-01T00:05Z] INFO  01:05:24,058 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:05Z] INFO  01:05:24,059 MicroScheduler -   -> 1936 reads (6.01% of total) failing DuplicateReadFilter
[2015-10-01T00:05Z] INFO  01:05:24,059 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:05Z] INFO  01:05:24,059 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:05Z] INFO  01:05:24,059 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:05Z] INFO  01:05:24,059 MicroScheduler -   -> 4 reads (0.01% of total) failing UnmappedReadFilter
[2015-10-01T00:05Z] INFO  01:05:25,017 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:05Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:05Z] tabix index syn3-21_0_31023863-raw.vcf.gz
[2015-10-01T00:05Z] GATK: VariantAnnotator
[2015-10-01T00:05Z] INFO  01:05:43,378 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:05Z] INFO  01:05:43,380 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:05Z] INFO  01:05:43,380 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:05Z] INFO  01:05:43,381 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:05Z] INFO  01:05:43,384 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/21/syn3-21_0_31023863-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/21/tx/tmp4RpsT1/syn3-21_0_31023863-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/21/syn3-21_0_31023863-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_0_31023863-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:05Z] INFO  01:05:43,390 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:05Z] INFO  01:05:43,390 HelpFormatter - Date/Time: 2015/10/01 01:05:43
[2015-10-01T00:05Z] INFO  01:05:43,390 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:05Z] INFO  01:05:43,390 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:05Z] INFO  01:05:43,486 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:05Z] INFO  01:05:43,563 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:05Z] INFO  01:05:43,572 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:05Z] INFO  01:05:43,595 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:05Z] INFO  01:05:43,967 IntervalUtils - Processing 754 bp from intervals
[2015-10-01T00:05Z] WARN  01:05:43,971 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:05Z] WARN  01:05:43,971 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:05Z] INFO  01:05:44,030 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:05Z] INFO  01:05:45,040 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:05Z] INFO  01:05:45,041 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:05Z] INFO  01:05:45,041 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:05Z] INFO  01:05:45,041 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:05Z] INFO  01:05:45,081 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:05Z] INFO  01:05:49,792 VariantAnnotator - Processed 699 loci.
[2015-10-01T00:05Z]
[2015-10-01T00:05Z] INFO  01:05:49,812 ProgressMeter -            done      4919.0     4.0 s      16.2 m       99.9%     4.0 s       0.0 s
[2015-10-01T00:05Z] INFO  01:05:49,813 ProgressMeter - Total runtime 4.77 secs, 0.08 min, 0.00 hours
[2015-10-01T00:05Z] INFO  01:05:49,813 MicroScheduler - 3172 reads were filtered out during the traversal out of approximately 59646 total reads (5.32%)
[2015-10-01T00:05Z] INFO  01:05:49,813 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:05Z] INFO  01:05:49,813 MicroScheduler -   -> 3157 reads (5.29% of total) failing DuplicateReadFilter
[2015-10-01T00:05Z] INFO  01:05:49,814 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:05Z] INFO  01:05:49,814 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:05Z] INFO  01:05:49,814 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:05Z] INFO  01:05:49,814 MicroScheduler -   -> 15 reads (0.03% of total) failing UnmappedReadFilter
[2015-10-01T00:05Z] INFO  01:05:50,361 VariantAnnotator - Processed 5615 loci.
[2015-10-01T00:05Z]
[2015-10-01T00:05Z] INFO  01:05:50,383 ProgressMeter -            done     40139.0    27.0 s      11.6 m      100.0%    27.0 s       0.0 s
[2015-10-01T00:05Z] INFO  01:05:50,383 ProgressMeter - Total runtime 27.89 secs, 0.46 min, 0.01 hours
[2015-10-01T00:05Z] INFO  01:05:50,384 MicroScheduler - 27356 reads were filtered out during the traversal out of approximately 516657 total reads (5.29%)
[2015-10-01T00:05Z] INFO  01:05:50,384 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:05Z] INFO  01:05:50,384 MicroScheduler -   -> 27234 reads (5.27% of total) failing DuplicateReadFilter
[2015-10-01T00:05Z] INFO  01:05:50,384 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:05Z] INFO  01:05:50,385 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:05Z] INFO  01:05:50,385 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:05Z] INFO  01:05:50,385 MicroScheduler -   -> 122 reads (0.02% of total) failing UnmappedReadFilter
[2015-10-01T00:05Z] INFO  01:05:50,772 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:05Z] INFO  01:05:51,442 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:05Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:05Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:07Z] tabix index syn3-21_31026814_48129895-raw.vcf.gz
[2015-10-01T00:07Z] GATK: VariantAnnotator
[2015-10-01T00:07Z] INFO  01:07:27,372 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:07Z] INFO  01:07:27,374 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:07Z] INFO  01:07:27,374 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:07Z] INFO  01:07:27,374 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:07Z] INFO  01:07:27,377 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/21/syn3-21_31026814_48129895-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/21/tx/tmp7xBZKz/syn3-21_31026814_48129895-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/21/syn3-21_31026814_48129895-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/21/1_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/21/2_2014-08-13_dream-syn3-sort-21_31026814_48129895-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:07Z] INFO  01:07:27,383 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:07Z] INFO  01:07:27,383 HelpFormatter - Date/Time: 2015/10/01 01:07:27
[2015-10-01T00:07Z] INFO  01:07:27,383 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:07Z] INFO  01:07:27,384 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:07Z] INFO  01:07:27,470 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:07Z] INFO  01:07:27,543 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:07Z] INFO  01:07:27,550 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:07Z] INFO  01:07:27,572 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:07Z] INFO  01:07:28,171 IntervalUtils - Processing 2445 bp from intervals
[2015-10-01T00:07Z] WARN  01:07:28,175 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:07Z] WARN  01:07:28,175 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:07Z] INFO  01:07:28,229 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:07Z] INFO  01:07:28,327 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:07Z] INFO  01:07:28,328 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:07Z] INFO  01:07:28,328 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:07Z] INFO  01:07:28,329 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:07Z] INFO  01:07:28,368 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:07Z] INFO  01:07:39,684 VariantAnnotator - Processed 2161 loci.
[2015-10-01T00:07Z]
[2015-10-01T00:07Z] INFO  01:07:39,703 ProgressMeter -            done     17584.0    11.0 s      10.8 m      100.0%    11.0 s       0.0 s
[2015-10-01T00:07Z] INFO  01:07:39,703 ProgressMeter - Total runtime 11.38 secs, 0.19 min, 0.00 hours
[2015-10-01T00:07Z] INFO  01:07:39,704 MicroScheduler - 10361 reads were filtered out during the traversal out of approximately 198440 total reads (5.22%)
[2015-10-01T00:07Z] INFO  01:07:39,704 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:07Z] INFO  01:07:39,704 MicroScheduler -   -> 10321 reads (5.20% of total) failing DuplicateReadFilter
[2015-10-01T00:07Z] INFO  01:07:39,704 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:07Z] INFO  01:07:39,705 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:07Z] INFO  01:07:39,705 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:07Z] INFO  01:07:39,705 MicroScheduler -   -> 40 reads (0.02% of total) failing UnmappedReadFilter
[2015-10-01T00:07Z] INFO  01:07:40,628 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:07Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:08Z] tabix index syn3-22_0_31019358-raw.vcf.gz
[2015-10-01T00:08Z] GATK: VariantAnnotator
[2015-10-01T00:08Z] INFO  01:08:13,310 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:08Z] INFO  01:08:13,312 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:08Z] INFO  01:08:13,312 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:08Z] INFO  01:08:13,313 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:08Z] INFO  01:08:13,316 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/22/syn3-22_0_31019358-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/22/tx/tmpZyeuGM/syn3-22_0_31019358-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/22/syn3-22_0_31019358-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_0_31019358-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:08Z] INFO  01:08:13,321 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:08Z] INFO  01:08:13,321 HelpFormatter - Date/Time: 2015/10/01 01:08:13
[2015-10-01T00:08Z] INFO  01:08:13,322 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:08Z] INFO  01:08:13,322 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:08Z] INFO  01:08:13,409 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:08Z] INFO  01:08:13,482 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:08Z] INFO  01:08:13,489 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:08Z] INFO  01:08:13,510 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:08Z] INFO  01:08:14,162 IntervalUtils - Processing 2941 bp from intervals
[2015-10-01T00:08Z] WARN  01:08:14,167 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:08Z] WARN  01:08:14,167 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:08Z] INFO  01:08:14,230 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:08Z] INFO  01:08:14,539 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:08Z] INFO  01:08:14,540 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:08Z] INFO  01:08:14,540 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:08Z] INFO  01:08:14,541 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:08Z] INFO  01:08:14,580 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:08Z] WARNING(freebayes): Could not find any mapped reads in target region X:16964896..16964991
[2015-10-01T00:08Z] INFO  01:08:27,588 VariantAnnotator - Processed 2590 loci.
[2015-10-01T00:08Z]
[2015-10-01T00:08Z] INFO  01:08:27,607 ProgressMeter -            done     19887.0    13.0 s      11.0 m       99.9%    13.0 s       0.0 s
[2015-10-01T00:08Z] INFO  01:08:27,607 ProgressMeter - Total runtime 13.07 secs, 0.22 min, 0.00 hours
[2015-10-01T00:08Z] INFO  01:08:27,608 MicroScheduler - 13444 reads were filtered out during the traversal out of approximately 249054 total reads (5.40%)
[2015-10-01T00:08Z] INFO  01:08:27,608 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:08Z] INFO  01:08:27,608 MicroScheduler -   -> 13385 reads (5.37% of total) failing DuplicateReadFilter
[2015-10-01T00:08Z] INFO  01:08:27,608 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:08Z] INFO  01:08:27,608 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:08Z] INFO  01:08:27,609 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:08Z] INFO  01:08:27,609 MicroScheduler -   -> 59 reads (0.02% of total) failing UnmappedReadFilter
[2015-10-01T00:08Z] INFO  01:08:28,527 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:08Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:08Z] WARNING(freebayes): Could not find any mapped reads in target region X:38150333..38150345
[2015-10-01T00:08Z] WARNING(freebayes): Could not find any mapped reads in target region 22:51112881..51112902
[2015-10-01T00:08Z] tabix index syn3-22_31022170_51304566-raw.vcf.gz
[2015-10-01T00:08Z] GATK: VariantAnnotator
[2015-10-01T00:08Z] INFO  01:08:52,357 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:08Z] INFO  01:08:52,359 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:08Z] INFO  01:08:52,359 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:08Z] INFO  01:08:52,359 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:08Z] INFO  01:08:52,363 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/22/syn3-22_31022170_51304566-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/22/tx/tmpGPidca/syn3-22_31022170_51304566-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/22/syn3-22_31022170_51304566-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/22/1_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/22/2_2014-08-13_dream-syn3-sort-22_31022170_51304566-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:08Z] INFO  01:08:52,368 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:08Z] INFO  01:08:52,369 HelpFormatter - Date/Time: 2015/10/01 01:08:52
[2015-10-01T00:08Z] INFO  01:08:52,369 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:08Z] INFO  01:08:52,369 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:08Z] INFO  01:08:52,462 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:08Z] INFO  01:08:52,541 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:08Z] INFO  01:08:52,549 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:08Z] INFO  01:08:52,571 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:08Z] tabix index syn3-X_0_31090302-raw.vcf.gz
[2015-10-01T00:08Z] GATK: VariantAnnotator
[2015-10-01T00:08Z] INFO  01:08:53,226 IntervalUtils - Processing 2768 bp from intervals
[2015-10-01T00:08Z] WARN  01:08:53,230 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:08Z] WARN  01:08:53,231 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:08Z] INFO  01:08:53,402 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:08Z] INFO  01:08:53,523 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:08Z] INFO  01:08:53,523 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:08Z] INFO  01:08:53,524 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:08Z] INFO  01:08:53,524 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:08Z] INFO  01:08:53,563 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:08Z] INFO  01:08:54,441 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:08Z] INFO  01:08:54,443 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:08Z] INFO  01:08:54,443 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:08Z] INFO  01:08:54,444 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:08Z] INFO  01:08:54,447 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/X/syn3-X_0_31090302-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/X/tx/tmpEkWrKZ/syn3-X_0_31090302-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/X/syn3-X_0_31090302-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_0_31090302-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:08Z] INFO  01:08:54,453 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:08Z] INFO  01:08:54,453 HelpFormatter - Date/Time: 2015/10/01 01:08:54
[2015-10-01T00:08Z] INFO  01:08:54,453 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:08Z] INFO  01:08:54,453 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:08Z] INFO  01:08:54,548 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:08Z] INFO  01:08:54,624 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:08Z] INFO  01:08:54,632 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:08Z] INFO  01:08:54,654 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:08Z] INFO  01:08:55,017 IntervalUtils - Processing 995 bp from intervals
[2015-10-01T00:08Z] WARN  01:08:55,021 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:08Z] WARN  01:08:55,021 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:08Z] INFO  01:08:55,144 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:08Z] INFO  01:08:55,226 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:08Z] INFO  01:08:55,226 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:08Z] INFO  01:08:55,227 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:08Z] INFO  01:08:55,227 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:08Z] INFO  01:08:55,268 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:09Z] INFO  01:09:00,428 VariantAnnotator - Processed 834 loci.
[2015-10-01T00:09Z]
[2015-10-01T00:09Z] INFO  01:09:00,446 ProgressMeter -            done      4609.0     5.0 s      18.9 m       99.9%     5.0 s       0.0 s
[2015-10-01T00:09Z] INFO  01:09:00,451 ProgressMeter - Total runtime 5.22 secs, 0.09 min, 0.00 hours
[2015-10-01T00:09Z] INFO  01:09:00,452 MicroScheduler - 3281 reads were filtered out during the traversal out of approximately 67063 total reads (4.89%)
[2015-10-01T00:09Z] INFO  01:09:00,453 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:09Z] INFO  01:09:00,453 MicroScheduler -   -> 3269 reads (4.87% of total) failing DuplicateReadFilter
[2015-10-01T00:09Z] INFO  01:09:00,453 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:09Z] INFO  01:09:00,453 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:09Z] INFO  01:09:00,454 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:09Z] INFO  01:09:00,454 MicroScheduler -   -> 12 reads (0.02% of total) failing UnmappedReadFilter
[2015-10-01T00:09Z] INFO  01:09:01,372 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:09Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:09Z] INFO  01:09:07,540 VariantAnnotator - Processed 2438 loci.
[2015-10-01T00:09Z]
[2015-10-01T00:09Z] INFO  01:09:07,560 ProgressMeter -            done     15497.0    14.0 s      15.1 m      100.0%    14.0 s       0.0 s
[2015-10-01T00:09Z] INFO  01:09:07,561 ProgressMeter - Total runtime 14.04 secs, 0.23 min, 0.00 hours
[2015-10-01T00:09Z] INFO  01:09:07,561 MicroScheduler - 13125 reads were filtered out during the traversal out of approximately 242613 total reads (5.41%)
[2015-10-01T00:09Z] INFO  01:09:07,561 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:09Z] INFO  01:09:07,561 MicroScheduler -   -> 13081 reads (5.39% of total) failing DuplicateReadFilter
[2015-10-01T00:09Z] INFO  01:09:07,562 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:09Z] INFO  01:09:07,562 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:09Z] INFO  01:09:07,562 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:09Z] INFO  01:09:07,562 MicroScheduler -   -> 44 reads (0.02% of total) failing UnmappedReadFilter
[2015-10-01T00:09Z] INFO  01:09:08,515 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:09Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:09Z] tabix index syn3-X_62568928_94148729-raw.vcf.gz
[2015-10-01T00:09Z] GATK: VariantAnnotator
[2015-10-01T00:09Z] tabix index syn3-X_31132529_62519711-raw.vcf.gz
[2015-10-01T00:09Z] GATK: VariantAnnotator
[2015-10-01T00:09Z] INFO  01:09:59,174 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:09Z] INFO  01:09:59,176 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:09Z] INFO  01:09:59,176 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:09Z] INFO  01:09:59,176 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:09Z] INFO  01:09:59,180 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/X/syn3-X_62568928_94148729-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/X/tx/tmpEEdSQl/syn3-X_62568928_94148729-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/X/syn3-X_62568928_94148729-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_62568928_94148729-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:09Z] INFO  01:09:59,185 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:09Z] INFO  01:09:59,186 HelpFormatter - Date/Time: 2015/10/01 01:09:59
[2015-10-01T00:09Z] INFO  01:09:59,186 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:09Z] INFO  01:09:59,186 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:09Z] INFO  01:09:59,277 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:09Z] INFO  01:09:59,355 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:09Z] INFO  01:09:59,363 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:09Z] INFO  01:09:59,386 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:09Z] INFO  01:09:59,719 IntervalUtils - Processing 466 bp from intervals
[2015-10-01T00:09Z] WARN  01:09:59,723 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:09Z] WARN  01:09:59,723 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:09Z] INFO  01:09:59,843 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:10Z] INFO  01:10:00,085 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:10Z] INFO  01:10:00,085 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:10Z] INFO  01:10:00,085 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:10Z] INFO  01:10:00,086 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:10Z] INFO  01:10:00,181 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:10Z] INFO  01:10:00,728 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:10Z] INFO  01:10:00,730 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:10Z] INFO  01:10:00,730 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:10Z] INFO  01:10:00,730 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:10Z] INFO  01:10:00,734 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/X/syn3-X_31132529_62519711-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/X/tx/tmpGWmkQw/syn3-X_31132529_62519711-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/X/syn3-X_31132529_62519711-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_31132529_62519711-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:10Z] INFO  01:10:00,738 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:10Z] INFO  01:10:00,739 HelpFormatter - Date/Time: 2015/10/01 01:10:00
[2015-10-01T00:10Z] INFO  01:10:00,739 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:10Z] INFO  01:10:00,739 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:10Z] INFO  01:10:01,011 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:10Z] INFO  01:10:01,088 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:10Z] INFO  01:10:01,096 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:10Z] INFO  01:10:01,119 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:10Z] INFO  01:10:01,478 IntervalUtils - Processing 677 bp from intervals
[2015-10-01T00:10Z] WARN  01:10:01,482 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:10Z] WARN  01:10:01,482 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:10Z] INFO  01:10:01,540 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:10Z] INFO  01:10:01,695 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:10Z] INFO  01:10:01,695 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:10Z] INFO  01:10:01,696 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:10Z] INFO  01:10:01,696 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:10Z] INFO  01:10:01,738 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:10Z] INFO  01:10:03,607 VariantAnnotator - Processed 387 loci.
[2015-10-01T00:10Z]
[2015-10-01T00:10Z] INFO  01:10:03,632 ProgressMeter -            done      1177.0     3.0 s      50.2 m       99.8%     3.0 s       0.0 s
[2015-10-01T00:10Z] INFO  01:10:03,632 ProgressMeter - Total runtime 3.55 secs, 0.06 min, 0.00 hours
[2015-10-01T00:10Z] INFO  01:10:03,632 MicroScheduler - 1232 reads were filtered out during the traversal out of approximately 28327 total reads (4.35%)
[2015-10-01T00:10Z] INFO  01:10:03,632 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:10Z] INFO  01:10:03,633 MicroScheduler -   -> 1226 reads (4.33% of total) failing DuplicateReadFilter
[2015-10-01T00:10Z] INFO  01:10:03,633 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:10Z] INFO  01:10:03,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:10Z] INFO  01:10:03,633 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:10Z] INFO  01:10:03,634 MicroScheduler -   -> 6 reads (0.02% of total) failing UnmappedReadFilter
[2015-10-01T00:10Z] INFO  01:10:04,570 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:10Z] INFO  01:10:06,319 VariantAnnotator - Processed 611 loci.
[2015-10-01T00:10Z]
[2015-10-01T00:10Z] INFO  01:10:06,339 ProgressMeter -            done      2297.0     4.0 s      33.7 m       99.9%     4.0 s       0.0 s
[2015-10-01T00:10Z] INFO  01:10:06,339 ProgressMeter - Total runtime 4.64 secs, 0.08 min, 0.00 hours
[2015-10-01T00:10Z] INFO  01:10:06,340 MicroScheduler - 2206 reads were filtered out during the traversal out of approximately 48078 total reads (4.59%)
[2015-10-01T00:10Z] INFO  01:10:06,340 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:10Z] INFO  01:10:06,340 MicroScheduler -   -> 2200 reads (4.58% of total) failing DuplicateReadFilter
[2015-10-01T00:10Z] INFO  01:10:06,341 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:10Z] INFO  01:10:06,341 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:10Z] INFO  01:10:06,341 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:10Z] INFO  01:10:06,341 MicroScheduler -   -> 6 reads (0.01% of total) failing UnmappedReadFilter
[2015-10-01T00:10Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:10Z] INFO  01:10:07,303 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:10Z] Genotyping paired variants with FreeBayes
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2654729..2655918
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2709354..2710291
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2711835..2712519
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2713428..2714033
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2722378..2723061
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2732849..2733019
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2733033..2733499
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2734587..2735175
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2803070..2803869
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2821715..2822291
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2844488..2845138
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2845743..2845818
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:2848430..2848994
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6115138..6116440
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6116547..6117051
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6133245..6133825
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6134337..6135062
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6258180..6258814
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6291846..6292428
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6317219..6317818
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6318200..6318906
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6320692..6321288
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6321442..6322103
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6340697..6341215
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6341237..6341292
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6341344..6341852
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6733806..6734387
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6735803..6737147
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6738172..6738326
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6740324..6740906
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6892827..6893447
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6910725..6911436
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6931706..6932333
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6937930..6939191
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6939352..6940115
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6942319..6942894
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6948502..6949135
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6953678..6954747
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6955235..6955733
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6957882..6958438
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:6959210..6959754
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7171693..7171726
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7223961..7224508
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7227181..7227206
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7227255..7227365
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7235095..7235711
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7249189..7249836
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7635953..7635999
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7644323..7644978
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7666696..7666879
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7666901..7667241
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7721483..7722319
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7781258..7781439
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7781461..7782010
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7858952..7859547
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:7936793..7937883
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:8141152..8141832
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:8147980..8150515
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:8492616..8493133
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:8498219..8498335
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:8498354..8498814
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:8499044..8499732
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:8651873..8652483
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:8656755..8657550
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9148648..9149535
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9149558..9149967
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9151072..9151663
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9152148..9152734
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9154275..9154936
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9156321..9157008
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9159518..9160317
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9160354..9160773
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9173750..9174379
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9174813..9175918
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9175976..9177273
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9177399..9177884
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9177960..9177964
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9194062..9194719
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9195216..9196064
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9196281..9197605
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9197695..9198199
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9198277..9198293
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9214354..9214997
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9215440..9216456
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9216590..9217822
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9217973..9218476
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9234686..9235336
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9236905..9238190
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9238338..9238823
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9238899..9238903
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9303236..9303879
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9305439..9306713
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9306851..9307355
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9307429..9307435
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9323546..9324189
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9324616..9325690
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9325790..9327042
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9327183..9327687
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9343850..9344465
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9344988..9345998
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9346082..9347391
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9347465..9347969
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9348039..9348063
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9364145..9364795
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9365258..9366271
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9366364..9367627
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9367804..9368282
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9368348..9368362
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9385768..9386480
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9528488..9529031
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9529083..9529139
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9529157..9529644
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9548262..9548958
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9549078..9549678
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9551472..9552159
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9552542..9553142
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9577918..9578524
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9611449..9612179
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:9867751..9868406
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14460440..14460976
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14467673..14468283
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14486371..14486429
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14486478..14486952
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14491304..14491856
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14821143..14821721
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14833783..14834277
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14834351..14834374
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14836805..14837388
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14838259..14838944
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14847244..14848727
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14849839..14850452
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14850494..14850498
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14851228..14851411
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14851452..14851810
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14870142..14870843
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14872113..14872760
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14882745..14883337
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14885299..14886011
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14887145..14887735
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14889743..14889901
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14889949..14890972
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14891148..14891815
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14897889..14898400
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14898450..14898965
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14902091..14902742
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14903127..14903828
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14904710..14905336
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14921881..14923020
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14923293..14923711
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14924516..14925200
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14927856..14928502
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14930091..14930789
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14945343..14946017
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14949595..14949759
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14949784..14950260
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14951497..14953315
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14953940..14954399
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14954417..14954560
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14954691..14955400
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14957983..14959391
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14968001..14968767
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14968784..14968955
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14970911..14971071
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:14971089..14971599
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15016592..15017147
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15017406..15017986
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15019179..15019725
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15020982..15021555
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15023463..15024098
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15024347..15025125
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15026211..15026649
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15026671..15028383
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15028408..15029461
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15029712..15030632
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15030771..15032182
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15360738..15361412
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15361436..15361887
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15361917..15362029
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15362633..15363262
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15371848..15372573
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15409296..15409977
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15414451..15415166
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15416994..15417588
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15417686..15418377
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15435251..15435273
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15435310..15435849
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15436235..15436780
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15437797..15438473
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15447170..15448214
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15448229..15448425
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15466601..15467454
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15469493..15470077
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15470095..15470696
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15470727..15470786
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15470924..15471357
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15480874..15481472
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15505444..15506042
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15508522..15509115
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15522570..15523272
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15526354..15526879
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15526893..15526911
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15560611..15561208
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15581740..15582340
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15590853..15591806
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15779504..15780073
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15815957..15816557
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:15816813..15817668
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:16098545..16098546
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:16167908..16167935
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:16733740..16734669
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:16831076..16831647
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:16845064..16845647
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:16860191..16860735
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:16860838..16860900
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:16935831..16936490
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:16941374..16941375
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:18174489..18174637
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:18174701..18175041
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:19167813..19168600
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:19171181..19171729
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:19171770..19172331
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:19734675..19735238
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:19881029..19881884
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:19881907..19882012
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:19989896..19991956
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:19993892..19994543
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20016792..20017594
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20023699..20023962
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20024000..20024176
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20137738..20139819
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20297687..20297855
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20297887..20298617
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20444478..20445085
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20708420..20709430
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20709468..20710471
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20711685..20712284
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20712381..20712971
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20743836..20744530
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20749011..20749697
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20826086..20826363
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20894492..20895125
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20899649..20900338
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20931195..20931839
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20931890..20932393
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:20933574..20935775
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21039400..21040299
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21147915..21148501
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21238877..21239505
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21618220..21618968
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21620632..21621490
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21621617..21622203
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21622797..21623371
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21636349..21636958
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21641761..21642303
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21643301..21646808
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21728998..21729674
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21748815..21748863
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21748892..21749611
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21750080..21750577
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21751173..21751743
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21751763..21752355
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21753419..21754040
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21755007..21755686
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21757654..21758035
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21758050..21758143
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21759222..21759796
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21763837..21764403
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21765486..21766411
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21867723..21871962
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21872017..21872579
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21876944..21878894
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21882468..21883354
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21893409..21894194
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21894276..21894623
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21894656..21894838
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21896948..21897914
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21901113..21901819
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21902971..21903931
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21904779..21905279
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:21905996..21906678
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22737454..22738022
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22741227..22741806
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22746123..22746695
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22749653..22750245
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22751108..22751211
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22751235..22751704
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22753937..22754516
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22781581..22782054
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22917743..22918342
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22918411..22918975
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22921492..22922180
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22922911..22923514
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22930415..22930864
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22930890..22931081
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22941106..22941787
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:22942570..22943165
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23545080..23545265
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23545292..23546080
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23547842..23548430
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23556835..23558094
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23559005..23559549
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23562570..23563318
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23563347..23563702
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23655135..23655786
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23657278..23657892
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23659378..23659999
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23660435..23661022
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23661050..23663032
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23663047..23664109
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23674929..23675357
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23675406..23675511
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23675571..23676182
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23678696..23679347
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23680767..23681432
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23682933..23683539
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23683975..23684616
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23684649..23686559
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23686587..23687573
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23698470..23698898
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23698947..23699086
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23699132..23699767
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23702237..23702880
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23704288..23704973
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23706459..23707091
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23707587..23710111
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23710127..23711173
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23749130..23749762
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:23750878..23751456
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24026352..24027295
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24027319..24029903
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24030349..24030985
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24032431..24033135
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24034501..24035162
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24037661..24038314
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24038341..24038485
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24038536..24038945
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24049799..24050846
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24050860..24052843
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24052896..24053444
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24053890..24054502
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24055961..24056630
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24058070..24058719
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24061193..24061822
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24061877..24062015
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24062077..24062495
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24073608..24074903
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24075245..24075931
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24077397..24078083
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24079494..24080159
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24082382..24082941
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24082962..24083590
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24218226..24218989
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24219622..24220098
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24227912..24228163
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24228199..24228634
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24230654..24231250
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24290909..24291948
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24292473..24293076
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24314707..24315770
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24315784..24317175
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24317195..24317769
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24317811..24318369
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24318829..24319439
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24320898..24321572
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24323007..24323647
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24326212..24326759
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24326792..24326943
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24326992..24327386
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24443353..24444182
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24456747..24457946
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24460446..24461105
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24462495..24463118
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24464713..24465263
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24466929..24468124
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24551280..24551711
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24551758..24552499
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24555016..24555017
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24555052..24555717
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24557103..24557818
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24559264..24559885
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24560331..24560904
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24561004..24562911
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24562943..24563247
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24563283..24564017
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24585620..24586226
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24586677..24587805
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24647436..24648044
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24650053..24650495
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24650531..24650692
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24659709..24660392
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24795071..24795694
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24798522..24799192
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24800614..24801277
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24802774..24803386
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:24803762..24805073
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25012533..25013752
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25138218..25138857
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25140324..25140969
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25143343..25143944
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25144095..25144686
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25276433..25276970
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25281070..25281194
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25281221..25281677
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25282524..25282687
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25282749..25283106
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25284080..25284479
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25284527..25284672
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25285711..25286238
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25286523..25287187
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25288896..25289371
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25298013..25298201
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25298580..25299257
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25301048..25301574
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25303448..25303926
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25305086..25305572
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25305827..25306353
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25308220..25308702
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25310623..25311208
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25313055..25313654
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25314630..25315847
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25315889..25316927
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25325407..25326666
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25326721..25327729
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25336239..25337535
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25337590..25338627
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25344637..25345253
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25365562..25366170
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25372265..25373227
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25373297..25374583
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25375468..25376077
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25376352..25376533
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25377911..25378437
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25380435..25380908
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25382782..25383297
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25383565..25384059
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25385213..25385686
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25387560..25388075
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25389993..25390466
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25392340..25392855
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25394663..25395342
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25397148..25397621
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25399495..25400004
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25401798..25402389
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25411710..25412180
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25414094..25414564
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25416479..25416949
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25418863..25419333
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25421247..25421717
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25423631..25424101
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25425829..25426486
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25426681..25426911
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25426972..25427264
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25428324..25428481
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25428521..25428906
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25429128..25429183
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25429211..25429651
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25429919..25430249
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25430303..25430458
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25431807..25431914
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25435973..25436554
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25537044..25537939
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25602754..25602924
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25602963..25603294
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25683395..25684680
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25685132..25685721
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25687168..25687861
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25689314..25689951
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25692761..25693327
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25827901..25828615
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25837669..25837840
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25837876..25838311
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:25840329..25840938
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26191515..26194023
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26195938..26196589
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26318208..26318643
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26320269..26320639
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26329278..26329877
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26333861..26334460
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26378722..26379315
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26384781..26385359
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26391457..26391519
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26424736..26425231
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26437267..26437328
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26646324..26647526
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26774090..26774755
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26777085..26777659
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26777878..26778428
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26914794..26914911
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26916239..26916821
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26917071..26917503
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26917528..26917597
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26917813..26918404
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26919426..26919750
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26919808..26919961
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26920238..26920904
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26929931..26930607
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26931647..26932142
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26932409..26932914
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26934677..26935364
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26936404..26936899
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26937145..26937665
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26938866..26939039
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26939433..26940120
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26941165..26941655
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26941901..26942427
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26944294..26944776
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26946684..26947281
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26949146..26949710
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26950659..26951883
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26951973..26952991
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26959022..26959638
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26979948..26980528
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26986606..26987639
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26987668..26988981
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26997445..26998446
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:26998532..26999786
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27000715..27001277
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27003146..27003684
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27005669..27006142
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27008016..27008531
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27008799..27009293
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27010449..27010922
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27012796..27013311
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27013579..27014073
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27015099..27015798
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27017563..27018062
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27018336..27018830
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27019856..27020555
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27020637..27020895
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27020934..27021122
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27029767..27030237
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27032152..27032622
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27034537..27035007
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27036921..27037391
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27039306..27039776
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27041488..27042136
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27042357..27042591
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27042648..27042960
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27043990..27044582
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27045558..27046117
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27046983..27047454
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27047481..27047565
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27183941..27184550
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27184723..27185280
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27187607..27188305
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27189831..27190410
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27314834..27316095
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27525109..27525174
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27535576..27536112
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27537030..27537704
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27538362..27538834
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27577066..27577635
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27583119..27583199
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27583225..27583698
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27601214..27601729
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27627949..27628550
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27632535..27633151
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27641575..27641759
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27641780..27642171
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27644253..27644362
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27645062..27645605
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27673632..27674188
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:27768414..27770936
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28121420..28122024
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28124058..28124484
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28124526..28124687
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28133727..28134475
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28269500..28270140
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28272950..28273621
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28275026..28275699
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28277183..28277787
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28278217..28279502
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28359588..28359935
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28359979..28360137
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28424932..28425787
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28481530..28482149
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28557593..28557647
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28661392..28661478
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28680258..28680419
[2015-10-01T00:10Z] WARNING(freebayes): Could not find any mapped reads in target region Y:28715771..28715927
[2015-10-01T00:10Z] tabix index syn3-Y_0_28716339-raw.vcf.gz
[2015-10-01T00:10Z] GATK: VariantAnnotator
[2015-10-01T00:10Z] INFO  01:10:17,707 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:10Z] INFO  01:10:17,709 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:10Z] INFO  01:10:17,709 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:10Z] INFO  01:10:17,709 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:10Z] INFO  01:10:17,713 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/Y/syn3-Y_0_28716339-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/Y/tx/tmpyWNDXw/syn3-Y_0_28716339-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/Y/syn3-Y_0_28716339-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/Y/1_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/Y/2_2014-08-13_dream-syn3-sort-Y_0_28716339-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:10Z] INFO  01:10:17,718 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:10Z] INFO  01:10:17,718 HelpFormatter - Date/Time: 2015/10/01 01:10:17
[2015-10-01T00:10Z] INFO  01:10:17,718 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:10Z] INFO  01:10:17,719 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:10Z] INFO  01:10:17,810 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:10Z] INFO  01:10:17,885 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:10Z] INFO  01:10:17,893 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:10Z] INFO  01:10:17,914 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:10Z] INFO  01:10:18,223 IntervalUtils - Processing 411 bp from intervals
[2015-10-01T00:10Z] WARN  01:10:18,227 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:10Z] WARN  01:10:18,228 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:10Z] INFO  01:10:18,281 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:10Z] INFO  01:10:18,321 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:10Z] INFO  01:10:18,321 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:10Z] INFO  01:10:18,321 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:10Z] INFO  01:10:18,322 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:10Z] INFO  01:10:18,609 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:10Z] INFO  01:10:20,999 VariantAnnotator - Processed 388 loci.
[2015-10-01T00:10Z]
[2015-10-01T00:10Z] INFO  01:10:21,037 ProgressMeter -            done     11473.0     2.0 s       3.9 m       99.8%     2.0 s       0.0 s
[2015-10-01T00:10Z] INFO  01:10:21,038 ProgressMeter - Total runtime 2.72 secs, 0.05 min, 0.00 hours
[2015-10-01T00:10Z] INFO  01:10:21,038 MicroScheduler - 1048 reads were filtered out during the traversal out of approximately 12799 total reads (8.19%)
[2015-10-01T00:10Z] INFO  01:10:21,038 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:10Z] INFO  01:10:21,039 MicroScheduler -   -> 1026 reads (8.02% of total) failing DuplicateReadFilter
[2015-10-01T00:10Z] INFO  01:10:21,039 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:10Z] INFO  01:10:21,039 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:10Z] INFO  01:10:21,039 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:10Z] INFO  01:10:21,039 MicroScheduler -   -> 22 reads (0.17% of total) failing UnmappedReadFilter
[2015-10-01T00:10Z] tabix index syn3-X_94317773_125687021-raw.vcf.gz
[2015-10-01T00:10Z] GATK: VariantAnnotator
[2015-10-01T00:10Z] INFO  01:10:22,008 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:10Z] INFO  01:10:22,847 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:10Z] INFO  01:10:22,849 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:10Z] INFO  01:10:22,849 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:10Z] INFO  01:10:22,849 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:10Z] INFO  01:10:22,852 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/X/syn3-X_94317773_125687021-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/X/tx/tmpMa0XFl/syn3-X_94317773_125687021-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/X/syn3-X_94317773_125687021-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_94317773_125687021-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:10Z] INFO  01:10:22,858 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:10Z] INFO  01:10:22,859 HelpFormatter - Date/Time: 2015/10/01 01:10:22
[2015-10-01T00:10Z] INFO  01:10:22,859 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:10Z] INFO  01:10:22,859 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:10Z] INFO  01:10:22,951 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:10Z] INFO  01:10:23,025 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:10Z] INFO  01:10:23,033 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:10Z] INFO  01:10:23,055 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:10Z] INFO  01:10:23,423 IntervalUtils - Processing 669 bp from intervals
[2015-10-01T00:10Z] WARN  01:10:23,427 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:10Z] WARN  01:10:23,428 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:10Z] INFO  01:10:23,483 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:10Z] INFO  01:10:23,642 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:10Z] INFO  01:10:23,642 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:10Z] INFO  01:10:23,642 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:10Z] INFO  01:10:23,643 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:10Z] INFO  01:10:23,683 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:10Z] INFO  01:10:27,780 VariantAnnotator - Processed 570 loci.
[2015-10-01T00:10Z]
[2015-10-01T00:10Z] INFO  01:10:27,800 ProgressMeter -            done      2382.0     4.0 s      29.1 m       99.9%     4.0 s       0.0 s
[2015-10-01T00:10Z] INFO  01:10:27,800 ProgressMeter - Total runtime 4.16 secs, 0.07 min, 0.00 hours
[2015-10-01T00:10Z] INFO  01:10:27,801 MicroScheduler - 1924 reads were filtered out during the traversal out of approximately 42497 total reads (4.53%)
[2015-10-01T00:10Z] INFO  01:10:27,801 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:10Z] INFO  01:10:27,801 MicroScheduler -   -> 1915 reads (4.51% of total) failing DuplicateReadFilter
[2015-10-01T00:10Z] INFO  01:10:27,801 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:10Z] INFO  01:10:27,801 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:10Z] INFO  01:10:27,802 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:10Z] INFO  01:10:27,802 MicroScheduler -   -> 9 reads (0.02% of total) failing UnmappedReadFilter
[2015-10-01T00:10Z] INFO  01:10:28,833 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:11Z] WARNING(freebayes): Could not find any mapped reads in target region X:152953794..152953843
[2015-10-01T00:11Z] tabix index syn3-X_125953527_155270560-raw.vcf.gz
[2015-10-01T00:11Z] GATK: VariantAnnotator
[2015-10-01T00:11Z] INFO  01:11:35,646 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:11Z] INFO  01:11:35,648 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
[2015-10-01T00:11Z] INFO  01:11:35,648 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2015-10-01T00:11Z] INFO  01:11:35,648 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2015-10-01T00:11Z] INFO  01:11:35,652 HelpFormatter - Program Args: -T VariantAnnotator -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --variant /home/cancer-dream-syn3/work/freebayes/X/syn3-X_125953527_155270560-raw.vcf.gz --out /home/cancer-dream-syn3/work/freebayes/X/tx/tmp5puZA4/syn3-X_125953527_155270560-raw-gatkann.vcf.gz -L /home/cancer-dream-syn3/work/freebayes/X/syn3-X_125953527_155270560-raw.vcf.gz --dbsnp /data/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -I /home/cancer-dream-syn3/work/bamprep/syn3-normal/X/1_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam -I /home/cancer-dream-syn3/work/bamprep/syn3-tumor/X/2_2014-08-13_dream-syn3-sort-X_125953527_155270560-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment
[2015-10-01T00:11Z] INFO  01:11:35,657 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:11Z] INFO  01:11:35,657 HelpFormatter - Date/Time: 2015/10/01 01:11:35
[2015-10-01T00:11Z] INFO  01:11:35,657 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:11Z] INFO  01:11:35,657 HelpFormatter - --------------------------------------------------------------------------------
[2015-10-01T00:11Z] INFO  01:11:35,729 GenomeAnalysisEngine - Strictness is SILENT
[2015-10-01T00:11Z] INFO  01:11:35,816 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2015-10-01T00:11Z] INFO  01:11:35,823 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2015-10-01T00:11Z] INFO  01:11:35,845 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2015-10-01T00:11Z] INFO  01:11:36,267 IntervalUtils - Processing 992 bp from intervals
[2015-10-01T00:11Z] WARN  01:11:36,271 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:11Z] WARN  01:11:36,271 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2015-10-01T00:11Z] INFO  01:11:36,325 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
[2015-10-01T00:11Z] INFO  01:11:36,410 GenomeAnalysisEngine - Done preparing for traversal
[2015-10-01T00:11Z] INFO  01:11:36,410 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2015-10-01T00:11Z] INFO  01:11:36,411 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2015-10-01T00:11Z] INFO  01:11:36,411 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2015-10-01T00:11Z] INFO  01:11:36,450 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2015-10-01T00:11Z] INFO  01:11:42,179 VariantAnnotator - Processed 890 loci.
[2015-10-01T00:11Z]
[2015-10-01T00:11Z] INFO  01:11:42,200 ProgressMeter -            done      3966.0     5.0 s      24.3 m       99.9%     5.0 s       0.0 s
[2015-10-01T00:11Z] INFO  01:11:42,200 ProgressMeter - Total runtime 5.79 secs, 0.10 min, 0.00 hours
[2015-10-01T00:11Z] INFO  01:11:42,200 MicroScheduler - 4142 reads were filtered out during the traversal out of approximately 79944 total reads (5.18%)
[2015-10-01T00:11Z] INFO  01:11:42,201 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2015-10-01T00:11Z] INFO  01:11:42,201 MicroScheduler -   -> 4130 reads (5.17% of total) failing DuplicateReadFilter
[2015-10-01T00:11Z] INFO  01:11:42,201 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2015-10-01T00:11Z] INFO  01:11:42,201 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2015-10-01T00:11Z] INFO  01:11:42,201 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2015-10-01T00:11Z] INFO  01:11:42,202 MicroScheduler -   -> 12 reads (0.02% of total) failing UnmappedReadFilter
[2015-10-01T00:11Z] INFO  01:11:43,278 GATKRunReport - Uploaded run statistics report to AWS S3
[2015-10-01T00:11Z] multiprocessing: concat_variant_files
[2015-10-01T00:11Z] Resource requests: ; memory: 1.00; cores: 1
[2015-10-01T00:11Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-10-01T00:11Z] tabix index syn3-1_0_31187470.vcf.gz
[2015-10-01T00:11Z] Resource requests: ; memory: 1.00; cores: 1
[2015-10-01T00:11Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-10-01T00:11Z] tabix index syn3-1_31187762_62229084.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-1_62231753_93258244.vcf.gz
[2015-10-01T00:11Z] Resource requests: ; memory: 1.00; cores: 1
[2015-10-01T00:11Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-10-01T00:11Z] tabix index syn3-1_93297335_142653959.vcf.gz
[2015-10-01T00:11Z] Concat variant files
[2015-10-01T00:11Z] tabix index syn3-1_142666976_173685474.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-1_173702591_204798081.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-1_204839842_235860787.vcf.gz
[2015-10-01T00:11Z] Concat variant files
[2015-10-01T00:11Z] tabix index syn3-1_235865791_249250621.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-2_0_31134137.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-2_31134801_62196287.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-2_62227535_95457199.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-2_95457728_127315933.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-2_127413596_158444156.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-2_158484801_189599894.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-2_189838937_221056966.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-2_221341378_243199373.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-3_0_31203562.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-3_31494593_62516713.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-3_62518267_93593495.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-3_93595554_124625281.vcf.gz
[2015-10-01T00:11Z] INFO  01:11:46,020 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:11Z] INFO  01:11:46,022 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2015-10-01T00:11Z] INFO  01:11:46,026 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /home/cancer-dream-syn3/work/varscan/syn3-files.list -out /home/cancer-dream-syn3/work/varscan/tx/tmpQFHsLx/syn3.vcf.gz -assumeSorted
[2015-10-01T00:11Z] INFO  01:11:46,033 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:11Z] INFO  01:11:46,033 HelpFormatter - Date/Time: 2015/10/01 01:11:46
[2015-10-01T00:11Z] INFO  01:11:46,033 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:11Z] INFO  01:11:46,034 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:11Z] tabix index syn3-3_124626733_155649953.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-3_155652401_186761310.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-3_186768753_198022430.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-4_0_31018607.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-4_31031389_62067173.vcf.gz
[2015-10-01T00:11Z] INFO  01:11:46,566 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:11Z] INFO  01:11:46,568 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2015-10-01T00:11Z] INFO  01:11:46,572 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /home/cancer-dream-syn3/work/mutect/syn3-files.list -out /home/cancer-dream-syn3/work/mutect/tx/tmpopebZ7/syn3.vcf.gz -assumeSorted
[2015-10-01T00:11Z] tabix index syn3-4_62292837_93511697.vcf.gz
[2015-10-01T00:11Z] INFO  01:11:46,578 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:11Z] INFO  01:11:46,579 HelpFormatter - Date/Time: 2015/10/01 01:11:46
[2015-10-01T00:11Z] INFO  01:11:46,579 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:11Z] INFO  01:11:46,579 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:11Z] tabix index syn3-4_94005855_125588163.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-4_125589908_156618518.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-4_156624795_188926424.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-4_189012293_191154276.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-5_0_31268043.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-5_31293868_62597714.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-5_63256014_94276127.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-5_94277739_125696417.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-5_125759062_156781785.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-5_156785743_180915260.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-6_0_31080572.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-6_31082315_62284583.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-6_62389878_93953543.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-6_93954776_124979769.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-6_125064552_156268261.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-6_156275378_171115067.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-7_0_31019109.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-7_31022897_62585293.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-7_62708318_93925745.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-7_94024041_125680568.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-7_126078434_157151579.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-7_157155595_159138663.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-8_0_31024990.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-8_31030285_62213090.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-8_62288979_93648031.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-8_93896832_124968568.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-8_124975213_146364022.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-9_0_32405837.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-9_32406980_65488652.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-9_65505265_96581951.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-9_96714155_127734373.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-9_127737328_141213431.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-10_0_31134673.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-10_31137165_62208748.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-10_62267938_93388847.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-10_93389481_124436664.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-10_124438084_135534747.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-11_0_31082819.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-11_31085657_62105890.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-11_62123540_93141822.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-11_93147865_124180877.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-11_124188917_135006516.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-12_0_31107241.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-12_31116488_62142833.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-12_62147092_93167456.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-12_93169109_124189486.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-12_124191013_133851895.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-13_0_31036104.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-13_31036377_62334609.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-13_63745563_94765401.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-13_94938309_115169878.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-14_0_31050569.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-14_31055710_62162825.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-14_62186823_93262365.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-14_93263525_107349540.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-15_0_31041107.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-15_31042312_62147370.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-15_62148224_93170844.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-15_93173163_102531392.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-16_0_31021934.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-16_31044089_62860191.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-16_64294277_90354753.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-17_0_31039439.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-17_31047756_62076645.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-17_62078196_81195210.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-18_0_31142016.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-18_31158315_63430522.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-18_63476668_78077248.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-19_0_31026185.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-19_31038548_59128983.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-20_0_31018105.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-20_31018873_62038916.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-20_62039427_63025520.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-21_0_31023863.vcf.gz
[2015-10-01T00:11Z] tabix index syn3-21_31026814_48129895.vcf.gz
[2015-10-01T00:11Z] .........10.........20.........30.........40.........50.........60.........70.........80.........90.........100.........
[2015-10-01T00:11Z] .........10.........20.........30.........40.........50.........60.........70.........80.........90.........100.........
[2015-10-01T00:11Z] tabix index syn3-22_0_31019358.vcf.gz
[2015-10-01T00:11Z] Resource requests: ; memory: 1.00; cores: 1
[2015-10-01T00:11Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-10-01T00:11Z] tabix index syn3-22_31022170_51304566.vcf.gz
[2015-10-01T00:11Z] Concat variant files
[2015-10-01T00:11Z] tabix index syn3-X_0_31090302.vcf.gz
[2015-10-01T00:12Z] tabix index syn3-X_31132529_62519711.vcf.gz
[2015-10-01T00:12Z] tabix index syn3-X_62568928_94148729.vcf.gz
[2015-10-01T00:12Z] tabix index syn3-X_94317773_125687021.vcf.gz
[2015-10-01T00:12Z] tabix index syn3-X_125953527_155270560.vcf.gz
[2015-10-01T00:12Z] tabix index syn3-Y_0_28716339.vcf.gz
[2015-10-01T00:12Z] Concat variant files
[2015-10-01T00:12Z] INFO  01:12:01,178 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:12Z] INFO  01:12:01,180 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2015-10-01T00:12Z] INFO  01:12:01,184 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /home/cancer-dream-syn3/work/freebayes/syn3-files.list -out /home/cancer-dream-syn3/work/freebayes/tx/tmpPDu7Cz/syn3.vcf.gz -assumeSorted
[2015-10-01T00:12Z] INFO  01:12:01,190 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:12Z] INFO  01:12:01,191 HelpFormatter - Date/Time: 2015/10/01 01:12:01
[2015-10-01T00:12Z] INFO  01:12:01,191 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:12Z] INFO  01:12:01,191 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:12Z] INFO  01:12:01,875 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:12Z] INFO  01:12:01,877 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2015-10-01T00:12Z] INFO  01:12:01,881 HelpFormatter - Program Args: -R /data/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /home/cancer-dream-syn3/work/vardict/syn3-files.list -out /home/cancer-dream-syn3/work/vardict/tx/tmpN_nQ08/syn3.vcf.gz -assumeSorted
[2015-10-01T00:12Z] INFO  01:12:01,887 HelpFormatter - Executing as user@node01 on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_71-mockbuild_2014_12_18_14_23-b00.
[2015-10-01T00:12Z] INFO  01:12:01,887 HelpFormatter - Date/Time: 2015/10/01 01:12:01
[2015-10-01T00:12Z] INFO  01:12:01,888 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:12Z] INFO  01:12:01,888 HelpFormatter - -------------------------------------------------------
[2015-10-01T00:12Z] .........10.........20.........30.........40.........50.........60.........70.........80.........90.........100.........
[2015-10-01T00:12Z] .........10.........20.........30.........40.........50.........60.........70.........80.........90.........100.........
[2015-10-01T00:12Z] Resource requests: bamtools, bcbio_variation, fastqc, gatk, gemini, qsignature, samtools, snpeff; memory: 2.50, 3.70, 0.25, 2.75, 6.00; cores: 1, 1, 1, 1, 16, 1, 16, 1
[2015-10-01T00:12Z] Configuring 1 jobs to run, using 7 cores each with 47.1g of memory reserved for each job
[2015-10-01T00:12Z] Timing: joint squaring off/backfilling
[2015-10-01T00:12Z] Timing: variant post-processing
[2015-10-01T00:12Z] multiprocessing: postprocess_variants
[2015-10-01T00:12Z] Finalizing variant calls: syn3-tumor, vardict
[2015-10-01T00:12Z] Calculating variation effects for syn3-tumor, vardict
[2015-10-01T00:12Z] snpEff effects : syn3-tumor
[2015-10-01T00:15Z] tabix index syn3-effects.vcf.gz
[2015-10-01T00:15Z] Filtering for syn3-tumor, vardict
[2015-10-01T00:15Z] Prioritization for syn3-tumor, vardict
[2015-10-01T00:15Z] Finalizing variant calls: syn3-tumor, varscan
[2015-10-01T00:15Z] Calculating variation effects for syn3-tumor, varscan
[2015-10-01T00:15Z] snpEff effects : syn3-tumor
[2015-10-01T00:18Z] tabix index syn3-effects.vcf.gz
[2015-10-01T00:19Z] Filtering for syn3-tumor, varscan
[2015-10-01T00:19Z] Prioritization for syn3-tumor, varscan
[2015-10-01T00:19Z] Finalizing variant calls: syn3-tumor, mutect
[2015-10-01T00:19Z] Calculating variation effects for syn3-tumor, mutect
[2015-10-01T00:19Z] snpEff effects : syn3-tumor
[2015-10-01T00:21Z] tabix index syn3-effects.vcf.gz
[2015-10-01T00:21Z] Filtering for syn3-tumor, mutect
[2015-10-01T00:21Z] Prioritization for syn3-tumor, mutect
[2015-10-01T00:21Z] Finalizing variant calls: syn3-tumor, freebayes
[2015-10-01T00:21Z] Calculating variation effects for syn3-tumor, freebayes
[2015-10-01T00:21Z] snpEff effects : syn3-tumor
[2015-10-01T00:24Z] tabix index syn3-effects.vcf.gz
[2015-10-01T00:24Z] Filtering for syn3-tumor, freebayes
[2015-10-01T00:24Z] Hard filtering /home/cancer-dream-syn3/work/freebayes/syn3-effects.vcf.gz with (AF[0] <= 0.5 && (DP < 4 || (DP < 13 && %QUAL < 10))) || (AF[0] > 0.5 && (DP < 4 && %QUAL < 50)) : syn3-tumor
[2015-10-01T00:24Z] tabix index syn3-effects-filter.vcf.gz
[2015-10-01T00:24Z] Prioritization for syn3-tumor, freebayes
[2015-10-01T00:24Z] multiprocessing: split_variants_by_sample
[2015-10-01T00:24Z] Timing: prepped BAM merging
[2015-10-01T00:24Z] multiprocessing: delayed_bam_merge
[2015-10-01T00:24Z] Merge bam files to 1_2014-08-13_dream-syn3-sort-prep.bam
[2015-10-01T00:31Z] Merge bam files to 2_2014-08-13_dream-syn3-sort-prep.bam
[2015-10-01T00:38Z] Timing: validation
[2015-10-01T00:38Z] multiprocessing: compare_to_rm
[2015-10-01T00:38Z] Select sample: syn3-tumor
[2015-10-01T00:38Z] tabix index syn3-effects-syn3-tumor.vcf.gz
[2015-10-01T00:38Z] Resource requests: ; memory: 1.00; cores: 1
[2015-10-01T00:38Z] Configuring 7 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-10-01T00:38Z] Intersect callable intervals for rtg vcfeval
[2015-10-01T00:38Z] Validate calls using rtg vcfeval : syn3-tumor
[2015-10-01T00:38Z] Reference sequence Y is declared in calls but not declared in baseline (variants will be treated as FP).
[2015-10-01T00:39Z] There were 1 called variants skipped due to being too long, overlapping or starting outside the expected reference sequence length.
[2015-10-01T00:39Z] There were 1655 variants not included in ROC data files due to missing or invalid GQ (FORMAT) values.
[2015-10-01T00:39Z] Not enough ROC data to maximize F-measure, only un-thresholded statistics will be computed. Consider selecting a different scoring attribute with --vcf-score-field
[2015-10-01T00:39Z] Threshold  True-pos  False-pos  False-neg  Precision  Sensitivity  F-measure
[2015-10-01T00:39Z] ----------------------------------------------------------------------------
[2015-10-01T00:39Z]      None       710        945         36     0.4290       0.9517     0.5914
[2015-10-01T00:39Z]
[2015-10-01T00:39Z] Select sample: syn3-tumor
[2015-10-01T00:39Z] tabix index syn3-effects-syn3-tumor.vcf.gz
[2015-10-01T00:39Z] Resource requests: ; memory: 1.00; cores: 1
[2015-10-01T00:39Z] Configuring 7 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-10-01T00:39Z] Intersect callable intervals for rtg vcfeval
[2015-10-01T00:39Z] Validate calls using rtg vcfeval : syn3-tumor
[2015-10-01T00:39Z] Reference sequence Y is declared in calls but not declared in baseline (variants will be treated as FP).
[2015-10-01T00:40Z] There were 1267 variants not included in ROC data files due to missing or invalid GQ (FORMAT) values.
[2015-10-01T00:40Z] Not enough ROC data to maximize F-measure, only un-thresholded statistics will be computed. Consider selecting a different scoring attribute with --vcf-score-field
[2015-10-01T00:40Z] Threshold  True-pos  False-pos  False-neg  Precision  Sensitivity  F-measure
[2015-10-01T00:40Z] ----------------------------------------------------------------------------
[2015-10-01T00:40Z]      None       543        724        203     0.4286       0.7279     0.5395
[2015-10-01T00:40Z]
[2015-10-01T00:40Z] Select sample: syn3-tumor
[2015-10-01T00:40Z] tabix index syn3-effects-syn3-tumor.vcf.gz
[2015-10-01T00:40Z] Resource requests: ; memory: 1.00; cores: 1
[2015-10-01T00:40Z] Configuring 7 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-10-01T00:40Z] Intersect callable intervals for rtg vcfeval
[2015-10-01T00:40Z] Validate calls using rtg vcfeval : syn3-tumor
[2015-10-01T00:40Z] Reference sequence Y is declared in calls but not declared in baseline (variants will be treated as FP).
[2015-10-01T00:40Z] There were 461 variants not included in ROC data files due to missing or invalid GQ (FORMAT) values.
[2015-10-01T00:40Z] Not enough ROC data to maximize F-measure, only un-thresholded statistics will be computed. Consider selecting a different scoring attribute with --vcf-score-field
[2015-10-01T00:40Z] Threshold  True-pos  False-pos  False-neg  Precision  Sensitivity  F-measure
[2015-10-01T00:40Z] ----------------------------------------------------------------------------
[2015-10-01T00:40Z]      None       368         93        378     0.7983       0.4933     0.6098
[2015-10-01T00:40Z]
[2015-10-01T00:40Z] Select sample: syn3-tumor
[2015-10-01T00:41Z] tabix index syn3-effects-filter-syn3-tumor.vcf.gz
[2015-10-01T00:41Z] Resource requests: ; memory: 1.00; cores: 1
[2015-10-01T00:41Z] Configuring 7 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-10-01T00:41Z] Intersect callable intervals for rtg vcfeval
[2015-10-01T00:41Z] Validate calls using rtg vcfeval : syn3-tumor
[2015-10-01T00:41Z] Reference sequence Y is declared in calls but not declared in baseline (variants will be treated as FP).
[2015-10-01T00:41Z] Threshold  True-pos  False-pos  False-neg  Precision  Sensitivity  F-measure
[2015-10-01T00:41Z] ----------------------------------------------------------------------------
[2015-10-01T00:41Z]     9.000       520        113        226     0.8215       0.6971     0.7542
[2015-10-01T00:41Z]      None       526        132        220     0.7994       0.7051     0.7493
[2015-10-01T00:41Z]
[2015-10-01T00:41Z] Timing: ensemble calling
[2015-10-01T00:41Z] multiprocessing: combine_calls
[2015-10-01T00:41Z] Ensemble consensus calls for syn3: mutect,freebayes,vardict,varscan
[2015-10-01T00:41Z] Ensemble intersection calling: syn3
[2015-10-01T00:42Z] 2015-10-01 01:42:06 node01 INFO [bcbio.run.itx] - Note: -w option not given, printing list of sites...
[2015-10-01T00:42Z] Select sample: syn3-tumor
[2015-10-01T00:42Z] tabix index syn3-ensemble-syn3-tumor.vcf.gz
[2015-10-01T00:42Z] Resource requests: ; memory: 1.00; cores: 1
[2015-10-01T00:42Z] Configuring 7 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2015-10-01T00:42Z] Intersect callable intervals for rtg vcfeval
[2015-10-01T00:42Z] Validate calls using rtg vcfeval : syn3-tumor
[2015-10-01T00:42Z] There were 531 variants not included in ROC data files due to missing or invalid GQ (FORMAT) values.
[2015-10-01T00:42Z] Threshold  True-pos  False-pos  False-neg  Precision  Sensitivity  F-measure
[2015-10-01T00:42Z] ----------------------------------------------------------------------------
[2015-10-01T00:42Z]     7.000       172         46        574     0.7890       0.2306     0.3568
[2015-10-01T00:42Z]      None       597        156        149     0.7928       0.8003     0.7965
[2015-10-01T00:42Z]
[2015-10-01T00:42Z] Timing: validation summary
[2015-10-01T00:42Z] Timing: structural variation final
[2015-10-01T00:42Z] Timing: structural variation ensemble
[2015-10-01T00:42Z] Timing: structural variation validation
[2015-10-01T00:42Z] multiprocessing: validate_sv
[2015-10-01T00:42Z] Timing: heterogeneity
[2015-10-01T00:42Z] Timing: population database
[2015-10-01T00:42Z] multiprocessing: prep_gemini_db
[2015-10-01T00:42Z] Multi-allelic to single allele
[2015-10-01T00:42Z] decompose v0.5
[2015-10-01T00:42Z]
[2015-10-01T00:42Z] options:     input VCF file        -
[2015-10-01T00:42Z]          [s] smart decomposition   true (experimental)
[2015-10-01T00:42Z]          [o] output VCF file       -
[2015-10-01T00:42Z]
[2015-10-01T00:43Z]
[2015-10-01T00:43Z] stats: no. variants                 : 203088
[2015-10-01T00:43Z]        no. biallelic variants       : 203088
[2015-10-01T00:43Z]        no. multiallelic variants    : 0
[2015-10-01T00:43Z]
[2015-10-01T00:43Z]        no. additional biallelics    : 0
[2015-10-01T00:43Z]        total no. of biallelics      : 203088
[2015-10-01T00:43Z]
[2015-10-01T00:43Z] Time elapsed: 1.70s
[2015-10-01T00:43Z]
[2015-10-01T00:43Z] tabix index syn3-mutect-decompose.vcf.gz
[2015-10-01T00:43Z] snpEff effects : syn3-tumor
[2015-10-01T00:45Z] tabix index syn3-mutect-decompose-effects.vcf.gz
[2015-10-01T00:45Z] Create gemini database for /home/cancer-dream-syn3/work/gemini/syn3-mutect-decompose-effects.vcf.gz : syn3-tumor
[2015-10-01T00:45Z] pid 38581: 71 variants processed.
[2015-10-01T00:45Z] pid 38581: 28941 skipped due to having the FILTER field set.
[2015-10-01T00:45Z] pid 38593: 81 variants processed.
[2015-10-01T00:45Z] pid 38593: 28935 skipped due to having the FILTER field set.
[2015-10-01T00:45Z] pid 38590: 92 variants processed.
[2015-10-01T00:45Z] pid 38590: 28920 skipped due to having the FILTER field set.
[2015-10-01T00:45Z] pid 38575: 103 variants processed.
[2015-10-01T00:45Z] pid 38575: 28909 skipped due to having the FILTER field set.
[2015-10-01T00:45Z] pid 38584: 74 variants processed.
[2015-10-01T00:45Z] pid 38584: 28938 skipped due to having the FILTER field set.
[2015-10-01T00:45Z] pid 38578: 100 variants processed.
[2015-10-01T00:45Z] pid 38578: 28912 skipped due to having the FILTER field set.
[2015-10-01T00:45Z] pid 38587: 103 variants processed.
[2015-10-01T00:45Z] pid 38587: 28909 skipped due to having the FILTER field set.
[2015-10-01T00:48Z] Indexing /home/cancer-dream-syn3/work/gemini/syn3-mutect-decompose-effects.vcf.gz with grabix.
[2015-10-01T00:48Z] Loading 203088 variants.
[2015-10-01T00:48Z] Breaking /home/cancer-dream-syn3/work/gemini/syn3-mutect-decompose-effects.vcf.gz into 7 chunks.
[2015-10-01T00:48Z] Loading chunk 0.
[2015-10-01T00:48Z] Loading chunk 1.
[2015-10-01T00:48Z] Loading chunk 2.
[2015-10-01T00:48Z] Loading chunk 3.
[2015-10-01T00:48Z] Loading chunk 4.
[2015-10-01T00:48Z] Loading chunk 5.
[2015-10-01T00:48Z] Loading chunk 6.
[2015-10-01T00:48Z] Done loading 203088 variants in 7 chunks.
[2015-10-01T00:48Z] 2015-10-01 01:47:58 merging 7 chunks.
[2015-10-01T00:48Z] 2015-10-01 01:48:03 merging 3 chunks.
[2015-10-01T00:48Z] 2015-10-01 01:48:08 indexing final database.
[2015-10-01T00:48Z] Add PED file to gemini database : syn3-tumor
[2015-10-01T00:48Z] Multi-allelic to single allele
[2015-10-01T00:48Z] decompose v0.5
[2015-10-01T00:48Z]
[2015-10-01T00:48Z] options:     input VCF file        -
[2015-10-01T00:48Z]          [s] smart decomposition   true (experimental)
[2015-10-01T00:48Z]          [o] output VCF file       -
[2015-10-01T00:48Z]
[2015-10-01T00:48Z]
[2015-10-01T00:48Z] stats: no. variants                 : 182100
[2015-10-01T00:48Z]        no. biallelic variants       : 181888
[2015-10-01T00:48Z]        no. multiallelic variants    : 212
[2015-10-01T00:48Z]
[2015-10-01T00:48Z]        no. additional biallelics    : 212
[2015-10-01T00:48Z]        total no. of biallelics      : 182312
[2015-10-01T00:48Z]
[2015-10-01T00:48Z] Time elapsed: 5.01s
[2015-10-01T00:48Z]
[2015-10-01T00:48Z] tabix index syn3-freebayes-decompose.vcf.gz
[2015-10-01T00:48Z] snpEff effects : syn3-tumor
[2015-10-01T00:51Z] tabix index syn3-freebayes-decompose-effects.vcf.gz
[2015-10-01T00:51Z] Create gemini database for /home/cancer-dream-syn3/work/gemini/syn3-freebayes-decompose-effects.vcf.gz : syn3-tumor
[2015-10-01T00:51Z] pid 39296: 113 variants processed.
[2015-10-01T00:51Z] pid 39296: 25935 skipped due to having the FILTER field set.
[2015-10-01T00:51Z] pid 39278: 119 variants processed.
[2015-10-01T00:51Z] pid 39278: 25925 skipped due to having the FILTER field set.
[2015-10-01T00:51Z] pid 39284: 108 variants processed.
[2015-10-01T00:51Z] pid 39284: 25936 skipped due to having the FILTER field set.
[2015-10-01T00:51Z] pid 39281: 120 variants processed.
[2015-10-01T00:51Z] pid 39281: 25924 skipped due to having the FILTER field set.
[2015-10-01T00:51Z] pid 39287: 115 variants processed.
[2015-10-01T00:51Z] pid 39287: 25929 skipped due to having the FILTER field set.
[2015-10-01T00:51Z] pid 39290: 134 variants processed.
[2015-10-01T00:51Z] pid 39290: 25910 skipped due to having the FILTER field set.
[2015-10-01T00:51Z] pid 39293: 152 variants processed.
[2015-10-01T00:51Z] pid 39293: 25892 skipped due to having the FILTER field set.
[2015-10-01T00:54Z] Indexing /home/cancer-dream-syn3/work/gemini/syn3-freebayes-decompose-effects.vcf.gz with grabix.
[2015-10-01T00:54Z] Loading 182312 variants.
[2015-10-01T00:54Z] Breaking /home/cancer-dream-syn3/work/gemini/syn3-freebayes-decompose-effects.vcf.gz into 7 chunks.
[2015-10-01T00:54Z] Loading chunk 0.
[2015-10-01T00:54Z] Loading chunk 1.
[2015-10-01T00:54Z] Loading chunk 2.
[2015-10-01T00:54Z] Loading chunk 3.
[2015-10-01T00:54Z] Loading chunk 4.
[2015-10-01T00:54Z] Loading chunk 5.
[2015-10-01T00:54Z] Loading chunk 6.
[2015-10-01T00:54Z] Done loading 182312 variants in 7 chunks.
[2015-10-01T00:54Z] 2015-10-01 01:54:02 merging 7 chunks.
[2015-10-01T00:54Z] 2015-10-01 01:54:06 merging 3 chunks.
[2015-10-01T00:54Z] 2015-10-01 01:54:09 indexing final database.
[2015-10-01T00:54Z] Add PED file to gemini database : syn3-tumor
[2015-10-01T00:54Z] Multi-allelic to single allele
[2015-10-01T00:54Z] decompose v0.5
[2015-10-01T00:54Z]
[2015-10-01T00:54Z] options:     input VCF file        -
[2015-10-01T00:54Z]          [s] smart decomposition   true (experimental)
[2015-10-01T00:54Z]          [o] output VCF file       -
[2015-10-01T00:54Z]
[2015-10-01T00:54Z]
[2015-10-01T00:54Z] stats: no. variants                 : 1037
[2015-10-01T00:54Z]        no. biallelic variants       : 1037
[2015-10-01T00:54Z]        no. multiallelic variants    : 0
[2015-10-01T00:54Z]
[2015-10-01T00:54Z]        no. additional biallelics    : 0
[2015-10-01T00:54Z]        total no. of biallelics      : 1037
[2015-10-01T00:54Z]
[2015-10-01T00:54Z] Time elapsed: 0.01s
[2015-10-01T00:54Z]
[2015-10-01T00:54Z] tabix index syn3-ensemble-decompose.vcf.gz
[2015-10-01T00:54Z] snpEff effects : syn3-tumor
[2015-10-01T00:55Z] tabix index syn3-ensemble-decompose-effects.vcf.gz
[2015-10-01T00:55Z] Create gemini database for /home/cancer-dream-syn3/work/gemini/syn3-ensemble-decompose-effects.vcf.gz : syn3-tumor
[2015-10-01T00:56Z] pid 39872: 148 variants processed.
[2015-10-01T00:56Z] pid 39872: 0 skipped due to having the FILTER field set.
[2015-10-01T00:56Z] pid 39863: 148 variants processed.
[2015-10-01T00:56Z] pid 39863: 0 skipped due to having the FILTER field set.
[2015-10-01T00:56Z] pid 39857: 148 variants processed.
[2015-10-01T00:56Z] pid 39857: 0 skipped due to having the FILTER field set.
[2015-10-01T00:56Z] pid 39875: 149 variants processed.
[2015-10-01T00:56Z] pid 39875: 0 skipped due to having the FILTER field set.
[2015-10-01T00:56Z] pid 39866: 148 variants processed.
[2015-10-01T00:56Z] pid 39866: 0 skipped due to having the FILTER field set.
[2015-10-01T00:56Z] pid 39869: 148 variants processed.
[2015-10-01T00:56Z] pid 39869: 0 skipped due to having the FILTER field set.
[2015-10-01T00:56Z] pid 39860: 148 variants processed.
[2015-10-01T00:56Z] pid 39860: 0 skipped due to having the FILTER field set.
[2015-10-01T00:59Z] Indexing /home/cancer-dream-syn3/work/gemini/syn3-ensemble-decompose-effects.vcf.gz with grabix.
[2015-10-01T00:59Z] Loading 1037 variants.
[2015-10-01T00:59Z] Breaking /home/cancer-dream-syn3/work/gemini/syn3-ensemble-decompose-effects.vcf.gz into 7 chunks.
[2015-10-01T00:59Z] Loading chunk 0.
[2015-10-01T00:59Z] Loading chunk 1.
[2015-10-01T00:59Z] Loading chunk 2.
[2015-10-01T00:59Z] Loading chunk 3.
[2015-10-01T00:59Z] Loading chunk 4.
[2015-10-01T00:59Z] Loading chunk 5.
[2015-10-01T00:59Z] Loading chunk 6.
[2015-10-01T00:59Z] Done loading 1037 variants in 7 chunks.
[2015-10-01T00:59Z] 2015-10-01 01:59:03 merging 7 chunks.
[2015-10-01T00:59Z] 2015-10-01 01:59:08 merging 3 chunks.
[2015-10-01T00:59Z] 2015-10-01 01:59:10 indexing final database.
[2015-10-01T00:59Z] Add PED file to gemini database : syn3-tumor
[2015-10-01T00:59Z] Multi-allelic to single allele
[2015-10-01T00:59Z] decompose v0.5
[2015-10-01T00:59Z]
[2015-10-01T00:59Z] options:     input VCF file        -
[2015-10-01T00:59Z]          [s] smart decomposition   true (experimental)
[2015-10-01T00:59Z]          [o] output VCF file       -
[2015-10-01T00:59Z]
[2015-10-01T00:59Z] [W::vcf_parse] contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '3' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '4' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '5' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '6' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '7' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '8' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '9' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '10' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '11' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '12' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '13' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '14' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '15' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '16' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '18' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '19' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '21' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig '22' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig 'X' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z] [W::vcf_parse] contig 'Y' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T00:59Z]
[2015-10-01T00:59Z] stats: no. variants                 : 219425
[2015-10-01T00:59Z]        no. biallelic variants       : 219425
[2015-10-01T00:59Z]        no. multiallelic variants    : 0
[2015-10-01T00:59Z]
[2015-10-01T00:59Z]        no. additional biallelics    : 0
[2015-10-01T00:59Z]        total no. of biallelics      : 219425
[2015-10-01T00:59Z]
[2015-10-01T00:59Z] Time elapsed: 5.14s
[2015-10-01T00:59Z]
[2015-10-01T00:59Z] tabix index syn3-vardict-decompose.vcf.gz
[2015-10-01T00:59Z] snpEff effects : syn3-tumor
[2015-10-01T01:03Z] tabix index syn3-vardict-decompose-effects.vcf.gz
[2015-10-01T01:03Z] Create gemini database for /home/cancer-dream-syn3/work/gemini/syn3-vardict-decompose-effects.vcf.gz : syn3-tumor
[2015-10-01T01:04Z] [W::vcf_parse] contig '8' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '19' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '5' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '11' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '15' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '9' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '12' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '6' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '16' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '3' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '21' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '22' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '10' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '13' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '7' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig 'X' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '4' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '14' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '18' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig 'Y' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '11' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] pid 40836: 362 variants processed.
[2015-10-01T01:04Z] pid 40836: 30987 skipped due to having the FILTER field set.
[2015-10-01T01:04Z] pid 40818: 360 variants processed.
[2015-10-01T01:04Z] pid 40818: 30986 skipped due to having the FILTER field set.
[2015-10-01T01:04Z] [W::vcf_parse] contig '19' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] [W::vcf_parse] contig '15' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] pid 40827: 358 variants processed.
[2015-10-01T01:04Z] pid 40827: 30988 skipped due to having the FILTER field set.
[2015-10-01T01:04Z] pid 40833: 397 variants processed.
[2015-10-01T01:04Z] pid 40833: 30949 skipped due to having the FILTER field set.
[2015-10-01T01:04Z] pid 40830: 360 variants processed.
[2015-10-01T01:04Z] pid 40830: 30986 skipped due to having the FILTER field set.
[2015-10-01T01:04Z] [W::vcf_parse] contig '8' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] pid 40824: 382 variants processed.
[2015-10-01T01:04Z] pid 40824: 30964 skipped due to having the FILTER field set.
[2015-10-01T01:04Z] [W::vcf_parse] contig '5' is not defined in the header. (Quick workaround: index the file with tabix.)
[2015-10-01T01:04Z] pid 40821: 460 variants processed.
[2015-10-01T01:04Z] pid 40821: 30886 skipped due to having the FILTER field set.
[2015-10-01T01:07Z] Indexing /home/cancer-dream-syn3/work/gemini/syn3-vardict-decompose-effects.vcf.gz with grabix.
[2015-10-01T01:07Z] Loading 219425 variants.
[2015-10-01T01:07Z] Breaking /home/cancer-dream-syn3/work/gemini/syn3-vardict-decompose-effects.vcf.gz into 7 chunks.
[2015-10-01T01:07Z] Loading chunk 0.
[2015-10-01T01:07Z] Loading chunk 1.
[2015-10-01T01:07Z] Loading chunk 2.
[2015-10-01T01:07Z] Loading chunk 3.
[2015-10-01T01:07Z] Loading chunk 4.
[2015-10-01T01:07Z] Loading chunk 5.
[2015-10-01T01:07Z] Loading chunk 6.
[2015-10-01T01:07Z] Done loading 219425 variants in 7 chunks.
[2015-10-01T01:07Z] 2015-10-01 02:07:19 merging 7 chunks.
[2015-10-01T01:07Z] 2015-10-01 02:07:23 merging 3 chunks.
[2015-10-01T01:07Z] 2015-10-01 02:07:26 indexing final database.
[2015-10-01T01:07Z] Add PED file to gemini database : syn3-tumor
[2015-10-01T01:07Z] Multi-allelic to single allele
[2015-10-01T01:07Z] decompose v0.5
[2015-10-01T01:07Z]
[2015-10-01T01:07Z] options:     input VCF file        -
[2015-10-01T01:07Z]          [s] smart decomposition   true (experimental)
[2015-10-01T01:07Z]          [o] output VCF file       -
[2015-10-01T01:07Z]
[2015-10-01T01:07Z]
[2015-10-01T01:07Z] stats: no. variants                 : 191654
[2015-10-01T01:07Z]        no. biallelic variants       : 191654
[2015-10-01T01:07Z]        no. multiallelic variants    : 0
[2015-10-01T01:07Z]
[2015-10-01T01:07Z]        no. additional biallelics    : 0
[2015-10-01T01:07Z]        total no. of biallelics      : 191654
[2015-10-01T01:07Z]
[2015-10-01T01:07Z] Time elapsed: 2.87s
[2015-10-01T01:07Z]
[2015-10-01T01:07Z] tabix index syn3-varscan-decompose.vcf.gz
[2015-10-01T01:07Z] snpEff effects : syn3-tumor
[2015-10-01T01:11Z] tabix index syn3-varscan-decompose-effects.vcf.gz
[2015-10-01T01:11Z] Create gemini database for /home/cancer-dream-syn3/work/gemini/syn3-varscan-decompose-effects.vcf.gz : syn3-tumor
[2015-10-01T01:11Z] pid 41586: 286 variants processed.
[2015-10-01T01:11Z] pid 41586: 27093 skipped due to having the FILTER field set.
[2015-10-01T01:11Z] pid 41592: 341 variants processed.
[2015-10-01T01:11Z] pid 41592: 27038 skipped due to having the FILTER field set.
[2015-10-01T01:11Z] pid 41583: 340 variants processed.
[2015-10-01T01:11Z] pid 41583: 27039 skipped due to having the FILTER field set.
[2015-10-01T01:11Z] pid 41589: 265 variants processed.
[2015-10-01T01:11Z] pid 41589: 27114 skipped due to having the FILTER field set.
[2015-10-01T01:11Z] pid 41601: 353 variants processed.
[2015-10-01T01:11Z] pid 41601: 27027 skipped due to having the FILTER field set.
[2015-10-01T01:11Z] pid 41598: 344 variants processed.
[2015-10-01T01:11Z] pid 41598: 27035 skipped due to having the FILTER field set.
[2015-10-01T01:11Z] pid 41595: 326 variants processed.
[2015-10-01T01:11Z] pid 41595: 27053 skipped due to having the FILTER field set.
[2015-10-01T01:14Z] Indexing /home/cancer-dream-syn3/work/gemini/syn3-varscan-decompose-effects.vcf.gz with grabix.
[2015-10-01T01:14Z] Loading 191654 variants.
[2015-10-01T01:14Z] Breaking /home/cancer-dream-syn3/work/gemini/syn3-varscan-decompose-effects.vcf.gz into 7 chunks.
[2015-10-01T01:14Z] Loading chunk 0.
[2015-10-01T01:14Z] Loading chunk 1.
[2015-10-01T01:14Z] Loading chunk 2.
[2015-10-01T01:14Z] Loading chunk 3.
[2015-10-01T01:14Z] Loading chunk 4.
[2015-10-01T01:14Z] Loading chunk 5.
[2015-10-01T01:14Z] Loading chunk 6.
[2015-10-01T01:14Z] Done loading 191654 variants in 7 chunks.
[2015-10-01T01:14Z] 2015-10-01 02:14:10 merging 7 chunks.
[2015-10-01T01:14Z] 2015-10-01 02:14:18 merging 3 chunks.
[2015-10-01T01:14Z] 2015-10-01 02:14:21 indexing final database.
[2015-10-01T01:14Z] Add PED file to gemini database : syn3-tumor
[2015-10-01T01:14Z] Timing: quality control
[2015-10-01T01:14Z] multiprocessing: pipeline_summary
[2015-10-01T01:14Z] Generating summary files: ['', 'syn3-tumor']
[2015-10-01T01:14Z] Downsample BAM file: 2_2014-08-13_dream-syn3-sort-prep.bam
[2015-10-01T01:16Z] FastQC: syn3-tumor
[2015-10-01T01:16Z] Started analysis of 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 5% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 10% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 15% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 20% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 25% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 30% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 35% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 40% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 45% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:16Z] Approx 50% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 55% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 60% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 65% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 70% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 75% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 80% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 85% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 90% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 95% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Approx 100% complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] Analysis complete for 2_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:17Z] bamtools stats : syn3-tumor
[2015-10-01T01:22Z] Generating summary files: ['', 'syn3-normal']
[2015-10-01T01:22Z] Downsample BAM file: 1_2014-08-13_dream-syn3-sort-prep.bam
[2015-10-01T01:24Z] FastQC: syn3-normal
[2015-10-01T01:24Z] Started analysis of 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:24Z] Approx 5% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:24Z] Approx 10% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:24Z] Approx 15% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:24Z] Approx 20% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 25% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 30% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 35% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 40% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 45% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 50% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 55% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 60% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 65% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 70% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 75% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:25Z] Approx 80% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:26Z] Approx 85% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:26Z] Approx 90% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:26Z] Approx 95% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:26Z] Approx 100% complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:26Z] Analysis complete for 1_2014-08-13_dream-syn3-sort-prep-downsample.bam
[2015-10-01T01:26Z] bamtools stats : syn3-normal
[2015-10-01T01:31Z] multiprocessing: qsignature_summary
[2015-10-01T01:31Z] Timing: report
[2015-10-01T01:31Z] copy qsignature
[2015-10-01T01:31Z] summarize metrics
[2015-10-01T01:31Z] summarize fastqc
[2015-10-01T01:31Z] multiprocessing: coverage_report
[2015-10-01T01:31Z] Timing: archive
[2015-10-01T01:31Z] Timing: upload
[2015-10-01T01:31Z] multiprocessing: upload_samples
[2015-10-01T01:31Z] Storing directory in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/qc
[2015-10-01T01:31Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-ready.bam
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-ready.bam.bai
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-disc.bam
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-disc.bam.bai
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-sr.bam
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-sr.bam.bai
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-ensemble.vcf.gz
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-ensemble.vcf.gz.tbi
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-mutect.vcf.gz
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-mutect.vcf.gz.tbi
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-mutect-effects-stats.html
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-freebayes.vcf.gz
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-freebayes.vcf.gz.tbi
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-freebayes-effects-stats.html
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-vardict.vcf.gz
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-vardict.vcf.gz.tbi
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-vardict-effects-stats.html
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-varscan.vcf.gz
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-varscan.vcf.gz.tbi
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-varscan-effects-stats.html
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-tumor/syn3-tumor-validate.png
[2015-10-01T01:34Z] Storing directory in local filesystem: /home/cancer-dream-syn3/final/syn3-normal/qc
[2015-10-01T01:34Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-normal/syn3-normal-ready.bam
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-normal/syn3-normal-ready.bam.bai
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-normal/syn3-normal-disc.bam
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-normal/syn3-normal-disc.bam.bai
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-normal/syn3-normal-sr.bam
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/syn3-normal/syn3-normal-sr.bam.bai
[2015-10-01T01:36Z] multiprocessing: upload_samples_project
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/programs.txt
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/bcbio-nextgen.log
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/bcbio-nextgen-commands.log
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/project-summary.yaml
[2015-10-01T01:36Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-ensemble.db
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-ensemble.vcf.gz
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-ensemble.vcf.gz.tbi
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-mutect.db
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-mutect.vcf.gz
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-mutect.vcf.gz.tbi
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-freebayes.db
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-freebayes.vcf.gz
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-freebayes.vcf.gz.tbi
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-vardict.db
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-vardict.vcf.gz
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-vardict.vcf.gz.tbi
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-varscan.db
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-varscan.vcf.gz
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/syn3-varscan.vcf.gz.tbi
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/grading-summary-syn3.csv
[2015-10-01T01:37Z] multiprocessing: upload_samples_project
[2015-10-01T01:37Z] Storing in local filesystem: /home/cancer-dream-syn3/final/2014-08-13_dream-syn3/bcbio-nextgen.log
[2015-10-01T01:37Z] Timing: finished